Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D13
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: 64892201
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1760000 characters in sequence are not A, C, G, or T
File 181 of 221
Found at i:54008780 original size:30 final size:28
Alignment explanation
Indices: 54008670--54008787 Score: 94
Period size: 30 Copynumber: 4.0 Consensus size: 28
54008660 TAAAAAATAA
* * *
54008670 AAATTGCATTTTGACCCCTAAACTTTTCCT
1 AAATTTCATTTT-AACCCTAAAC-TTTCTT
*
54008700 AAATTTCATTTTGACCCTTAAACTTTCTTT
1 AAATTTCATTTTAACCC-TAAACTTTC-TT
*
54008730 AAATTTCA-CTTAGACCCCTAAACTTTCATT
1 AAATTTCATTTTA-A-CCCTAAACTTTC-TT
* *
54008760 AAATTTTCATTTTAATCCTAAATTTTCT
1 AAA-TTTCATTTTAACCCTAAACTTTCT
54008788 AAAAATTACA
Statistics
Matches: 72, Mismatches: 10, Indels: 13
0.76 0.11 0.14
Matches are distributed among these distances:
29 10 0.14
30 50 0.69
31 9 0.12
32 3 0.04
ACGTcount: A:0.30, C:0.22, G:0.03, T:0.45
Consensus pattern (28 bp):
AAATTTCATTTTAACCCTAAACTTTCTT
Found at i:54008794 original size:60 final size:60
Alignment explanation
Indices: 54008667--54008794 Score: 143
Period size: 60 Copynumber: 2.1 Consensus size: 60
54008657 ATTTAAAAAA
* * *
54008667 TAAAAATTGCATTTTGACCCCTAAACTTTTCCTAAATTTCATTTTGACCCTTAAACTTTC
1 TAAAAATTGCACTTAGACCCCTAAACTTTTCCTAAATTTCATTTTAACCCTTAAACTTTC
** * * * *
54008727 TTTAAATTTCACTTAGACCCCTAAAC-TTTCATTAAATTTTCATTTTAATCC-TAAATTTTC
1 TAAAAATTGCACTTAGACCCCTAAACTTTTC-CTAAA-TTTCATTTTAACCCTTAAACTTTC
54008787 TAAAAATT
1 TAAAAATT
54008795 ACATTTAGCC
Statistics
Matches: 55, Mismatches: 11, Indels: 4
0.79 0.16 0.06
Matches are distributed among these distances:
59 4 0.07
60 39 0.71
61 12 0.22
ACGTcount: A:0.33, C:0.20, G:0.03, T:0.44
Consensus pattern (60 bp):
TAAAAATTGCACTTAGACCCCTAAACTTTTCCTAAATTTCATTTTAACCCTTAAACTTTC
Found at i:54009059 original size:17 final size:17
Alignment explanation
Indices: 54009037--54009083 Score: 62
Period size: 17 Copynumber: 2.8 Consensus size: 17
54009027 TTCGAAGGAA
54009037 AAAAGAAGAAAGAGAAG
1 AAAAGAAGAAAGAGAAG
*
54009054 AAAAG-AGAAAGAGGAG
1 AAAAGAAGAAAGAGAAG
54009070 AAGAA-AAGAAAGAG
1 AA-AAGAAGAAAGAG
54009084 TACTGGCGTC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
16 12 0.44
17 15 0.56
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (17 bp):
AAAAGAAGAAAGAGAAG
Found at i:54009062 original size:19 final size:20
Alignment explanation
Indices: 54009034--54009083 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 20
54009024 TTTTTCGAAG
*
54009034 GAAAAAAGAAGA-AAGAGAA
1 GAAAAGAGAAGAGAAGAGAA
*
54009053 GAAAAGAGAA-AGAGGAGAA
1 GAAAAGAGAAGAGAAGAGAA
54009072 GAAAAGA-AAGAG
1 GAAAAGAGAAGAG
54009084 TACTGGCGTC
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
18 3 0.11
19 24 0.89
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (20 bp):
GAAAAGAGAAGAGAAGAGAA
Found at i:54009144 original size:3 final size:3
Alignment explanation
Indices: 54009138--54009208 Score: 60
Period size: 3 Copynumber: 24.0 Consensus size: 3
54009128 GCTAGACTTT
* *
54009138 GAA GAA GAA GAA GGAA GAA GAA GGAA GAA GAA -AA GAG GAA GAA AAA
1 GAA GAA GAA GAA -GAA GAA GAA -GAA GAA GAA GAA GAA GAA GAA GAA
*
54009184 GAAA GAA -AA -AA GAA AAA GAA -AA GAA
1 G-AA GAA GAA GAA GAA GAA GAA GAA GAA
54009209 ATAATAAAAA
Statistics
Matches: 56, Mismatches: 6, Indels: 12
0.76 0.08 0.16
Matches are distributed among these distances:
2 8 0.14
3 39 0.70
4 9 0.16
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:54009156 original size:10 final size:10
Alignment explanation
Indices: 54009141--54009169 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
54009131 AGACTTTGAA
54009141 GAAGAAGAAG
1 GAAGAAGAAG
54009151 GAAGAAGAAG
1 GAAGAAGAAG
54009161 GAAGAAGAA
1 GAAGAAGAA
54009170 AAGAGGAAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (10 bp):
GAAGAAGAAG
Found at i:54009185 original size:17 final size:17
Alignment explanation
Indices: 54009165--54009209 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
54009155 AAGAAGGAAG
**
54009165 AAGAAAAGAGGAAGAAA
1 AAGAAAAGAAAAAGAAA
54009182 AAG-AAAGAAAAAAGAAA
1 AAGAAAAG-AAAAAGAAA
54009199 AAGAAAAGAAA
1 AAGAAAAGAAA
54009210 TAATAAAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
16 4 0.17
17 16 0.67
18 4 0.17
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (17 bp):
AAGAAAAGAAAAAGAAA
Found at i:54009190 original size:34 final size:34
Alignment explanation
Indices: 54009141--54009207 Score: 89
Period size: 34 Copynumber: 2.0 Consensus size: 34
54009131 AGACTTTGAA
* * * * *
54009141 GAAGAAGAAGGAAGAAGAAGGAAGAAGAAAAGAG
1 GAAGAAAAAGAAAGAAAAAAGAAAAAGAAAAGAG
54009175 GAAGAAAAAGAAAGAAAAAAGAAAAAGAAAAGA
1 GAAGAAAAAGAAAGAAAAAAGAAAAAGAAAAGA
54009208 AATAATAAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
34 28 1.00
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (34 bp):
GAAGAAAAAGAAAGAAAAAAGAAAAAGAAAAGAG
Found at i:54009218 original size:18 final size:17
Alignment explanation
Indices: 54009176--54009209 Score: 59
Period size: 17 Copynumber: 1.9 Consensus size: 17
54009166 AGAAAAGAGG
54009176 AAGAAAAAGAAAGAAAA
1 AAGAAAAAGAAAGAAAA
54009193 AAGAAAAAGAAAAGAAA
1 AAGAAAAAG-AAAGAAA
54009210 TAATAAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (17 bp):
AAGAAAAAGAAAGAAAA
Found at i:54009486 original size:21 final size:21
Alignment explanation
Indices: 54009457--54009523 Score: 68
Period size: 21 Copynumber: 3.3 Consensus size: 21
54009447 GGCCCAGCAG
*
54009457 AGAAAAAAAAAGAAAAGAAAA
1 AGAAGAAAAAAGAAAAGAAAA
*
54009478 AGAAG-AAAAAGAGAAGGAAAA
1 AGAAGAAAAAAGA-AAAGAAAA
* *
54009499 AGAAGGAAAAA-AAGAGAAAA
1 AGAAGAAAAAAGAAAAGAAAA
54009519 A-AAGA
1 AGAAGA
54009524 GAGGTTCAAT
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
19 3 0.08
20 14 0.36
21 17 0.44
22 5 0.13
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (21 bp):
AGAAGAAAAAAGAAAAGAAAA
Found at i:54009524 original size:10 final size:10
Alignment explanation
Indices: 54009455--54009525 Score: 70
Period size: 10 Copynumber: 6.5 Consensus size: 10
54009445 TTGGCCCAGC
54009455 AGAGAAAAAA
1 AGAGAAAAAA
*
54009465 AAAGAAAAGAA
1 AGAGAAAA-AA
*
54009476 AAAGAAGAAAA
1 AGAGAA-AAAA
54009487 AGAGAAGGAAAA
1 AGAGAA--AAAA
54009499 AGAAGGAAAAAA
1 AG-A-GAAAAAA
54009511 AGAGAAAAAA
1 AGAGAAAAAA
54009521 AGAGA
1 AGAGA
54009526 GGTTCAATTC
Statistics
Matches: 54, Mismatches: 2, Indels: 10
0.82 0.03 0.15
Matches are distributed among these distances:
10 19 0.35
11 16 0.30
12 15 0.28
13 1 0.02
14 3 0.06
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (10 bp):
AGAGAAAAAA
Found at i:54009893 original size:18 final size:18
Alignment explanation
Indices: 54009859--54010356 Score: 212
Period size: 16 Copynumber: 29.3 Consensus size: 18
54009849 TCGTGCATTT
* *
54009859 AAAAATTCTCATG-TTTC
1 AAAAATTTTCGTGTTTTC
*
54009876 AAAAATCTTCGTGTTTTC
1 AAAAATTTTCGTGTTTTC
* *
54009894 -AAAATTCTAGTG-TTTC
1 AAAAATTTTCGTGTTTTC
*
54009910 -AAAATTTTCTTGTTTTC
1 AAAAATTTTCGTGTTTTC
54009927 AGAAAAATTTTCGTGTTTT-
1 --AAAAATTTTCGTGTTTTC
* * *
54009946 -ATAATTTCCGTATTTTC
1 AAAAATTTTCGTGTTTTC
* *
54009963 AAAAA--ATCATGTCTTTC
1 AAAAATTTTCGTGT-TTTC
54009980 AAAAATTTTCGTGTTTTC
1 AAAAATTTTCGTGTTTTC
***
54009998 AAAAAAATGACCGTG-TTTC
1 --AAAAATTTTCGTGTTTTC
* ***
54010017 -AAAATTTCCGTGTTAAAA
1 AAAAATTTTCGTGTT-TTC
* *
54010035 AAAAATCTTCGTATTTTC
1 AAAAATTTTCGTGTTTTC
54010053 AAAGAATTTTCGTG-TTTC
1 AAA-AATTTTCGTGTTTTC
*
54010071 -AAAATCTTCGTGTTTTC
1 AAAAATTTTCGTGTTTTC
54010088 AAAAA-TTTCG-GTGTTTC
1 AAAAATTTTCGTGT-TTTC
*
54010105 AAAGATTTTCGTGTTTTC
1 AAAAATTTTCGTGTTTTC
* * *
54010123 AAAAA-CTCCGGTGATTTTA
1 AAAAATTTTC-GTG-TTTTC
** *
54010142 AAAAAAATT-GT-TTTCTA
1 AAAAATTTTCGTGTTT-TC
*
54010159 AAAAATTTCCGTG-TTTC
1 AAAAATTTTCGTGTTTTC
*
54010176 -AAAATTTTCGTGTTTTT
1 AAAAATTTTCGTGTTTTC
54010193 AAAAATTTTCGTGTTTT-
1 AAAAATTTTCGTGTTTTC
* *
54010210 -AAAATTCTCGTATTTT-
1 AAAAATTTTCGTGTTTTC
***
54010226 --AAATTTT--T-TTAAG
1 AAAAATTTTCGTGTTTTC
*
54010239 AAAAA-ATT-GTG-TTTC
1 AAAAATTTTCGTGTTTTC
* * *
54010254 AAAAAATGTCTTGTTTT-
1 AAAAATTTTCGTGTTTTC
*
54010271 -AAAATTCTCGTG-TTTC
1 AAAAATTTTCGTGTTTTC
*
54010287 AAAAA-TGTCGTGTTTT-
1 AAAAATTTTCGTGTTTTC
54010303 -AAAATTTTCGTG-TTTC
1 AAAAATTTTCGTGTTTTC
** *
54010319 TGAAATTTCCGTG-TTT-
1 AAAAATTTTCGTGTTTTC
*
54010335 AAAAATTCTCGTGTTTT-
1 AAAAATTTTCGTGTTTTC
54010352 AAAAA
1 AAAAA
54010357 AAAACTTTCA
Statistics
Matches: 363, Mismatches: 74, Indels: 88
0.69 0.14 0.17
Matches are distributed among these distances:
12 2 0.01
13 1 0.00
14 2 0.01
15 26 0.07
16 109 0.30
17 95 0.26
18 63 0.17
19 39 0.11
20 26 0.07
ACGTcount: A:0.32, C:0.12, G:0.12, T:0.45
Consensus pattern (18 bp):
AAAAATTTTCGTGTTTTC
Found at i:54009924 original size:16 final size:16
Alignment explanation
Indices: 54009837--54009915 Score: 68
Period size: 16 Copynumber: 4.6 Consensus size: 16
54009827 AAAATTGTAA
*
54009837 TTTCAATAATCCTCGTG
1 TTTCAA-AATTCTCGTG
* *
54009854 CATTTAAAAATTCTCATG
1 --TTTCAAAATTCTCGTG
*
54009872 TTTCAAAAATCTTCGTG
1 TTTCAAAATTC-TCGTG
*
54009889 TTTTCAAAATTCTAGTG
1 -TTTCAAAATTCTCGTG
54009906 TTTCAAAATT
1 TTTCAAAATT
54009916 TTCTTGTTTT
Statistics
Matches: 50, Mismatches: 8, Indels: 7
0.77 0.12 0.11
Matches are distributed among these distances:
16 19 0.38
17 8 0.16
18 18 0.36
19 5 0.10
ACGTcount: A:0.32, C:0.16, G:0.09, T:0.43
Consensus pattern (16 bp):
TTTCAAAATTCTCGTG
Found at i:54009943 original size:36 final size:35
Alignment explanation
Indices: 54009859--54010126 Score: 151
Period size: 35 Copynumber: 7.6 Consensus size: 35
54009849 TCGTGCATTT
* * *
54009859 AAAAATTCTCATGTTTCAAAAATCTTCGTGTTTTC-
1 AAAAATTATCGTGTTTC-AAAATTTTCGTGTTTTCA
* * *
54009894 -AAAATTCTAGTGTTTCAAAATTTTCTTGTTTTCA
1 AAAAATTATCGTGTTTCAAAATTTTCGTGTTTTCA
* * * * *
54009928 GAAAAATTTTCGTGTTTTATAATTTCCGTATTTTCA
1 -AAAAATTATCGTGTTTCAAAATTTTCGTGTTTTCA
* *
54009964 AAAAATCAT-GTCTTTCAAAAATTTTCGTGTTTTCAA
1 AAAAATTATCGTGTTTC-AAAATTTTCGTGTTTTC-A
* * * ***
54010000 AAAAATGACCGTGTTTCAAAATTTCCGTGTTAAAA
1 AAAAATTATCGTGTTTCAAAATTTTCGTGTTTTCA
*
54010035 AAAAATCT-TCGTATTTTCAAAGAATTTTCGTG-TTTC-
1 AAAAAT-TATCGT-GTTTC-AA-AATTTTCGTGTTTTCA
*
54010071 -AAAATCT-TCGTGTTTTCAAAAATTTCG-GTGTTTC-
1 AAAAAT-TATCGTG-TTTCAAAATTTTCGTGT-TTTCA
* *
54010105 AAAGATTTTCGTGTTTTCAAAA
1 AAAAATTATCGTG-TTTCAAAA
54010127 ACTCCGGTGA
Statistics
Matches: 183, Mismatches: 35, Indels: 30
0.74 0.14 0.12
Matches are distributed among these distances:
32 1 0.01
33 22 0.12
34 26 0.14
35 64 0.35
36 52 0.28
37 9 0.05
38 9 0.05
ACGTcount: A:0.32, C:0.13, G:0.11, T:0.43
Consensus pattern (35 bp):
AAAAATTATCGTGTTTCAAAATTTTCGTGTTTTCA
Found at i:54009996 original size:71 final size:73
Alignment explanation
Indices: 54009906--54010074 Score: 184
Period size: 71 Copynumber: 2.4 Consensus size: 73
54009896 AATTCTAGTG
* * *** * * ***
54009906 TTTC-AAAATTTTCTTGTTTTCAGAAAAATTTTCGTGTTTTATAATTTCCGTATTTTCAAAAAAT
1 TTTCAAAAATTTTCGTGTTTTCAAAAAAATGACCGTGTTTCAAAATTTCCGTATTAAAAAAAAAT
54009970 CAT-GT-C
66 CATCGTAC
*
54009976 TTTCAAAAATTTTCGTGTTTTCAAAAAAATGACCGTGTTTCAAAATTTCCGTGTTAAAAAAAAAT
1 TTTCAAAAATTTTCGTGTTTTCAAAAAAATGACCGTGTTTCAAAATTTCCGTATTAAAAAAAAAT
* *
54010041 CTTCGTAT
66 CATCGTAC
54010049 TTTCAAAGAATTTTCGTG-TTTCAAAA
1 TTTCAAA-AATTTTCGTGTTTTCAAAA
54010075 TCTTCGTGTT
Statistics
Matches: 82, Mismatches: 13, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
70 4 0.05
71 51 0.62
72 2 0.02
73 15 0.18
74 10 0.12
ACGTcount: A:0.34, C:0.13, G:0.10, T:0.43
Consensus pattern (73 bp):
TTTCAAAAATTTTCGTGTTTTCAAAAAAATGACCGTGTTTCAAAATTTCCGTATTAAAAAAAAAT
CATCGTAC
Found at i:54010081 original size:35 final size:34
Alignment explanation
Indices: 54010036--54010214 Score: 150
Period size: 35 Copynumber: 5.1 Consensus size: 34
54010026 GTGTTAAAAA
*
54010036 AAAATCTTCGTATTTTCAAAGAATTTTC-GTGTTTC
1 AAAATCTTCGTGTTTTCAAA-AA-TTTCGGTGTTTC
54010071 AAAATCTTCGTGTTTTCAAAAATTTCGGTGTTTC
1 AAAATCTTCGTGTTTTCAAAAATTTCGGTGTTTC
* * * *
54010105 AAAGATTTTCGTGTTTTCAAAAACTCCGGTGATTTTAA
1 AAA-ATCTTCGTGTTTTCAAAAATTTCGGTG--TTT-C
** * *
54010143 AAAAAATT-GT-TTTCTAAAAAATTTCCGTGTTTC
1 AAAATCTTCGTGTTT-TCAAAAATTTCGGTGTTTC
* * *
54010176 AAAATTTTCGTGTTTTTAAAAATTTTC-GTGTTTT
1 AAAATCTTCGTGTTTTCAAAAA-TTTCGGTGTTTC
54010210 AAAAT
1 AAAAT
54010215 TCTCGTATTT
Statistics
Matches: 119, Mismatches: 16, Indels: 19
0.77 0.10 0.12
Matches are distributed among these distances:
33 10 0.08
34 34 0.29
35 53 0.45
36 13 0.11
37 6 0.05
38 3 0.03
ACGTcount: A:0.31, C:0.12, G:0.12, T:0.45
Consensus pattern (34 bp):
AAAATCTTCGTGTTTTCAAAAATTTCGGTGTTTC
Found at i:54010274 original size:15 final size:15
Alignment explanation
Indices: 54010256--54010307 Score: 52
Period size: 15 Copynumber: 3.3 Consensus size: 15
54010246 TGTGTTTCAA
54010256 AAAATGTCTTGTTTT
1 AAAATGTCTTGTTTT
*
54010271 AAAAT-TCTCGTGTTTCA
1 AAAATGTCT--TGTTT-T
*
54010288 AAAATGTCGTGTTTT
1 AAAATGTCTTGTTTT
54010303 AAAAT
1 AAAAT
54010308 TTTCGTGTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
14 3 0.10
15 10 0.33
16 10 0.33
