Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr06 ID=Chr06-JGI_221_v2.0
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: 51074515
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 971674 characters in sequence are not A, C, G, or T
File 141 of 168
Found at i:41488058 original size:57 final size:59
Alignment explanation
Indices: 41487986--41488099 Score: 187
Period size: 57 Copynumber: 2.0 Consensus size: 59
41487976 TATGGGTCAA
*
41487986 AATGTAATTTCGAGAAAGTTTAGGGGTCAAAATGTAA-TTTA-AAAAATTTAGGGGTTG
1 AATGTAATTTCGAGAAAGTTTAGGGGTCAAAATGCAATTTTAGAAAAATTTAGGGGTTG
* *
41488043 AATGTAATTTTGAGAAAGTTTAGGGGTCAAAATGCAATTTTAGAAAATTTTAGGGGT
1 AATGTAATTTCGAGAAAGTTTAGGGGTCAAAATGCAATTTTAGAAAAATTTAGGGGT
41488100 CAAAATGCAA
Statistics
Matches: 52, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
57 35 0.67
58 4 0.08
59 13 0.25
ACGTcount: A:0.38, C:0.04, G:0.25, T:0.34
Consensus pattern (59 bp):
AATGTAATTTCGAGAAAGTTTAGGGGTCAAAATGCAATTTTAGAAAAATTTAGGGGTTG
Found at i:41488109 original size:30 final size:30
Alignment explanation
Indices: 41487960--41488106 Score: 185
Period size: 30 Copynumber: 5.0 Consensus size: 30
41487950 GGCCAAAACA
*
41487960 TAATTTTGAGAAAGTTTATGGGTCAAAATG
1 TAATTTTGAGAAAGTTTAGGGGTCAAAATG
*
41487990 TAATTTCGAGAAAGTTTAGGGGTCAAAATG
1 TAATTTTGAGAAAGTTTAGGGGTCAAAATG
* * **
41488020 TAA-TTT-AAAAAATTTAGGGGT-TGAATG
1 TAATTTTGAGAAAGTTTAGGGGTCAAAATG
41488047 TAATTTTGAGAAAGTTTAGGGGTCAAAATG
1 TAATTTTGAGAAAGTTTAGGGGTCAAAATG
* *
41488077 CAATTTT-AGAAAATTTTAGGGGTCAAAATG
1 TAATTTTGAG-AAAGTTTAGGGGTCAAAATG
41488107 CAAAAAAATT
Statistics
Matches: 100, Mismatches: 13, Indels: 8
0.83 0.11 0.07
Matches are distributed among these distances:
27 7 0.07
28 16 0.16
29 17 0.17
30 60 0.60
ACGTcount: A:0.38, C:0.04, G:0.24, T:0.34
Consensus pattern (30 bp):
TAATTTTGAGAAAGTTTAGGGGTCAAAATG
Found at i:41488533 original size:77 final size:76
Alignment explanation
Indices: 41488305--41489038 Score: 784
Period size: 76 Copynumber: 9.6 Consensus size: 76
41488295 GAATAGCTTG
* * * * *
41488305 GCGTGCGACTCAAAGCTCAACTCATCTCTCGAAATATGAGTTGATTTTTGAAAAACAGAAATTTA
1 GCGTGCGACCCGAGGCTCAACTCACCTCTCGTAATATGAGTTGATTTTTGAAAAACAGAAATTT-
*
41488370 AAAGAAATACCTTA
65 -AA-AAATACCTCA
* * * * *
41488384 GCATGTG-TCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTG-AAAATAGAAATTTA
1 GCGTGCGACCCGAGGCTCAACTCACCTCTCGTAATATGAGTTGATTTTTGAAAAACAGAAATTT-
41488447 AAAGAAATACCTCA
65 -AA-AAATACCTCA
*
41488461 GCGTGCGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAACAGAAATTT
1 GCGTGCGACCCGAGGCTCAACTCACCTCTCGTAATATGAGTTGA-TTTTTGAAAAACAGAAATTT
41488526 AAAAATACCTCA
65 AAAAATACCTCA
* *
41488538 GCGTGCGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAATAGAAATTT
1 GCGTGCGACCCGAGGCTCAACTCACCTCTCGTAATATGAGTTGA-TTTTTGAAAAACAGAAATTT
41488603 AAAAATACCTCA
65 AAAAATACCTCA
*
41488615 GCGTGCGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAAGCAGAAATTT
1 GCGTGCGACCCGAGGCTCAACTCACCTCTCGTAATATGAGTTGATTTTTGAAAAA-CAGAAATTT
41488680 -AAAATACCTCA
65 AAAAATACCTCA
* * *** *
41488691 GCGTGCGACCCGAGGCTCAACTCACCTC-AGTATTATGAGTTGATTTAAAAAAAAAACATAAA-T
1 GCGTGCGACCCGAGGCTCAACTCACCTCTCGTAATATGAGTTGATTT--TTGAAAAACAGAAATT
*
41488754 TAAAAATACATCA
64 TAAAAATACCTCA
* * ** * *
41488767 GCGT--GACCCGAGGCTCAACTCACCT-TTGTATTATGAGTTGA-TTTAAAAAAAAAGACATAAA
1 GCGTGCGACCCGAGGCTCAACTCACCTCTCGTAATATGAGTTGATTTTTGAAAAACAG--A-AAT
41488828 TTAAAAATACCTCA
63 TTAAAAATACCTCA
* * * *
41488842 GCGT--GACCCGAGGCTCAACTCACCTCT-GTATTATGAGTTGATTTTTAAAAAAAAGACATAAA
1 GCGTGCGACCCGAGGCTCAACTCACCTCTCGTAATATGAGTTGATTTTTGAAAAACAG--A-AAT
*
41488904 TTAAAAACACCTCA
63 TTAAAAATACCTCA
* * * *** * *
41488918 GCGT--GACCCGAGACTCAACTCACCTCT-GTATTATGAGTTGACTTAAAAAAAAAAGACATAAA
1 GCGTGCGACCCGAGGCTCAACTCACCTCTCGTAATATGAGTTGATTTTTGAAAAACAG--A-AAT
41488980 TTAAAAATACCTCA
63 TTAAAAATACCTCA
*
41488994 GCGT--GACCCGAGGCTCAACTCACCTCT-GTATTATGAGTTGATTTT
1 GCGTGCGACCCGAGGCTCAACTCACCTCTCGTAATATGAGTTGATTTT
41489039 AAAAAAAAAC
Statistics
Matches: 602, Mismatches: 39, Indels: 31
0.90 0.06 0.05
Matches are distributed among these distances:
71 8 0.01
73 3 0.00
74 37 0.06
75 69 0.11
76 215 0.36
77 174 0.29
78 73 0.12
79 11 0.02
80 12 0.02
ACGTcount: A:0.36, C:0.21, G:0.16, T:0.27
Consensus pattern (76 bp):
GCGTGCGACCCGAGGCTCAACTCACCTCTCGTAATATGAGTTGATTTTTGAAAAACAGAAATTTA
AAAATACCTCA
Found at i:41489063 original size:227 final size:228
Alignment explanation
Indices: 41488392--41489063 Score: 848
Period size: 227 Copynumber: 2.9 Consensus size: 228
41488382 TAGCATGTGT
* ** *
41488392 CCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAATAGAA-ATTTAAA--AGAAA
1 CCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT-AAAA-AAAAGACATAAATTAAAAA
* * ****
41488454 TACCTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTT-TTTGAAAA-A
64 TACCTCAGCGT-CGACCCGAGGCTCAACTCACCTCT-GTATTATGAGTTGATTTAAAAAAAAAGA
* * *
41488517 CAGAAATTTAAAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA
127 CATAAA-TTAAAAATACCTCAGCGT--GACCCGAGGCTCAACTCACCTCT-GTATTATGAGTTGA
*** *
41488582 TTTT-TTGAAAAATAGAAATTTAAAAATACCTCAGCGTGCGAC
188 TTTTAAAAAAAAACAGAAA-TTAAAAATACCTCAGCGT-CGAC
* * *
41488624 CCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT--GAAAAAG-CAGAAATTTAAAATA
1 CCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTAAAAAAAAGACATAAATTAAAAATA
*
41488686 CCTCAGCGTGCGACCCGAGGCTCAACTCACCTCAGTATTATGAGTTGATTTAAAAAAAAA-ACAT
66 CCTCAGCGT-CGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTAAAAAAAAAGACAT
* * *
41488750 AAATTAAAAATACATCAGCGTGACCCGAGGCTCAACTCACCTTTGTATTATGAGTTGATTTAAAA
130 AAATTAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTAAA
*
41488815 AAAAAGACATAAATTAAAAATACCTCAGCGT-GAC
195 AAAAA-ACAGAAATTAAAAATACCTCAGCGTCGAC
* * *
41488849 CCGAGGCTCAACTCACCTCT-GTATTATGAGTTGATTTTTAAAAAAAAGACATAAATTAAAAACA
1 CCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTAAAAAAAAGACATAAATTAAAAATA
* *
41488913 CCTCAGCGT-GACCCGAGACTCAACTCACCTCTGTATTATGAGTTGACTTAAAAAAAAAAGACAT
66 CCTCAGCGTCGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGA-TTTAAAAAAAAAGACAT
41488977 AAATTAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTAAA
130 AAATTAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTAAA
*
41489042 AAAAAACAGAAAGTGAAAAATA
195 AAAAAACAGAAA-TTAAAAATA
41489064 TTTCTTGAAA
Statistics
Matches: 389, Mismatches: 39, Indels: 29
0.85 0.09 0.06
Matches are distributed among these distances:
224 17 0.04
225 58 0.15
226 38 0.10
227 144 0.37
228 11 0.03
229 33 0.08
230 48 0.12
232 40 0.10
ACGTcount: A:0.38, C:0.21, G:0.16, T:0.26
Consensus pattern (228 bp):
CCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTAAAAAAAAGACATAAATTAAAAATA
CCTCAGCGTCGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTAAAAAAAAAGACATA
AATTAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTAAAA
AAAAACAGAAATTAAAAATACCTCAGCGTCGAC
Found at i:41489940 original size:13 final size:13
Alignment explanation
Indices: 41489919--41489971 Score: 53
Period size: 13 Copynumber: 4.3 Consensus size: 13
41489909 TTCATCTTGA
41489919 TTTT-TCTT-TTT
1 TTTTGTCTTGTTT
41489930 TTTTGTGCTT-TTT
1 TTTTGT-CTTGTTT
41489943 TATTT-T-TTGTTT
1 T-TTTGTCTTGTTT
41489955 TTTTGTCTTGTTT
1 TTTTGTCTTGTTT
41489968 TTTT
1 TTTT
41489972 TAAGCATAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
11 9 0.25
12 6 0.17
13 18 0.50
14 3 0.08
ACGTcount: A:0.02, C:0.06, G:0.09, T:0.83
Consensus pattern (13 bp):
TTTTGTCTTGTTT
Found at i:41489947 original size:26 final size:24
Alignment explanation
Indices: 41489918--41489972 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 24
41489908 TTTCATCTTG
* *
41489918 ATTTTTCTTTTTTTTTGTGCTTTTTT
1 ATTTTT-TGTTTTTTTGT-CTTGTTT
41489944 ATTTTTTGTTTTTTTGTCTTGTTT
1 ATTTTTTGTTTTTTTGTCTTGTTT
41489968 -TTTTT
1 ATTTTT
41489973 AAGCATAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
23 5 0.19
24 6 0.22
25 10 0.37
26 6 0.22
ACGTcount: A:0.04, C:0.05, G:0.09, T:0.82
Consensus pattern (24 bp):
ATTTTTTGTTTTTTTGTCTTGTTT
Found at i:41495997 original size:35 final size:34
Alignment explanation
Indices: 41495960--41496179 Score: 135
Period size: 36 Copynumber: 6.2 Consensus size: 34
41495950 GACATAATAT
* *
41495960 TTTTTTAAAAAACGAAAATTTATGAAACACGAGATT
1 TTTTTTAAAACACGAAAATTT-TGAAACACGAGA-A
*
41495996 TTTTTTGAAAACACGAAAATTTTCAAAACACCGA-AA
1 TTTTTT-AAAACACGAAAATTTT-GAAACA-CGAGAA
* * *
41496032 TTTTTGAAAACACGAGGATTTTTGAAACACGAGAA
1 TTTTTTAAAACACGA-AAATTTTGAAACACGAGAA
* * *
41496067 TTTTCTGAAAACATGAAAAATTTTGAAA-ATTG-GAA
1 TTTT-TTAAAACACG-AAAATTTTGAAACA-CGAGAA
* *
41496102 TTTTTTTGAAAACACGAGAATTTTTGAAAACATGA-AA
1 -TTTTTT-AAAACACGA-AAATTTTG-AAACACGAGAA
* * * *
41496139 ATTTTTGAAACACGGGAATTTTTGAAAACACGA-AA
1 TTTTTTAAAACAC-GAAAATTTTG-AAACACGAGAA
41496174 TTTTTT
1 TTTTTT
41496180 TTATTTTTTA
Statistics
Matches: 150, Mismatches: 19, Indels: 31
0.75 0.09 0.16
Matches are distributed among these distances:
34 3 0.02
35 55 0.37
36 60 0.40
37 28 0.19
38 4 0.03
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (34 bp):
TTTTTTAAAACACGAAAATTTTGAAACACGAGAA
Found at i:41496087 original size:72 final size:69
Alignment explanation
Indices: 41495960--41496178 Score: 215
Period size: 72 Copynumber: 3.1 Consensus size: 69
41495950 GACATAATAT
* * * * * *
41495960 TTTTTTAAAAAACGAAAATTTATGAAACACGAGATTTTTTTTGAAAACACGAAAATTTTCAAAAC
1 TTTTTGAAAACACGAGAATTTTTGAAACACGAGA--ATTTTTGAAAACACGAAAATTTTGAAAAC
41496025 ACCGAAA
64 A-CGAAA
* * *
41496032 TTTTTGAAAACACGAGGATTTTTGAAACACGAGAATTTTCTGAAAACATGAAAAATTTTGAAAAT
1 TTTTTGAAAACACGAGAATTTTTGAAACACGAGAATTTT-TGAAAACACG-AAAATTTTGAAAAC
** *
41496097 TGGAATT
64 ACGAA-A
* * * *
41496104 TTTTTGAAAACACGAGAATTTTTGAAAACATGAAAATTTTTG-AAACACGGGAATTTTTGAAAAC
1 TTTTTGAAAACACGAGAATTTTTG-AAACACGAGAATTTTTGAAAACAC-GAAAATTTTGAAAAC
41496168 ACGAAA
64 ACGAAA
41496174 TTTTT
1 TTTTT
41496179 TTTATTTTTT
Statistics
Matches: 120, Mismatches: 22, Indels: 12
0.78 0.14 0.08
Matches are distributed among these distances:
70 9 0.08
71 31 0.26
72 67 0.56
73 13 0.11
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (69 bp):
TTTTTGAAAACACGAGAATTTTTGAAACACGAGAATTTTTGAAAACACGAAAATTTTGAAAACAC
GAAA
Found at i:41496179 original size:18 final size:17
Alignment explanation
Indices: 41495997--41496178 Score: 170
Period size: 18 Copynumber: 10.3 Consensus size: 17
41495987 CACGAGATTT
41495997 TTTTTGAAAACACGAAA
1 TTTTTGAAAACACGAAA
* *
41496014 ATTTTCAAAACACCGAAA
1 TTTTTGAAAACA-CGAAA
*
41496032 TTTTTGAAAACACGAGGA
1 TTTTTGAAAACACGA-AA
41496050 TTTTTG-AAACACGAGAA
1 TTTTTGAAAACACGA-AA
*
41496067 TTTTCTGAAAACATGAAAA
1 TTTT-TGAAAACACG-AAA
* *** *
41496086 ATTTTGAAAATTGGAATT
1 TTTTTGAAAACACGAA-A
41496104 TTTTTGAAAACACGAGAA
1 TTTTTGAAAACACGA-AA
*
41496122 TTTTTGAAAACATGAAAA
1 TTTTTGAAAACACG-AAA
*
41496140 TTTTTG-AAACACGGGAA
1 TTTTTGAAAACAC-GAAA
41496157 TTTTTGAAAACACGAAA
1 TTTTTGAAAACACGAAA
41496174 TTTTT
1 TTTTT
41496179 TTTATTTTTT
Statistics
Matches: 134, Mismatches: 21, Indels: 20
0.77 0.12 0.11
Matches are distributed among these distances:
17 50 0.37
18 70 0.52
19 13 0.10
20 1 0.01
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.32
Consensus pattern (17 bp):
TTTTTGAAAACACGAAA
Found at i:41496310 original size:22 final size:21
Alignment explanation
Indices: 41496283--41496325 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
41496273 CGTTACCTTA
*
41496283 TTTTTGAAAACACGAGAAATTT
1 TTTTTGAAAACAC-AAAAATTT
*
41496305 TTTTTGAAGACACAAAAATTT
1 TTTTTGAAAACACAAAAATTT
41496326 CGAAACCCGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.42, C:0.09, G:0.12, T:0.37
Consensus pattern (21 bp):
TTTTTGAAAACACAAAAATTT
Found at i:41496541 original size:14 final size:15
Alignment explanation
Indices: 41496522--41496556 Score: 54
Period size: 16 Copynumber: 2.3 Consensus size: 15
41496512 ATTGAAATTG
41496522 AAAATAT-AAATACA
1 AAAATATAAAATACA
41496536 AAAATATAAAAATACA
1 AAAATAT-AAAATACA
41496552 AAAAT
1 AAAAT
41496557 GCATAAAATG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 7 0.37
16 12 0.63
ACGTcount: A:0.74, C:0.06, G:0.00, T:0.20
Consensus pattern (15 bp):
AAAATATAAAATACA
Found at i:41496794 original size:58 final size:60
Alignment explanation
Indices: 41496726--41496841 Score: 200
Period size: 58 Copynumber: 2.0 Consensus size: 60
41496716 TTATGGGTCA
*
41496726 AAATGTAATTTTGAGAAAGTTTAGGGGTCAAAATGTAA-TTTA-AAAAATTTAGGGGTTG
1 AAATGTAATTTTGAGAAAGTTTAGGGGTCAAAATGCAATTTTAGAAAAATTTAGGGGTTG
*
41496784 AAATGTAATTTTGAGAAAGTTTAGGGGTCAAAATGCAATTTTAGAAAATTTTAGGGGT
1 AAATGTAATTTTGAGAAAGTTTAGGGGTCAAAATGCAATTTTAGAAAAATTTAGGGGT
41496842 CAAAATGCAA
Statistics
Matches: 54, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
58 37 0.69
59 4 0.07
60 13 0.24
ACGTcount: A:0.39, C:0.03, G:0.24, T:0.34
Consensus pattern (60 bp):
AAATGTAATTTTGAGAAAGTTTAGGGGTCAAAATGCAATTTTAGAAAAATTTAGGGGTTG
Found at i:41496851 original size:30 final size:30
Alignment explanation
Indices: 41496701--41496848 Score: 203
Period size: 30 Copynumber: 5.0 Consensus size: 30
41496691 GGCCAAAACA
*
41496701 TAATTTTGAGAAAGTTTATGGGTCAAAATG
1 TAATTTTGAGAAAGTTTAGGGGTCAAAATG
41496731 TAATTTTGAGAAAGTTTAGGGGTCAAAATG
1 TAATTTTGAGAAAGTTTAGGGGTCAAAATG
* * **
41496761 TAA-TTT-AAAAAATTTAGGGGTTGAAATG
1 TAATTTTGAGAAAGTTTAGGGGTCAAAATG
41496789 TAATTTTGAGAAAGTTTAGGGGTCAAAATG
1 TAATTTTGAGAAAGTTTAGGGGTCAAAATG
* *
41496819 CAATTTT-AGAAAATTTTAGGGGTCAAAATG
1 TAATTTTGAG-AAAGTTTAGGGGTCAAAATG
41496849 CAAAAAAAAT
Statistics
Matches: 104, Mismatches: 11, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
28 21 0.20
29 8 0.08
30 75 0.72
ACGTcount: A:0.39, C:0.03, G:0.24, T:0.34
Consensus pattern (30 bp):
TAATTTTGAGAAAGTTTAGGGGTCAAAATG
Found at i:41496864 original size:2 final size:2
Alignment explanation
Indices: 41496859--41496889 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
41496849 CAAAAAAAAT
41496859 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
41496890 TTATTTATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:41505450 original size:22 final size:22
Alignment explanation
Indices: 41505425--41505467 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
41505415 ACAAATGAGT
41505425 TTTTATATTTATAATTTATTAA
1 TTTTATATTTATAATTTATTAA
* *
41505447 TTTTATTTTTATATTTTATTA
1 TTTTATATTTATAATTTATTA
41505468 TTGTTCGATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (22 bp):
TTTTATATTTATAATTTATTAA
Found at i:41505454 original size:13 final size:13
Alignment explanation
Indices: 41505424--41505466 Score: 52
Period size: 13 Copynumber: 3.2 Consensus size: 13
41505414 AACAAATGAG
41505424 TTTTTATATTTATAA
1 TTTTTATATTT-T-A
41505439 TTTATTA-ATTTTA
1 TTT-TTATATTTTA
41505452 TTTTTATATTTTA
1 TTTTTATATTTTA
41505465 TT
1 TT
41505467 ATTGTTCGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
12 3 0.12
13 12 0.46
14 1 0.04
15 7 0.27
16 3 0.12
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (13 bp):
TTTTTATATTTTA
Found at i:41507850 original size:39 final size:40
Alignment explanation
Indices: 41507788--41507876 Score: 126
Period size: 39 Copynumber: 2.2 Consensus size: 40
41507778 TACAAAGTAT
* * * * *
41507788 TTATATTAAAAAATATACCATAAATATAATAGATGTTTTA
1 TTATATTAAAAAACACACAATAAATATAATAAATATTTTA
41507828 TTATATTAAAAAACACA-AATAAATATAATAAATATTTTA
1 TTATATTAAAAAACACACAATAAATATAATAAATATTTTA
41507867 TTATATTAAA
1 TTATATTAAA
41507877 TAAAATTTTT
Statistics
Matches: 44, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
39 29 0.66
40 15 0.34
ACGTcount: A:0.54, C:0.04, G:0.02, T:0.39
Consensus pattern (40 bp):
TTATATTAAAAAACACACAATAAATATAATAAATATTTTA
Found at i:41510006 original size:23 final size:25
Alignment explanation
Indices: 41509977--41510028 Score: 81
Period size: 24 Copynumber: 2.1 Consensus size: 25
41509967 CATTCTATAT
41509977 TTAAAAAATCAT-TATATTTATAA-A
1 TTAAAAAA-CATATATATTTATAATA
41510001 TTAAAAAACATATATATTTATAATA
1 TTAAAAAACATATATATTTATAATA
41510026 TTA
1 TTA
41510029 TCTTTTAAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
23 3 0.12
24 19 0.73
25 4 0.15
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (25 bp):
TTAAAAAACATATATATTTATAATA
Found at i:41511404 original size:99 final size:99
Alignment explanation
Indices: 41511231--41511535 Score: 544
Period size: 99 Copynumber: 3.1 Consensus size: 99
41511221 ATTACTTTAG
41511231 AAAAAAAAAATCGTCGTCTTTGCAATTTATTTTGAGAAAAGACTCTAAAAATGGCCATTTTATCT
1 AAAAAAAAAATCGTCGTCTTTGCAATTTATTTTGAGAAAAGACTCTAAAAATGGCCATTTTATCT
*
41511296 CTATCTCCACGGTCATTTGTTTACTTTGTGGAAA
66 ATATCTCCACGGTCATTTGTTTACTTTGTGGAAA
41511330 AAAAAAAAACATCGTCGTCTTTGCAATTTATTTTGAGAAAAGACT-TAAAAATGGCCATTTTATC
1 AAAAAAAAA-ATCGTCGTCTTTGCAATTTATTTTGAGAAAAGACTCTAAAAATGGCCATTTTATC
*
41511394 TATATCTCCACGGTCATTTGTTTACTTTGTGG--G
65 TATATCTCCACGGTCATTTGTTTACTTTGTGGAAA
* *
41511427 GAAAAAAAAATCGTCTTCTTTGCAATTTATTTTGAGAAAAGACTCTAAAAATGGCCATTTTATCT
1 AAAAAAAAAATCGTCGTCTTTGCAATTTATTTTGAGAAAAGACTCTAAAAATGGCCATTTTATCT
41511492 ATATCTCCACGGTCATTTGTTTACTTTGTGGAAA
66 ATATCTCCACGGTCATTTGTTTACTTTGTGGAAA
41511526 AAAAAAAAAA
1 AAAAAAAAAA
41511536 CCTTAGTATA
Statistics
Matches: 196, Mismatches: 6, Indels: 8
0.93 0.03 0.04
Matches are distributed among these distances:
96 34 0.17
97 59 0.30
99 68 0.35
100 35 0.18
ACGTcount: A:0.35, C:0.15, G:0.14, T:0.36
Consensus pattern (99 bp):
AAAAAAAAAATCGTCGTCTTTGCAATTTATTTTGAGAAAAGACTCTAAAAATGGCCATTTTATCT
ATATCTCCACGGTCATTTGTTTACTTTGTGGAAA
Found at i:41511500 original size:97 final size:97
Alignment explanation
Indices: 41511231--41511533 Score: 536
Period size: 97 Copynumber: 3.1 Consensus size: 97
41511221 ATTACTTTAG
41511231 AAAAAAAAAATCGTCGTCTTTGCAATTTATTTTGAGAAAAGACTCTAAAAATGGCCATTTTATCT
1 AAAAAAAAAATCGTCGTCTTTGCAATTTATTTTGAGAAAAGACTCTAAAAATGGCCATTTTATCT
*
41511296 CTATCTCCACGGTCATTTGTTTACTTTGTGGAAA
66 ATATCTCCACGGTCATTTGTTTACTTTGTGG--A
41511330 AAAAAAAAACATCGTCGTCTTTGCAATTTATTTTGAGAAAAGACT-TAAAAATGGCCATTTTATC
1 AAAAAAAAA-ATCGTCGTCTTTGCAATTTATTTTGAGAAAAGACTCTAAAAATGGCCATTTTATC
*
41511394 TATATCTCCACGGTCATTTGTTTACTTTGTGGG
65 TATATCTCCACGGTCATTTGTTTACTTTGTGGA
* *
41511427 GAAAAAAAAATCGTCTTCTTTGCAATTTATTTTGAGAAAAGACTCTAAAAATGGCCATTTTATCT
1 AAAAAAAAAATCGTCGTCTTTGCAATTTATTTTGAGAAAAGACTCTAAAAATGGCCATTTTATCT
41511492 ATATCTCCACGGTCATTTGTTTACTTTGTGGA
66 ATATCTCCACGGTCATTTGTTTACTTTGTGGA
41511524 AAAAAAAAAA
1 AAAAAAAAAA
41511534 AACCTTAGTA
Statistics
Matches: 196, Mismatches: 6, Indels: 6
0.94 0.03 0.03
Matches are distributed among these distances:
96 34 0.17
97 68 0.35
99 59 0.30
100 35 0.18
ACGTcount: A:0.35, C:0.15, G:0.14, T:0.36
Consensus pattern (97 bp):
AAAAAAAAAATCGTCGTCTTTGCAATTTATTTTGAGAAAAGACTCTAAAAATGGCCATTTTATCT
ATATCTCCACGGTCATTTGTTTACTTTGTGGA
Found at i:41516093 original size:21 final size:24
Alignment explanation
Indices: 41516054--41516107 Score: 60
Period size: 22 Copynumber: 2.4 Consensus size: 24
41516044 TCTAAAAAAA
* **
41516054 TAAAAAAAATACATAAATATTTTC
1 TAAAAAATATACATAAATAGATTC
41516078 -AAAAAATATA-AT-AATAGATTC
1 TAAAAAATATACATAAATAGATTC
41516099 TAAAAAATA
1 TAAAAAATA
41516108 CATGGAAATG
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
21 7 0.27
22 10 0.38
23 9 0.35
ACGTcount: A:0.63, C:0.06, G:0.02, T:0.30
Consensus pattern (24 bp):
TAAAAAATATACATAAATAGATTC
Found at i:41516203 original size:21 final size:21
Alignment explanation
Indices: 41516179--41516226 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 21
41516169 AAAATAGATA
41516179 AATATTTTTAAAAAGTATAAT
1 AATATTTTTAAAAAGTATAAT
** ** *
41516200 AATAAATTTAAAATTTATATT
1 AATATTTTTAAAAAGTATAAT
41516221 AATATT
1 AATATT
41516227 AATATTAAAT
Statistics
Matches: 20, Mismatches: 7, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (21 bp):
AATATTTTTAAAAAGTATAAT
Found at i:41516532 original size:16 final size:16
Alignment explanation
Indices: 41516497--41516528 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
41516487 AATTGACCTA
41516497 TATTTTTTTAAATATT
1 TATTTTTTTAAATATT
41516513 TATTTTTTT-AATATT
1 TATTTTTTTAAATATT
41516528 T
1 T
41516529 TATTATGTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (16 bp):
TATTTTTTTAAATATT
Found at i:41520244 original size:7 final size:7
Alignment explanation
Indices: 41520232--41520264 Score: 66
Period size: 7 Copynumber: 4.7 Consensus size: 7
41520222 ATTTCATTTT
41520232 ATTTACA
1 ATTTACA
41520239 ATTTACA
1 ATTTACA
41520246 ATTTACA
1 ATTTACA
41520253 ATTTACA
1 ATTTACA
41520260 ATTTA
1 ATTTA
41520265 TTTTTATTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.42, C:0.12, G:0.00, T:0.45
Consensus pattern (7 bp):
ATTTACA
Found at i:41537407 original size:18 final size:19
Alignment explanation
Indices: 41537384--41537421 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
41537374 TTTTTAAAAA
41537384 TATAAAT-TTTGGAATTTT
1 TATAAATATTTGGAATTTT
*
41537402 TATAAATATTTTGAATTTT
1 TATAAATATTTGGAATTTT
41537421 T
1 T
41537422 GAAAATTATG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.34, C:0.00, G:0.08, T:0.58
Consensus pattern (19 bp):
TATAAATATTTGGAATTTT
Found at i:41537427 original size:19 final size:20
Alignment explanation
Indices: 41537389--41537440 Score: 56
Period size: 19 Copynumber: 2.6 Consensus size: 20
41537379 AAAAATATAA
41537389 ATTTTGGAATTTTTATAAA-T
1 ATTTT-GAATTTTTATAAATT
41537409 ATTTTGAATTTTTGA-AAATT
1 ATTTTGAATTTTT-ATAAATT
*