17 5 0.17
18 2 0.07
ACGTcount: A:0.33, C:0.10, G:0.13, T:0.44
Consensus pattern (15 bp):
AAAATGTCTTGTTTT
Found at i:54010356 original size:17 final size:17
Alignment explanation
Indices: 54009856--54010356 Score: 147
Period size: 17 Copynumber: 29.5 Consensus size: 17
54009846 TCCTCGTGCA
*
54009856 TTTAAAAATTCTCATGT
1 TTTAAAAATTCTCGTGT
*
54009873 TTCAAAAA-TCTTCGTGT
1 TTTAAAAATTC-TCGTGT
* *
54009890 TTTCAAAATTCTAGTG-
1 TTTAAAAATTCTCGTGT
* * *
54009906 TTTCAAAATTTTCTTGT
1 TTTAAAAATTCTCGTGT
*
54009923 TTTCAGAAAAATTTTCGTGT
1 TTT---AAAAATTCTCGTGT
* * *
54009943 TTTATAATTTC-CGTAT
1 TTTAAAAATTCTCGTGT
* *
54009959 TTTCAAAAAATCAT-GTCT
1 TTT-AAAAATTC-TCGTGT
* *
54009977 TTCAAAAATTTTCGTGT
1 TTTAAAAATTCTCGTGT
*
54009994 TTTCAAAAAAATGAC-CGTGT
1 TTT---AAAAAT-TCTCGTGT
* *
54010014 TTCAAAATTTC-CGTGT
1 TTTAAAAATTCTCGTGT
** * *
54010030 TAAAAAAAAATCTTCGTAT
1 T-TTAAAAATTC-TCGTGT
*
54010049 TTTCAAAGAATTTTCGTG-
1 TTT-AAA-AATTCTCGTGT
*
54010067 TTTCAAAA-TCTTCGTGT
1 TTTAAAAATTC-TCGTGT
54010084 TTTCAAAAATT-TCGGTGT
1 TTT-AAAAATTCTC-GTGT
* * *
54010102 TTCAAAGATTTTCGTGT
1 TTTAAAAATTCTCGTGT
*
54010119 TTTCAAAAACTC-CGGTGAT
1 TTT-AAAAATTCTC-GTG-T
*** *
54010138 TTTAAAAAAAATTGT-T
1 TTTAAAAATTCTCGTGT
54010154 TTCTAAAAAATT-TCCGTG-
1 TT-T-AAAAATTCT-CGTGT
* *
54010172 TTTCAAAATTTTCGTGTT
1 TTTAAAAATTCTCGTG-T
*
54010190 TTTAAAAATTTTCGTGT
1 TTTAAAAATTCTCGTGT
*
54010207 TTT-AAAATTCTCGTAT
1 TTTAAAAATTCTCGTGT
54010223 TTT--AAATT-T--T-T
1 TTTAAAAATTCTCGTGT
* *
54010234 TTAAGAAAAAAT-T-GTGT
1 TT--TAAAAATTCTCGTGT
* * * *
54010251 TTCAAAAAATGTCTTGT
1 TTTAAAAATTCTCGTGT
54010268 TTT-AAAATTCTCGTGT
1 TTTAAAAATTCTCGTGT
* *
54010284 TTCAAAAA-TGTCGTGT
1 TTTAAAAATTCTCGTGT
*
54010300 TTT-AAAATTTTCGTGT
1 TTTAAAAATTCTCGTGT
* *
54010316 TTCTGAAATTTC-CGTG-
1 TT-TAAAAATTCTCGTGT
54010332 TTTAAAAATTCTCGTGT
1 TTTAAAAATTCTCGTGT
54010349 TTTAAAAA
1 TTTAAAAA
54010357 AAAACTTTCA
Statistics
Matches: 360, Mismatches: 74, Indels: 100
0.67 0.14 0.19
Matches are distributed among these distances:
11 3 0.01
12 1 0.00
14 1 0.00
15 29 0.08
16 102 0.28
17 110 0.31
18 66 0.18
19 17 0.05
20 31 0.09
ACGTcount: A:0.32, C:0.12, G:0.12, T:0.45
Consensus pattern (17 bp):
TTTAAAAATTCTCGTGT
Found at i:54010360 original size:21 final size:20
Alignment explanation
Indices: 54010335--54010387 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
54010325 TTCCGTGTTT
54010335 AAAAATTCTCGTGTTTTAAAA
1 AAAAATT-TCGTGTTTTAAAA
* *
54010356 AAAAACTTTCAT-TTTTTAAA
1 AAAAA-TTTCGTGTTTTAAAA
54010376 AAAAATTTCGTG
1 AAAAATTTCGTG
54010388 CTTCAAAATT
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
19 5 0.19
20 12 0.44
21 8 0.30
22 2 0.07
ACGTcount: A:0.43, C:0.09, G:0.08, T:0.40
Consensus pattern (20 bp):
AAAAATTTCGTGTTTTAAAA
Found at i:54010395 original size:16 final size:17
Alignment explanation
Indices: 54010376--54010412 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
54010366 ATTTTTTAAA
54010376 AAAAATT-TCGTG-CTT
1 AAAAATTCTCGTGTCTT
*
54010391 CAAAATTCTCGTGTCTT
1 AAAAATTCTCGTGTCTT
54010408 AAAAA
1 AAAAA
54010413 AAGTTTTCAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
15 6 0.33
16 5 0.28
17 7 0.39
ACGTcount: A:0.38, C:0.16, G:0.11, T:0.35
Consensus pattern (17 bp):
AAAAATTCTCGTGTCTT
Found at i:54018732 original size:192 final size:192
Alignment explanation
Indices: 54018405--54019421 Score: 1921
Period size: 192 Copynumber: 5.3 Consensus size: 192
54018395 CTTTCCAAGG
54018405 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAAATTTT
1 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAAATTTT
54018470 TTAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTTAG
66 TTAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTTAG
54018535 TTTATGTTTTAAATTGAGTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTC
131 TTTATGTTTTAAATTGAGTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTC
54018597 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAAATTTT
1 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAAATTTT
54018662 TTAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTTAG
66 TTAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTTAG
54018727 TTTATGTTTTAAATTGAGTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTC
131 TTTATGTTTTAAATTGAGTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTC
54018789 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAAATTTT
1 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAAATTTT
** * *
54018854 AAAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGGGCATGCCGAGGTATTTTTAG
66 TTAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTTAG
54018919 TTTATGTTTTAAATTGAGTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTC
131 TTTATGTTTTAAATTGAGTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTC
*
54018981 AAAATCAACTCATATTGTGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAAA-TTT
1 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAAATTTT
*
54019045 TTAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGAGGCACGCCGAGGTATTTTTAG
66 TTAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTTAG
*
54019110 TTTATGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTC
131 TTTATGTTTTAAATTGAGTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTC
54019172 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAAATTTT
1 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAAATTTT
54019237 TTAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTTAG
66 TTAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTTAG
54019302 TTTATGTTTTAAATTGAGTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTC
131 TTTATGTTTTAAATTGAGTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTC
* * **
54019364 -AAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCGAGGCACGCCGAGGTATTTTTA
1 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTA
54019422 GTTTATGTTT
Statistics
Matches: 806, Mismatches: 18, Indels: 3
0.97 0.02 0.00
Matches are distributed among these distances:
191 238 0.30
192 568 0.70
ACGTcount: A:0.30, C:0.13, G:0.21, T:0.35
Consensus pattern (192 bp):
AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAAATTTT
TTAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTTAG
TTTATGTTTTAAATTGAGTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTC
Found at i:54019179 original size:383 final size:384
Alignment explanation
Indices: 54018405--54019421 Score: 1921
Period size: 383 Copynumber: 2.7 Consensus size: 384
54018395 CTTTCCAAGG
54018405 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAAATTTT
1 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAAATTTT
54018470 TTAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTTAG
66 TTAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTTAG
54018535 TTTATGTTTTAAATTGAGTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTCAAA
131 TTTATGTTTTAAATTGAGTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTCAAA
54018600 ATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAAATTTTTTA
196 ATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAAATTTTTTA
*
54018665 AAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTTAGTTT
261 AAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGAGGCACGCCGAGGTATTTTTAGTTT
*
54018730 ATGTTTTAAATTGAGTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTC
326 ATGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTC
54018789 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAAATTTT
1 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAAATTTT
** * *
54018854 AAAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGGGCATGCCGAGGTATTTTTAG
66 TTAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTTAG
54018919 TTTATGTTTTAAATTGAGTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTCAAA
131 TTTATGTTTTAAATTGAGTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTCAAA
*
54018984 ATCAACTCATATTGTGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAAA-TTTTTA
196 ATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAAATTTTTTA
54019048 AAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGAGGCACGCCGAGGTATTTTTAGTTT
261 AAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGAGGCACGCCGAGGTATTTTTAGTTT
54019113 ATGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTC
326 ATGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTC
54019172 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAAATTTT
1 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAAATTTT
54019237 TTAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTTAG
66 TTAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTTAG
54019302 TTTATGTTTTAAATTGAGTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTC-AA
131 TTTATGTTTTAAATTGAGTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTCAAA
* * **
54019366 ATCAACTCATATTGCGAGAAATGAGTTGAGCCTCGAGGCACGCCGAGGTATTTTTA
196 ATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTA
54019422 GTTTATGTTT
Statistics
Matches: 617, Mismatches: 16, Indels: 2
0.97 0.03 0.00
Matches are distributed among these distances:
382 53 0.09
383 316 0.51
384 248 0.40
ACGTcount: A:0.30, C:0.13, G:0.21, T:0.35
Consensus pattern (384 bp):
AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAAATTTT
TTAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTTAG
TTTATGTTTTAAATTGAGTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTCAAA
ATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAAATTTTTTA
AAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGAGGCACGCCGAGGTATTTTTAGTTT
ATGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTC
Found at i:54019391 original size:121 final size:122
Alignment explanation
Indices: 54019242--54019557 Score: 492
Period size: 121 Copynumber: 2.6 Consensus size: 122
54019232 ATTTTTTAAA
*
54019242 AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTTAGTTTAT
1 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTTAGTTTAT
*
54019307 GTTTTAAATTGAGTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTC
66 GTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTC
*
54019364 -AAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCGAGGCACGCCGAGGTATTTTTAGTTTAT
1 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTTAGTTTAT
54019428 GTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTC
66 GTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTC
* * ** * * *
54019485 AAAAATCAACTCATATTGCAAGAGGA-GAGTTGAGCCTCGGCTCACATGCTGAGGTATTTTCAAT
1 -AAAATCAACTCATATTGCGAGA-AATGAGTTGAGCCTCGGGGCAC--GCCGAGGTATTTTTAGT
54019549 TTATGTTTT
62 TTATGTTTT
54019558 TTTCAATCTA
Statistics
Matches: 178, Mismatches: 11, Indels: 7
0.91 0.06 0.04
Matches are distributed among these distances:
121 118 0.66
123 36 0.20
124 1 0.01
125 23 0.13
ACGTcount: A:0.27, C:0.14, G:0.22, T:0.37
Consensus pattern (122 bp):
AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTTAGTTTAT
GTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTC
Found at i:54019562 original size:16 final size:17
Alignment explanation
Indices: 54019541--54019574 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
54019531 TGCTGAGGTA
*
54019541 TTTTCAATTTATG-TTT
1 TTTTCAATCTATGCTTT
54019557 TTTTCAATCTATGCTTT
1 TTTTCAATCTATGCTTT
54019574 T
1 T
54019575 CAAAAATCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.18, C:0.12, G:0.06, T:0.65
Consensus pattern (17 bp):
TTTTCAATCTATGCTTT
Found at i:54019686 original size:85 final size:87
Alignment explanation
Indices: 54019480--54019723 Score: 273
Period size: 91 Copynumber: 2.7 Consensus size: 87
54019470 TAATTTTTGT
*
54019480 TTTTCAAAAATCAACTCATATTGCAAGAGGAGAGTTGAGCCTC-GGCTCACATGCTGAGGTATTT
1 TTTTC-AAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAGG--C-CATGCTGAGGTATTT
* **
54019544 TCAATTTATGTTTTTTTCAATCTATGC
62 TCAATTTATGCTTTACTCAATCTA-GC
* *
54019571 TTTTCAAAAATCAACTTATATTGCGAGAGGTGAGTTGAGCCTCAAGG-CATGCTGAGGTATTTTC
1 TTTTC-AAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTC-AGGCCATGCTGAGGTATTTTC
*
54019635 AATTTCTGCTTTACT-AATTCTA-C
64 AATTTATGCTTTACTCAA-TCTAGC
* * *
54019658 TTTTC-AAATCAACTCATATTGCAAGAGGTGAGTTGAGTCTCAGGCCACACGCTGAGGTCTTTTC
1 TTTTCAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAGG-C-CATGCTGAGGTATTTTC
54019722 AA
64 AA
54019724 ATTCTGTTTT
Statistics
Matches: 135, Mismatches: 12, Indels: 16
0.83 0.07 0.10
Matches are distributed among these distances:
84 3 0.02
85 33 0.24
87 23 0.17
88 2 0.01
89 32 0.24
91 40 0.30
93 2 0.01
ACGTcount: A:0.27, C:0.18, G:0.19, T:0.35
Consensus pattern (87 bp):
TTTTCAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAGGCCATGCTGAGGTATTTTCAA
TTTATGCTTTACTCAATCTAGC
Found at i:54019738 original size:85 final size:88
Alignment explanation
Indices: 54019480--54019738 Score: 300
Period size: 85 Copynumber: 2.9 Consensus size: 88
54019470 TAATTTTTGT
*
54019480 TTTTCAAAAATCAACTCATATTGCAAGAGGAGAGTTGAGCCTC-GGCTCACATGCTGAGGTATTT
1 TTTTC-AAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAGGC-CACATGCTGAGGTATTT