41537429 ATGTTG-ATTTTT
1 ATTTTGAATTTTT
41537441 TTTTGTAATT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.58
Consensus pattern (20 bp):
ATTTTGAATTTTTATAAATT
Found at i:41540731 original size:25 final size:23
Alignment explanation
Indices: 41540650--41540749 Score: 114
Period size: 22 Copynumber: 4.3 Consensus size: 23
41540640 TGCACTATTA
*
41540650 AACAGAGAGCACTAAAGTGCTAT
1 AACAGAGAGCACTAATGTGCTAT
*
41540673 -ACAGAGAGCACAAATGTGCTA-
1 AACAGAGAGCACTAATGTGCTAT
41540694 AACAGAGAGCACTAATGTGCTAAT
1 AACAGAGAGCACTAATGTGCT-AT
* *
41540718 AATTAGAGAGCACTAACGTGCTAAT
1 AA-CAGAGAGCACTAATGTGCT-AT
41540743 AATCAGA
1 AA-CAGA
41540750 AAGGGCGCTA
Statistics
Matches: 67, Mismatches: 6, Indels: 6
0.85 0.08 0.08
Matches are distributed among these distances:
22 38 0.57
23 1 0.01
24 2 0.03
25 26 0.39
ACGTcount: A:0.43, C:0.17, G:0.21, T:0.19
Consensus pattern (23 bp):
AACAGAGAGCACTAATGTGCTAT
Found at i:41543522 original size:37 final size:39
Alignment explanation
Indices: 41543462--41543535 Score: 109
Period size: 37 Copynumber: 1.9 Consensus size: 39
41543452 ATTAGAAAAA
*
41543462 TATAAAAATTGTTAAAAAATATAAAAT-TATA-AAATTT
1 TATAAAAATTCTTAAAAAATATAAAATATATAGAAATTT
41543499 TATAAAAA-TCTTAAAAAATTATAAAATATATAGAAAT
1 TATAAAAATTCTTAAAAAA-TATAAAATATATAGAAAT
41543536 ATAAAATTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
36 9 0.27
37 16 0.48
38 4 0.12
39 4 0.12
ACGTcount: A:0.61, C:0.01, G:0.03, T:0.35
Consensus pattern (39 bp):
TATAAAAATTCTTAAAAAATATAAAATATATAGAAATTT
Found at i:41543524 original size:46 final size:44
Alignment explanation
Indices: 41543465--41543578 Score: 129
Period size: 46 Copynumber: 2.5 Consensus size: 44
41543455 AGAAAAATAT
* *
41543465 AAAAATTGTTAAAAAATATAAAATTATAAAATTTTATAAAAATCTTA
1 AAAAATT-ATAAAAAATATAAAA-TATAAAATTTTAT-AAAATCGTA
* *
41543512 AAAAATTATAAAATATATAGAAATATAAAATTTTATAAAGTCGTA
1 AAAAATTATAAAAAATATA-AAATATAAAATTTTATAAAATCGTA
* *
41543557 AGAAAATTATACAAAATGTAAA
1 A-AAAATTATAAAAAATATAAA
41543579 GAAATATAAA
Statistics
Matches: 58, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
45 10 0.17
46 38 0.66
47 10 0.17
ACGTcount: A:0.60, C:0.03, G:0.05, T:0.32
Consensus pattern (44 bp):
AAAAATTATAAAAAATATAAAATATAAAATTTTATAAAATCGTA
Found at i:41543834 original size:19 final size:18
Alignment explanation
Indices: 41543811--41543874 Score: 60
Period size: 19 Copynumber: 3.4 Consensus size: 18
41543801 TAATAAAATT
41543811 TAAATTTTTATATTTTTA
1 TAAATTTTTATATTTTTA
41543829 TTAAATTTTAATAATATTTTTA
1 -TAAATTTT--T-ATATTTTTA
*
41543851 -AAATTTATTAT-TTATTA
1 TAAATTT-TTATATTTTTA
41543868 TAAATTT
1 TAAATTT
41543875 ATTTCTAATT
Statistics
Matches: 39, Mismatches: 1, Indels: 11
0.76 0.02 0.22
Matches are distributed among these distances:
17 5 0.13
18 8 0.21
19 9 0.23
20 6 0.15
21 2 0.05
22 9 0.23
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (18 bp):
TAAATTTTTATATTTTTA
Found at i:41543874 original size:18 final size:16
Alignment explanation
Indices: 41543843--41543877 Score: 52
Period size: 18 Copynumber: 2.1 Consensus size: 16
41543833 ATTTTAATAA
41543843 TATTTTTAAAATTTAT
1 TATTTTTAAAATTTAT
41543859 TATTTATTATAAATTTAT
1 TATTT-TTA-AAATTTAT
41543877 T
1 T
41543878 TCTAATTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.29
17 3 0.18
18 9 0.53
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (16 bp):
TATTTTTAAAATTTAT
Found at i:41553643 original size:27 final size:27
Alignment explanation
Indices: 41553606--41553677 Score: 99
Period size: 27 Copynumber: 2.6 Consensus size: 27
41553596 ATTATATAGT
41553606 GATTCAATTCGGTTAATTCAGGTAATCC
1 GATT-AATTCGGTTAATTCAGGTAATCC
* *
41553634 GATTAATTCGGTTAATTCGGGTAATTC
1 GATTAATTCGGTTAATTCAGGTAATCC
* *
41553661 GGTTAATTCTGTTAATT
1 GATTAATTCGGTTAATT
41553678 TTTAACCAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
27 36 0.90
28 4 0.10
ACGTcount: A:0.26, C:0.12, G:0.19, T:0.42
Consensus pattern (27 bp):
GATTAATTCGGTTAATTCAGGTAATCC
Found at i:41553674 original size:9 final size:9
Alignment explanation
Indices: 41553611--41553677 Score: 82
Period size: 9 Copynumber: 7.4 Consensus size: 9
41553601 ATAGTGATTC
41553611 AATTCGGTT
1 AATTCGGTT
41553620 AATTCAGG-T
1 AATTC-GGTT
* *
41553629 AATCCGATT
1 AATTCGGTT
41553638 AATTCGGTT
1 AATTCGGTT
*
41553647 AATTCGGGT
1 AATTCGGTT
41553656 AATTCGGTT
1 AATTCGGTT
*
41553665 AATTCTGTT
1 AATTCGGTT
41553674 AATT
1 AATT
41553678 TTTAACCAAA
Statistics
Matches: 49, Mismatches: 7, Indels: 4
0.82 0.12 0.07
Matches are distributed among these distances:
8 1 0.02
9 46 0.94
10 2 0.04
ACGTcount: A:0.27, C:0.12, G:0.19, T:0.42
Consensus pattern (9 bp):
AATTCGGTT
Found at i:41559497 original size:18 final size:18
Alignment explanation
Indices: 41559474--41559521 Score: 60
Period size: 18 Copynumber: 2.7 Consensus size: 18
41559464 AAATTATATT
41559474 TTTTTATAATTTTTTTTA
1 TTTTTATAATTTTTTTTA
* * *
41559492 TTTTTAAAAATATTTTTA
1 TTTTTATAATTTTTTTTA
*
41559510 TTTTTTTAATTT
1 TTTTTATAATTT
41559522 ATGCTCGTTA
Statistics
Matches: 23, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (18 bp):
TTTTTATAATTTTTTTTA
Found at i:41559518 original size:20 final size:19
Alignment explanation
Indices: 41559470--41559518 Score: 57
Period size: 20 Copynumber: 2.6 Consensus size: 19
41559460 CAAAAAATTA
*
41559470 TATTTTTTT-ATAATTTTT
1 TATTTTTTTAAAAATTTTT
41559488 T-TTATTTTTAAAAATATTTT
1 TATT-TTTTTAAAAAT-TTTT
41559508 TATTTTTTTAA
1 TATTTTTTTAA
41559519 TTTATGCTCG
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 2 0.08
18 6 0.23
19 4 0.15
20 12 0.46
21 2 0.08
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (19 bp):
TATTTTTTTAAAAATTTTT
Found at i:41571706 original size:22 final size:22
Alignment explanation
Indices: 41571664--41571707 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
41571654 AAAGCAAAAC
*
41571664 GAAACAGAAAGAAGGAAAAAGA
1 GAAACAGAAAGAAGAAAAAAGA
*
41571686 GAAAGAGAAAG-AGAAAGAAAGA
1 GAAACAGAAAGAAGAAA-AAAGA
41571708 AGAACCCATG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.68, C:0.02, G:0.30, T:0.00
Consensus pattern (22 bp):
GAAACAGAAAGAAGAAAAAAGA
Found at i:41572138 original size:19 final size:20
Alignment explanation
Indices: 41572114--41572154 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
41572104 GAATTTAGGC
41572114 AAATATTGAATA-AAAATTG
1 AAATATTGAATATAAAATTG
* *
41572133 AAATATTTAATATGAAATTG
1 AAATATTGAATATAAAATTG
41572153 AA
1 AA
41572155 TTGTGTTGTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.56, C:0.00, G:0.10, T:0.34
Consensus pattern (20 bp):
AAATATTGAATATAAAATTG
Found at i:41573597 original size:3 final size:3
Alignment explanation
Indices: 41573589--41573621 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
41573579 GTTTTTTGTT
41573589 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
41573622 ACAAATAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:41575920 original size:10 final size:10
Alignment explanation
Indices: 41575905--41575929 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
41575895 ACAATTACAA
41575905 CATTTCATGC
1 CATTTCATGC
41575915 CATTTCATGC
1 CATTTCATGC
41575925 CATTT
1 CATTT
41575930 TAAACCATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.20, C:0.28, G:0.08, T:0.44
Consensus pattern (10 bp):
CATTTCATGC
Found at i:41577856 original size:13 final size:13
Alignment explanation
Indices: 41577835--41577866 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
41577825 TTTGATTAAT
*
41577835 TAATGTAATATAA
1 TAATATAATATAA
41577848 TAATATAATATAA
1 TAATATAATATAA
41577861 TAATAT
1 TAATAT
41577867 TTTAATCTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (13 bp):
TAATATAATATAA
Found at i:41577966 original size:22 final size:22
Alignment explanation
Indices: 41577938--41578090 Score: 225
Period size: 22 Copynumber: 7.0 Consensus size: 22
41577928 TGTTGATAGT
*
41577938 ACGTACTAAGCTCTCATGTTTC
1 ACGTACTAAGCTCTCATGTTTA
41577960 ACGTACTAAGCTCTCATGTTTA
1 ACGTACTAAGCTCTCATGTTTA
41577982 ACGTACTAAGCTCTCATGTTTA
1 ACGTACTAAGCTCTCATGTTTA
* * * **
41578004 ACGAACTAAACCCTCATGGCTA
1 ACGTACTAAGCTCTCATGTTTA
**
41578026 ACGTACTAAGCTCTCATGGCTA
1 ACGTACTAAGCTCTCATGTTTA
*
41578048 ACGTACTAAGCTCTCATGTTTC
1 ACGTACTAAGCTCTCATGTTTA
41578070 ACGTACTAAGCTCTCATGTTT
1 ACGTACTAAGCTCTCATGTTT
41578091 GAACAATAAA
Statistics
Matches: 119, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 119 1.00
ACGTcount: A:0.27, C:0.26, G:0.14, T:0.33
Consensus pattern (22 bp):
ACGTACTAAGCTCTCATGTTTA
Found at i:41582789 original size:24 final size:24
Alignment explanation
Indices: 41582762--41582807 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
41582752 CACACACCAC
41582762 AGCTCAT-ATGAGCTTACCGATTTA
1 AGCTCATGA-GAGCTTACCGATTTA
*
41582786 AGCTCGTGAGAGCTTACCGATT
1 AGCTCATGAGAGCTTACCGATT
41582808 CACAGCCCGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
24 19 0.95
25 1 0.05
ACGTcount: A:0.26, C:0.22, G:0.22, T:0.30
Consensus pattern (24 bp):
AGCTCATGAGAGCTTACCGATTTA
Found at i:41605683 original size:28 final size:28
Alignment explanation
Indices: 41605651--41605709 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
41605641 TTGATTTTAT
*
41605651 AAATAA-AAAGGTTATTAATTAAAAATAA
1 AAATAATAAA-GTTATTAATTAAAAACAA
* *
41605679 AAATAATATATTTATTAATTAAAAACAA
1 AAATAATAAAGTTATTAATTAAAAACAA
41605707 AAA
1 AAA
41605710 GCTTGAAATA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
28 25 0.93
29 2 0.07
ACGTcount: A:0.64, C:0.02, G:0.03, T:0.31
Consensus pattern (28 bp):
AAATAATAAAGTTATTAATTAAAAACAA
Found at i:41617403 original size:12 final size:12
Alignment explanation
Indices: 41617360--41617407 Score: 50
Period size: 11 Copynumber: 4.3 Consensus size: 12
41617350 TTAGCAACTT
41617360 AAAATTATA-AA
1 AAAATTATATAA
*
41617371 AAAATTGT-T-A
1 AAAATTATATAA
*
41617381 AAAACTA-ATAA
1 AAAATTATATAA
41617392 AAAATTATATAA
1 AAAATTATATAA
41617404 AAAA
1 AAAA
41617408 GCATTTATAT
Statistics
Matches: 29, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
10 7 0.24
11 14 0.48
12 8 0.28
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.27
Consensus pattern (12 bp):
AAAATTATATAA
Found at i:41617837 original size:20 final size:18
Alignment explanation
Indices: 41617783--41617842 Score: 50
Period size: 20 Copynumber: 3.1 Consensus size: 18
41617773 TTTGATAACT
41617783 ATTTTTGATGACTTTTTATA
1 ATTTTTG-TGA-TTTTTATA
*
41617803 ATTTATTAGAT-TTTTTTATA
1 ATTT-TT-G-TGATTTTTATA
41617823 AGTTTTTGTGATTTTTATA
1 A-TTTTTGTGATTTTTATA
41617842 A
1 A
41617843 AATATATAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
18 1 0.03
19 10 0.29
20 15 0.44
21 5 0.15
22 3 0.09
ACGTcount: A:0.27, C:0.02, G:0.10, T:0.62
Consensus pattern (18 bp):
ATTTTTGTGATTTTTATA
Found at i:41617907 original size:17 final size:17
Alignment explanation
Indices: 41617885--41617917 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
41617875 TTTATAATGT
41617885 TTTATAAATTTTTTTAG
1 TTTATAAATTTTTTTAG
*
41617902 TTTATATATTTTTTTA
1 TTTATAAATTTTTTTA
41617918 TAATTTTTAT
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:0.27, C:0.00, G:0.03, T:0.70
Consensus pattern (17 bp):
TTTATAAATTTTTTTAG
Found at i:41618410 original size:17 final size:16
Alignment explanation
Indices: 41618371--41618411 Score: 50
Period size: 14 Copynumber: 2.6 Consensus size: 16
41618361 AATAAATAAT
41618371 TTAATCTAATATTTTTA
1 TTAAT-TAATATTTTTA
41618388 TT--TTAATATTATTTA
1 TTAATTAATATT-TTTA
41618403 TTAATTAAT
1 TTAATTAAT
41618412 TTTGATAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 6
0.78 0.00 0.22
Matches are distributed among these distances:
14 7 0.33
15 7 0.33
17 7 0.33
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (16 bp):
TTAATTAATATTTTTA
Found at i:41621716 original size:28 final size:28
Alignment explanation
Indices: 41621684--41621742 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
41621674 TTGATTTTAT
*
41621684 AAATAA-AAAGGTTATTAATTAAAAATAA
1 AAATAATAAA-GTTATTAATTAAAAACAA
* *
41621712 AAATAATATATTTATTAATTAAAAACAA
1 AAATAATAAAGTTATTAATTAAAAACAA
41621740 AAA
1 AAA
41621743 GCTTGAAATA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
28 25 0.93
29 2 0.07
ACGTcount: A:0.64, C:0.02, G:0.03, T:0.31
Consensus pattern (28 bp):
AAATAATAAAGTTATTAATTAAAAACAA
Found at i:41630923 original size:18 final size:16
Alignment explanation
Indices: 41630886--41630929 Score: 52
Period size: 18 Copynumber: 2.6 Consensus size: 16
41630876 TTTTCAAGTT
41630886 TGTAATGTTTTATATTA
1 TGTAAT-TTTTATATTA
*
41630903 TGTTATTTTTATATATAA
1 TGTAATTTTTATAT-T-A
41630921 TGTAATTTT
1 TGTAATTTT
41630930 GTAACACATA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
16 8 0.35
17 6 0.26
18 9 0.39
ACGTcount: A:0.30, C:0.00, G:0.09, T:0.61
Consensus pattern (16 bp):
TGTAATTTTTATATTA
Found at i:41631051 original size:15 final size:17
Alignment explanation
Indices: 41631033--41631069 Score: 51
Period size: 15 Copynumber: 2.3 Consensus size: 17
41631023 AATAAAAATC
41631033 ATATAAAATT-AT-TAA
1 ATATAAAATTAATATAA
*
41631048 ATATTAAATTAATATAA
1 ATATAAAATTAATATAA
41631065 ATATA
1 ATATA
41631070 TTTTTAACAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
15 9 0.50
16 2 0.11
17 7 0.39
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
ATATAAAATTAATATAA
Found at i:41634209 original size:11 final size:13
Alignment explanation
Indices: 41634193--41634226 Score: 54
Period size: 11 Copynumber: 2.8 Consensus size: 13
41634183 AATTTTACGG
41634193 AAAAATTTCG-T-
1 AAAAATTTCGTTC
41634204 AAAAATTTCGTTC
1 AAAAATTTCGTTC
41634217 AAAAATTTCG
1 AAAAATTTCG
41634227 ACGTTTGGGC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 10 0.48
12 1 0.05
13 10 0.48
ACGTcount: A:0.44, C:0.12, G:0.09, T:0.35
Consensus pattern (13 bp):
AAAAATTTCGTTC
Found at i:41653504 original size:22 final size:25
Alignment explanation
Indices: 41653474--41653519 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
41653464 TGACGAATTT
41653474 TGCACGTA-TTA-CT-TTTTACCTC
1 TGCACGTATTTACCTCTTTTACCTC
*
41653496 TGCAGGTATTTACCTCTTTTACCT
1 TGCACGTATTTACCTCTTTTACCT
41653520 TTTGTATCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 7 0.35
23 3 0.15
24 2 0.10
25 8 0.40
ACGTcount: A:0.17, C:0.26, G:0.11, T:0.46
Consensus pattern (25 bp):
TGCACGTATTTACCTCTTTTACCTC
Found at i:41665875 original size:22 final size:21
Alignment explanation
Indices: 41665847--41665893 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 21
41665837 ATTTTGATAA
41665847 AATTTTTGTA-CTAAAAATACTT
1 AATTTTT-TATCTAAAAAT-CTT
*
41665869 AATTTTTTATTTAAAAATCTT
1 AATTTTTTATCTAAAAATCTT
41665890 AATT
1 AATT
41665894 GTATCATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
21 9 0.39
22 14 0.61
ACGTcount: A:0.40, C:0.06, G:0.02, T:0.51
Consensus pattern (21 bp):
AATTTTTTATCTAAAAATCTT
Found at i:41690858 original size:25 final size:25
Alignment explanation
Indices: 41690759--41690902 Score: 80
Period size: 25 Copynumber: 5.7 Consensus size: 25
41690749 TAACGGGTAA
* * *
41690759 CTCCGAAGAGCTATTAATCAGGAAG
1 CTCCGGAGAGCCATTAATCAAGAAG
* * *
41690784 CTTCGGATAGCCA-TATATCTAGAAG
1 CTCCGGAGAGCCATTA-ATCAAGAAG
* ** * *
41690809 TTCAAGCGAGCCA-T-ATCGAGAAG
1 CTCCGGAGAGCCATTAATCAAGAAG
41690832 CTCCGGAGAGCCATTAATCAAGAAG
1 CTCCGGAGAGCCATTAATCAAGAAG
** * *
41690857 CTCACAAAGAGCCTTTAATCGAGAAG
1 CTC-CGGAGAGCCATTAATCAAGAAG
41690883 CT-CGAGAAGAGCCATATAAT
1 CTCCG-G-AGAGCCAT-TAAT
41690903 GGGACACTCA
Statistics
Matches: 87, Mismatches: 25, Indels: 12
0.70 0.20 0.10
Matches are distributed among these distances:
23 17 0.20
24 4 0.05
25 35 0.40
26 27 0.31
27 4 0.05
ACGTcount: A:0.36, C:0.22, G:0.22, T:0.20
Consensus pattern (25 bp):
CTCCGGAGAGCCATTAATCAAGAAG
Found at i:41690892 original size:26 final size:26
Alignment explanation
Indices: 41690816--41690902 Score: 85
Period size: 26 Copynumber: 3.4 Consensus size: 26
41690806 AAGTTCAAGC
41690816 GAGCCA-T-ATCGAGAAGCTCCG-G-A
1 GAGCCATTAATCGAGAAGCT-CGAGAA
* *
41690839 GAGCCATTAATCAAGAAGCTC-ACAAA
1 GAGCCATTAATCGAGAAGCTCGA-GAA
*
41690865 GAGCCTTTAATCGAGAAGCTCGAGAA
1 GAGCCATTAATCGAGAAGCTCGAGAA
41690891 GAGCCATATAAT
1 GAGCCAT-TAAT
41690903 GGGACACTCA
Statistics
Matches: 51, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
23 6 0.12
24 2 0.04
25 10 0.20
26 28 0.55
27 5 0.10
ACGTcount: A:0.38, C:0.22, G:0.23, T:0.17
Consensus pattern (26 bp):
GAGCCATTAATCGAGAAGCTCGAGAA
Found at i:41707778 original size:2 final size:2
Alignment explanation
Indices: 41707771--41707803 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
41707761 TTGAGTGATT
41707771 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
41707804 TTNNNNNNNN
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:41708098 original size:2 final size:2
Alignment explanation
Indices: 41708091--41708147 Score: 107
Period size: 2 Copynumber: 29.0 Consensus size: 2
41708081 TTCTTTGAAC
41708091 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
41708133 TA TA TA TA TA -A TA TA
1 TA TA TA TA TA TA TA TA
41708148 GTCATTTAGT
Statistics
Matches: 54, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 53 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:41709266 original size:19 final size:19
Alignment explanation
Indices: 41709242--41709286 Score: 90
Period size: 19 Copynumber: 2.4 Consensus size: 19
41709232 GTAGCGGGTA
41709242 AAAATGAAATGATGATATT
1 AAAATGAAATGATGATATT
41709261 AAAATGAAATGATGATATT
1 AAAATGAAATGATGATATT
41709280 AAAATGA
1 AAAATGA
41709287 TAGGTAAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.56, C:0.00, G:0.16, T:0.29
Consensus pattern (19 bp):
AAAATGAAATGATGATATT
Found at i:41711539 original size:15 final size:14
Alignment explanation
Indices: 41711521--41711551 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
41711511 TTGAAAATGG
41711521 TTTTTGAAAAATAA
1 TTTTTGAAAAATAA
*
41711535 TTTTTGGAAAATAA
1 TTTTTGAAAAATAA
41711549 TTT
1 TTT
41711552 ATTTTTCTGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.42, C:0.00, G:0.10, T:0.48
Consensus pattern (14 bp):
TTTTTGAAAAATAA
Found at i:41716177 original size:20 final size:21
Alignment explanation
Indices: 41716142--41716180 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
41716132 TAAAAATAAT
*
41716142 ATAAATATTTATATAATCCTA
1 ATAAATATTTAAATAATCCTA
41716163 ATAAAT-TTTAAATAATCC
1 ATAAATATTTAAATAATCC
41716181 ATGGATTGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.49, C:0.10, G:0.00, T:0.41
Consensus pattern (21 bp):
ATAAATATTTAAATAATCCTA
Found at i:41719382 original size:11 final size:10
Alignment explanation
Indices: 41719362--41719394 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
41719352 TGTTTTAAGC
41719362 TTTT-TTAAT
1 TTTTATTAAT
41719371 TTTTAATTAAT
1 TTTT-ATTAAT
41719382 TTTTATTAAT
1 TTTTATTAAT
41719392 TTT
1 TTT
41719395 ATCCTTAAGT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 4 0.18
10 9 0.41
11 9 0.41
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (10 bp):
TTTTATTAAT
Found at i:41721212 original size:27 final size:24
Alignment explanation
Indices: 41721150--41721214 Score: 67
Period size: 24 Copynumber: 2.6 Consensus size: 24
41721140 CCGAGCCATA
*
41721150 TAATTTGGAAGCTCATGAGAACCG
1 TAATTGGGAAGCTCATGAGAACCG
* * *
41721174 TAATCGGGAAGCTCATGAAAGAGCCTT
1 TAATTGGGAAGCTCATG--AGAACC-G
41721201 TAATTGGGAAGCTC
1 TAATTGGGAAGCTC
41721215 CGGAGAGCCA
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
24 15 0.45
26 5 0.15
27 13 0.39
ACGTcount: A:0.32, C:0.17, G:0.26, T:0.25
Consensus pattern (24 bp):
TAATTGGGAAGCTCATGAGAACCG
Found at i:41727055 original size:10 final size:10
Alignment explanation
Indices: 41727032--41727073 Score: 52
Period size: 10 Copynumber: 4.3 Consensus size: 10
41727022 TTGATCGCTA
41727032 AAAAACTTAT
1 AAAAACTTAT
*
41727042 -AAAATTTAT
1 AAAAACTTAT
41727051 AAAAA-TTAAT
1 AAAAACTT-AT
41727061 AAAAACTTAT
1 AAAAACTTAT
41727071 AAA
1 AAA
41727074 TATTACAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
9 10 0.36
10 16 0.57
11 2 0.07
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.31
Consensus pattern (10 bp):
AAAAACTTAT
Found at i:41727073 original size:29 final size:30
Alignment explanation
Indices: 41727032--41727090 Score: 86
Period size: 29 Copynumber: 2.0 Consensus size: 30
41727022 TTGATCGCTA
*
41727032 AAAAACTTATAAA-ATTTATAAAAAT-TAAT
1 AAAAACTTATAAATA-TTACAAAAATCTAAT
41727061 AAAAACTTATAAATATTACAAAAATCTAAT
1 AAAAACTTATAAATATTACAAAAATCTAAT
41727091 GAATGTAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 22 0.81
30 5 0.19
ACGTcount: A:0.61, C:0.07, G:0.00, T:0.32
Consensus pattern (30 bp):
AAAAACTTATAAATATTACAAAAATCTAAT
Found at i:41727136 original size:32 final size:32
Alignment explanation
Indices: 41727100--41727161 Score: 90
Period size: 32 Copynumber: 1.9 Consensus size: 32
41727090 TGAATGTAAT
* *
41727100 AAATTTTA-ATAAATTATAAAAAAAATTATTTA
1 AAATTTTACAAAAATAAT-AAAAAAATTATTTA
41727132 AAATTTTACAAAAATAATAAAAAAATTATT
1 AAATTTTACAAAAATAATAAAAAAATTATT
41727162 AACAATTATT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
32 20 0.74
33 7 0.26
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (32 bp):
AAATTTTACAAAAATAATAAAAAAATTATTTA
Found at i:41727184 original size:31 final size:31
Alignment explanation
Indices: 41727100--41727174 Score: 89
Period size: 32 Copynumber: 2.3 Consensus size: 31
41727090 TGAATGTAAT
* *