*
54019544 TCAATTTATGTTTTTTTCAA-TCTATGC
64 TCAATTTCTG-TTTTTT-AATTCTA-GC
* *
54019571 TTTTCAAAAATCAACTTATATTGCGAGAGGTGAGTTGAGCCTCAAGG---CATGCTGAGGTATTT
1 TTTTC-AAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTC-AGGCCACATGCTGAGGTATTT
**
54019633 TCAATTTCTGCTTTACTAATTCTA-C
64 TCAATTTCTG-TTTTTTAATTCTAGC
* * *
54019658 TTTTC-AAATCAACTCATATTGCAAGAGGTGAGTTGAGTCTCAGGCCACACGCTGAGGTCTTTTC
1 TTTTCAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAGGCCACATGCTGAGGTATTTTC
*
54019722 AAATTCTG-TTTTTAATT
66 AATTTCTGTTTTTTAATT
54019739 TCTGTTTTTT
Statistics
Matches: 147, Mismatches: 15, Indels: 18
0.82 0.08 0.10
Matches are distributed among these distances:
84 3 0.02
85 40 0.27
87 28 0.19
88 2 0.01
89 32 0.22
91 40 0.27
93 2 0.01
ACGTcount: A:0.27, C:0.18, G:0.18, T:0.37
Consensus pattern (88 bp):
TTTTCAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAGGCCACATGCTGAGGTATTTTC
AATTTCTGTTTTTTAATTCTAGC
Found at i:54019921 original size:54 final size:55
Alignment explanation
Indices: 54019837--54020054 Score: 315
Period size: 54 Copynumber: 4.1 Consensus size: 55
54019827 TCAATTTCTA
*
54019837 CTTTTCAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
1 CTTTTCAATTTCTATTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
* *
54019892 CTTTT-AATTTCTATTTTTCAAAAACCAACTCATATTGCGAAAGGTGAGTTGAGC
1 CTTTTCAATTTCTATTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
54019946 C--TT---TTTCTATTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
1 CTTTTCAATTTCTATTTTTC-AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
* * *
54019997 CTTTTGCAAATTCT-GTTTTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGC
1 CTTTT-CAATTTCTATTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
54020052 CTT
1 CTT
54020055 GGCTCACGTG
Statistics
Matches: 148, Mismatches: 8, Indels: 14
0.87 0.05 0.08
Matches are distributed among these distances:
50 12 0.08
51 34 0.23
52 2 0.01
53 2 0.01
54 47 0.32
55 42 0.28
56 5 0.03
57 4 0.03
ACGTcount: A:0.29, C:0.17, G:0.17, T:0.37
Consensus pattern (55 bp):
CTTTTCAATTTCTATTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
Found at i:54020359 original size:30 final size:31
Alignment explanation
Indices: 54020325--54020426 Score: 122
Period size: 30 Copynumber: 3.4 Consensus size: 31
54020315 TTAAAAATAA
*
54020325 AAATTGCATTTTGACCCCTAAACTTTTC-CT
1 AAATTTCATTTTGACCCCTAAACTTTTCTCT
* *
54020355 AAATTTCATTTTGACCCTTAAAC-TTTCTTT
1 AAATTTCATTTTGACCCCTAAACTTTTCTCT
* *
54020385 AAATTTCACTTAGACCCCTAAAC-TTTCAT-T
1 AAATTTCATTTTGACCCCTAAACTTTTC-TCT
54020415 AAATTTCATTTT
1 AAATTTCATTTT
54020427 AATCCTAAAT
Statistics
Matches: 62, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
29 4 0.06
30 57 0.92
31 1 0.02
ACGTcount: A:0.29, C:0.23, G:0.04, T:0.44
Consensus pattern (31 bp):
AAATTTCATTTTGACCCCTAAACTTTTCTCT
Found at i:54020791 original size:3 final size:3
Alignment explanation
Indices: 54020785--54020855 Score: 60
Period size: 3 Copynumber: 24.0 Consensus size: 3
54020775 GCTAGACTTT
* *
54020785 GAA GAA GAA GAA GGAA GAA GAA GGAA GAA GAA -AA GAG GAA GAA AAA
1 GAA GAA GAA GAA -GAA GAA GAA -GAA GAA GAA GAA GAA GAA GAA GAA
*
54020831 GAAA GAA -AA -AA GAA AAA GAA -AA GAA
1 G-AA GAA GAA GAA GAA GAA GAA GAA GAA
54020856 ATAATAAAAA
Statistics
Matches: 56, Mismatches: 6, Indels: 12
0.76 0.08 0.16
Matches are distributed among these distances:
2 8 0.14
3 39 0.70
4 9 0.16
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:54020803 original size:10 final size:10
Alignment explanation
Indices: 54020788--54020816 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
54020778 AGACTTTGAA
54020788 GAAGAAGAAG
1 GAAGAAGAAG
54020798 GAAGAAGAAG
1 GAAGAAGAAG
54020808 GAAGAAGAA
1 GAAGAAGAA
54020817 AAGAGGAAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (10 bp):
GAAGAAGAAG
Found at i:54020832 original size:17 final size:17
Alignment explanation
Indices: 54020812--54020856 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
54020802 AAGAAGGAAG
**
54020812 AAGAAAAGAGGAAGAAA
1 AAGAAAAGAAAAAGAAA
54020829 AAG-AAAGAAAAAAGAAA
1 AAGAAAAG-AAAAAGAAA
54020846 AAGAAAAGAAA
1 AAGAAAAGAAA
54020857 TAATAAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
16 4 0.17
17 16 0.67
18 4 0.17
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (17 bp):
AAGAAAAGAAAAAGAAA
Found at i:54020837 original size:34 final size:34
Alignment explanation
Indices: 54020788--54020854 Score: 89
Period size: 34 Copynumber: 2.0 Consensus size: 34
54020778 AGACTTTGAA
* * * * *
54020788 GAAGAAGAAGGAAGAAGAAGGAAGAAGAAAAGAG
1 GAAGAAAAAGAAAGAAAAAAGAAAAAGAAAAGAG
54020822 GAAGAAAAAGAAAGAAAAAAGAAAAAGAAAAGA
1 GAAGAAAAAGAAAGAAAAAAGAAAAAGAAAAGA
54020855 AATAATAAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
34 28 1.00
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (34 bp):
GAAGAAAAAGAAAGAAAAAAGAAAAAGAAAAGAG
Found at i:54020865 original size:18 final size:17
Alignment explanation
Indices: 54020823--54020856 Score: 59
Period size: 17 Copynumber: 1.9 Consensus size: 17
54020813 AGAAAAGAGG
54020823 AAGAAAAAGAAAGAAAA
1 AAGAAAAAGAAAGAAAA
54020840 AAGAAAAAGAAAAGAAA
1 AAGAAAAAG-AAAGAAA
54020857 TAATAAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (17 bp):
AAGAAAAAGAAAGAAAA
Found at i:54020952 original size:18 final size:20
Alignment explanation
Indices: 54020929--54020972 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
54020919 CCAGCAGCCC
54020929 AAGAAA-AA-ACAAAAAAAA
1 AAGAAACAACACAAAAAAAA
*
54020947 AAGAAACAAGCCCAAAAAAAA
1 AAGAAACAA-CACAAAAAAAA
54020968 AAGAA
1 AAGAA
54020973 GAGCAGGCCA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 6 0.27
19 2 0.09
21 14 0.64
ACGTcount: A:0.80, C:0.11, G:0.09, T:0.00
Consensus pattern (20 bp):
AAGAAACAACACAAAAAAAA
Found at i:54021119 original size:9 final size:9
Alignment explanation
Indices: 54021107--54021157 Score: 50
Period size: 9 Copynumber: 5.6 Consensus size: 9
54021097 CCCAGCAGAG
54021107 AAAAA-AAA
1 AAAAAGAAA
*
54021115 GAAAAGAAA
1 AAAAAGAAA
*
54021124 AAGAAGAAA
1 AAAAAGAAA
*
54021133 AAGAGAAGGAA
1 AA-A-AAGAAA
54021144 AAAAAGAAA
1 AAAAAGAAA
54021153 AAAAA
1 AAAAA
54021158 AGAGGTTCAA
Statistics
Matches: 34, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
8 4 0.12
9 22 0.65
10 1 0.03
11 7 0.21
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (9 bp):
AAAAAGAAA
Found at i:54021124 original size:14 final size:14
Alignment explanation
Indices: 54021105--54021157 Score: 54
Period size: 14 Copynumber: 3.7 Consensus size: 14
54021095 GGCCCAGCAG
54021105 AGAAAAAAAAGAAA
1 AGAAAAAAAAGAAA
*
54021119 AGAAAAAGAAGAAAA
1 AGAAAAAAAAG-AAA
**
54021134 AGAGAAGGAAA-AAA
1 AGA-AAAAAAAGAAA
54021148 AGAAAAAAAA
1 AGAAAAAAAA
54021158 AGAGGTTCAA
Statistics
Matches: 31, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
13 5 0.16
14 16 0.52
15 6 0.19
16 4 0.13
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (14 bp):
AGAAAAAAAAGAAA
Found at i:54021133 original size:20 final size:20
Alignment explanation
Indices: 54021105--54021160 Score: 71
Period size: 20 Copynumber: 2.9 Consensus size: 20
54021095 GGCCCAGCAG
*
54021105 AGAAAAAAAAGAAAAGAAAA
1 AGAAGAAAAAGAAAAGAAAA
*
54021125 AGAAGAAAAAGAGAAGGAAAA
1 AGAAGAAAAAGA-AAAGAAAA
54021146 A-AAGAAAAA-AAAAGA
1 AGAAGAAAAAGAAAAGA
54021161 GGTTCAATTC
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
18 4 0.12
19 1 0.03
20 19 0.59
21 8 0.25
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (20 bp):
AGAAGAAAAAGAAAAGAAAA
Found at i:54021529 original size:18 final size:18
Alignment explanation
Indices: 54021491--54022003 Score: 276
Period size: 17 Copynumber: 29.6 Consensus size: 18
54021481 ATCCTCGTTC
* *
54021491 TTTT-AAAAATTCTCATG
1 TTTTCAAAAATTTTCGTG
*
54021508 -TTTCAAAAATCTTCGTG
1 TTTTCAAAAATTTTCGTG
* *
54021525 TTTTC-AAAATTCTAGTG
1 TTTTCAAAAATTTTCGTG
*
54021542 -TTTCAAAAATTTTCTTG
1 TTTTCAAAAATTTTCGTG
54021559 TTTTCAGAAAAAATTTTCGTG
1 TTTTC---AAAAATTTTCGTG
* * *
54021580 TTTT-ATAAATTTCCGTA
1 TTTTCAAAAATTTTCGTG
** *
54021597 TTTTCAAAAA-AATCATG
1 TTTTCAAAAATTTTCGTG
54021614 TCTTTCAAAAATTTTCGTG
1 T-TTTCAAAAATTTTCGTG
****
54021633 TTTTCAAAAAAAAGACCGTG
1 TTTTC--AAAAATTTTCGTG
*
54021653 -TTTCAAAAATTTCCGTG
1 TTTTCAAAAATTTTCGTG
*** * *
54021670 TTAAAAAAAATCTTCGTA
1 TTTTCAAAAATTTTCGTG
54021688 TTTTCAAAAAATTTTCGTG
1 TTTTC-AAAAATTTTCGTG
*
54021707 -TTTCAAAAATCTTCGTG
1 TTTTCAAAAATTTTCGTG
54021724 TTTTCAAAAA-TTTCG-G
1 TTTTCAAAAATTTTCGTG
*
54021740 TGTTTCAAAGATTTTCGTG
1 T-TTTCAAAAATTTTCGTG
* *
54021759 TTTTCAAAAA-CTCCGGTG
1 TTTTCAAAAATTTTC-GTG
***
54021777 ATTTT-AAAAAAAATCGT-
1 -TTTTCAAAAATTTTCGTG
* *
54021794 TTTCTAAAAAATTTCCGTG
1 TTT-TCAAAAATTTTCGTG
54021813 -TTTCAAAAATTTTCGTG
1 TTTTCAAAAATTTTCGTG
*
54021830 TTTTTAAAAATTTTCGTG
1 TTTTCAAAAATTTTCGTG
* *
54021848 TTTT-AAAAATTCTCGTA
1 TTTTCAAAAATTTTCGTG
54021865 TTTT---AAATTTT--T-
1 TTTTCAAAAATTTTCGTG
*** **
54021877 TTAAGAAAAAAATT-GTG
1 TTTTCAAAAATTTTCGTG
* * *
54021894 -TTTCAAAAAATGTCTTG
1 TTTTCAAAAATTTTCGTG
*
54021911 TTTT-AAAAATTCTCGTG
1 TTTTCAAAAATTTTCGTG
* *
54021928 -TTTCAAAAAATGTCGTG
1 TTTTCAAAAATTTTCGTG
54021945 TTTT-AAAAATTTTCGTG
1 TTTTCAAAAATTTTCGTG
** *
54021962 -TTTCTGAAATTTCCGTG
1 TTTTCAAAAATTTTCGTG
*
54021979 -TTT-AAAAATTCTCGTG
1 TTTTCAAAAATTTTCGTG
54021995 TTTT-AAAAA
1 TTTTCAAAAA
54022004 AAAACTTTCA
Statistics
Matches: 377, Mismatches: 83, Indels: 72
0.71 0.16 0.14
Matches are distributed among these distances:
12 2 0.01
13 1 0.00
15 11 0.03
16 36 0.10
17 165 0.44
18 110 0.29
19 27 0.07
20 9 0.02
21 16 0.04
ACGTcount: A:0.34, C:0.12, G:0.11, T:0.44
Consensus pattern (18 bp):
TTTTCAAAAATTTTCGTG
Found at i:54021535 original size:34 final size:34
Alignment explanation
Indices: 54021473--54021641 Score: 108
Period size: 34 Copynumber: 4.8 Consensus size: 34
54021463 AAAATTGTAA
* * * *
54021473 TTTCAATAATCCTCGTTCTTTTAAAAATTCTCATG
1 TTTCAAAAATCTTCG-TGTTTTCAAAATTCTCATG
54021508 TTTCAAAAATCTTCGTGTTTTCAAAATTCT-AGTG
1 TTTCAAAAATCTTCGTGTTTTCAAAATTCTCA-TG
* * * *
54021542 TTTCAAAAATTTTCTTGTTTTCAGAAAAAATTTTCGTG
1 TTTCAAAAATCTTCGTGTTTTC----AAAATTCTCATG
* * * ***
54021580 TTTTATAAAT-TTCCGTATTTTCAAAAAAATCATG
1 TTTCAAAAATCTT-CGTGTTTTCAAAATTCTCATG
*
54021614 TCTTTCAAAAATTTTCGTGTTTTCAAAA
1 --TTTCAAAAATCTTCGTGTTTTCAAAA
54021642 AAAAGACCGT
Statistics
Matches: 105, Mismatches: 19, Indels: 19
0.73 0.13 0.13
Matches are distributed among these distances:
33 1 0.01
34 43 0.41
35 13 0.12
36 20 0.19
37 4 0.04
38 24 0.23
ACGTcount: A:0.32, C:0.14, G:0.08, T:0.46
Consensus pattern (34 bp):
TTTCAAAAATCTTCGTGTTTTCAAAATTCTCATG
Found at i:54021547 original size:16 final size:16
Alignment explanation
Indices: 54021496--54021549 Score: 56
Period size: 16 Copynumber: 3.2 Consensus size: 16
54021486 CGTTCTTTTA
54021496 AAAATTCTCA-TGTTTC
1 AAAATTCT-AGTGTTTC
* *
54021512 AAAAATCTTCGTGTTTTC
1 AAAATTC-TAGTG-TTTC
54021530 AAAATTCTAGTGTTTC
1 AAAATTCTAGTGTTTC
54021546 AAAA
1 AAAA
54021550 ATTTTCTTGT
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
16 14 0.45
17 7 0.23
18 10 0.32
ACGTcount: A:0.35, C:0.15, G:0.09, T:0.41
Consensus pattern (16 bp):
AAAATTCTAGTGTTTC
Found at i:54021626 original size:36 final size:37
Alignment explanation
Indices: 54021586--54021668 Score: 105
Period size: 36 Copynumber: 2.3 Consensus size: 37
54021576 CGTGTTTTAT
* *
54021586 AAATTTCCGTATTTTCAAAAAAATCA-TGTCTTTCAA
1 AAATTTCCGTATTTTCAAAAAAAACACCGTCTTTCAA
* * * *
54021622 AAATTTTCGTGTTTTCAAAAAAAAGACCGTGTTTCAA
1 AAATTTCCGTATTTTCAAAAAAAACACCGTCTTTCAA
54021659 AAATTTCCGT
1 AAATTTCCGT
54021669 GTTAAAAAAA
Statistics
Matches: 39, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
36 22 0.56
37 17 0.44
ACGTcount: A:0.37, C:0.16, G:0.10, T:0.37
Consensus pattern (37 bp):
AAATTTCCGTATTTTCAAAAAAAACACCGTCTTTCAA
Found at i:54021743 original size:35 final size:34
Alignment explanation
Indices: 54021508--54022004 Score: 197
Period size: 35 Copynumber: 14.3 Consensus size: 34
54021498 AATTCTCATG
* *
54021508 TTTCAAAAATCTTCGTGTTTTCAAAATTC-TAGTG-
1 TTTCAAAAAT-TTCGTG-TTTCAAAAATCTTCGTGT
* *
54021542 TTTCAAAAATTTTCTTGTTTTCAGAAAAAATTTTCGTGT
1 TTTCAAAAA-TTTCGTG-TTTC---AAAAATCTTCGTGT
* * ** *
54021581 TTT-ATAAATTTCCGTATTTTCAAAAA-AATCATGT
1 TTTCAAAAATTT-CGT-GTTTCAAAAATCTTCGTGT
****
54021615 CTTTCAAAAATTTTCGTGTTTTCAAAAAAAAGACCGTG-
1 -TTTCAAAAA-TTTCGTG-TTTC--AAAAATCTTCGTGT
** *
54021653 TTTCAAAAATTTCCGTGTTAAAAAAAATCTTCGTAT
1 TTTCAAAAATTT-CGTGTT-TCAAAAATCTTCGTGT
54021689 TTTCAAAAAATTTTCGTGTTTCAAAAATCTTCGTGT
1 TTTC-AAAAA-TTTCGTGTTTCAAAAATCTTCGTGT
* *
54021725 TTTCAAAAATTTCGGTGTTTCAAAGATTTTCGTGT
1 TTTCAAAAATTTC-GTGTTTCAAAAATCTTCGTGT
* * * ***
54021760 TTTCAAAAACTCCGGTGATTTTAAAAAAAATCGT-T
1 TTTCAAAAATTTC-GTG-TTTCAAAAATCTTCGTGT
* *
54021795 TTCTAAAAAATTTCCGTGTTTCAAAAATTTTCGTGT
1 TT-TCAAAAATTT-CGTGTTTCAAAAATCTTCGTGT
* * *
54021831 TTTTAAAAATTTTCGTGTTTTAAAAAT-TCTCGTAT
1 TTTCAAAAA-TTTCGTGTTTCAAAAATCT-TCGTGT
* **
54021866 TTT---AAATTT--T-TTTAAGAAAAAAATT-GTG-
1 TTTCAAAAATTTCGTGTTT--CAAAAATCTTCGTGT
* * *
54021894 TTTCAAAAAATGTCTTGTTTTAAAAAT-TCTCGTG-