41727100 AAATTTTAATAAATTATAAAAAAAATTATTTA
1 AAATTTTAAAAAATAAT-AAAAAAATTATTTA
41727132 AAATTTTACAAAAATAATAAAAAAATTA-TTA
1 AAATTTTA-AAAAATAATAAAAAAATTATTTA
41727163 ACAATTATTAAA
1 A-AATT-TTAAA
41727175 CATATTAAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
31 4 0.11
32 24 0.63
33 10 0.26
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (31 bp):
AAATTTTAAAAAATAATAAAAAAATTATTTA
Found at i:41727198 original size:10 final size:10
Alignment explanation
Indices: 41727121--41727214 Score: 54
Period size: 10 Copynumber: 9.5 Consensus size: 10
41727111 AATTATAAAA
*
41727121 AAAATTATTT
1 AAAATTATAT
* *
41727131 AAAATTTTACA
1 AAAATTATA-T
* *
41727142 AAAATAATAAA
1 AAAATTAT-AT
41727153 AAAATTAT-T
1 AAAATTATAT
41727162 AACAATTAT-T
1 AA-AATTATAT
41727172 AAACA-TAT-T
1 AAA-ATTATAT
41727181 AAAATTATAT
1 AAAATTATAT
*
41727191 AAACTTATA-
1 AAAATTATAT
*
41727200 AAAATTATAA
1 AAAATTATAT
41727210 AAAAT
1 AAAAT
41727215 CATAAAAGCT
Statistics
Matches: 68, Mismatches: 9, Indels: 14
0.75 0.10 0.15
Matches are distributed among these distances:
8 1 0.01
9 21 0.31
10 31 0.46
11 14 0.21
12 1 0.01
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.35
Consensus pattern (10 bp):
AAAATTATAT
Found at i:41727209 original size:9 final size:9
Alignment explanation
Indices: 41727032--41727212 Score: 62
Period size: 9 Copynumber: 18.6 Consensus size: 9
41727022 TTGATCGCTA
41727032 AAAAACTTAT
1 AAAAA-TTAT
*
41727042 AAAATTTAT
1 AAAAATTAT
41727051 AAAAATTAAT
1 AAAAATT-AT
41727061 AAAAACTTAT
1 AAAAA-TTAT
* *
41727071 AAATATTAC
1 AAAAATTAT
41727080 AAAAATCTA-
1 AAAAAT-TAT
**
41727089 ATGAATGTA-
1 AAAAAT-TAT
* *
41727098 ATAAATTTT
1 AAAAATTAT
41727107 AATAAATTAT
1 AA-AAATTAT
41727117 AAAAAAAATTATTT
1 ---AAAAATTA--T
* *
41727131 AAAATTTTAC
1 AAAA-ATTAT
*
41727141 AAAAATAATAA
1 AAAAAT--TAT
41727152 AAAAATTATT
1 AAAAATTA-T
*
41727162 AACAATTATT
1 AAAAATTA-T
*
41727172 AAACA-TAT
1 AAAAATTAT
*
41727180 TAAAATTAT
1 AAAAATTAT
*
41727189 ATAAACTTAT
1 A-AAAATTAT
41727199 AAAAATTAT
1 AAAAATTAT
41727208 AAAAA
1 AAAAA
41727213 ATCATAAAAG
Statistics
Matches: 130, Mismatches: 25, Indels: 33
0.69 0.13 0.18
Matches are distributed among these distances:
8 5 0.04
9 50 0.38
10 49 0.38
11 14 0.11
12 9 0.07
13 2 0.02
14 1 0.01
ACGTcount: A:0.60, C:0.04, G:0.01, T:0.34
Consensus pattern (9 bp):
AAAAATTAT
Found at i:41727219 original size:19 final size:19
Alignment explanation
Indices: 41727030--41727221 Score: 70
Period size: 19 Copynumber: 9.8 Consensus size: 19
41727020 TATTGATCGC
*
41727030 TAAAAAACTTATAAAATTTA
1 TAAAAAA-TTATAAAAATTA
41727050 T-AAAAATTAATAAAAACTTA
1 TAAAAAATT-ATAAAAA-TTA
* * *
41727070 T-AAATATTACAAAAA-TC
1 TAAAAAATTATAAAAATTA
** * *
41727087 TAATGAATGTA-ATAAATTT
1 TAAAAAAT-TATAAAAATTA
*
41727106 TAATAAATTATAAAAAAAATTA
1 TAAAAAATTAT---AAAAATTA
** * *
41727128 TTTAAAATTTTACAAAAATAA
1 --TAAAAAATTATAAAAATTA
*
41727149 TAAAAAAATTATTAACAATTA
1 T-AAAAAATTA-TAAAAATTA
* * *
41727170 TTAAACA-TATTAAAATTA
1 TAAAAAATTATAAAAATTA
* *
41727188 TATAAACTTATAAAAATTA
1 TAAAAAATTATAAAAATTA
*
41727207 TAAAAAATCATAAAA
1 TAAAAAATTATAAAA
41727222 GCTTGAATTG
Statistics
Matches: 124, Mismatches: 34, Indels: 29
0.66 0.18 0.16
Matches are distributed among these distances:
17 2 0.02
18 21 0.17
19 52 0.42
20 22 0.18
21 14 0.11
22 6 0.05
24 7 0.06
ACGTcount: A:0.60, C:0.05, G:0.01, T:0.34
Consensus pattern (19 bp):
TAAAAAATTATAAAAATTA
Found at i:41730478 original size:10 final size:10
Alignment explanation
Indices: 41730463--41730556 Score: 68
Period size: 10 Copynumber: 9.3 Consensus size: 10
41730453 CTAGTTCATG
41730463 TTTTTATAAT
1 TTTTTATAAT
41730473 TTTTTATAAT
1 TTTTTATAAT
*
41730483 TTTATATCAA-
1 TTTTTAT-AAT
*
41730493 TTTTAAT-AT
1 TTTTTATAAT
* *
41730502 TTTTAATAAG
1 TTTTTATAAT
**
41730512 TTTTTATTCT
1 TTTTTATAAT
41730522 TTTCTTATAAT
1 TTT-TTATAAT
*
41730533 TTTTT-TAGAA
1 TTTTTATA-AT
41730543 TTTTTATATAT
1 TTTTTATA-AT
41730554 TTT
1 TTT
41730557 CATAAAATTT
Statistics
Matches: 65, Mismatches: 13, Indels: 11
0.73 0.15 0.12
Matches are distributed among these distances:
8 1 0.02
9 9 0.14
10 39 0.60
11 16 0.25
ACGTcount: A:0.29, C:0.03, G:0.02, T:0.66
Consensus pattern (10 bp):
TTTTTATAAT
Found at i:41734937 original size:136 final size:135
Alignment explanation
Indices: 41734694--41734965 Score: 526
Period size: 136 Copynumber: 2.0 Consensus size: 135
41734684 TAAATTCTAA
41734694 TATGGAAACAAGTAAAGAGTCCTGCTTGTGTCTTTTAAATGTACTTGATACAATAAGTATTTTGA
1 TATGGAAACAAGTAAAGAGTCCTGCTTGTGTCTTTTAAATGTACTTGATACAATAAGTATTTTGA
41734759 AATCTTAGATGGACCTTTTAAATTTGACCCAAACCTAAATAAAACCATTTCCGAACAAAGCATTT
66 AATCTTAGATGGACCTTTTAAATTTGACCCAAACCTAAATAAAACCATTTCCGAACAAAGCATTT
41734824 GGATT
131 GGATT
*
41734829 TATGGAAACAAGTAAATAGTCCTGCTTGTGTCTTTTAAATGTACTTGATACAATTAAGTATTTTG
1 TATGGAAACAAGTAAAGAGTCCTGCTTGTGTCTTTTAAATGTACTTGATACAA-TAAGTATTTTG
41734894 AAATCTTAGATGGACCTTTTAAATTTGACCCAAACCTAAATAAAACCATTTCCGAACAAAGCATT
65 AAATCTTAGATGGACCTTTTAAATTTGACCCAAACCTAAATAAAACCATTTCCGAACAAAGCATT
41734959 TGGATT
130 TGGATT
41734965 T
1 T
41734966 TGAAATCCAA
Statistics
Matches: 135, Mismatches: 1, Indels: 1
0.99 0.01 0.01
Matches are distributed among these distances:
135 52 0.39
136 83 0.61
ACGTcount: A:0.36, C:0.15, G:0.14, T:0.34
Consensus pattern (135 bp):
TATGGAAACAAGTAAAGAGTCCTGCTTGTGTCTTTTAAATGTACTTGATACAATAAGTATTTTGA
AATCTTAGATGGACCTTTTAAATTTGACCCAAACCTAAATAAAACCATTTCCGAACAAAGCATTT
GGATT
Found at i:41746375 original size:34 final size:33
Alignment explanation
Indices: 41746332--41746404 Score: 137
Period size: 34 Copynumber: 2.2 Consensus size: 33
41746322 AAAAAATGCA
41746332 TATGCATCAGCACAGATTGTGCACGCATGGATC
1 TATGCATCAGCACAGATTGTGCACGCATGGATC
41746365 GTATGCATCAGCACAGATTGTGCACGCATGGATC
1 -TATGCATCAGCACAGATTGTGCACGCATGGATC
41746399 TATGCA
1 TATGCA
41746405 CAGATTGATG
Statistics
Matches: 39, Mismatches: 0, Indels: 1
0.98 0.00 0.03
Matches are distributed among these distances:
33 6 0.15
34 33 0.85
ACGTcount: A:0.27, C:0.23, G:0.25, T:0.25
Consensus pattern (33 bp):
TATGCATCAGCACAGATTGTGCACGCATGGATC
Found at i:41754953 original size:70 final size:71
Alignment explanation
Indices: 41754867--41755006 Score: 246
Period size: 70 Copynumber: 2.0 Consensus size: 71
41754857 ATTTATTTGT
41754867 TAAAATTTAATCTTTTTATTGGATTAAACAAAATTATAGGGAAAATAATGAAAA-CCTTTTTTAG
1 TAAAATTTAATCTTTTTATTGGATTAAACAAAATTATAGGGAAAATAATGAAAACCCTTTTTTAG
41754931 TTTCTC
66 TTTCTC
* * *
41754937 TAAAATTTAATTTTTTTATTGGATTAAACAATATTATAGGGAAATTAATGAAAACCCTTTTTTAG
1 TAAAATTTAATCTTTTTATTGGATTAAACAAAATTATAGGGAAAATAATGAAAACCCTTTTTTAG
41755002 TTTCT
66 TTTCT
41755007 TTATTTTTTA
Statistics
Matches: 66, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
70 51 0.77
71 15 0.23
ACGTcount: A:0.39, C:0.08, G:0.10, T:0.44
Consensus pattern (71 bp):
TAAAATTTAATCTTTTTATTGGATTAAACAAAATTATAGGGAAAATAATGAAAACCCTTTTTTAG
TTTCTC
Found at i:41756942 original size:21 final size:21
Alignment explanation
Indices: 41756889--41756943 Score: 92
Period size: 21 Copynumber: 2.6 Consensus size: 21
41756879 ACTATTGTTT
*
41756889 CTAATCTCACCACTACAATAA
1 CTAATCTCACCGCTACAATAA
*
41756910 CTAATCTCACCGCTACAGTAA
1 CTAATCTCACCGCTACAATAA
41756931 CTAATCTCACCGC
1 CTAATCTCACCGC
41756944 CACCATTGTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.35, C:0.36, G:0.05, T:0.24
Consensus pattern (21 bp):
CTAATCTCACCGCTACAATAA
Found at i:41762538 original size:209 final size:210
Alignment explanation
Indices: 41762166--41762588 Score: 670
Period size: 209 Copynumber: 2.0 Consensus size: 210
41762156 AACCATATAA
* * * *
41762166 ATGTTGTCTCGGGGTACAAACAAACTAGACCAAGAGCTTTAAACTAGTAATTGTTGTCTGGACGC
1 ATGTTGTCTCGAGGTACAAACAAACTAGACCAAGAGCTTTAAACAAATAATTGTTGTCTAGACGC
* *
41762231 CAAGAAAAACAATCATGCGAAATTCTTAACAAGAAGTCCTCATTCATACCTCTTCATGAATTTTA
66 CAAGAAAAACAATCATGCAAAATTCTTAACAAGAAGTCCTCATTCATACCTCTTCATGAATCTTA
* * *
41762296 TCCATTAGCAACTACTTTCTCTAAGAGCAATTAGAACTCGATTTTTCGCAACAATTTTGAGAAGC
131 TCCATTAGCAACTACTTTCTCTAAAAACAATTAGAACTCGATTTTTCGCAACAATTTTGAGAAAC
41762361 TCTTCATCTATGATT
196 TCTTCATCTATGATT
* *
41762376 ATGTTGTCTTGAGGTACAAACGAACTAGACCAAGAGCTTTAAACAAATAATTGTTGTCTAGACGC
1 ATGTTGTCTCGAGGTACAAACAAACTAGACCAAGAGCTTTAAACAAATAATTGTTGTCTAGACGC
* **
41762441 CAAGGAAAACAAT-ATGCAAAATTCTTAAC-AGAAAGTCCTCATTTGTACCTCTTCATGAATCTT
66 CAAGAAAAACAATCATGCAAAATTCTTAACAAG-AAGTCCTCATTCATACCTCTTCATGAATCTT
* *
41762504 ATCCATTAGCAATTACTTTCTCTAAAAACAATTAGAACTCGATTTTTCGCAACAATTTTTAGAAA
130 ATCCATTAGCAACTACTTTCTCTAAAAACAATTAGAACTCGATTTTTCGCAACAATTTTGAGAAA
*
41762569 CTTTTCATCTATGATT
195 CTCTTCATCTATGATT
41762585 ATGT
1 ATGT
41762589 GGAAGATTAC
Statistics
Matches: 195, Mismatches: 17, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
208 2 0.01
209 122 0.63
210 71 0.36
ACGTcount: A:0.35, C:0.19, G:0.14, T:0.32
Consensus pattern (210 bp):
ATGTTGTCTCGAGGTACAAACAAACTAGACCAAGAGCTTTAAACAAATAATTGTTGTCTAGACGC
CAAGAAAAACAATCATGCAAAATTCTTAACAAGAAGTCCTCATTCATACCTCTTCATGAATCTTA
TCCATTAGCAACTACTTTCTCTAAAAACAATTAGAACTCGATTTTTCGCAACAATTTTGAGAAAC
TCTTCATCTATGATT
Found at i:41762947 original size:9 final size:9
Alignment explanation
Indices: 41762930--41763000 Score: 54
Period size: 9 Copynumber: 7.4 Consensus size: 9
41762920 TTATTTTTTT
41762930 AAATATAAA
1 AAATATAAA
*
41762939 AAATTTAAA
1 AAATATAAA
41762948 AAAGTATAAA
1 AAA-TATAAA
* *
41762958 AATTATTTAA
1 AAATA-TAAA
41762968 AAATGA-AAA
1 AAAT-ATAAA
41762977 AAAGTATAAA
1 AAA-TATAAA
*
41762987 AATTATAAA
1 AAATATAAA
41762996 TAAAT
1 -AAAT
41763001 TTTAATATTT
Statistics
Matches: 48, Mismatches: 8, Indels: 11
0.72 0.12 0.16
Matches are distributed among these distances:
9 25 0.52
10 22 0.46
11 1 0.02
ACGTcount: A:0.68, C:0.00, G:0.04, T:0.28
Consensus pattern (9 bp):
AAATATAAA
Found at i:41763000 original size:29 final size:29
Alignment explanation
Indices: 41762935--41763000 Score: 89
Period size: 29 Copynumber: 2.3 Consensus size: 29
41762925 TTTTTAAATA
**
41762935 TAAAAAATTTAAAAAAGTATAAAAATTAT
1 TAAAAAATGAAAAAAAGTATAAAAATTAT
*
41762964 TTAAAAATGAAAAAAAGTATAAAAATTA-
1 TAAAAAATGAAAAAAAGTATAAAAATTAT
41762992 TAAATAAAT
1 TAAA-AAAT
41763001 TTTAATATTT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
28 3 0.09
29 29 0.91
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.29
Consensus pattern (29 bp):
TAAAAAATGAAAAAAAGTATAAAAATTAT
Found at i:41766861 original size:129 final size:129
Alignment explanation
Indices: 41766629--41766885 Score: 442
Period size: 129 Copynumber: 2.0 Consensus size: 129
41766619 TTATAGGGTC
* *
41766629 ACAGTTATTGACCCTGGATTTTGCTTGTAATTGCCGGTTTGCTTCAGACTGACAGTTCCTATCTG
1 ACAGTTATTGACCCAGGACTTTGCTTGTAATTGCCGGTTTGCTTCAGACTGACAGTTCCTATCTG
*
41766694 ATTGTTCAATTGGCTGGAGTAAGGGCAGGGCCTGTTGATCAATGATGACAGCATGGTTATGACT
66 ATTGTTCAATTGGCTGGAGTAAGGGCAGGGCCTGTTGATCAATAATGACAGCATGGTTATGACT
* *
41766758 ACAGTTATTGACCCAGGACTTTGCTTGTAATTGCTGGTTTGCTTCAGGCTGACAGTTCCTATCTG
1 ACAGTTATTGACCCAGGACTTTGCTTGTAATTGCCGGTTTGCTTCAGACTGACAGTTCCTATCTG
* * *
41766823 ATTGTTCAATTGGCTGGGGTAGGGGCAGGGCCTTTTGATCAATAATGACAGCATGGTTATGAC
66 ATTGTTCAATTGGCTGGAGTAAGGGCAGGGCCTGTTGATCAATAATGACAGCATGGTTATGAC
41766886 CAGGTTTTCT
Statistics
Matches: 120, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
129 120 1.00
ACGTcount: A:0.21, C:0.18, G:0.27, T:0.34
Consensus pattern (129 bp):
ACAGTTATTGACCCAGGACTTTGCTTGTAATTGCCGGTTTGCTTCAGACTGACAGTTCCTATCTG
ATTGTTCAATTGGCTGGAGTAAGGGCAGGGCCTGTTGATCAATAATGACAGCATGGTTATGACT
Found at i:41770714 original size:39 final size:39
Alignment explanation
Indices: 41770658--41770789 Score: 183
Period size: 39 Copynumber: 3.4 Consensus size: 39
41770648 AGACAACAAG
41770658 TGCATTCTGCTCTTTGTATCTCATATTGTAGGGGACGAC
1 TGCATTCTGCTCTTTGTATCTCATATTGTAGGGGACGAC
* * * *
41770697 TGCATTCTGCTCCTTGTATCTCAGATTGTAAGGGACGAT
1 TGCATTCTGCTCTTTGTATCTCATATTGTAGGGGACGAC
* ** *
41770736 TGCATTCTGCTTTTTGTATCTCATATTGTAGGGGATAAT
1 TGCATTCTGCTCTTTGTATCTCATATTGTAGGGGACGAC
*
41770775 TGCCTTCTGCTCTTT
1 TGCATTCTGCTCTTT
41770790 ATGTGTAATA
Statistics
Matches: 81, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
39 81 1.00
ACGTcount: A:0.17, C:0.20, G:0.21, T:0.42
Consensus pattern (39 bp):
TGCATTCTGCTCTTTGTATCTCATATTGTAGGGGACGAC
Found at i:41776392 original size:20 final size:20
Alignment explanation
Indices: 41776367--41776404 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
41776357 TGGGTGGGCA
*
41776367 AGTTAACTTGCCACATCAGC
1 AGTTAACTTACCACATCAGC
41776387 AGTTAACTTACCACATCA
1 AGTTAACTTACCACATCA
41776405 TCGACACCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.34, C:0.29, G:0.11, T:0.26
Consensus pattern (20 bp):
AGTTAACTTACCACATCAGC
Found at i:41776493 original size:29 final size:31
Alignment explanation
Indices: 41776436--41776496 Score: 81
Period size: 30 Copynumber: 2.0 Consensus size: 31
41776426 AATTAATAAC
* * *
41776436 TGTTTTGTTTCTTTTTTACAATGTTAGTAAT
1 TGTTTTGTTTATTTTTTAAAATGTGAGTAAT
41776467 TGTTTTG-TTATTTTTTAAAAT-TGAGTAAT
1 TGTTTTGTTTATTTTTTAAAATGTGAGTAAT
41776496 T
1 T
41776497 AAAATAAGAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
29 8 0.30
30 12 0.44
31 7 0.26
ACGTcount: A:0.23, C:0.03, G:0.13, T:0.61
Consensus pattern (31 bp):
TGTTTTGTTTATTTTTTAAAATGTGAGTAAT
Found at i:41777521 original size:2 final size:2
Alignment explanation
Indices: 41777514--41777543 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
41777504 TCGCATATGG
41777514 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
41777544 CTTTGGAGAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:41784571 original size:23 final size:21
Alignment explanation
Indices: 41784545--41784600 Score: 53
Period size: 23 Copynumber: 2.5 Consensus size: 21
41784535 AAATTTTCCA
41784545 ATAAAGGAAAAAC-CTAAGGTTTT
1 ATAAA-GAAAAACTCT--GGTTTT
41784568 AT-AAGAAAAACTCTGGTTTT
1 ATAAAGAAAAACTCTGGTTTT
41784588 ATAATAAGAAAAA
1 AT-A-AAGAAAAA
41784601 GTTATTTTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
20 8 0.28
21 7 0.24
22 4 0.14
23 10 0.34
ACGTcount: A:0.52, C:0.07, G:0.14, T:0.27
Consensus pattern (21 bp):
ATAAAGAAAAACTCTGGTTTT
Found at i:41789019 original size:21 final size:22
Alignment explanation
Indices: 41788975--41789020 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
41788965 TATTTGGTTT
*
41788975 TTTAATTGGTTTTTATGTTCAA
1 TTTAATTGATTTTTATGTTCAA
41788997 TTTAATTGATTTATTA-G-TCAA
1 TTTAATTGATTT-TTATGTTCAA
41789018 TTT
1 TTT
41789021 TTTTATTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 7 0.32
22 12 0.55
23 3 0.14
ACGTcount: A:0.26, C:0.04, G:0.11, T:0.59
Consensus pattern (22 bp):
TTTAATTGATTTTTATGTTCAA
Found at i:41794300 original size:23 final size:23
Alignment explanation
Indices: 41794271--41794328 Score: 75
Period size: 22 Copynumber: 2.6 Consensus size: 23
41794261 GGCCGGCCCG
* *
41794271 TTTTTAATTAAAATTAAAATTAT
1 TTTTTAATTAAAATTAAAACTAA
41794294 TTTTTAA-TAAAATTAAAACTAA
1 TTTTTAATTAAAATTAAAACTAA
*
41794316 TTGTT-ATTAAAAT
1 TTTTTAATTAAAAT
41794329 AAATTGTTAG
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
21 1 0.03
22 23 0.74
23 7 0.23
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (23 bp):
TTTTTAATTAAAATTAAAACTAA
Found at i:41794324 original size:16 final size:16
Alignment explanation
Indices: 41794305--41794344 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
41794295 TTTTAATAAA
41794305 ATTAAAACT-AATTGTT
1 ATTAAAA-TAAATTGTT
41794321 ATTAAAATAAATTGTT
1 ATTAAAATAAATTGTT
*
41794337 AGTAAAAT
1 ATTAAAAT
41794345 TATCAAATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 1 0.05
16 21 0.95
ACGTcount: A:0.50, C:0.03, G:0.07, T:0.40
Consensus pattern (16 bp):
ATTAAAATAAATTGTT
Found at i:41794405 original size:66 final size:67
Alignment explanation
Indices: 41794335--41794477 Score: 252
Period size: 68 Copynumber: 2.1 Consensus size: 67
41794325 AAATAAATTG
*
41794335 TTAGTAAAATTATCAAATTATTAATTG-TTAATTGTATTAATTGTTGTAATAAAATCTAACATTT
1 TTAGTAAAATTATCAAATTATTAATTGATTAATTGTATTAATTGTTGTAACAAAATCTAACATTT
41794399 GA
66 GA
*
41794401 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAACAAAATCTAACATT
1 TTAGTAAAATTATCAAATTATTAATTG-ATTAATTGTATTAATTGTTGTAACAAAATCTAACATT
41794466 TGA
65 TGA
41794469 TTAGTAAAA
1 TTAGTAAAA
41794478 CAAACTTGAT
Statistics
Matches: 72, Mismatches: 3, Indels: 2
0.94 0.04 0.03
Matches are distributed among these distances:
66 26 0.36
68 46 0.64
ACGTcount: A:0.41, C:0.05, G:0.09, T:0.45
Consensus pattern (67 bp):
TTAGTAAAATTATCAAATTATTAATTGATTAATTGTATTAATTGTTGTAACAAAATCTAACATTT
GA
Found at i:41794431 original size:9 final size:9
Alignment explanation
Indices: 41794419--41794446 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
41794409 TTTATCAAAT
41794419 TATTAATTG
1 TATTAATTG
41794428 TATTAATTG
1 TATTAATTG
41794437 TATTAATTG
1 TATTAATTG
41794446 T
1 T
41794447 TGTAACAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.57
Consensus pattern (9 bp):
TATTAATTG
Found at i:41794583 original size:22 final size:24
Alignment explanation
Indices: 41794543--41794586 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
41794533 AAATAAACTT
41794543 AAAATAAAAAACTATTATATTTTA
1 AAAATAAAAAACTATTATATTTTA
41794567 AAAATAAAAAA-TA-TATATTT
1 AAAATAAAAAACTATTATATTT
41794587 AATATTTTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 7 0.35
23 2 0.10
24 11 0.55
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.36
Consensus pattern (24 bp):
AAAATAAAAAACTATTATATTTTA
Found at i:41800684 original size:6 final size:6
Alignment explanation
Indices: 41800673--41800698 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
41800663 GGAAAATCAG
41800673 AAAATA AAAATA AAAATA AAAATA AA
1 AAAATA AAAATA AAAATA AAAATA AA
41800699 GAACCAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (6 bp):
AAAATA
Found at i:41802857 original size:10 final size:10
Alignment explanation
Indices: 41802842--41802873 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
41802832 CAACACAAGT
*
41802842 AAGCTTAATG
1 AAGCTTAATA
41802852 AAGCTTAATA
1 AAGCTTAATA
41802862 AAGCTTAATA
1 AAGCTTAATA
41802872 AA
1 AA
41802874 TTCGTTGGCT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.50, C:0.09, G:0.12, T:0.28
Consensus pattern (10 bp):
AAGCTTAATA
Found at i:41803184 original size:42 final size:42
Alignment explanation
Indices: 41803116--41803251 Score: 157
Period size: 42 Copynumber: 3.2 Consensus size: 42
41803106 AGGCTGCACA
* * *
41803116 GAAGCACATAAGTGCTAAAC-AGAAACCCATAAGGGTTGAACG
1 GAAGCTCATAAGAGCTAAACGA-AAACCCATAAGGGTTAAACG
* *
41803158 GAAGCTCATAAGAGCTGAACGAAAACCCATAAGGGTTAAACT
1 GAAGCTCATAAGAGCTAAACGAAAACCCATAAGGGTTAAACG
* * * *
41803200 GAAGCTCAAAAGAGCTAAACGGAAACCCATTAGAGTTAAACG
1 GAAGCTCATAAGAGCTAAACGAAAACCCATAAGGGTTAAACG
* *
41803242 AAAACTCATA
1 GAAGCTCATA
41803252 TGAGTTAACT
Statistics
Matches: 79, Mismatches: 14, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
42 78 0.99
43 1 0.01
ACGTcount: A:0.45, C:0.19, G:0.21, T:0.15
Consensus pattern (42 bp):
GAAGCTCATAAGAGCTAAACGAAAACCCATAAGGGTTAAACG
Found at i:41803234 original size:21 final size:21
Alignment explanation
Indices: 41803122--41803286 Score: 89
Period size: 21 Copynumber: 7.9 Consensus size: 21
41803112 CACAGAAGCA
* *
41803122 CATAAGTGCTAAACAGAAACC
1 CATAAGAGCTAAACGGAAACC
* * * * *
41803143 CATAAGGGTTGAACGGAAGCT
1 CATAAGAGCTAAACGGAAACC
* *
41803164 CATAAGAGCTGAACGAAAACC
1 CATAAGAGCTAAACGGAAACC
* * * * *
41803185 CATAAGGGTTAAACTGAAGCT
1 CATAAGAGCTAAACGGAAACC
*
41803206 CAAAAGAGCTAAACGGAAACC
1 CATAAGAGCTAAACGGAAACC
* * * *
41803227 CATTAGAGTTAAACGAAAACT
1 CATAAGAGCTAAACGGAAACC
* * * * *
41803248 CATATGAG-TTAACTGAAGCT
1 CATAAGAGCTAAACGGAAACC
* *
41803268 CATGAGAGCTAAACAGAAA
1 CATAAGAGCTAAACGGAAA
41803287 GTAAACACAA
Statistics
Matches: 103, Mismatches: 40, Indels: 2
0.71 0.28 0.01
Matches are distributed among these distances:
20 14 0.14
21 89 0.86
ACGTcount: A:0.44, C:0.18, G:0.21, T:0.17
Consensus pattern (21 bp):
CATAAGAGCTAAACGGAAACC
Found at i:41805072 original size:18 final size:16
Alignment explanation
Indices: 41805030--41805086 Score: 62
Period size: 17 Copynumber: 3.4 Consensus size: 16
41805020 TTTCAGAGAT
41805030 TATAAAAGAAGAAAAAA
1 TATAAAAG-AGAAAAAA
41805047 TATAAAAGAGATAAATAA
1 TATAAAAGAGA-AAA-AA
*
41805065 TGTAAAAGA-AAAAAA
1 TATAAAAGAGAAAAAA
*
41805080 TTTAAAA
1 TATAAAA
41805087 TATATTTTTA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
15 8 0.22
16 6 0.17
17 12 0.33
18 10 0.28
ACGTcount: A:0.70, C:0.00, G:0.11, T:0.19
Consensus pattern (16 bp):
TATAAAAGAGAAAAAA
Found at i:41805243 original size:29 final size:29
Alignment explanation
Indices: 41805174--41805244 Score: 94
Period size: 28 Copynumber: 2.5 Consensus size: 29
41805164 ATTGAGTAAC
*
41805174 AAAAAAATTA-TTTAGGTACAACTTGTGA
1 AAAAAAAATAGTTTAGGTACAACTTGTGA
*
41805202 TAAAAAAAT-GTTTAGGTACTAACTT-TGA
1 AAAAAAAATAGTTTAGGTAC-AACTTGTGA
41805230 AAAAAAAATAGTTTA
1 AAAAAAAATAGTTTA
41805245 AATGTCAATT
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
28 27 0.73
29 10 0.27
ACGTcount: A:0.49, C:0.06, G:0.13, T:0.32
Consensus pattern (29 bp):
AAAAAAAATAGTTTAGGTACAACTTGTGA
Found at i:41809299 original size:17 final size:18
Alignment explanation
Indices: 41809267--41809301 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
41809257 AACATTAATC
*
41809267 TTAATTATTCTAAATATT
1 TTAATTAATCTAAATATT