1 TTTC-AAAAATTTCGTGTTTCAAAAATCT-TCGTGT
* * *
54021928 TTTCAAAAAATGTCGTGTTTTAAAAATTTTCGTG-
1 TTTC-AAAAATTTCGTGTTTCAAAAATCTTCGTGT
**
54021962 TTTCTGAAATTTCCGTGTTT-AAAAAT-TCTCGTGT
1 TTTCAAAAATTT-CGTGTTTCAAAAATCT-TCGTGT
*
54021996 TTTAAAAAA
1 TTTCAAAAA
54022005 AAACTTTCAT
Statistics
Matches: 363, Mismatches: 57, Indels: 86
0.72 0.11 0.17
Matches are distributed among these distances:
28 6 0.02
29 3 0.01
30 6 0.02
31 4 0.01
32 10 0.03
33 22 0.06
34 81 0.22
35 102 0.28
36 64 0.18
37 36 0.10
38 22 0.06
39 7 0.02
ACGTcount: A:0.34, C:0.12, G:0.11, T:0.43
Consensus pattern (34 bp):
TTTCAAAAATTTCGTGTTTCAAAAATCTTCGTGT
Found at i:54026706 original size:169 final size:162
Alignment explanation
Indices: 54026423--54026722 Score: 456
Period size: 169 Copynumber: 1.8 Consensus size: 162
54026413 TTGGGTTTTT
* * *
54026423 TAGGCTTGCAAATATTTTAGCCCAATACATAATCTTTTTTTTCCTCGTAGAACTCAGTTTGGAAT
1 TAGGCCTGCAAATATTTTAGCCCAATACATAATCTTTTTTTTCCTCGCAGAACTCAGTTTGAAAT
*
54026488 TAAAAAAGAGTTAATGGCTCTTTTAATTCAAACATTAATTTGTGATTAATGGCTCCTTAATTCAC
66 TAAAAAAGAGTTAATGGCTCTTTTAATTCAAACATTAATTTGGGATTAATGGCTCCTTAATTCAC
54026553 AAACATATAATGTTTGGACCAGTCAGGCCTTC
131 AAACATATAATGTTTGGACCAGTCAGGCCTTC
* *
54026585 TAGGCCTGCAAATATTTTAGCCCAATACGTTATCTTATTTTTTTTCCTCAGCAGAACTTATCAGT
1 TAGGCCTGCAAATATTTTAGCCCAATACATAATC---TTTTTTTTCCTC-GCAGAAC---TCAGT
* * *
54026650 TTGAAATTAAAAAGGAGTTAATTGCTCTTTTAATTCAAACGTTAATTTGGGATTAATGGCTCCTT
59 TTGAAATTAAAAAAGAGTTAATGGCTCTTTTAATTCAAACATTAATTTGGGATTAATGGCTCCTT
54026715 AATTCACA
124 AATTCACA
54026723 GACACATTAT
Statistics
Matches: 122, Mismatches: 9, Indels: 7
0.88 0.07 0.05
Matches are distributed among these distances:
162 31 0.25
165 12 0.10
166 6 0.05
169 73 0.60
ACGTcount: A:0.31, C:0.17, G:0.14, T:0.38
Consensus pattern (162 bp):
TAGGCCTGCAAATATTTTAGCCCAATACATAATCTTTTTTTTCCTCGCAGAACTCAGTTTGAAAT
TAAAAAAGAGTTAATGGCTCTTTTAATTCAAACATTAATTTGGGATTAATGGCTCCTTAATTCAC
AAACATATAATGTTTGGACCAGTCAGGCCTTC
Found at i:54027964 original size:27 final size:27
Alignment explanation
Indices: 54027918--54028000 Score: 94
Period size: 27 Copynumber: 3.1 Consensus size: 27
54027908 CCTCTACAAA
***
54027918 AGATGGTCCTAACAAACTTCCCACATT
1 AGATGGTCCTAACGGGCTTCCCACATT
* *
54027945 AGATGGTCCTAACGGGCTTCCCATAGT
1 AGATGGTCCTAACGGGCTTCCCACATT
* * *
54027972 AGATAGTCCTGACGGGCTTCCAACATT
1 AGATGGTCCTAACGGGCTTCCCACATT
54027999 AG
1 AG
54028001 TTTGGTTGGT
Statistics
Matches: 46, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 46 1.00
ACGTcount: A:0.28, C:0.27, G:0.20, T:0.25
Consensus pattern (27 bp):
AGATGGTCCTAACGGGCTTCCCACATT
Found at i:54032101 original size:13 final size:12
Alignment explanation
Indices: 54032064--54032098 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
54032054 TCGATCTTCT
* *
54032064 TTTTATTATCTA
1 TTTTATTTTTTA
54032076 TTTTATTTTTTA
1 TTTTATTTTTTA
54032088 TTTTATTTTTT
1 TTTTATTTTTT
54032099 TATAAACGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.17, C:0.03, G:0.00, T:0.80
Consensus pattern (12 bp):
TTTTATTTTTTA
Found at i:54032815 original size:9 final size:10
Alignment explanation
Indices: 54032793--54032832 Score: 52
Period size: 9 Copynumber: 4.4 Consensus size: 10
54032783 TATTGTTTAA
54032793 ATTAATCATT
1 ATTAATCATT
54032803 -TTAAT-ATT
1 ATTAATCATT
54032811 ATTAAT-ATT
1 ATTAATCATT
54032820 ATT-ATCATT
1 ATTAATCATT
54032829 ATTA
1 ATTA
54032833 TTAGTTTTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
8 5 0.19
9 22 0.81
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.55
Consensus pattern (10 bp):
ATTAATCATT
Found at i:54033540 original size:19 final size:20
Alignment explanation
Indices: 54033513--54033554 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
54033503 CTTAGGTATA
*
54033513 TTTTTATAT-TGTATA-ATT
1 TTTTTATATATATATATATT
54033531 TTTTTAATATATATATATATT
1 TTTTT-ATATATATATATATT
54033552 TTT
1 TTT
54033555 ATTTTCACGA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
18 5 0.25
19 4 0.20
20 5 0.25
21 6 0.30
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (20 bp):
TTTTTATATATATATATATT
Found at i:54033555 original size:19 final size:18
Alignment explanation
Indices: 54033509--54033555 Score: 51
Period size: 19 Copynumber: 2.6 Consensus size: 18
54033499 CATACTTAGG
*
54033509 TATATTTTT-ATATTGTA
1 TATATTTTTAATATTATA
*
54033526 TAATTTTTTTAATATATATA
1 T-ATATTTTTAATAT-TATA
54033546 TATATTTTTA
1 TATATTTTTA
54033556 TTTTCACGAA
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
17 1 0.04
18 7 0.29
19 12 0.50
20 4 0.17
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (18 bp):
TATATTTTTAATATTATA
Found at i:54040462 original size:12 final size:12
Alignment explanation
Indices: 54040445--54040470 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
54040435 CTTGATGCGC
54040445 CCAAAATTGGTA
1 CCAAAATTGGTA
54040457 CCAAAATTGGTA
1 CCAAAATTGGTA
54040469 CC
1 CC
54040471 TAGTTGATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.38, C:0.23, G:0.15, T:0.23
Consensus pattern (12 bp):
CCAAAATTGGTA
Found at i:54041041 original size:12 final size:12
Alignment explanation
Indices: 54041026--54041068 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
54041016 AAATGACAAT
*
54041026 ATAATAATAACA
1 ATAATAACAACA
54041038 ATAATAACAACA
1 ATAATAACAACA
* * *
54041050 ACAATAACTATA
1 ATAATAACAACA
54041062 ATAATAA
1 ATAATAA
54041069 ATCTAAATTT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.65, C:0.12, G:0.00, T:0.23
Consensus pattern (12 bp):
ATAATAACAACA
Found at i:54043905 original size:10 final size:10
Alignment explanation
Indices: 54043892--54043932 Score: 50
Period size: 9 Copynumber: 4.2 Consensus size: 10
54043882 ACATATATTT
54043892 ATATTTTATA
1 ATATTTTATA
54043902 ATATTTTTATA
1 ATA-TTTTATA
*
54043913 GT-TTTTA-A
1 ATATTTTATA
54043921 ATATTTTATA
1 ATATTTTATA
54043931 AT
1 AT
54043933 CCAAATATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
8 2 0.08
9 10 0.38
10 6 0.23
11 8 0.31
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (10 bp):
ATATTTTATA
Found at i:54043905 original size:18 final size:18
Alignment explanation
Indices: 54043884--54043926 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
54043874 ATATACGTAC
54043884 ATATATTTATA-TTTTATA
1 ATATATTTATAGTTTT-TA
*
54043902 ATATTTTTATAGTTTTTA
1 ATATATTTATAGTTTTTA
54043920 A-ATATTT
1 ATATATTT
54043927 TATAATCCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 5 0.23
18 13 0.59
19 4 0.18
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (18 bp):
ATATATTTATAGTTTTTA
Found at i:54052738 original size:44 final size:44
Alignment explanation
Indices: 54052683--54053129 Score: 301
Period size: 44 Copynumber: 10.1 Consensus size: 44
54052673 GGACCTACTA
* * *
54052683 TCTTTGATCTACTTCACGCCAGTACATGAAGATAAGATCTATTT
1 TCTTTGATCTACTTCACACCAGTACATGAAGACAAGATCTGTTT
* * *** *
54052727 TCTTCGATCTACTCCACCACCAGTATGGGGAGACAAGATCTG-TT
1 TCTTTGATCTACTTCA-CACCAGTACATGAAGACAAGATCTGTTT
* *
54052771 TCTTTGATCTACTTCACGCTAGTACATGAAGACAAGATCTGTTT
1 TCTTTGATCTACTTCACACCAGTACATGAAGACAAGATCTGTTT
* * * *** ** *
54052815 TCTTCGATCTACTTCGCCACCGGTATGGGAAGACAAGATCTACTA
1 TCTTTGATCTACTTC-ACACCAGTACATGAAGACAAGATCTGTTT
* ** * *
54052860 TCTTTGATCTATTTCATGCCAGTACATGAAGACAAGATCTGCTA
1 TCTTTGATCTACTTCACACCAGTACATGAAGACAAGATCTGTTT
* **
54052904 TCTTTGATCTACTCCACCACCAGT--ATGGGGACAAGATCTGTTT
1 TCTTTGATCTACTTCA-CACCAGTACATGAAGACAAGATCTGTTT
* * * *** * * *
54052947 TCTTCGATCTGCTTCGCCACCAGTATGGGAAGACATGATCTGGTA
1 TCTTTGATCTACTTC-ACACCAGTACATGAAGACAAGATCTGTTT
* * **
54052992 TCTCTGATCTACTTCACGCCAGTATGTGAAGACAAGATCTG-TT
1 TCTTTGATCTACTTCACACCAGTACATGAAGACAAGATCTGTTT
* * *** * * * *
54053035 TCTTTGATCTGCTTTGC-CACCAATATGGGAAGGCAGGATCTGGTA
1 TCTTTGATCTAC-TT-CACACCAGTACATGAAGACAAGATCTGTTT
* * ***
54053080 GCTATGATCTACTTCACGTTAGTACATGAAGACAAGATCTGCTTT
1 TCTTTGATCTACTTCACACCAGTACATGAAGACAAGATCTG-TTT
54053125 TCTTT
1 TCTTT
54053130 TCAGCCTGCT
Statistics
Matches: 302, Mismatches: 89, Indels: 23
0.73 0.21 0.06
Matches are distributed among these distances:
43 65 0.22
44 143 0.47
45 94 0.31
ACGTcount: A:0.26, C:0.23, G:0.19, T:0.32
Consensus pattern (44 bp):
TCTTTGATCTACTTCACACCAGTACATGAAGACAAGATCTGTTT
Found at i:54052775 original size:88 final size:88
Alignment explanation
Indices: 54052683--54053044 Score: 417
Period size: 88 Copynumber: 4.1 Consensus size: 88
54052673 GGACCTACTA
* * *
54052683 TCTTTGATCTACTTCACGCCAGTACATGAAGATAAGATCTATTTTCTTCGATCTACTCCACCACC
1 TCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGTTATCTTCGATCTACTCCACCACC
*
54052748 AGTATGGGGAGACAAGATCTGTT
66 AGTATGGGAAGACAAGATCTGTT
* * * *
54052771 TCTTTGATCTACTTCACGCTAGTACATGAAGACAAGATCTGTTTTCTTCGATCTACTTCGCCACC
1 TCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGTTATCTTCGATCTACTCCACCACC
* * *
54052836 GGTATGGGAAGACAAGATCTACTA
66 AGTATGGGAAGACAAGATCT-GTT
* * * *
54052860 TCTTTGATCTATTTCATGCCAGTACATGAAGACAAGATCTGCTATCTTTGATCTACTCCACCACC
1 TCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGTTATCTTCGATCTACTCCACCACC
54052925 AGTATGGG--GACAAGATCTGTTT
66 AGTATGGGAAGACAAGATCTG-TT
* * * * *** * * * *
54052947 TCTTCGATCTGCTTCGCCACCAGTATGGGAAGACATGATCTGGTATC-TCTGATCTACTTCA-CG
1 TCTTTGATCTACTTC-ACGCCAGTACATGAAGACAAGATCTGTTATCTTC-GATCTACTCCACCA
*
54053010 CCAGTATGTGAAGACAAGATCTGTT
64 CCAGTATGGGAAGACAAGATCTGTT
54053035 TCTTTGATCT
1 TCTTTGATCT
54053045 GCTTTGCCAC
Statistics
Matches: 232, Mismatches: 36, Indels: 12
0.83 0.13 0.04
Matches are distributed among these distances:
87 34 0.15
88 122 0.53
89 76 0.33
ACGTcount: A:0.26, C:0.23, G:0.18, T:0.33
Consensus pattern (88 bp):
TCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGTTATCTTCGATCTACTCCACCACC
AGTATGGGAAGACAAGATCTGTT
Found at i:54052893 original size:132 final size:131
Alignment explanation
Indices: 54052757--54053044 Score: 398
Period size: 132 Copynumber: 2.2 Consensus size: 131
54052747 CAGTATGGGG
* * *
54052757 AGACAAGATCTGTTTCTTTGATCTACTTCA-CGCTAGTACATGAAGACAAGATCTGTTTTCTTCG
1 AGACAAGATCTGTTTCTTTGATCTACTCCACCACCAGT--ATGAAGACAAGATCTGTTTTCTTCG
* * * *
54052821 ATCTACTTCGCCACCGGTATGGGAAGACAAGATCTACTATCTTTGATCTATTTCATGCCAGTACA
64 ATCTACTTCGCCACCAGTATGGGAAGACAAGATCTACTATCTCTGATCTACTTCACGCCAGTACA
54052886 TGA
129 TGA
* **
54052889 AGACAAGATCTGCTATCTTTGATCTACTCCACCACCAGTATGGGGACAAGATCTGTTTTCTTCGA
1 AGACAAGATCTG-TTTCTTTGATCTACTCCACCACCAGTATGAAGACAAGATCTGTTTTCTTCGA
* * ** **
54052954 TCTGCTTCGCCACCAGTATGGGAAGACATGATCTGGTATCTCTGATCTACTTCACGCCAGTATGT
65 TCTACTTCGCCACCAGTATGGGAAGACAAGATCTACTATCTCTGATCTACTTCACGCCAGTACAT
54053019 GA
130 GA
54053021 AGACAAGATCTGTTTCTTTGATCT
1 AGACAAGATCTGTTTCTTTGATCT
54053045 GCTTTGCCAC
Statistics
Matches: 137, Mismatches: 17, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
131 11 0.08
132 105 0.77
133 16 0.12
134 5 0.04
ACGTcount: A:0.26, C:0.23, G:0.19, T:0.33
Consensus pattern (131 bp):
AGACAAGATCTGTTTCTTTGATCTACTCCACCACCAGTATGAAGACAAGATCTGTTTTCTTCGAT
CTACTTCGCCACCAGTATGGGAAGACAAGATCTACTATCTCTGATCTACTTCACGCCAGTACATG
A
Found at i:54052981 original size:177 final size:177
Alignment explanation
Indices: 54052574--54053044 Score: 488
Period size: 177 Copynumber: 2.7 Consensus size: 177
54052564 CTACTGCTTA
* * * * * * *
54052574 GGGAGGCAAGATCTGTAATCTTCAATCTAATATTCGCCACCAGTATGGGAAGATAAAATATGTAT
1 GGGAGACAAGATCTGT-TTCTTCGATCT-A-CTTCGCCACCAGTATGGGAAGACAAGATCTGTAT
* * * * * * *
54052639 ATTCGATCCACTTCGCTACTGATATAGGG-AGACAGGACCTACTATCTTTGATCTACTTCACGCC
63 CTTCGATCTACTTCGCCACCGGTAT-GGGAAGACAAGATCTACTATCTTTGATCTACTTCACGCC
* * *
54052703 AGTACATGAAGATAAGATCTATTTTCTTCGATCTACTCCACCACCAGTATG
127 AGTACATGAAGACAAGATCTACTATCTTCGATCTACTCCACCACCAGTATG
* * * * *** *
54052754 GGGAGACAAGATCTGTTTCTTTGATCTACTTC-ACGCTAGTACATGAAGACAAGATCTGTTTTCT
1 GGGAGACAAGATCTGTTTCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTG-TATCT
* *
54052818 TCGATCTACTTCGCCACCGGTATGGGAAGACAAGATCTACTATCTTTGATCTATTTCATGCCAGT
65 TCGATCTACTTCGCCACCGGTATGGGAAGACAAGATCTACTATCTTTGATCTACTTCACGCCAGT
* *
54052883 ACATGAAGACAAGATCTGCTATCTTTGATCTACTCCACCACCAGTAT-
130 ACATGAAGACAAGATCTACTATCTTCGATCTACTCCACCACCAGTATG
* *
54052930 GGG-GACAAGATCTGTTTTCTTCGATCTGCTTCGCCACCAGTATGGGAAGACATGATCTGGTATC
1 GGGAGACAAGATCTG-TTTCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCT-GTATC
* * * * * *
54052994 -TCTGATCTACTTC-ACGCCAGTATGTGAAGACAAGATCT-GTTTCTTTGATCT
64 TTC-GATCTACTTCGCCACCGGTATGGGAAGACAAGATCTACTATCTTTGATCT
54053045 GCTTTGCCAC
Statistics
Matches: 240, Mismatches: 45, Indels: 17
0.79 0.15 0.06
Matches are distributed among these distances:
175 22 0.09
176 61 0.25
177 132 0.55
178 2 0.01
179 8 0.03
180 15 0.06
ACGTcount: A:0.27, C:0.23, G:0.19, T:0.31
Consensus pattern (177 bp):
GGGAGACAAGATCTGTTTCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGTATCTT
CGATCTACTTCGCCACCGGTATGGGAAGACAAGATCTACTATCTTTGATCTACTTCACGCCAGTA
CATGAAGACAAGATCTACTATCTTCGATCTACTCCACCACCAGTATG
Found at i:54053045 original size:88 final size:86
Alignment explanation
Indices: 54052683--54053096 Score: 348