41809285 TTAATTAAT-TAAATATT
1 TTAATTAATCTAAATATT
41809302 ATAGTATATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (18 bp):
TTAATTAATCTAAATATT
Found at i:41814404 original size:13 final size:15
Alignment explanation
Indices: 41814380--41814427 Score: 50
Period size: 13 Copynumber: 3.5 Consensus size: 15
41814370 AATGTAAAAA
41814380 TTATTAATTAAAT-T
1 TTATTAATTAAATAT
41814394 TTATT-ATTAAATAT
1 TTATTAATTAAATAT
*
41814408 TTA--AATAAAATAT
1 TTATTAATTAAATAT
*
41814421 TTGTTAA
1 TTATTAA
41814428 GAATAAAGTT
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
13 17 0.61
14 9 0.32
15 2 0.07
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (15 bp):
TTATTAATTAAATAT
Found at i:41816701 original size:37 final size:39
Alignment explanation
Indices: 41816660--41816752 Score: 104
Period size: 37 Copynumber: 2.4 Consensus size: 39
41816650 TAATAATATT
*
41816660 TTAATAGTTTAATATTAAATTTAAT-TT-AA-TACTTATC
1 TTAATAGTTTAATATT-AATTTAATATTAAAGTAATTATC
*
41816697 TTAATAGTATT-TTATTAATTTAATATTAAAGTAATTATC
1 TTAATAGT-TTAATATTAATTTAATATTAAAGTAATTATC
*
41816736 TTAATAAATTTAATATT
1 TTAAT-AGTTTAATATT
41816753 TATCTTGTAG
Statistics
Matches: 46, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
36 8 0.17
37 14 0.30
38 4 0.09
39 14 0.30
40 6 0.13
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.52
Consensus pattern (39 bp):
TTAATAGTTTAATATTAATTTAATATTAAAGTAATTATC
Found at i:41818005 original size:106 final size:106
Alignment explanation
Indices: 41817809--41818085 Score: 310
Period size: 106 Copynumber: 2.6 Consensus size: 106
41817799 ATTTAGTCGG
* * * *
41817809 ACGAGACATCGAAACCCAGCACGTTAGGGCACGTTCTCTCGAATTTCTAAACGCAAGACATTG-T
1 ACGAGAAATCGAAACCCAGCACGTTAGGGCACGTT-TCTCGAATTTCCAAACGCAAAATATTGCT
** *
41817873 CTCGTTTTAAAATTTTGAAAGAATATTCGACTATTTGGCCAA
65 CTCGTTTTAAAATTTAAAAAGAATATTCGACCATTTGGCCAA
* * *
41817915 ACGAGTAATCGAAACCCAACACGTTAGGGCCCGTATTCTCGAATTTCCAAACGCAAAATATTGCA
1 ACGAGAAATCGAAACCCAGCACGTTAGGGCACGT-TTCTCGAATTTCCAAACGCAAAATATTGC-
* * * * *
41817980 T-TC-TTTTGAAAGTTTAAAAAG-ATATTTGGCCATTTGGTCGA
64 TCTCGTTTT-AAAATTTAAAAAGAATATTCGACCATTTGGCCAA
* * *
41818021 ACGAGAAAGCGAAACCCAGCACATTAGGGCACGTTTTCTCGAATTTTCCAAACGCGAAATATTGC
1 ACGAGAAATCGAAACCCAGCACGTTAGGGCACG-TTTCTCGAA-TTTCCAAACGCAAAATATTGC
41818086 CTTATTTAGG
Statistics
Matches: 144, Mismatches: 21, Indels: 11
0.82 0.12 0.06
Matches are distributed among these distances:
106 109 0.76
107 34 0.24
108 1 0.01
ACGTcount: A:0.33, C:0.22, G:0.18, T:0.27
Consensus pattern (106 bp):
ACGAGAAATCGAAACCCAGCACGTTAGGGCACGTTTCTCGAATTTCCAAACGCAAAATATTGCTC
TCGTTTTAAAATTTAAAAAGAATATTCGACCATTTGGCCAA
Found at i:41818956 original size:20 final size:20
Alignment explanation
Indices: 41818928--41818980 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
41818918 TGTAAGTATG
41818928 TATATATATATAAGGCATAAA
1 TATATATATATAA-GCATAAA
* * *
41818949 TA-ATATATGTAAGTATATA
1 TATATATATATAAGCATAAA
41818968 TATATATATATAA
1 TATATATATATAA
41818981 ATAAAAATTA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
19 7 0.26
20 18 0.67
21 2 0.07
ACGTcount: A:0.51, C:0.02, G:0.08, T:0.40
Consensus pattern (20 bp):
TATATATATATAAGCATAAA
Found at i:41819778 original size:2 final size:2
Alignment explanation
Indices: 41819771--41819812 Score: 52
Period size: 2 Copynumber: 22.0 Consensus size: 2
41819761 CTCTCGTTTT
* *
41819771 TA TA TA TA TA TA TA TA TA T- TC T- TA TA TA CA TA 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
41819811 TA
1 TA
41819813 CATAATAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
1 2 0.06
2 34 0.94
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:41823866 original size:180 final size:180
Alignment explanation
Indices: 41823558--41824001 Score: 682
Period size: 180 Copynumber: 2.5 Consensus size: 180
41823548 TATTAATAAT
* ** *
41823558 TTAATTTTAGCATAATTATTATTTATA----GATTTGTTTTATAGTAATATAGGTAAGGTGGATT
1 TTAA-TTTAGCATCATTATTATTTATATTGTGATTTGTTTTATAGTAATATACATATGGTGGATT
41823619 TATAATTGTCACATTATTTTATATTAATGGTAGGAAAGTAGGGACATTGAAAATAAATCGCAATG
65 TATAATTGTCACATTATTTTATATTAATGGT---AAAGTAGGGACATTGAAAATAAATCGCAATG
*
41823684 TGTTACTATTAATAATAATTTAATTTCAAATTACATTATTGCAATATGAGGAGAC
127 TGTTACTATTAATAATAAATTAATTTCAAATTACATTATTGCAATATGAGGA-AC
41823739 TTAATTTAGCATCATTATTATTTATATTGTGATTTGTTTTATAGTAATATACATATGGTGGATTT
1 TTAATTTAGCATCATTATTATTTATATTGTGATTTGTTTTATAGTAATATACATATGGTGGATTT
*
41823804 ATAATTGTCACATTATTTTATATTAATGGT-AAGTAGGGACATTGAAAATAAATCGTAATGTGTT
66 ATAATTGTCACATTATTTTATATTAATGGTAAAGTAGGGACATTGAAAATAAATCGCAATGTGTT
* * *
41823868 ATTTTTTATAATAAATTAATTTCAAATTACATTATTGCAATATGAGGAAC
131 ACTATTAATAATAAATTAATTTCAAATTACATTATTGCAATATGAGGAAC
* * *
41823918 TTAATTTAGCATCACTATTATTTATATTGTGATTTGTTTTATCGTAATGTACATATGGTGGATTT
1 TTAATTTAGCATCATTATTATTTATATTGTGATTTGTTTTATAGTAATATACATATGGTGGATTT
* *
41823983 ATAATTGTGAAATTATTTT
66 ATAATTGTCACATTATTTT
41824002 TGAATCTCGT
Statistics
Matches: 245, Mismatches: 14, Indels: 10
0.91 0.05 0.04
Matches are distributed among these distances:
179 81 0.33
180 98 0.40
181 4 0.02
184 62 0.25
ACGTcount: A:0.35, C:0.06, G:0.14, T:0.44
Consensus pattern (180 bp):
TTAATTTAGCATCATTATTATTTATATTGTGATTTGTTTTATAGTAATATACATATGGTGGATTT
ATAATTGTCACATTATTTTATATTAATGGTAAAGTAGGGACATTGAAAATAAATCGCAATGTGTT
ACTATTAATAATAAATTAATTTCAAATTACATTATTGCAATATGAGGAAC
Found at i:41824000 original size:179 final size:181
Alignment explanation
Indices: 41823585--41824001 Score: 676
Period size: 179 Copynumber: 2.3 Consensus size: 181
41823575 ATTATTTATA
** *
41823585 GATTTGTTTTATAGTAATATAGGTAAGGTGGATTTATAATTGTCACATTATTTTATATTAATGGT
1 GATTTGTTTTATAGTAATATACATATGGTGGATTTATAATTGTCACATTATTTTATATTAATGGT
*
41823650 AGGAAAGTAGGGACATTGAAAATAAATCGCAATGTGTTACTATTAATAATAATTTAATTTCAAAT
66 ---AAAGTAGGGACATTGAAAATAAATCGCAATGTGTTACTATTAATAATAAATTAATTTCAAAT
*
41823715 TACATTATTGCAATATGAGGAGACTTAATTTAGCATCATTATTATTTATATTGT
128 TACATTATTGCAATATGAGGAGACTTAATTTAGCATCACTATTATTTATATTGT
41823769 GATTTGTTTTATAGTAATATACATATGGTGGATTTATAATTGTCACATTATTTTATATTAATGGT
1 GATTTGTTTTATAGTAATATACATATGGTGGATTTATAATTGTCACATTATTTTATATTAATGGT
* * * *
41823834 -AAGTAGGGACATTGAAAATAAATCGTAATGTGTTATTTTTTATAATAAATTAATTTCAAATTAC
66 AAAGTAGGGACATTGAAAATAAATCGCAATGTGTTACTATTAATAATAAATTAATTTCAAATTAC
41823898 ATTATTGCAATATGAGGA-ACTTAATTTAGCATCACTATTATTTATATTGT
131 ATTATTGCAATATGAGGAGACTTAATTTAGCATCACTATTATTTATATTGT
* * * *
41823948 GATTTGTTTTATCGTAATGTACATATGGTGGATTTATAATTGTGAAATTATTTT
1 GATTTGTTTTATAGTAATATACATATGGTGGATTTATAATTGTCACATTATTTT
41824002 TGAATCTCGT
Statistics
Matches: 220, Mismatches: 13, Indels: 5
0.92 0.05 0.02
Matches are distributed among these distances:
179 81 0.37
180 77 0.35
184 62 0.28
ACGTcount: A:0.35, C:0.06, G:0.15, T:0.44
Consensus pattern (181 bp):
GATTTGTTTTATAGTAATATACATATGGTGGATTTATAATTGTCACATTATTTTATATTAATGGT
AAAGTAGGGACATTGAAAATAAATCGCAATGTGTTACTATTAATAATAAATTAATTTCAAATTAC
ATTATTGCAATATGAGGAGACTTAATTTAGCATCACTATTATTTATATTGT
Found at i:41827152 original size:24 final size:22
Alignment explanation
Indices: 41827115--41827159 Score: 54
Period size: 24 Copynumber: 2.0 Consensus size: 22
41827105 AATTATTTTT
41827115 ATATTTAAAGTAATCTAATATATC
1 ATATTTAAAGTAAT-T-ATATATC
* *
41827139 ATATTTATATTAATTATATAT
1 ATATTTAAAGTAATTATATAT
41827160 TATCTACAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 6 0.32
23 1 0.05
24 12 0.63
ACGTcount: A:0.44, C:0.04, G:0.02, T:0.49
Consensus pattern (22 bp):
ATATTTAAAGTAATTATATATC
Found at i:41832915 original size:101 final size:102
Alignment explanation
Indices: 41832737--41832923 Score: 259
Period size: 101 Copynumber: 1.8 Consensus size: 102
41832727 AGTTGCGAGT
* * * * * *
41832737 TGCTAATGAGATTCTGTTTTTTAACTTACTGTTACCATGTTTGGGCTTGGTAACCATCTATCTGT
1 TGCTAATGAGACTCCGCTTTTTAACTCACTGATACCATGTTGGGGCTTGGTAACCATCTATCTGT
* *
41832802 GGTAACACACACTGCCTTTGTGGTAAAACACGTGAGC
66 GGTAAAACACACTGCATTTGTGGTAAAACACGTGAGC
* *
41832839 TGCTAATGAGACTCCGCTTTTT-ACTCACTGATATCATGTTGGGGCTTGGTAACCATCTTTCTGT
1 TGCTAATGAGACTCCGCTTTTTAACTCACTGATACCATGTTGGGGCTTGGTAACCATCTATCTGT
* *
41832903 TGTAAAATACACTGCATTTGT
66 GGTAAAACACACTGCATTTGT
41832924 TCAGGTTTTC
Statistics
Matches: 73, Mismatches: 12, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
101 54 0.74
102 19 0.26
ACGTcount: A:0.23, C:0.20, G:0.20, T:0.37
Consensus pattern (102 bp):
TGCTAATGAGACTCCGCTTTTTAACTCACTGATACCATGTTGGGGCTTGGTAACCATCTATCTGT
GGTAAAACACACTGCATTTGTGGTAAAACACGTGAGC
Found at i:41833432 original size:62 final size:62
Alignment explanation
Indices: 41833335--41833457 Score: 237
Period size: 62 Copynumber: 2.0 Consensus size: 62
41833325 CTTCCTCTGC
41833335 GGTATTTATTCATCCTAATGATTCTATTGTGAATAATGTTTTTATCATTGTAAGGTAGTGGT
1 GGTATTTATTCATCCTAATGATTCTATTGTGAATAATGTTTTTATCATTGTAAGGTAGTGGT
*
41833397 GGTATTTATTCATCCTAATGATTCTATTGTGAATAATGTTTTTATCATTGTAATGTAGTGG
1 GGTATTTATTCATCCTAATGATTCTATTGTGAATAATGTTTTTATCATTGTAAGGTAGTGG
41833458 CCTTTACCAA
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
62 60 1.00
ACGTcount: A:0.26, C:0.08, G:0.19, T:0.47
Consensus pattern (62 bp):
GGTATTTATTCATCCTAATGATTCTATTGTGAATAATGTTTTTATCATTGTAAGGTAGTGGT
Found at i:41836831 original size:17 final size:17
Alignment explanation
Indices: 41836791--41836824 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
41836781 TTGTTATAGA
41836791 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
41836808 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
41836825 TGTTAATAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:41836896 original size:20 final size:21
Alignment explanation
Indices: 41836857--41836896 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
41836847 AATTTACTAA
*
41836857 TAAAATCATAATATATAATAC
1 TAAAATCATAATATAAAATAC
*
41836878 TAAAAT-ATAATTTAAAATA
1 TAAAATCATAATATAAAATA
41836897 ATTATTATTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (21 bp):
TAAAATCATAATATAAAATAC
Found at i:41836909 original size:26 final size:28
Alignment explanation
Indices: 41836864--41836943 Score: 92
Period size: 28 Copynumber: 2.8 Consensus size: 28
41836854 TAATAAAATC
41836864 ATAATATATAATACTAAAATATAATTTAA-A
1 ATAATATATAAT--T-AAATATAATTTAATA
*
41836894 ATAAT-TATTATTAAATATAATTTAATA
1 ATAATATATAATTAAATATAATTTAATA
* *
41836921 ATAATATATAATTTAATAAAATT
1 ATAATATATAATTAAATATAATT
41836944 CTTATTCTTA
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
26 13 0.30
27 7 0.16
28 14 0.32
29 5 0.11
30 5 0.11
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.42
Consensus pattern (28 bp):
ATAATATATAATTAAATATAATTTAATA
Found at i:41836976 original size:44 final size:41
Alignment explanation
Indices: 41836875--41836976 Score: 98
Period size: 44 Copynumber: 2.3 Consensus size: 41
41836865 TAATATATAA
41836875 TACTAAAATATAATTTAAAATAATTATTATTAAATATAATT
1 TACTAAAATATAATTTAAAATAATTATTATTAAATATAATT
* * **
41836916 TAATAATAATATATAATTTAATAA-AATTCTTATTCTTATATGAATT
1 TACT-A-AA-ATATAATTTAA-AATAATTATTATT-AAATAT-AATT
41836962 TACTAAAATCATAAT
1 TACTAAAAT-ATAAT
41836977 ATATAATACT
Statistics
Matches: 49, Mismatches: 5, Indels: 11
0.75 0.08 0.17
Matches are distributed among these distances:
41 3 0.06
42 1 0.02
43 4 0.08
44 27 0.55
45 7 0.14
46 7 0.14
ACGTcount: A:0.50, C:0.05, G:0.01, T:0.44
Consensus pattern (41 bp):
TACTAAAATATAATTTAAAATAATTATTATTAAATATAATT
Found at i:41836986 original size:108 final size:113
Alignment explanation
Indices: 41836771--41837030 Score: 358
Period size: 117 Copynumber: 2.3 Consensus size: 113
41836761 TTAATCATAT
* *
41836771 TTTAACATAATTGTTA-TAGAATATAATTTAATAA-AATATATAATTTAATAAAATTGTTAATAA
1 TTTAAAATAATTATTATTA-AATATAATTTAATAATAATATATAATTTAATAAAA-T-TTAAT--
41836834 ATATTCTTATATGAATTTACTAATAAAATCATAATATATAATAC-TAAAATATAA
61 ATATTCTTATATGAATTTAC--ATAAAATCATAATATATAATACATAAAATATAA
*
41836888 TTTAAAATAATTATTATTAAATATAATTTAATAATAATATATAATTTAATAAAA-TT-CT-TATT
1 TTTAAAATAATTATTATTAAATATAATTTAATAATAATATATAATTTAATAAAATTTAATATATT
41836950 CTTATATGAATTTAC-TAAAATCATAATATATAATACTATAAAATATAA
66 CTTATATGAATTTACATAAAATCATAATATATAATAC-ATAAAATATAA
41836998 TTT-AAATAATTATTATTAAATATAATTT-ATAAT
1 TTTAAAATAATTATTATTAAATATAATTTAATAAT
41837031 CTACTTTATT
Statistics
Matches: 136, Mismatches: 3, Indels: 17
0.87 0.02 0.11
Matches are distributed among these distances:
108 26 0.19
109 25 0.18
110 13 0.10
111 19 0.14
114 1 0.01
115 2 0.01
117 29 0.21
118 21 0.15
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.43
Consensus pattern (113 bp):
TTTAAAATAATTATTATTAAATATAATTTAATAATAATATATAATTTAATAAAATTTAATATATT
CTTATATGAATTTACATAAAATCATAATATATAATACATAAAATATAA
Found at i:41837022 original size:32 final size:32
Alignment explanation
Indices: 41836986--41837049 Score: 74
Period size: 32 Copynumber: 2.0 Consensus size: 32
41836976 TATATAATAC
*
41836986 TATAAAATATAATTTAAATAATTATTATTAAA
1 TATAAAATATAATCTAAATAATTATTATTAAA
** ** *
41837018 TATAATTTATAATCTACTTTATTATTATTAAA
1 TATAAAATATAATCTAAATAATTATTATTAAA
41837050 CTGCAATACA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (32 bp):
TATAAAATATAATCTAAATAATTATTATTAAA
Found at i:41839603 original size:30 final size:30
Alignment explanation
Indices: 41839567--41839626 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
41839557 TCAACTAACT
41839567 TCATTTTATCCCTTTTCTAGATTTTGGACC
1 TCATTTTATCCCTTTTCTAGATTTTGGACC
41839597 TCATTTTATCCCTTTTCTAGATTTTGGACC
1 TCATTTTATCCCTTTTCTAGATTTTGGACC
41839627 GACCTTTTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.17, C:0.23, G:0.10, T:0.50
Consensus pattern (30 bp):
TCATTTTATCCCTTTTCTAGATTTTGGACC
Found at i:41840451 original size:15 final size:15
Alignment explanation
Indices: 41840433--41840485 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
41840423 CACTGCCTCA
* * *
41840433 TCATCGTCGTCTTCG
1 TCATCGTCCTCATCC
* *
41840448 TCATCATCCTCGTCC
1 TCATCGTCCTCATCC
*
41840463 TCATCGTCCTCATCT
1 TCATCGTCCTCATCC
41840478 TCATCGTC
1 TCATCGTC
41840486 ATCCTCTTCT
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
15 31 1.00
ACGTcount: A:0.11, C:0.40, G:0.11, T:0.38
Consensus pattern (15 bp):
TCATCGTCCTCATCC
Found at i:41844537 original size:7 final size:7
Alignment explanation
Indices: 41844525--41844551 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
41844515 AAATAAATTT
41844525 TATTATA
1 TATTATA
41844532 TATTATA
1 TATTATA
41844539 TATTATA
1 TATTATA
41844546 TATTAT
1 TATTAT
41844552 TTTTAAACAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (7 bp):
TATTATA
Found at i:41853018 original size:2 final size:2
Alignment explanation
Indices: 41853011--41853037 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
41853001 AAAGCAAAGA
41853011 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 A
41853038 AAAGAAATGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:41866966 original size:66 final size:65
Alignment explanation
Indices: 41866890--41867131 Score: 200
Period size: 66 Copynumber: 3.7 Consensus size: 65
41866880 AGCTGTCACG
* * * *
41866890 TCCTTCGCTTCCTTCGCTTTTTCAGCTGCATAGTCTTTATACTCGGTCGCTTTTTCCATTGTAGT
1 TCCTTTGCTTCCTTAGCTTTCTCAGCTGCATAGTCTTTATACTCGGTCGC-TTTTCCATTGCAGT
41866955 A
65 A
* * * ** * * ** *
41866956 TCTTTTGCTTCCTTAGCTTTCTGC-GCTGCGTAGTCTGTCA-ACTCGGAAGCCTTCTGCGCTGCC
1 TCCTTTGCTTCCTTAGCTTTCT-CAGCTGCATAGTCT-TTATACTCGGTCG-CTTTTCCATTGCA
41867019 GTA
63 GTA
* * * * * *
41867022 TCCTTTGCTCCCTTGGCTTTCTCAGCTGCATAGTCCTTATATTCAGTCGCTTTTCCAATTGCAGC
1 TCCTTTGCTTCCTTAGCTTTCTCAGCTGCATAGTCTTTATACTCGGTCGCTTTTCC-ATTGCAGT
41867087 A
65 A
* ** * *
41867088 TCCTTTGCATCCTTAGCTTTCTGTGCTGCATAATCTGTATACTC
1 TCCTTTGCTTCCTTAGCTTTCTCAGCTGCATAGTCTTTATACTC
41867132 AGAAGCCTTT
Statistics
Matches: 131, Mismatches: 39, Indels: 12
0.72 0.21 0.07
Matches are distributed among these distances:
65 8 0.06
66 119 0.91
67 4 0.03
ACGTcount: A:0.13, C:0.29, G:0.17, T:0.41
Consensus pattern (65 bp):
TCCTTTGCTTCCTTAGCTTTCTCAGCTGCATAGTCTTTATACTCGGTCGCTTTTCCATTGCAGTA
Found at i:41867167 original size:66 final size:66
Alignment explanation
Indices: 41866949--41867533 Score: 314
Period size: 66 Copynumber: 8.9 Consensus size: 66
41866939 CTTTTTCCAT
* * * * * * * *
41866949 TGTAGTATCTTTTGCTTCCTTAGCTTTCTGCGCTGCGTAGTCTGTCA-ACTCGGAAGCCTTCTGC
1 TGTAGTATCCTTTGCCTCCTTAGCTTTCTGGGCTGCATAATCTGT-ATACTCAGAAGCCTTTTGG
*
41867013 GC
65 GA
** * ** * * ** *
41867015 TGCCGTATCCTTTG-CTCCCTTGGCTTTCTCAGCTGCATAGTCCT-TATATTCAGTCG-CTTTTC
1 TGTAGTATCCTTTGCCT-CCTTAGCTTTCTGGGCTGCATAAT-CTGTATACTCAGAAGCCTTTTG
**
41867077 CAA
64 GGA
* * * *
41867080 TTGCAGCATCCTTTGCATCCTTAGCTTTCTGTGCTGCATAATCTGTATACTCAGAAGCCTTTTGG
1 -TGTAGTATCCTTTGCCTCCTTAGCTTTCTGGGCTGCATAATCTGTATACTCAGAAGCCTTTTGG
41867145 GA
65 GA
* * * * ** **
41867147 TGTAGTAT-CTCTTGCCTCCTTGGCTTTGTGGGCTGTATAATCCT-TATATTCAGTCG-CTTTCC
1 TGTAGTATCCT-TTGCCTCCTTAGCTTTCTGGGCTGCATAAT-CTGTATACTCAGAAGCCTTTTG
**
41867209 CCA
64 GGA
* * * * ** * *
41867212 TTGTAGCATCCTTTGCATCCTTAGTTTTCTGTGCTGCATAGCCTGTATACTCGGAAGCCTTCTGT
1 -TGTAGTATCCTTTGCCTCCTTAGCTTTCTGGGCTGCATAATCTGTATACTCAGAAGCCTTTTG-
*
41867277 GCA
64 GGA
* * * * *
41867280 -GTGGTGTCTTTTGCGTCCTTAGCTTTCTGGGCAGCATAATCTGTATACTCAGAAGCCTTTTGGG
1 TGTAGTATCCTTTGCCTCCTTAGCTTTCTGGGCTGCATAATCTGTATACTCAGAAGCCTTTTGGG
*
41867344 C
66 A
* * * * * ** *
41867345 TGTGGTAT-CTCTTGCCTCCTTGGCTTTCTCGGCTGTATAATCCT-TATATTCAGTCG-CTTTCC
1 TGTAGTATCCT-TTGCCTCCTTAGCTTTCTGGGCTGCATAAT-CTGTATACTCAGAAGCCTTT-T
** *
41867407 CCGT
63 GGGA
* * * * *
41867411 TGTAGCATCCTTTGCAC-CCTTAG-TTTGCTGTGCTGCATAGTCTGTATACTCGGAAGCCTTTTT
1 TGTAGTATCCTTTGC-CTCCTTAGCTTT-CTGGGCTGCATAATCTGTATACTCAGAAGCCTTTTG
* *
41867474 TGC
64 GGA
* * * *
41867477 TGTGGTGTCCTTTGCGTCCTTAGCTTTCTGGGCAGCATAATCTGTATACTCAGAAGC
1 TGTAGTATCCTTTGCCTCCTTAGCTTTCTGGGCTGCATAATCTGTATACTCAGAAGC
41867534 TTTACCTGTT
Statistics
Matches: 383, Mismatches: 111, Indels: 50
0.70 0.20 0.09
Matches are distributed among these distances:
65 29 0.08
66 324 0.85
67 28 0.07
68 2 0.01
ACGTcount: A:0.15, C:0.26, G:0.21, T:0.39
Consensus pattern (66 bp):
TGTAGTATCCTTTGCCTCCTTAGCTTTCTGGGCTGCATAATCTGTATACTCAGAAGCCTTTTGGG
A
Found at i:41867299 original size:132 final size:130
Alignment explanation
Indices: 41866914--41867320 Score: 447
Period size: 132 Copynumber: 3.1 Consensus size: 130
41866904 CGCTTTTTCA
* * * * * * * *
41866914 GCTGCATAGTCTTTATACTCGGTCGCTTTTTCCATTGTAGTATCTTTTGCTTCCTTAGCTTTCTG
1 GCTGCATAATCCTTATATTCAGTCGCTTTTCCCATTGTAGCATCCTTTGCATCCTTAGCTTTCTG
* * * ** *
41866979 CGCTGCGTAGTCTGTCA-ACTCGGAAGCCTTCTGCGCTGCCGTATCCTTTGCTCCCTTGGCTTTC
66 TGCTGCATAGTCTGT-ATACTCGGAAGCCTTCTG-GCAGTAGTATCTTTTGCT-CCTTGGCTTTC
**
41867043 TCA
128 TGG
* * *
41867046 GCTGCATAGTCCTTATATTCAGTCGCTTTTCCAATTGCAGCATCCTTTGCATCCTTAGCTTTCTG
1 GCTGCATAATCCTTATATTCAGTCGCTTTTCCCATTGTAGCATCCTTTGCATCCTTAGCTTTCTG
* * * * * *
41867111 TGCTGCATAATCTGTATACTCAGAAGCCTTTTGGGATGTAGTATCTCTTGCCTCCTTGGCTTTGT
66 TGCTGCATAGTCTGTATACTCGGAAGCCTTCTGGCA-GTAGTATCTTTTG-CTCCTTGGCTTTCT
41867176 GG
129 GG
* * *
41867178 GCTGTATAATCCTTATATTCAGTCGCTTTCCCCATTGTAGCATCCTTTGCATCCTTAGTTTTCTG
1 GCTGCATAATCCTTATATTCAGTCGCTTTTCCCATTGTAGCATCCTTTGCATCCTTAGCTTTCTG
* * * *
41867243 TGCTGCATAGCCTGTATACTCGGAAGCCTTCTGTGCAGTGGTGTCTTTTGCGTCCTTAGCTTTCT
66 TGCTGCATAGTCTGTATACTCGGAAGCCTTCTG-GCAGTAGTATCTTTTGC-TCCTTGGCTTTCT
41867308 GG
129 GG
*
41867310 GCAGCATAATC
1 GCTGCATAATC
41867321 TGTATACTCA
Statistics
Matches: 229, Mismatches: 41, Indels: 10
0.82 0.15 0.04
Matches are distributed among these distances:
131 3 0.01
132 222 0.97
133 4 0.02
ACGTcount: A:0.15, C:0.26, G:0.20, T:0.39
Consensus pattern (130 bp):
GCTGCATAATCCTTATATTCAGTCGCTTTTCCCATTGTAGCATCCTTTGCATCCTTAGCTTTCTG
TGCTGCATAGTCTGTATACTCGGAAGCCTTCTGGCAGTAGTATCTTTTGCTCCTTGGCTTTCTGG
Found at i:41867308 original size:198 final size:198
Alignment explanation
Indices: 41867088--41867533 Score: 757
Period size: 198 Copynumber: 2.3 Consensus size: 198
41867078 AATTGCAGCA
* * *
41867088 TCCTTTGCATCCTTAGCTTTCTGTGCTGCATAATCTGTATACTCAGAAGCCTTTTGGGATGTAGT
1 TCCTTTGCGTCCTTAGCTTTCTGGGCAGCATAATCTGTATACTCAGAAGCCTTTTGGGATGTAGT
* *
41867153 ATCTCTTGCCTCCTTGGCTTTGTGGGCTGTATAATCCTTATATTCAGTCGCTTTCCCCATTGTAG
66 ATCTCTTGCCTCCTTGGCTTTCTCGGCTGTATAATCCTTATATTCAGTCGCTTTCCCCATTGTAG
* *
41867218 CATCCTTTGCATCCTTAGTTTTCTGTGCTGCATAGCCTGTATACTCGGAAGCCTTCTGTGCAGTG
131 CATCCTTTGCACCCTTAGTTTGCTGTGCTGCATAGCCTGTATACTCGGAAGCCTTCTGTGCAGTG
41867283 GTG
196 GTG
* * *
41867286 TCTTTTGCGTCCTTAGCTTTCTGGGCAGCATAATCTGTATACTCAGAAGCCTTTTGGGCTGTGGT
1 TCCTTTGCGTCCTTAGCTTTCTGGGCAGCATAATCTGTATACTCAGAAGCCTTTTGGGATGTAGT
*
41867351 ATCTCTTGCCTCCTTGGCTTTCTCGGCTGTATAATCCTTATATTCAGTCGCTTTCCCCGTTGTAG
66 ATCTCTTGCCTCCTTGGCTTTCTCGGCTGTATAATCCTTATATTCAGTCGCTTTCCCCATTGTAG
* * * *
41867416 CATCCTTTGCACCCTTAGTTTGCTGTGCTGCATAGTCTGTATACTCGGAAGCCTTTTTTGCTGTG
131 CATCCTTTGCACCCTTAGTTTGCTGTGCTGCATAGCCTGTATACTCGGAAGCCTTCTGTGCAGTG
41867481 GTG
196 GTG
41867484 TCCTTTGCGTCCTTAGCTTTCTGGGCAGCATAATCTGTATACTCAGAAGC
1 TCCTTTGCGTCCTTAGCTTTCTGGGCAGCATAATCTGTATACTCAGAAGC
41867534 TTTACCTGTT
Statistics
Matches: 232, Mismatches: 16, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
198 232 1.00
ACGTcount: A:0.15, C:0.25, G:0.21, T:0.39
Consensus pattern (198 bp):
TCCTTTGCGTCCTTAGCTTTCTGGGCAGCATAATCTGTATACTCAGAAGCCTTTTGGGATGTAGT
ATCTCTTGCCTCCTTGGCTTTCTCGGCTGTATAATCCTTATATTCAGTCGCTTTCCCCATTGTAG
CATCCTTTGCACCCTTAGTTTGCTGTGCTGCATAGCCTGTATACTCGGAAGCCTTCTGTGCAGTG
GTG
Done.