Period size: 88 Copynumber: 4.7 Consensus size: 86
54052673 GGACCTACTA
* * * ** * *
54052683 TCTTTGATCTACTTCACGCCAGTACATGAAGATAAGATCTATTTTCTTCGATCTACTCCACCACC
1 TCTTTGATCTACTTCACACCAGTACAGGAAGACAAGATCTGGTATCTT-GATCTACTTCA-CACC
*
54052748 AGTATGGGGAGACAAGATCTGTT
64 AGTATGGGAAGACAAGATCTGTT
* * * * * *
54052771 TCTTTGATCTACTTCACGCTAGTACATGAAGACAAGATCTGTTTTCTTCGATCTACTTCGCCACC
1 TCTTTGATCTACTTCACACCAGTACAGGAAGACAAGATCTGGTATCTT-GATCTACTTC-ACACC
* * *
54052836 GGTATGGGAAGACAAGATCTACTA
64 AGTATGGGAAGACAAGATCT-GTT
* ** * * *
54052860 TCTTTGATCTATTTCATGCCAGTACATGAAGACAAGATCTGCTATCTTTGATCTACTCCACCACC
1 TCTTTGATCTACTTCACACCAGTACAGGAAGACAAGATCTGGTATC-TTGATCTACTTCA-CACC
54052925 AGTATGGG--GACAAGATCTGTTT
64 AGTATGGGAAGACAAGATCTG-TT
* * * ** * *
54052947 TCTTCGATCTGCTTCGCCACCAGTATGGGAAGACATGATCTGGTATCTCTGATCTACTTCACGCC
1 TCTTTGATCTACTTC-ACACCAGTACAGGAAGACAAGATCTGGTATCT-TGATCTACTTCACACC
*
54053012 AGTATGTGAAGACAAGATCTGTT
64 AGTATGGGAAGACAAGATCTGTT
* * ** * * *
54053035 TCTTTGATCTGCTTTGC-CACCAATATGGGAAGGCAGGATCTGGTAGCTATGATCTACTTCAC
1 TCTTTGATCTAC-TT-CACACCAGTACAGGAAGACAAGATCTGGTATCT-TGATCTACTTCAC
54053097 GTTAGTACAT
Statistics
Matches: 276, Mismatches: 39, Indels: 22
0.82 0.12 0.07
Matches are distributed among these distances:
87 34 0.12
88 164 0.59
89 75 0.27
90 3 0.01
ACGTcount: A:0.26, C:0.23, G:0.19, T:0.32
Consensus pattern (86 bp):
TCTTTGATCTACTTCACACCAGTACAGGAAGACAAGATCTGGTATCTTGATCTACTTCACACCAG
TATGGGAAGACAAGATCTGTT
Found at i:54053090 original size:220 final size:220
Alignment explanation
Indices: 54052680--54053122 Score: 566
Period size: 220 Copynumber: 2.0 Consensus size: 220
54052670 ACAGGACCTA
* * *
54052680 CTATCTTTGATCTACTTCACGCCAGTACATGAAGATAAGATCTATTTTCTTCGATCTACTCCACC
1 CTATCTTTGATCTACTCCACACCAGTA-ATGAAGACAAGATCTATTTTCTTCGATCTACTCCACC
* * * *
54052745 ACCAGTATGGGGAGACAAGATCTGTTTCTTTGATCTACTTCACGCTAGTACATGAAGACAAGATC
65 ACCAGTATGGGAAGACAAGATCTGTATCTCTGATCTACTTCACGCCAGTACATGAAGACAAGATC
** * * *
54052810 TGTTTTCTTCGATCTACTTCGCCACCGGTATGGGAAGACAAGATCTACTATCTTTGATCTATTTC
130 TGTTTTCTTCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTACTAGCTATGATCTACTTC
*
54052875 ATGCCAGTACATGAAGACAAGATCTG
195 ACGCCAGTACATGAAGACAAGATCTG
** * * * *
54052901 CTATCTTTGATCTACTCCACCACCAGT-ATGGGGACAAGATCTGTTTTCTTCGATCTGCTTCGCC
1 CTATCTTTGATCTACTCCA-CACCAGTAATGAAGACAAGATCTATTTTCTTCGATCTACTCCACC
* **
54052965 ACCAGTATGGGAAGACATGATCTGGTATCTCTGATCTACTTCACGCCAGTATGTGAAGACAAGAT
65 ACCAGTATGGGAAGACAAGATCT-GTATCTCTGATCTACTTCACGCCAGTACATGAAGACAAGAT
* * * * * **
54053030 CTG-TTTCTTTGATCTGCTTTGCCACCAATATGGGAAGGCAGGATCTGGTAGCTATGATCTACTT
129 CTGTTTTCTTCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTACTAGCTATGATCTACTT
**
54053094 CACGTTAGTACATGAAGACAAGATCTG
194 CACGCCAGTACATGAAGACAAGATCTG
54053121 CT
1 CT
54053123 TTTCTTTTCA
Statistics
Matches: 189, Mismatches: 31, Indels: 5
0.84 0.14 0.02
Matches are distributed among these distances:
220 126 0.67
221 57 0.30
222 6 0.03
ACGTcount: A:0.26, C:0.23, G:0.19, T:0.32
Consensus pattern (220 bp):
CTATCTTTGATCTACTCCACACCAGTAATGAAGACAAGATCTATTTTCTTCGATCTACTCCACCA
CCAGTATGGGAAGACAAGATCTGTATCTCTGATCTACTTCACGCCAGTACATGAAGACAAGATCT
GTTTTCTTCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTACTAGCTATGATCTACTTCA
CGCCAGTACATGAAGACAAGATCTG
Found at i:54067929 original size:48 final size:48
Alignment explanation
Indices: 54067858--54067954 Score: 194
Period size: 48 Copynumber: 2.0 Consensus size: 48
54067848 TCCTTGGTTA
54067858 TTGTCTTTATGACTTGTGTCTTGATCCATATAGTAATTAAATACATTC
1 TTGTCTTTATGACTTGTGTCTTGATCCATATAGTAATTAAATACATTC
54067906 TTGTCTTTATGACTTGTGTCTTGATCCATATAGTAATTAAATACATTC
1 TTGTCTTTATGACTTGTGTCTTGATCCATATAGTAATTAAATACATTC
54067954 T
1 T
54067955 ATTAAATTTA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 49 1.00
ACGTcount: A:0.27, C:0.14, G:0.12, T:0.46
Consensus pattern (48 bp):
TTGTCTTTATGACTTGTGTCTTGATCCATATAGTAATTAAATACATTC
Found at i:54070965 original size:34 final size:34
Alignment explanation
Indices: 54070927--54071018 Score: 139
Period size: 34 Copynumber: 2.7 Consensus size: 34
54070917 CTTTAGGAAC
* * *
54070927 TTGTGAATGAGTAATGGTTTACTGTGGAGGAAAG
1 TTGTGAATGAGTGATGGTTTACTCTGAAGGAAAG
54070961 TTGTGAATGAGTGATGGTTTACTCTGAAGGAAAG
1 TTGTGAATGAGTGATGGTTTACTCTGAAGGAAAG
* *
54070995 TTGTTAATGATTGATGGTTTACTC
1 TTGTGAATGAGTGATGGTTTACTC
54071019 CAGAGTCTAG
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 53 1.00
ACGTcount: A:0.27, C:0.05, G:0.30, T:0.37
Consensus pattern (34 bp):
TTGTGAATGAGTGATGGTTTACTCTGAAGGAAAG
Found at i:54072253 original size:31 final size:31
Alignment explanation
Indices: 54072218--54072279 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
54072208 ACTTGTAAGA
54072218 TATATTTCTTTTTCTGTCTTCTTAGCGATTG
1 TATATTTCTTTTTCTGTCTTCTTAGCGATTG
54072249 TATATTTCTTTTTCTGTCTTCTTAGCGATTG
1 TATATTTCTTTTTCTGTCTTCTTAGCGATTG
54072280 GTACAATTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.13, C:0.16, G:0.13, T:0.58
Consensus pattern (31 bp):
TATATTTCTTTTTCTGTCTTCTTAGCGATTG
Found at i:54091297 original size:11 final size:11
Alignment explanation
Indices: 54091276--54091314 Score: 51
Period size: 12 Copynumber: 3.4 Consensus size: 11
54091266 TATGCCTAAA
54091276 AAAACAAGAAAC
1 AAAA-AAGAAAC
54091288 AAAAAAGAAAAC
1 AAAAAAG-AAAC
*
54091300 AAAAAAGAAAG
1 AAAAAAGAAAC
54091311 AAAA
1 AAAA
54091315 GAAAAAGAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
11 10 0.40
12 15 0.60
ACGTcount: A:0.82, C:0.08, G:0.10, T:0.00
Consensus pattern (11 bp):
AAAAAAGAAAC
Found at i:54091299 original size:12 final size:12
Alignment explanation
Indices: 54091284--54091309 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
54091274 AAAAAACAAG
54091284 AAACAAAAAAGA
1 AAACAAAAAAGA
54091296 AAACAAAAAAGA
1 AAACAAAAAAGA
54091308 AA
1 AA
54091310 GAAAAGAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.85, C:0.08, G:0.08, T:0.00
Consensus pattern (12 bp):
AAACAAAAAAGA
Found at i:54091310 original size:16 final size:15
Alignment explanation
Indices: 54091291--54091324 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
54091281 AAGAAACAAA
54091291 AAAGAAAACAAAAAAG
1 AAAGAAAA-AAAAAAG
*
54091307 AAAGAAAAGAAAAAG
1 AAAGAAAAAAAAAAG
54091322 AAA
1 AAA
54091325 AATCAAGATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.82, C:0.03, G:0.15, T:0.00
Consensus pattern (15 bp):
AAAGAAAAAAAAAAG
Found at i:54091311 original size:27 final size:27
Alignment explanation
Indices: 54091273--54091325 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
54091263 TATTATGCCT
54091273 AAAAAAACAAGAAACA-AAAAAGAAAAC
1 AAAAAAACAAGAAA-AGAAAAAGAAAAC
54091300 AAAAAAGA-AAGAAAAGAAAAAGAAAA
1 AAAAAA-ACAAGAAAAGAAAAAGAAAA
54091326 ATCAAGATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
26 1 0.04
27 22 0.92
28 1 0.04
ACGTcount: A:0.83, C:0.06, G:0.11, T:0.00
Consensus pattern (27 bp):
AAAAAAACAAGAAAAGAAAAAGAAAAC
Found at i:54092291 original size:75 final size:74
Alignment explanation
Indices: 54092167--54092906 Score: 637
Period size: 75 Copynumber: 9.7 Consensus size: 74
54092157 CAAGAAATAT
*** * * *
54092167 TTTTCAATTTCTGTTTTTTTTTTAAATCAACTCATAATGCAAGAGGTGAGTTGAGCCTTGGGCAC
1 TTTTCAATTTCTG--TTTTTCAAAAATCAACTCATAATGCGAGAAGTGAGTTGAGCCTCGGGCAC
* **
54092232 ATTCCAAGGTA
64 ATGCTGAGGTA
* * *
54092243 TTTCTCAATTTCTATTTTTCAAAAATCAACTCATAATGCTAGAAGTGAGTTGAGCCTCAGGCTAC
1 TTT-TCAATTTCTGTTTTTCAAAAATCAACTCATAATGCGAGAAGTGAGTTGAGCCTCGGGC-AC
54092308 --GCTGAGGTA
64 ATGCTGAGGTA
*
54092317 TTTTCAATTTCTGCTTTTTCAAAAATCAACTCATAATACGAGAAGTGAGTTGAGCCTCGGGC-CA
1 TTTTCAATTTCTG-TTTTTCAAAAATCAACTCATAATGCGAGAAGTGAGTTGAGCCTCGGGCACA
* *
54092381 CGCTGATGTA
65 TGCTGAGGTA
* * *
54092391 TTTTCAATTTCTGCTTTTCAAAAATATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCA
1 TTTTCAATTTCTGTTTTTC-AAAA-ATCAACTCATAATGCGAGAAGTGAGTTGAGCCTCGGG-CA
*
54092456 C--GCCGAGGTA
63 CATGCTGAGGTA
* * *
54092466 TTTTCAATTTGTGTTTTTCAAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGGTC
1 TTTTCAATTTCTGTTTTTC---AAAAATCAACTCATAATGCGAGAAGTGAGTTGAGCCTC-GGGC
54092531 ACATGCTGAGGTA
62 ACATGCTGAGGTA
* * * * * * *
54092544 TATTTTAATTTCTATTTTCCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGA-CTCTTTGGTC
1 T-TTTCAATTTCTGTTTTTC-AAAAATCAACTCATAATGCGAGAAGTGAGTTGAGC-C-TCGGGC
** *
54092608 ACACACTGAGGTTTTT
62 ACATGCTGAGG---TA
* * * * *
54092624 TTCTTCAATTTATGTTTTTCAAAAAATCAACTCATATTGTGAGAGGTGAGTTGAGCCTCGGGCTG
1 TT-TTCAATTTCTGTTTTTC-AAAAATCAACTCATAATGCGAGAAGTGAGTTGAGCCTCGGGC-A
** *
54092689 CACACCGAGGTA
63 CATGCTGAGGTA
* * * * *
54092701 TTTTTAATTTCTTTTTTTAAGAAAAAATCAACTCATAATGCGAGAAGTGAGTTGAGTCTTGGGCT
1 TTTTCAATTTCTGTTTTT---CAAAAATCAACTCATAATGCGAGAAGTGAGTTGAGCCTCGGGC-
* **
54092766 ATACACTGAGGTA
62 ACATGCTGAGGTA
* * * * * * *
54092779 TTTTTAATTTCTGTTTTTCAAAAATCAACTTATATTGCGAGAGGTGAGTTGAGCCTTGGTTCATA
1 TTTTCAATTTCTGTTTTTCAAAAATCAACTCATAATGCGAGAAGTGAGTTGAGCCTCGG-GCACA
54092844 TGCTGAGGTA
65 TGCTGAGGTA
* ** * **
54092854 TTTTCCAATTTCTATTTTTCAAAGCTCAACTTATAATTTGAGAAGTGAGTTGA
1 TTTT-CAATTTCTGTTTTTCAAAAATCAACTCATAATGCGAGAAGTGAGTTGA
54092907 ACTTTGGATC
Statistics
Matches: 561, Mismatches: 75, Indels: 56
0.81 0.11 0.08
Matches are distributed among these distances:
72 1 0.00
73 14 0.02
74 79 0.14
75 150 0.27
76 97 0.17
77 67 0.12
78 75 0.13
79 19 0.03
80 58 0.10
81 1 0.00
ACGTcount: A:0.28, C:0.16, G:0.19, T:0.36
Consensus pattern (74 bp):
TTTTCAATTTCTGTTTTTCAAAAATCAACTCATAATGCGAGAAGTGAGTTGAGCCTCGGGCACAT
GCTGAGGTA
Found at i:54092593 original size:153 final size:149
Alignment explanation
Indices: 54092167--54092906 Score: 699
Period size: 149 Copynumber: 4.9 Consensus size: 149
54092157 CAAGAAATAT
*** * * *
54092167 TTTTCAATTTCTGTTTTTTTTTTAAATCAACTCATAATGCAAGAGGTGAGTTGAGCCT-TGGGCA
1 TTTTCAATTTCTG--TTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCTGGTCA
* ** *
54092231 CATTCCAAGGTATTTCTCAATTTCTATTTTTC-AAAAATCAACTCATAATGCTAGAAGTGAGTTG
64 CATGCTGAGGTATTT-TCAATTTCTATTTTTCAAAAAATCAACTCATAATGCGAGAAGTGAGTTG
* * *
54092295 AGCCTCAGG-CTACGCTGAGGTA
128 AGCCTCGGGTC-ACACCGAGGTA
* * * *
54092317 TTTTCAATTTCTGCTTTTTCAAAAATCAACTCATAATACGAGAAGTGAGTTGAGCCTC-GGGC-C
1 TTTTCAATTTCTG-TTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCTGGTCAC
* * ** * *
54092380 ACGCTGATGTATTTTCAATTTCTGCTTTTCAAAAATATCAACTCATATTGCGAGAGGTGAGTTGA
65 ATGCTGAGGTATTTTCAATTTCTATTTTTCAAAAA-ATCAACTCATAATGCGAGAAGTGAGTTGA
*
54092445 GCCTCGGGTCACGCCGAGGTA
129 GCCTCGGGTCACACCGAGGTA
* * *
54092466 TTTTCAATTTGTGTTTTTCAAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGGTC
1 TTTTCAATTTCTGTTTTTC---AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCTGGTC
* * * *
54092531 ACATGCTGAGGTATATTTTAATTTCTATTTTCCAAAAAATCAACTCATATTGCGAGAGGTGAGTT
63 ACATGCTGAGGTAT-TTTCAATTTCTATTTTTCAAAAAATCAACTCATAATGCGAGAAGTGAGTT
** *
54092596 GA-CTCTTTGGTCACACACTGAGGTTTTT
127 GAGC-CTCGGGTCACAC-C-GAGG---TA
* * *
54092624 TTCTTCAATTTATGTTTTTCAAAAAATCAACTCATATTGTGAGAGGTGAGTTGAGCCTCGGGCTG
1 TT-TTCAATTTCTGTTTTTC-AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCTGG-T-
* * * *
54092689 CACA--CCGAGGTATTTTTAATTTCTTTTTTTAAGAAAAAATCAACTCATAATGCGAGAAGTGAG
62 CACATGCTGAGGTATTTTCAATTTCTATTTTT--CAAAAAATCAACTCATAATGCGAGAAGTGAG
* * * *
54092752 TTGAGTCTTGGGCTATACACTGAGGTA
125 TTGAGCCTCGGG-T-CACACCGAGGTA
* * *
54092779 TTTTTAATTTCTGTTTTTCAAAAATCAACTTATATTGCGAGAGGTGAGTTGAGCCT-TGGTTCAT
1 TTTTCAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCTGG-TCAC
** * **
54092843 ATGCTGAGGTATTTTCCAATTTCTATTTTTC-AAAGCTCAACTTATAATTTGAGAAGTGAGTTGA
65 ATGCTGAGGTATTTT-CAATTTCTATTTTTCAAAAAATCAACTCATAATGCGAGAAGTGAGTTGA
54092907 ACTTTGGATC
Statistics
Matches: 499, Mismatches: 64, Indels: 53
0.81 0.10 0.09
Matches are distributed among these distances:
147 14 0.03
148 20 0.04
149 96 0.19
150 14 0.03
151 67 0.13
152 7 0.01
153 95 0.19
154 47 0.09
155 7 0.01
156 15 0.03
157 47 0.09
158 45 0.09
159 21 0.04
160 4 0.01
ACGTcount: A:0.28, C:0.16, G:0.19, T:0.36
Consensus pattern (149 bp):
TTTTCAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCTGGTCACA
TGCTGAGGTATTTTCAATTTCTATTTTTCAAAAAATCAACTCATAATGCGAGAAGTGAGTTGAGC
CTCGGGTCACACCGAGGTA
Found at i:54093840 original size:15 final size:16
Alignment explanation
Indices: 54093817--54093872 Score: 59
Period size: 15 Copynumber: 3.8 Consensus size: 16
54093807 GAGCAAGGTT
* *
54093817 GAAGGGAAGGAAG-AA
1 GAAGAGAAGAAAGAAA
54093832 GAAGAGAAGAAAGAAA
1 GAAGAGAAGAAAGAAA
54093848 GAAGA-AA-AAA-AAA
1 GAAGAGAAGAAAGAAA
54093861 GAA-AGAAGAAAG
1 GAAGAGAAGAAAG
54093873 GGAAATAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
12 1 0.03
13 8 0.23
14 6 0.17
15 13 0.37
16 7 0.20
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (16 bp):
GAAGAGAAGAAAGAAA
Found at i:54093854 original size:7 final size:7
Alignment explanation
Indices: 54093822--54093872 Score: 50
Period size: 7 Copynumber: 7.1 Consensus size: 7
54093812 AGGTTGAAGG
*
54093822 GAAGGAA
1 GAAGAAA
54093829 GAAGAAGA
1 GAAGAA-A
54093837 GAAGAAA
1 GAAGAAA
54093844 GAA-AGAA
1 GAAGA-AA
*
54093851 GAAAAAA
1 GAAGAAA
*
54093858 AAAGAAA
1 GAAGAAA
54093865 GAAGAAA
1 GAAGAAA
54093872 G
1 G
54093873 GGAAATAAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
6 1 0.03
7 28 0.76
8 8 0.22
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (7 bp):
GAAGAAA
Found at i:54093869 original size:24 final size:24
Alignment explanation
Indices: 54093833--54093902 Score: 67
Period size: 21 Copynumber: 3.0 Consensus size: 24
54093823 AAGGAAGAAG
54093833 AAGAGAAGAAAGAAAGAAGAAAAAAA
1 AAGA-AAG-AAGAAAGAAGAAAAAAA
* *
54093859 AAGAAAGAAGAAAG-GGAAATAAA
1 AAGAAAGAAGAAAGAAGAAAAAAA
*
54093882 AAG-AA-AAGAAATAA-AAAAAAA
1 AAGAAAGAAGAAAGAAGAAAAAAA
54093903 GAAAATAGAA
Statistics
Matches: 38, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
21 12 0.32
22 2 0.05
23 10 0.26
24 7 0.18
25 3 0.08
26 4 0.11
ACGTcount: A:0.77, C:0.00, G:0.20, T:0.03
Consensus pattern (24 bp):
AAGAAAGAAGAAAGAAGAAAAAAA
Found at i:54093872 original size:11 final size:11
Alignment explanation
Indices: 54093826--54093867 Score: 52
Period size: 11 Copynumber: 3.9 Consensus size: 11
54093816 TGAAGGGAAG
54093826 GAAG-AAGAAGA
1 GAAGAAAGAA-A
54093837 GAAGAAAGAAA
1 GAAGAAAGAAA
54093848 GAAGAAA-AAA
1 GAAGAAAGAAA
*
54093858 AAAGAAAGAA
1 GAAGAAAGAA
54093868 GAAAGGGAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
10 9 0.32
11 14 0.50
12 5 0.18
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (11 bp):
GAAGAAAGAAA
Found at i:54093887 original size:16 final size:16
Alignment explanation
Indices: 54093866--54093915 Score: 59
Period size: 15 Copynumber: 3.2 Consensus size: 16
54093856 AAAAAGAAAG
*
54093866 AAGAAAGGGAAATAAA
1 AAGAAAGAGAAATAAA
54093882 AAGAAA-AGAAATAAA
1 AAGAAAGAGAAATAAA
*
54093897 AAAAAAGA-AAATAGAA
1 AAGAAAGAGAAATA-AA
54093913 AAG
1 AAG
54093916 TCGGTCGACC
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
15 18 0.62
16 11 0.38
ACGTcount: A:0.76, C:0.00, G:0.18, T:0.06
Consensus pattern (16 bp):
AAGAAAGAGAAATAAA
Found at i:54093909 original size:15 final size:15
Alignment explanation
Indices: 54093833--54093906 Score: 60
Period size: 17 Copynumber: 4.7 Consensus size: 15
54093823 AAGGAAGAAG
* *
54093833 AAGAGAAGAAAGAAA
1 AAGAAAAGAAATAAA
* *
54093848 GAAGAAAAAAAAAGAAA
1 -AAG-AAAAGAAATAAA
*
54093865 GAAGAAAGGGAAATAAA
1 -AAGAAA-AGAAATAAA
54093882 AAGAAAAGAAATAAA
1 AAGAAAAGAAATAAA
54093897 AA-AAAAGAAA
1 AAGAAAAGAAA
54093907 ATAGAAAAGT
Statistics
Matches: 50, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
14 8 0.16
15 10 0.20
16 12 0.24
17 20 0.40
ACGTcount: A:0.77, C:0.00, G:0.20, T:0.03
Consensus pattern (15 bp):
AAGAAAAGAAATAAA
Found at i:54093931 original size:5 final size:5
Alignment explanation
Indices: 54093921--54093977 Score: 55
Period size: 5 Copynumber: 11.4 Consensus size: 5
54093911 AAAAGTCGGT
* * *
54093921 CGACC CGACC CGACC CGAGCTT CGACC CGACT C-A-C CGACC TGACC CGACC
1 CGACC CGACC CGACC CGA-C-C CGACC CGACC CGACC CGACC CGACC CGACC
54093971 CGACC CG
1 CGACC CG
54093978 CGCTCCAGCA
Statistics
Matches: 42, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
3 1 0.02
4 2 0.05
5 34 0.81
6 2 0.05
7 3 0.07
ACGTcount: A:0.19, C:0.53, G:0.21, T:0.07
Consensus pattern (5 bp):
CGACC
Found at i:54094075 original size:24 final size:25
Alignment explanation
Indices: 54094028--54094077 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 25
54094018 AAAAGAAAAC
54094028 AAAAAAAAACAGCAGGCCTGCAACAG
1 AAAAAAAAACAGCAGGCC-GCAACAG
54094054 AAAAAAACAA-AGCAGGCC-CAACAG
1 AAAAAAA-AACAGCAGGCCGCAACAG
54094078 CAGGCCATTG
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
24 6 0.26
26 15 0.65
27 2 0.09
ACGTcount: A:0.56, C:0.24, G:0.18, T:0.02
Consensus pattern (25 bp):
AAAAAAAAACAGCAGGCCGCAACAG
Found at i:54094586 original size:16 final size:18
Alignment explanation
Indices: 54094567--54094603 Score: 60
Period size: 16 Copynumber: 2.2 Consensus size: 18
54094557 TTTTCCGTTT
54094567 TTTATTTTT-TATTT-TA
1 TTTATTTTTGTATTTATA
54094583 TTTATTTTTGTATTTATA
1 TTTATTTTTGTATTTATA
54094601 TTT
1 TTT
54094604 TCTTAAATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 9 0.47
17 5 0.26
18 5 0.26
ACGTcount: A:0.19, C:0.00, G:0.03, T:0.78
Consensus pattern (18 bp):
TTTATTTTTGTATTTATA
Found at i:54094821 original size:17 final size:17
Alignment explanation
Indices: 54094756--54094955 Score: 142
Period size: 16 Copynumber: 11.5 Consensus size: 17
54094746 AAAAAAGATC
*
54094756 TCGTGTTTCGAAAAAATAT
1 TCGTGTTTC--AAAAATTT
54094775 TCGTGTTTC-AAAATTT
1 TCGTGTTTCAAAAATTT
54094791 TCGTGTTT-AAAAATTT
1 TCGTGTTTCAAAAATTT
*
54094807 TCGTGTTTCAAAAATTC
1 TCGTGTTTCAAAAATTT
* ** *
54094824 TAGTGAATGAAAAATTTT
1 TCGTGTTTCAAAAA-TTT
*
54094842 TCGTGTTTTCAAAAAATTC
1 TCGTG-TTTC-AAAAATTT
54094861 TCGTGTTT-AAAAATTT
1 TCGTGTTTCAAAAATTT
* *
54094877 TCGCAT-TTTCAAAAAACTC
1 TCG--TGTTTC-AAAAATTT
* *
54094896 TCGTGTTTTAAAATTTT
1 TCGTGTTTCAAAAATTT
*
54094913 TCGTGTTTTCCAAAAAATTA
1 TCGTG-TTT-C-AAAAATTT
*
54094933 T--TGTTTCAAAAATTC
1 TCGTGTTTCAAAAATTT
54094948 TCGTGTTT
1 TCGTGTTT
54094956 TTTAAAAAAA
Statistics
Matches: 143, Mismatches: 23, Indels: 32
0.72 0.12 0.16
Matches are distributed among these distances:
15 8 0.06
16 40 0.28
17 39 0.27
18 18 0.13
19 26 0.18
20 12 0.08
ACGTcount: A:0.32, C:0.12, G:0.12, T:0.45
Consensus pattern (17 bp):
TCGTGTTTCAAAAATTT
Found at i:54094865 original size:70 final size:71
Alignment explanation
Indices: 54094784--54095037 Score: 225
Period size: 74 Copynumber: 3.5 Consensus size: 71
54094774 TTCGTGTTTC
* *
54094784 AAAATTTTCGTGTTTAAAAATTTTCGTGTTTC-AAAAATTCTAGTGAATGAAAAATTTTTCGTGT
1 AAAATTATCGTGTTTAAAAATTTTCGTGTTTCAAAAAACTCTAGTG-ATGAAAAATTTTTCGTGT
54094848 TTT-CAA
65 TTTCCAA
* * * **
54094854 AAAATTCTCGTGTTTAAAAATTTTCGCAT-TTTCAAAAAACTCTCGTGTTTTAAAATTTTTCGTG
1 AAAATTATCGTGTTTAAAAATTTTCG--TGTTTCAAAAAACTCTAGTGATGAAAAATTTTTCGTG
54094918 TTTTCCAA
64 TTTTCCAA
* * * * * **
54094926 AAAATTAT--TGTTTCAAAAATTCTCGTGTTTTTTAAAAAAAACTGTCGTGTTTTAAAATTTTTC
1 AAAATTATCGTGTTT-AAAAATTTTCGTG---TTT-CAAAAAACTCTAGTGATGAAAAATTTTTC
54094989 GTGTTTTCCAA
61 GTGTTTTCCAA
* *
54095000 AAAATTAT--TGTTTCAGAAATTTTTGTGTTTTCAAAAAA
1 AAAATTATCGTGTTT-AAAAATTTTCGTG-TTTCAAAAAA
54095038 AAAAATTCAT
Statistics
Matches: 160, Mismatches: 14, Indels: 19
0.83 0.07 0.10
Matches are distributed among these distances:
69 1 0.01
70 30 0.19
71 38 0.24
72 26 0.16
73 3 0.02
74 62 0.39
ACGTcount: A:0.33, C:0.11, G:0.11, T:0.45
Consensus pattern (71 bp):
AAAATTATCGTGTTTAAAAATTTTCGTGTTTCAAAAAACTCTAGTGATGAAAAATTTTTCGTGTT
TTCCAA
Found at i:54094878 original size:35 final size:35
Alignment explanation
Indices: 54094767--54095037 Score: 218
Period size: 35 Copynumber: 7.7 Consensus size: 35
54094757 CGTGTTTCGA
* *
54094767 AAAAATATTCGTG-TTTC--AAAATTTTCGTGTTT
1 AAAAATTTTCGTGTTTTCAAAAAATTCTCGTGTTT
* * *
54094799 AAAAATTTTCGTG-TTTC-AAAAATTCTAGTGAATG
1 AAAAATTTTCGTGTTTTCAAAAAATTCTCGTG-TTT
54094833 AAAAATTTTTCGTGTTTTCAAAAAATTCTCGTGTTT
1 AAAAA-TTTTCGTGTTTTCAAAAAATTCTCGTGTTT
** *
54094869 AAAAATTTTCGCATTTTCAAAAAACTCTCGTGTTTT
1 AAAAATTTTCGTGTTTTCAAAAAATTCTCGTG-TTT
* *
54094905 AAAATTTTTCGTGTTTTCCAAAAAATTAT--TGTTT
1 AAAAATTTTCGTGTTTT-CAAAAAATTCTCGTGTTT
* * * *
54094939 CAAAAATTCTCGTGTTTTTTAAAAAAAACTGTCGTGTTTT
1 -AAAAATTTTCGTG--TTTT-CAAAAAATTCTCGTG-TTT
* *
54094979 AAAATTTTTCGTGTTTTCCAAAAAATTAT--TGTTT
1 AAAAATTTTCGTGTTTT-CAAAAAATTCTCGTGTTT
* *
54095013 CAGAAATTTTTGTGTTTTCAAAAAA
1 -AAAAATTTTCGTGTTTTCAAAAAA
54095038 AAAAATTCAT
Statistics
Matches: 194, Mismatches: 31, Indels: 26
0.77 0.12 0.10
Matches are distributed among these distances:
32 16 0.08
33 10 0.05
34 19 0.10
35 61 0.31
36 27 0.14
37 45 0.23
39 13 0.07
40 3 0.02
ACGTcount: A:0.34, C:0.11, G:0.11, T:0.45
Consensus pattern (35 bp):
AAAAATTTTCGTGTTTTCAAAAAATTCTCGTGTTT
Found at i:54094993 original size:74 final size:74
Alignment explanation
Indices: 54094834--54095040 Score: 271
Period size: 74 Copynumber: 2.8 Consensus size: 74
54094824 TAGTGAATGA
* ** *
54094834 AAAATTTTTCGTGTTTT-CAAAAAATTCTCGTGTTT-AAAAATTTTC--GCATTTT-CAAAAAAC
1 AAAATTTTTCGTGTTTTCCAAAAAATTAT--TGTTTCAAAAATTTTCGTGTTTTTTAAAAAAAAC
54094894 TCTCGTGTTTT
64 TCTCGTGTTTT
* *
54094905 AAAATTTTTCGTGTTTTCCAAAAAATTATTGTTTCAAAAATTCTCGTGTTTTTTAAAAAAAACTG
1 AAAATTTTTCGTGTTTTCCAAAAAATTATTGTTTCAAAAATTTTCGTGTTTTTTAAAAAAAACTC
54094970 TCGTGTTTT
66 TCGTGTTTT
* * **
54094979 AAAATTTTTCGTGTTTTCCAAAAAATTATTGTTTCAGAAATTTTTGTGTTTTCAAAAAAAAA
1 AAAATTTTTCGTGTTTTCCAAAAAATTATTGTTTCAAAAATTTTCGTGTTTTTTAAAAAAAA
54095041 AATTCATGTT
Statistics
Matches: 120, Mismatches: 11, Indels: 7
0.87 0.08 0.05
Matches are distributed among these distances:
70 5 0.04
71 26 0.22
72 10 0.08
73 5 0.04
74 74 0.62
ACGTcount: A:0.34, C:0.11, G:0.10, T:0.45
Consensus pattern (74 bp):
AAAATTTTTCGTGTTTTCCAAAAAATTATTGTTTCAAAAATTTTCGTGTTTTTTAAAAAAAACTC
TCGTGTTTT
Found at i:54095075 original size:74 final size:74
Alignment explanation
Indices: 54094899--54095070 Score: 193
Period size: 74 Copynumber: 2.3 Consensus size: 74
54094889 AAAACTCTCG
** * **
54094899 TGTTTTAAAATTTTTCGTGTTTTCCAAAAAATTATTGTTTCAAAAATTCTCGTGTTTTTTAAAAA
1 TGTTTTAAAAACTCTCGTGTTTTCCAAAAAATTATTGTTTCAAAAATTCTCGTGTTTTAAAAAAA
* *
54094964 AAACTGTCG
66 AAAATGTCA
** * * * *
54094973 TGTTTTAAAATTTTTCGTGTTTTCCAAAAAATTATTGTTTCAGAAATTTTTGTGTTTTCAAAAAA
1 TGTTTTAAAAACTCTCGTGTTTTCCAAAAAATTATTGTTTCAAAAATTCTCGTGTTTT-AAAAAA
54095038 AAAAAT-TCA
65 AAAAATGTCA
54095047 TGTTTTCAAAAAACTCTCGTGTTT
1 TGTTTT--AAAAACTCTCGTGTTT
54095071 CAAAATCTTA
Statistics
Matches: 85, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
74 63 0.74
75 9 0.11
76 13 0.15
ACGTcount: A:0.33, C:0.10, G:0.10, T:0.46
Consensus pattern (74 bp):
TGTTTTAAAAACTCTCGTGTTTTCCAAAAAATTATTGTTTCAAAAATTCTCGTGTTTTAAAAAAA
AAAATGTCA
Found at i:54106826 original size:36 final size:35
Alignment explanation
Indices: 54106779--54106850 Score: 99
Period size: 36 Copynumber: 2.0 Consensus size: 35
54106769 CATCTACAGA
54106779 GCTTGGAAAATAAGGAAAGTGATCTTCTAAAGATAT
1 GCTTGGAAAATAAGGAAAGTGATCTT-TAAAGATAT
* * * *
54106815 GCTTGGCAAATATGGAAGGTGATCTTTAGAGATAT
1 GCTTGGAAAATAAGGAAAGTGATCTTTAAAGATAT
54106850 G
1 G
54106851 TGATCCTAGA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
35 9 0.28
36 23 0.72
ACGTcount: A:0.36, C:0.08, G:0.26, T:0.29
Consensus pattern (35 bp):
GCTTGGAAAATAAGGAAAGTGATCTTTAAAGATAT
Found at i:54111935 original size:36 final size:35
Alignment explanation
Indices: 54111889--54111960 Score: 99
Period size: 36 Copynumber: 2.0 Consensus size: 35
54111879 CATCTCCGGA
*
54111889 GCTTGGCAAATAGAGAAAGTGATCTTCTAAAGATAT
1 GCTTGACAAATAGAGAAAGTGATCTT-TAAAGATAT
* * *
54111925 GCTTGACAAATATAGAATGTGATCTTTAGAGATAT
1 GCTTGACAAATAGAGAAAGTGATCTTTAAAGATAT
54111960 G
1 G
54111961 TAATCCTAGA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
35 9 0.28
36 23 0.72
ACGTcount: A:0.38, C:0.10, G:0.22, T:0.31
Consensus pattern (35 bp):
GCTTGACAAATAGAGAAAGTGATCTTTAAAGATAT
Found at i:54112425 original size:20 final size:20
Alignment explanation
Indices: 54112400--54112441 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
54112390 TTAGTTGGGG
54112400 AATTTGTGAGTTGGCTACTA
1 AATTTGTGAGTTGGCTACTA
*
54112420 AATTTGTGAGTTGGCTGCTA
1 AATTTGTGAGTTGGCTACTA
54112440 AA
1 AA
54112442 CCAGGTGTGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.26, C:0.10, G:0.26, T:0.38
Consensus pattern (20 bp):
AATTTGTGAGTTGGCTACTA
Found at i:54124229 original size:18 final size:19
Alignment explanation
Indices: 54124206--54124246 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
54124196 AAGAATAAAA
54124206 AGAGA-GAATGTTGTTTTG
1 AGAGAGGAATGTTGTTTTG
* *
54124224 AGAGAGGGATTTTGTTTTG
1 AGAGAGGAATGTTGTTTTG
54124243 AGAG
1 AGAG
54124247 GATTCGAGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 5 0.25
19 15 0.75
ACGTcount: A:0.27, C:0.00, G:0.37, T:0.37
Consensus pattern (19 bp):
AGAGAGGAATGTTGTTTTG
Found at i:54125556 original size:21 final size:21
Alignment explanation
Indices: 54125522--54125562 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
54125512 TACAAGAAAC
54125522 TTAAGAATAAAAAATAAATAT
1 TTAAGAATAAAAAATAAATAT
54125543 TTAA-AATAATAAAATAAATA
1 TTAAGAATAA-AAAATAAATA
54125563 AATAAACAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.29
Consensus pattern (21 bp):
TTAAGAATAAAAAATAAATAT
Found at i:54129942 original size:23 final size:24
Alignment explanation
Indices: 54129916--54129960 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
54129906 GAAAGATAAA
*
54129916 ATTCACATT-AAAATAAAATAATT
1 ATTCACATTGAAAAGAAAATAATT
*
54129939 ATTCATATTGAAAAGAAAATAA
1 ATTCACATTGAAAAGAAAATAA
54129961 CAAAATCTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 8 0.42
24 11 0.58
ACGTcount: A:0.58, C:0.07, G:0.04, T:0.31
Consensus pattern (24 bp):
ATTCACATTGAAAAGAAAATAATT
Found at i:54132179 original size:43 final size:43
Alignment explanation
Indices: 54132132--54132217 Score: 138
Period size: 43 Copynumber: 2.0 Consensus size: 43
54132122 CAATTCATCA
54132132 TTTCTCATCTCATAATCATTTCTCATATTTGT-CATTTCAATAT
1 TTTCTCATCTCATAATCATTTCTCATATTT-TCCATTTCAATAT
* *
54132175 TTTCTCATCTCATATTCATTTCTCATCTTTTCCATTTCAATAT
1 TTTCTCATCTCATAATCATTTCTCATATTTTCCATTTCAATAT
54132218 CAATTGGATA
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
42 1 0.03
43 39 0.98
ACGTcount: A:0.23, C:0.23, G:0.01, T:0.52
Consensus pattern (43 bp):
TTTCTCATCTCATAATCATTTCTCATATTTTCCATTTCAATAT
Found at i:54135222 original size:21 final size:21
Alignment explanation
Indices: 54135196--54135271 Score: 111
Period size: 21 Copynumber: 3.7 Consensus size: 21
54135186 AATCATATCT
54135196 TCTAAGATTGTATATATCATA
1 TCTAAGATTGTATATATCATA
**
54135217 TCTAAGATTACATATATCATA
1 TCTAAGATTGTATATATCATA
*
54135238 TCTAAGATTG--CATATCATA
1 TCTAAGATTGTATATATCATA
54135257 TCTAAGATTGTATAT
1 TCTAAGATTGTATAT
54135272 CCTCGAAAAT
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
19 18 0.38
21 30 0.62
ACGTcount: A:0.38, C:0.12, G:0.09, T:0.41
Consensus pattern (21 bp):
TCTAAGATTGTATATATCATA
Found at i:54135266 original size:19 final size:19
Alignment explanation
Indices: 54135209--54135272 Score: 92
Period size: 19 Copynumber: 3.3 Consensus size: 19
54135199 AAGATTGTAT
*
54135209 ATATCATATCTAAGATTAC
1 ATATCATATCTAAGATTGC
54135228 ATATATCATATCTAAGATTGC
1 --ATATCATATCTAAGATTGC
*
54135249 ATATCATATCTAAGATTGT
1 ATATCATATCTAAGATTGC
54135268 ATATC
1 ATATC
54135273 CTCGAAAATT
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
19 23 0.56
21 18 0.44
ACGTcount: A:0.39, C:0.14, G:0.08, T:0.39
Consensus pattern (19 bp):
ATATCATATCTAAGATTGC
Found at i:54136411 original size:9 final size:9
Alignment explanation
Indices: 54136389--54136444 Score: 71
Period size: 9 Copynumber: 6.4 Consensus size: 9
54136379 TGGTTAAAAA
54136389 TTAACCGA-
1 TTAACCGAT
54136397 TTAACCGAT
1 TTAACCGAT
*
54136406 TTAACCTAT
1 TTAACCGAT
54136415 TTAACCGA-
1 TTAACCGAT
* *
54136423 TTAACTGAC
1 TTAACCGAT
54136432 TTAACCGAT
1 TTAACCGAT
54136441 TTAA
1 TTAA
54136445 ATCACTATAT
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
8 15 0.37
9 26 0.63
ACGTcount: A:0.36, C:0.21, G:0.09, T:0.34
Consensus pattern (9 bp):
TTAACCGAT
Found at i:54136411 original size:17 final size:18
Alignment explanation
Indices: 54136389--54136444 Score: 71
Period size: 17 Copynumber: 3.2 Consensus size: 18
54136379 TGGTTAAAAA
54136389 TTAACCGA-TTAACCGAT
1 TTAACCGACTTAACCGAT
* *
54136406 TTAACCTATTTAACCGA-
1 TTAACCGACTTAACCGAT
*
54136423 TTAACTGACTTAACCGAT
1 TTAACCGACTTAACCGAT
54136441 TTAA
1 TTAA
54136445 ATCACTATAT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
17 21 0.64
18 12 0.36
ACGTcount: A:0.36, C:0.21, G:0.09, T:0.34
Consensus pattern (18 bp):
TTAACCGACTTAACCGAT
Found at i:54136422 original size:26 final size:26
Alignment explanation
Indices: 54136389--54136444 Score: 85
Period size: 26 Copynumber: 2.2 Consensus size: 26
54136379 TGGTTAAAAA
* *
54136389 TTAACCGATTAACCGATTTAACCTAT
1 TTAACCGATTAACCGACTTAACCGAT
*
54136415 TTAACCGATTAACTGACTTAACCGAT
1 TTAACCGATTAACCGACTTAACCGAT
54136441 TTAA
1 TTAA
54136445 ATCACTATAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.36, C:0.21, G:0.09, T:0.34
Consensus pattern (26 bp):
TTAACCGATTAACCGACTTAACCGAT
Found at i:54138063 original size:18 final size:19
Alignment explanation
Indices: 54138042--54138078 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
54138032 CCAAATTCGG
54138042 TCGG-TTAACCGAATTTTT
1 TCGGTTTAACCGAATTTTT
54138060 TCGGTTTTAACCGAATTTT
1 TCGG-TTTAACCGAATTTT
54138079 GCACACCCCT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 4 0.24
20 13 0.76
ACGTcount: A:0.22, C:0.16, G:0.16, T:0.46
Consensus pattern (19 bp):
TCGGTTTAACCGAATTTTT
Found at i:54139904 original size:35 final size:35
Alignment explanation
Indices: 54139864--54139932 Score: 111
Period size: 35 Copynumber: 2.0 Consensus size: 35
54139854 ACGATAGCGG
*
54139864 AAACCCAACTCTAAACTGATAAAATCCTCCATATT
1 AAACCCAACTCTAAACCGATAAAATCCTCCATATT
* *
54139899 AAACCCAGCTCTAAACCGATAAAATCCTTCATAT
1 AAACCCAACTCTAAACCGATAAAATCCTCCATAT
54139933 CAACCCCTAC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.42, C:0.29, G:0.04, T:0.25
Consensus pattern (35 bp):
AAACCCAACTCTAAACCGATAAAATCCTCCATATT
Found at i:54158655 original size:20 final size:19
Alignment explanation
Indices: 54158609--54158681 Score: 76
Period size: 20 Copynumber: 3.8 Consensus size: 19
54158599 AAAAAATTTT
* *
54158609 AAAAAAAGGGAAAA-AAGA
1 AAAAAAAAGAAAAAGAAGA
*
54158627 AAAAGAAAGAAAAAGAAGA
1 AAAAAAAAGAAAAAGAAGA
* *
54158646 AAAAACAAAGAATAAGATGA
1 AAAAA-AAAGAAAAAGAAGA
54158666 AAAGAAAAAGAAAAAG
1 AAA-AAAAAGAAAAAG
54158682 GAAAGGCCAA
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
18 11 0.24
19 8 0.18
20 24 0.53
21 2 0.04
ACGTcount: A:0.77, C:0.01, G:0.19, T:0.03
Consensus pattern (19 bp):
AAAAAAAAGAAAAAGAAGA
Found at i:54158685 original size:7 final size:6
Alignment explanation
Indices: 54158620--54158681 Score: 56
Period size: 6 Copynumber: 10.0 Consensus size: 6
54158610 AAAAAAGGGA
* *
54158620 AAAAAG AAAAAG AAAGAA- AAAGAAG AAAAA- ACAAAG AATAAG ATGAAAAG
1 AAAAAG AAAAAG AAA-AAG AAA-AAG AAAAAG AAAAAG AAAAAG A--AAAAG
54158670 AAAAAG AAAAAG
1 AAAAAG AAAAAG
54158682 GAAAGGCCAA
Statistics
Matches: 47, Mismatches: 4, Indels: 10
0.77 0.07 0.16
Matches are distributed among these distances:
5 4 0.09
6 33 0.70
7 5 0.11
8 5 0.11
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.03
Consensus pattern (6 bp):
AAAAAG
Found at i:54159979 original size:45 final size:45
Alignment explanation
Indices: 54159893--54160157 Score: 157
Period size: 45 Copynumber: 5.9 Consensus size: 45
54159883 AATAAAGTTA
* *
54159893 CAGATCTTGTCTTCCTGTACTGGCAGC-AGAGTAGA-CTGAAGATAG
1 CAGATCTTGCCTTCCTGTACTGGCAGCGA-AGCAGATC-GAAGATAG
* * * *
54159938 CAGATGTTGTCTTCCTGTACTGGCAGCGAAGCAGATCGAAGACAC
1 CAGATCTTGCCTTCCTGTACTGGCAGCGAAGCAGATCGAAGATAG
* * ** * *
54159983 CAG-CCTTGCCTTCCTATACTCACAGTGAAGCAGATTGAAGATAG
1 CAGATCTTGCCTTCCTGTACTGGCAGCGAAGCAGATCGAAGATAG
* ** * * *
54160027 CAGATCATGCCTTTATGTA-TCGGTAGCGAAGCAGATCGAAGACAC
1 CAGATCTTGCCTTCCTGTACT-GGCAGCGAAGCAGATCGAAGATAG
* * ** *** *
54160072 CTG-CCTTGCCTTTTTGTACTAATAGC-AGAGCA-AACTGAAGATAG
1 CAGATCTTGCCTTCCTGTACTGGCAGCGA-AGCAGATC-GAAGATAG
* * ** *
54160116 CAAATCTTGCCTTCTTGTACTAACAGTGAAGCAGATCGAAGA
1 CAGATCTTGCCTTCCTGTACTGGCAGCGAAGCAGATCGAAGA
54160158 CACCACAGTT
Statistics
Matches: 168, Mismatches: 42, Indels: 20
0.73 0.18 0.09
Matches are distributed among these distances:
43 3 0.02
44 62 0.37
45 98 0.58
46 5 0.03
ACGTcount: A:0.29, C:0.22, G:0.23, T:0.25
Consensus pattern (45 bp):
CAGATCTTGCCTTCCTGTACTGGCAGCGAAGCAGATCGAAGATAG
Found at i:54160111 original size:89 final size:89
Alignment explanation
Indices: 54159898--54160162 Score: 273
Period size: 89 Copynumber: 3.0 Consensus size: 89
54159888 AGTTACAGAT
* * ** * * * *
54159898 CTTGTCTTCCTGTACTGGCAGCAGAGTAGACTGAAGATAGCAGATGTTGTCTTCCTGTACTGGCA
1 CTTGCCTTCCTATACTAACAGCAGAGCAGACTGAAGATAGCAGATCTTGCCTTCATGTACTGGCA
54159963 GCGAAGCAGATCGAAGACACCAGC
66 GCGAAGCAGATCGAAGACACCAGC
* * * * *
54159987 CTTGCCTTCCTATACTCACAG-TGAAGCAGATTGAAGATAGCAGATCATGCCTTTATGTA-TCGG
1 CTTGCCTTCCTATACTAACAGCAG-AGCAGACTGAAGATAGCAGATCTTGCCTTCATGTACT-GG
* *
54160050 TAGCGAAGCAGATCGAAGACACCTGC
64 CAGCGAAGCAGATCGAAGACACCAGC
** * * * * * **
54160076 CTTGCCTTTTTGTACTAATAGCAGAGCAAACTGAAGATAGCAAATCTTGCCTTCTTGTACTAACA
1 CTTGCCTTCCTATACTAACAGCAGAGCAGACTGAAGATAGCAGATCTTGCCTTCATGTACTGGCA
*
54160141 GTGAAGCAGATCGAAGACACCA
66 GCGAAGCAGATCGAAGACACCA
54160163 CAGTTTGCAA
Statistics
Matches: 141, Mismatches: 31, Indels: 8
0.78 0.17 0.04
Matches are distributed among these distances:
88 2 0.01
89 137 0.97
90 2 0.01
ACGTcount: A:0.29, C:0.23, G:0.23, T:0.25
Consensus pattern (89 bp):
CTTGCCTTCCTATACTAACAGCAGAGCAGACTGAAGATAGCAGATCTTGCCTTCATGTACTGGCA
GCGAAGCAGATCGAAGACACCAGC
Found at i:54160430 original size:44 final size:44
Alignment explanation
Indices: 54160368--54160771 Score: 260
Period size: 44 Copynumber: 9.4 Consensus size: 44
54160358 AGCCAACAAA
* * *
54160368 TCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTGAAGTTACTAG
1 TCTTATCTCTCTGAAGTTGCAGTGGAGTAGATTGAAGTTACTAG
* * ** * * * *
54160412 TCCTATCTCTCTGAAGTTGCAGTAGAACAGATCGCA--T-CCAA
1 TCTTATCTCTCTGAAGTTGCAGTGGAGTAGATTGAAGTTACTAG
* *
54160453 TCTTACCTCCCTGAAGTTGCAGTGGAGTAGATTGAAGTTACTAG
1 TCTTATCTCTCTGAAGTTGCAGTGGAGTAGATTGAAGTTACTAG
* * * ***
54160497 TCCTATCT-TCCTGAAGTTGCAGTGGAGTGGATTAAAACCAC-AG
1 TCTTATCTCT-CTGAAGTTGCAGTGGAGTAGATTGAAGTTACTAG
* *** * *
54160540 ATCTTATCTCTCTGAAGTTGCAGTAGAGTAGATCCCA--T-CCAA
1 -TCTTATCTCTCTGAAGTTGCAGTGGAGTAGATTGAAGTTACTAG
* * **
54160582 TCTTATCTCCCTGAATTTTTAGTGGAGTAGATTGAAGTTACTAG
1 TCTTATCTCTCTGAAGTTGCAGTGGAGTAGATTGAAGTTACTAG
* * * * ***
54160626 TCCTATCT-TCCTGAAGTTACAGTGGAGTGGATTAAAACCAC-AG
1 TCTTATCTCT-CTGAAGTTGCAGTGGAGTAGATTGAAGTTACTAG
* * * * * *
54160669 ATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCGCA--T-CCAA
1 -TCTTATCTCTCTGAAGTTGCAGTGGAGTAGATTGAAGTTACTAG
* *
54160711 TCTTATCTCCCTGAAGTTGCTGTGGAGTAGATTGAAGTTACTAG
1 TCTTATCTCTCTGAAGTTGCAGTGGAGTAGATTGAAGTTACTAG
*
54160755 TCCTATCT-TCCTGAAGT
1 TCTTATCTCT-CTGAAGT
54160772 AGAGCAGATC
Statistics
Matches: 269, Mismatches: 73, Indels: 36
0.71 0.19 0.10
Matches are distributed among these distances:
41 90 0.33
42 3 0.01
43 7 0.03
44 167 0.62
45 2 0.01
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.32
Consensus pattern (44 bp):
TCTTATCTCTCTGAAGTTGCAGTGGAGTAGATTGAAGTTACTAG
Found at i:54160548 original size:129 final size:129
Alignment explanation
Indices: 54160415--54160771 Score: 633
Period size: 129 Copynumber: 2.8 Consensus size: 129
54160405 TTACTAGTCC
* *
54160415 TATCTCTCTGAAGTTGCAGTAGAACAGATCGCATCCAATCTTACCTCCCTGAAGTTGCAGTGGAG
1 TATCTCTCTGAAGTTGCAGTAGAGCAGATCGCATCCAATCTTATCTCCCTGAAGTTGCAGTGGAG
*
54160480 TAGATTGAAGTTACTAGTCCTATCTTCCTGAAGTTGCAGTGGAGTGGATTAAAACCACAGATCT
66 TAGATTGAAGTTACTAGTCCTATCTTCCTGAAGTTACAGTGGAGTGGATTAAAACCACAGATCT
* * * **
54160544 TATCTCTCTGAAGTTGCAGTAGAGTAGATCCCATCCAATCTTATCTCCCTGAATTTTTAGTGGAG
1 TATCTCTCTGAAGTTGCAGTAGAGCAGATCGCATCCAATCTTATCTCCCTGAAGTTGCAGTGGAG
54160609 TAGATTGAAGTTACTAGTCCTATCTTCCTGAAGTTACAGTGGAGTGGATTAAAACCACAGATCT
66 TAGATTGAAGTTACTAGTCCTATCTTCCTGAAGTTACAGTGGAGTGGATTAAAACCACAGATCT
*
54160673 TATCTCTCTGAAGTTGCAGTAGAGCAGATCGCATCCAATCTTATCTCCCTGAAGTTGCTGTGGAG
1 TATCTCTCTGAAGTTGCAGTAGAGCAGATCGCATCCAATCTTATCTCCCTGAAGTTGCAGTGGAG
54160738 TAGATTGAAGTTACTAGTCCTATCTTCCTGAAGT
66 TAGATTGAAGTTACTAGTCCTATCTTCCTGAAGT
54160772 AGAGCAGATC
Statistics
Matches: 214, Mismatches: 14, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
129 214 1.00
ACGTcount: A:0.27, C:0.20, G:0.21, T:0.32
Consensus pattern (129 bp):
TATCTCTCTGAAGTTGCAGTAGAGCAGATCGCATCCAATCTTATCTCCCTGAAGTTGCAGTGGAG
TAGATTGAAGTTACTAGTCCTATCTTCCTGAAGTTACAGTGGAGTGGATTAAAACCACAGATCT
Found at i:54160724 original size:85 final size:85
Alignment explanation
Indices: 54160366--54160771 Score: 311
Period size: 85 Copynumber: 4.7 Consensus size: 85
54160356 AAAGCCAACA
* * * *
54160366 AATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTGAAGTTACTAGTCCTATCTCTCTGAAGTTG
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTGAAATCACTAGTCCTATCTCTCTGAAGTTG
* *
54160431 CAGTAGAACAGATCGCATCC
66 CAGTAGAGCAGATCGAATCC
* * *
54160451 AATCTTACCTCCCTGAAGTTGCAGTGGAGTAGATTGAAGTTACTAGTCCTATCT-TCCTGAAGTT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTGAAATCACTAGTCCTATCTCT-CTGAAGTT
* ** ** *
54160515 GCAGTGGAGTGGATTAAAACCAC
65 GCAGTAGAGCAGA-TCGAATC-C
* * *** * * * *
54160538 AGATCTTATCTCTCTGAAGTTGCAGTAGAGTAGA-TCCCATC-C-AATCTTATCTCCCTGAATTT
1 A-ATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTGAAATCACTAGTCCTATCTCTCTGAAGTT
** * * * *
54160600 TTAGTGGAGTAGATTGAAGTTACT
65 GCAGTAGAGCAGATCGAA--T-CC
* * * * * * * *
54160624 AGTCCTATCTTCCTGAAGTTACAGTGGAGTGGATTAAAACCAC-AGATCTTATCTCTCTGAAGTT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTGAAATCACTAG-TCCTATCTCTCTGAAGTT
*
54160688 GCAGTAGAGCAGATCGCATCC
65 GCAGTAGAGCAGATCGAATCC
* * *
54160709 AATCTTATCTCCCTGAAGTTGCTGTGGAGTAGATTGAAGTTACTAGTCCTATCT-TCCTGAAGT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTGAAATCACTAGTCCTATCTCT-CTGAAGT
54160772 AGAGCAGATC
Statistics
Matches: 246, Mismatches: 62, Indels: 26
0.74 0.19 0.08
Matches are distributed among these distances:
84 5 0.02
85 166 0.67
86 11 0.04
87 7 0.03
88 57 0.23
ACGTcount: A:0.27, C:0.20, G:0.21, T:0.32
Consensus pattern (85 bp):
AATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTGAAATCACTAGTCCTATCTCTCTGAAGTTG
CAGTAGAGCAGATCGAATCC
Found at i:54162188 original size:20 final size:19
Alignment explanation
Indices: 54162163--54162230 Score: 109
Period size: 20 Copynumber: 3.4 Consensus size: 19
54162153 AATTGAAATG
54162163 AATGTGATATTGAGTTATGA
1 AATGTGATATTG-GTTATGA
54162183 AATGTGATATTGGGTTATGA
1 AATGTGATATT-GGTTATGA
54162203 AATGTGATATTGGTTTATGA
1 AATGTGATATTGG-TTATGA
54162223 AATGTGAT
1 AATGTGAT
54162231 TTTATGGACT
Statistics
Matches: 46, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
19 2 0.04
20 43 0.93
21 1 0.02
ACGTcount: A:0.32, C:0.00, G:0.26, T:0.41
Consensus pattern (19 bp):
AATGTGATATTGGTTATGA
Found at i:54162276 original size:35 final size:35
Alignment explanation
Indices: 54162237--54162497 Score: 192
Period size: 35 Copynumber: 7.5 Consensus size: 35
54162227 TGATTTTATG
*
54162237 GACTAGCGTTGGGCACAACTTCTGTCAGTTTATCT
1 GACTAGCGCTGGGCACAACTTCTGTCAGTTTATCT
* * * ** *
54162272 GACTAGTGCTGGGCACAACCATC-GT-TGGCTATTT
1 GACTAGCGCTGGGCACAA-CTTCTGTCAGTTTATCT
** ** *
54162306 GACTAGCATTGGGTGCAACTTCTGTCAATTTATCT
1 GACTAGCGCTGGGCACAACTTCTGTCAGTTTATCT
** * * *
54162341 GACTAGTACTGGGCACAACCATC-GTC-GGTTATCC
1 GACTAGCGCTGGGCACAA-CTTCTGTCAGTTTATCT
* * * *
54162375 GAGTAGCACTGGGCGCAACTTCTATCAGTTTATCT
1 GACTAGCGCTGGGCACAACTTCTGTCAGTTTATCT
* * * *
54162410 GACTAGTGTTAGGCACAACCATC-GTCAG-TTATCT
1 GACTAGCGCTGGGCACAA-CTTCTGTCAGTTTATCT
* *
54162444 GACTACCGCTGGGCGCAACTTCTGTCAGTTTATCT
1 GACTAGCGCTGGGCACAACTTCTGTCAGTTTATCT
* *
54162479 GACTAGTGCTAGGCACAAC
1 GACTAGCGCTGGGCACAAC
54162498 CATCGTCAAT
Statistics
Matches: 166, Mismatches: 51, Indels: 18
0.71 0.22 0.08
Matches are distributed among these distances:
33 9 0.05
34 66 0.40
35 82 0.49
36 9 0.05
ACGTcount: A:0.23, C:0.25, G:0.23, T:0.30
Consensus pattern (35 bp):
GACTAGCGCTGGGCACAACTTCTGTCAGTTTATCT
Found at i:54162353 original size:69 final size:69
Alignment explanation
Indices: 54162237--54162504 Score: 365
Period size: 69 Copynumber: 3.9 Consensus size: 69
54162227 TGATTTTATG
** * * * *
54162237 GACTAGCGTTGGGCACAACTTCTGTCAGTTTATCTGACTAGTGCTGGGCACAACCATCGTTGGCT
1 GACTAGCACTGGGCGCAACTTCTGTCAGTTTATCTGACTAGTGCTAGGCACAACCATCGTCGGTT
*
54162302 ATTT
66 ATCT
* * * * *
54162306 GACTAGCATTGGGTGCAACTTCTGTCAATTTATCTGACTAGTACTGGGCACAACCATCGTCGGTT
1 GACTAGCACTGGGCGCAACTTCTGTCAGTTTATCTGACTAGTGCTAGGCACAACCATCGTCGGTT
*
54162371 ATCC
66 ATCT
* * * *
54162375 GAGTAGCACTGGGCGCAACTTCTATCAGTTTATCTGACTAGTGTTAGGCACAACCATCGTCAGTT
1 GACTAGCACTGGGCGCAACTTCTGTCAGTTTATCTGACTAGTGCTAGGCACAACCATCGTCGGTT
54162440 ATCT
66 ATCT
* *
54162444 GACTACCGCTGGGCGCAACTTCTGTCAGTTTATCTGACTAGTGCTAGGCACAACCATCGTC
1 GACTAGCACTGGGCGCAACTTCTGTCAGTTTATCTGACTAGTGCTAGGCACAACCATCGTC
54162505 AATTATCTTG
Statistics
Matches: 175, Mismatches: 24, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
69 175 1.00
ACGTcount: A:0.22, C:0.25, G:0.23, T:0.30
Consensus pattern (69 bp):
GACTAGCACTGGGCGCAACTTCTGTCAGTTTATCTGACTAGTGCTAGGCACAACCATCGTCGGTT
ATCT
Found at i:54163036 original size:20 final size:20
Alignment explanation
Indices: 54163011--54163054 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
54163001 AACTGAAATG
54163011 AATGTGATATTGAGTTATGA
1 AATGTGATATTGAGTTATGA
*
54163031 AATGTGATATTGGGTTATGA
1 AATGTGATATTGAGTTATGA
54163051 AATG
1 AATG
54163055 CGATTTTATG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.34, C:0.00, G:0.27, T:0.39
Consensus pattern (20 bp):
AATGTGATATTGAGTTATGA
Found at i:54163104 original size:35 final size:35
Alignment explanation
Indices: 54163076--54163325 Score: 179
Period size: 35 Copynumber: 7.2 Consensus size: 35
54163066 ACTAGCGTTA
54163076 GGCACAACTTCTGTCAGTTTATCTGACTAGTGCTG
1 GGCACAACTTCTGTCAGTTTATCTGACTAGTGCTG
* * * **
54163111 GGCACAACCATC-GT-TGGTTATCTGACTAGTATTG
1 GGCACAA-CTTCTGTCAGTTTATCTGACTAGTGCTG
** *
54163145 GGTGCAACTTCTGTCAATTTATCTGACTAGTGCTG
1 GGCACAACTTCTGTCAGTTTATCTGACTAGTGCTG
* * * * * **
54163180 GGCACAACAATC-GT-TGGTTATCCGAGTAGCACTG
1 GGCACAAC-TTCTGTCAGTTTATCTGACTAGTGCTG
* * *
54163214 GGCACAACTTCTATCAGTTTATCTGACTAGTGTTA
1 GGCACAACTTCTGTCAGTTTATCTGACTAGTGCTG
* * *** *
54163249 GGCACAACCAT-TGTCAG-TTATCTCACTACCACTA
1 GGCACAA-CTTCTGTCAGTTTATCTGACTAGTGCTG
* * *
54163283 GGCGCAACTTCTGTTAGTTTATCTGACTAGTGCTA
1 GGCACAACTTCTGTCAGTTTATCTGACTAGTGCTG
*
54163318 AGCACAAC
1 GGCACAAC
54163326 CATCGTCGAT
Statistics
Matches: 157, Mismatches: 49, Indels: 18
0.70 0.22 0.08
Matches are distributed among these distances:
33 7 0.04
34 68 0.43
35 75 0.48
36 7 0.04
ACGTcount: A:0.24, C:0.23, G:0.21, T:0.32
Consensus pattern (35 bp):
GGCACAACTTCTGTCAGTTTATCTGACTAGTGCTG
Found at i:54163137 original size:34 final size:34
Alignment explanation
Indices: 54163094--54163340 Score: 117
Period size: 34 Copynumber: 7.2 Consensus size: 34
54163084 TTCTGTCAGT
54163094 TTATCTGACTAGTGCTGGGCACAACCATCGTTGG
1 TTATCTGACTAGTGCTGGGCACAACCATCGTTGG
** ** * ***
54163128 TTATCTGACTAGTATTGGGTGCAA-CTTCTGTCAAT
1 TTATCTGACTAGTGCTGGGCACAACCATC-GT-TGG
*
54163163 TTATCTGACTAGTGCTGGGCACAACAATCGTTGG
1 TTATCTGACTAGTGCTGGGCACAACCATCGTTGG
* * **
54163197 TTATCCGAGTAGCACTGGGCACAACTTCTATCAG-T--
1 TTATCTGACTAGTGCTGGGCACAAC--C-ATC-GTTGG
* * * **
54163232 TTATCTGACTAGTGTTAGGCACAACCATTGTCAG
1 TTATCTGACTAGTGCTGGGCACAACCATCGTTGG
* *** * * * *
54163266 TTATCTCACTACCACTAGGCGCAA-CTTCTGTTAGT
1 TTATCTGACTAGTGCTGGGCACAACCATC-GTT-GG
** * *
54163301 TTATCTGACTAGTGCTAAGCACAACCATCGTCGA
1 TTATCTGACTAGTGCTGGGCACAACCATCGTTGG
54163335 TTATCT
1 TTATCT
54163341 TGAACTAAAT
Statistics
Matches: 150, Mismatches: 50, Indels: 26
0.66 0.22 0.12
Matches are distributed among these distances:
31 1 0.01
32 2 0.01
33 6 0.04
34 70 0.47
35 61 0.41
36 5 0.03
37 4 0.03
38 1 0.01
ACGTcount: A:0.24, C:0.23, G:0.20, T:0.32
Consensus pattern (34 bp):
TTATCTGACTAGTGCTGGGCACAACCATCGTTGG
Found at i:54163176 original size:69 final size:69
Alignment explanation
Indices: 54163080--54163340 Score: 324
Period size: 69 Copynumber: 3.8 Consensus size: 69
54163070 GCGTTAGGCA
* * * *
54163080 CAACTTCTGTCAGTTTATCTGACTAGTGCTGGGCACAACCATCGTTGGTTATCTGACTAGTATTG
1 CAACTTCTGTCAGTTTATCTGACTAGTGCTAGGCACAACCATCGTCGGTTATCTGACTAGCACTG
*
54163145 GGTG
66 GGCG
* * * * * *
54163149 CAACTTCTGTCAATTTATCTGACTAGTGCTGGGCACAACAATCGTTGGTTATCCGAGTAGCACTG
1 CAACTTCTGTCAGTTTATCTGACTAGTGCTAGGCACAACCATCGTCGGTTATCTGACTAGCACTG
*
54163214 GGCA
66 GGCG
* * * * * * *
54163218 CAACTTCTATCAGTTTATCTGACTAGTGTTAGGCACAACCATTGTCAGTTATCTCACTACCACTA
1 CAACTTCTGTCAGTTTATCTGACTAGTGCTAGGCACAACCATCGTCGGTTATCTGACTAGCACTG
54163283 GGCG
66 GGCG
* * *
54163287 CAACTTCTGTTAGTTTATCTGACTAGTGCTAAGCACAACCATCGTCGATTATCT
1 CAACTTCTGTCAGTTTATCTGACTAGTGCTAGGCACAACCATCGTCGGTTATCT
54163341 TGAACTAAAT
Statistics
Matches: 163, Mismatches: 29, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
69 163 1.00
ACGTcount: A:0.24, C:0.23, G:0.20, T:0.33
Consensus pattern (69 bp):
CAACTTCTGTCAGTTTATCTGACTAGTGCTAGGCACAACCATCGTCGGTTATCTGACTAGCACTG
GGCG
Found at i:54163324 original size:138 final size:138
Alignment explanation
Indices: 54163076--54163331 Score: 359
Period size: 138 Copynumber: 1.9 Consensus size: 138
54163066 ACTAGCGTTA
* * ** * **
54163076 GGCACAACTTCTGTCAGTTTATCTGACTAGTGCTGGGCACAACCATCGTTGGTTATCTGACTAGT
1 GGCACAACTTCTATCAGTTTATCTGACTAGTGCTAGGCACAACCATCGTCAGTTATCTCACTACC
* * * **
54163141 ATTGGGTGCAACTTCTGTCAATTTATCTGACTAGTGCTGGGCACAACAATCGTTGGTTATCCGAG
66 ACTAGGCGCAACTTCTGTCAATTTATCTGACTAGTGCTAAGCACAACAATCGTTGGTTATCCGAG
54163206 TAGCACTG
131 TAGCACTG
* *
54163214 GGCACAACTTCTATCAGTTTATCTGACTAGTGTTAGGCACAACCATTGTCAGTTATCTCACTACC
1 GGCACAACTTCTATCAGTTTATCTGACTAGTGCTAGGCACAACCATCGTCAGTTATCTCACTACC
* * *
54163279 ACTAGGCGCAACTTCTGTTAGTTTATCTGACTAGTGCTAAGCACAACCATCGT
66 ACTAGGCGCAACTTCTGTCAATTTATCTGACTAGTGCTAAGCACAACAATCGT
54163332 CGATTATCTT
Statistics
Matches: 101, Mismatches: 17, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
138 101 1.00
ACGTcount: A:0.24, C:0.23, G:0.21, T:0.32
Consensus pattern (138 bp):
GGCACAACTTCTATCAGTTTATCTGACTAGTGCTAGGCACAACCATCGTCAGTTATCTCACTACC
ACTAGGCGCAACTTCTGTCAATTTATCTGACTAGTGCTAAGCACAACAATCGTTGGTTATCCGAG
TAGCACTG
Found at i:54163457 original size:828 final size:828
Alignment explanation
Indices: 54161663--54164139 Score: 4140
Period size: 828 Copynumber: 3.0 Consensus size: 828
54161653 AACATCCATG
* *
54161663 TGAAGTAAATAAATATTTTCTTTAATGCTAATTAAGTAAGTTTGTAATTCTTTAACTTGAACTAT
1 TGAACTAAATAAATATTTTCTTTAATGC----TAAGTAAGTTCGTAATTCTTTAACTTGAACTAT
*
54161728 TTAAATATTTACTTGTGAATTTCG--ATATATATATATGATACTTGTATACATTTATTAGCTATT
62 TTAAATATTTACTTGTGAATTTTGATATATATATATATGATACTTGTATACATTTATTAGCTATT
* * *
54161791 TGGAGACATGATAAAATGTATATTTAATCCAATGAATGGTTGATAAAATGAATAAACGAATAATT
127 TGGAGATATGATAAAATGTATATTTAATCCAATGAATGGTTGATAAAATGAATAAATGAACAATT
* * *
54161856 AGCCTTAAACTAATAGTATGGAAATGTTATATATGGAGATGTATTACCGAACTGATGAGATTGAA
192 AGCCTTAAACTAATAGTATAGAAATTTTATATATGGAGATGTATTGCCGAACTGATGAGATTGAA
* * * * **
54161921 GTTGAATAATGGTTAATGTATGGAGTTAAATAAAGTTTTCTGTCCACATACTAGGTAAGTT-AGT
257 GTTGAATAATGGTTAATGTATGCAGTTAAATAAAATCTTGTGTTTACATACTAGGTAAGTTCA-T
* *
54161985 AGTCTTGGAACTAGAACGTTATTTACTTAACTTAATTAGATAATTGTTAATTATTATTTAACTAT
321 AGTCTTGGAACTCGAACGTTATTTACTTAACTTAATTAGTTAATTGTTAATTATTATTTAACTAT
* * * *
54162050 ATTTTTATTTGGGTTTGGTTAAGCTCTATTGAACGGATATTGATAAAATCATAAATAGATAAAAC
386 GTTTTTAATTGGGTTTGATTAAGCTCTATTGAACGGATATTGATAAAATCATATATAGATAAAAC
* *
54162115 GTGGCTTTATGGAATAAATTAATGGATGATTAATAGATAATTGAAATGAATGTGATATTGAGTTA
451 GTGGCATTATGGAATAAATTAATGGATGATTAATAGATAACTGAAATGAATGTGATATTGAGTTA
*
54162180 TGAAATGTGATATTGGGTTATGAAATGTGATATTGGTTTATGAAATGTGATTTTATGGACTAGCG
516 TGAAA--TG----T--G--AT---AT-TG-----GG-TTATGAAATGCGATTTTATGGACTAGCG
* * *
54162245 TTGGGCACAACTTCTGTCAGTTTATCTGACTAGTGCTGGGCACAACCATCGTTGGCTATTTGACT
561 TTAGGCACAACTTCTGTCAGTTTATCTGACTAGTGCTGGGCACAACCATCGTTGGTTATCTGACT
* *
54162310 AGCATTGGGTGCAACTTCTGTCAATTTATCTGACTAGTACTGGGCACAACCATCGTCGGTTATCC
626 AGTATTGGGTGCAACTTCTGTCAATTTATCTGACTAGTGCTGGGCACAACCATCGTCGGTTATCC
*
54162375 GAGTAGCACTGGGCGCAACTTCTATCAGTTTATCTGACTAGTGTTAGGCACAACCATCGTCAGTT
691 GAGTAGCACTGGGCACAACTTCTATCAGTTTATCTGACTAGTGTTAGGCACAACCATCGTCAGTT
* * *
54162440 ATCTGACTACCGCTGGGCGCAACTTCTGTCAGTTTATCTGACTAGTGCTAGGCACAACCATCGTC
756 ATCTCACTACCGCTGGGCGCAACTTCTGTTAGTTTATCTGACTAGTGCTAAGCACAACCATCGTC
54162505 AATTATCT
821 AATTATCT
54162513 TGAACTAAATAAATATTTTCTTTAATGCTAAGTAAGTTCGTAATTCTTTAACTTGAACTATTTAA
1 TGAACTAAATAAATATTTTCTTTAATGCTAAGTAAGTTCGTAATTCTTTAACTTGAACTATTTAA
*
54162578 ATATTTACTTGTTAATTTTGATATATATATATATGATACTTGTATACATTTATTAGCTATTTGGA
66 ATATTTACTTGTGAATTTTGATATATATATATATGATACTTGTATACATTTATTAGCTATTTGGA
54162643 GATATGATAAAATGTATATTTAATCCAATGAATGGTTGATAAAATGAATAAATGAACAATTAGCC
131 GATATGATAAAATGTATATTTAATCCAATGAATGGTTGATAAAATGAATAAATGAACAATTAGCC
54162708 TTAAACTAATAGTATAGAAATTTTATATATGGAGATGTATTGCCGAACTGATGAGATTGAAGTTG
196 TTAAACTAATAGTATAGAAATTTTATATATGGAGATGTATTGCCGAACTGATGAGATTGAAGTTG
54162773 AATAATGGTTAATGTATGCAGTTAAATAAAATCTTGTGTTTACATACTAGGTAAGTTCATAGTCT
261 AATAATGGTTAATGTATGCAGTTAAATAAAATCTTGTGTTTACATACTAGGTAAGTTCATAGTCT
*
54162838 TGGAACTCGTACGTTATTTACTTAACTTAATTAGTTAATTGTTAATTATTATTTAACTATGTTTT
326 TGGAACTCGAACGTTATTTACTTAACTTAATTAGTTAATTGTTAATTATTATTTAACTATGTTTT
54162903 TAATTGGGTTTGATTAAGCTCTATTGAACGGATATTGATAAAATCATATATAGATAAAACGTGGC
391 TAATTGGGTTTGATTAAGCTCTATTGAACGGATATTGATAAAATCATATATAGATAAAACGTGGC
54162968 ATTATGGAATAAATTAATGGATGATTAATAGATAACTGAAATGAATGTGATATTGAGTTATGAAA
456 ATTATGGAATAAATTAATGGATGATTAATAGATAACTGAAATGAATGTGATATTGAGTTATGAAA
54163033 TGTGATATTGGGTTATGAAATGCGATTTTATGGACTAGCGTTAGGCACAACTTCTGTCAGTTTAT
521 TGTGATATTGGGTTATGAAATGCGATTTTATGGACTAGCGTTAGGCACAACTTCTGTCAGTTTAT
54163098 CTGACTAGTGCTGGGCACAACCATCGTTGGTTATCTGACTAGTATTGGGTGCAACTTCTGTCAAT
586 CTGACTAGTGCTGGGCACAACCATCGTTGGTTATCTGACTAGTATTGGGTGCAACTTCTGTCAAT
* *
54163163 TTATCTGACTAGTGCTGGGCACAACAATCGTTGGTTATCCGAGTAGCACTGGGCACAACTTCTAT
651 TTATCTGACTAGTGCTGGGCACAACCATCGTCGGTTATCCGAGTAGCACTGGGCACAACTTCTAT
* * *
54163228 CAGTTTATCTGACTAGTGTTAGGCACAACCATTGTCAGTTATCTCACTACCACTAGGCGCAACTT
716 CAGTTTATCTGACTAGTGTTAGGCACAACCATCGTCAGTTATCTCACTACCGCTGGGCGCAACTT
*
54163293 CTGTTAGTTTATCTGACTAGTGCTAAGCACAACCATCGTCGATTATCT
781 CTGTTAGTTTATCTGACTAGTGCTAAGCACAACCATCGTCAATTATCT
*
54163341 TGAACTAAATAAATATTTTCTTTAATGCTAAGTAAGTTCGTAATTCTTTAGCTTGAACTATTTAA
1 TGAACTAAATAAATATTTTCTTTAATGCTAAGTAAGTTCGTAATTCTTTAACTTGAACTATTTAA
54163406 ATATTTACTTGTGAATTTTGATATATATATATATGATACTTGTATACATTTATTAGCTATTTGGA
66 ATATTTACTTGTGAATTTTGATATATATATATATGATACTTGTATACATTTATTAGCTATTTGGA
54163471 GATATGATAAAATGTATATTTAATCCAATGAATGGTTGATAAAATGAATAAATGAACAATTAGCC
131 GATATGATAAAATGTATATTTAATCCAATGAATGGTTGATAAAATGAATAAATGAACAATTAGCC
54163536 TTAAACTAATAGTATAGAAATTTTATATATGGAGATGTATTGCCGAACTGATGAGATTGAAGTTG
196 TTAAACTAATAGTATAGAAATTTTATATATGGAGATGTATTGCCGAACTGATGAGATTGAAGTTG
54163601 AATAATGGTTAATGTATGCAGTTAAATAAAATCTTGTGTTTACATACTAGGTAAGTTCATAGTCT
261 AATAATGGTTAATGTATGCAGTTAAATAAAATCTTGTGTTTACATACTAGGTAAGTTCATAGTCT
54163666 TGGAACTCGAACGTTATTTACTTAACTTAATTAGTTAATTGTTAATTATTATTTAACTATG-TTT
326 TGGAACTCGAACGTTATTTACTTAACTTAATTAGTTAATTGTTAATTATTATTTAACTATGTTTT
54163730 TAATTGGGTTTGATTAAGCTCTATTGAACGGATATTGATAAAATCATATATAGATAAAACGTGGC
391 TAATTGGGTTTGATTAAGCTCTATTGAACGGATATTGATAAAATCATATATAGATAAAACGTGGC
*
54163795 ATTATGGAATAAATTAATGGATGATTAATAGATAACTGAAATGAATGTGATATTAAGTTATGAAA
456 ATTATGGAATAAATTAATGGATGATTAATAGATAACTGAAATGAATGTGATATTGAGTTATGAAA
54163860 TGTGATATTGGGTTATGAAATGCGATTTTATGGACTAGCGTTAGGCACAACTTCTGTCAGTTTAT
521 TGTGATATTGGGTTATGAAATGCGATTTTATGGACTAGCGTTAGGCACAACTTCTGTCAGTTTAT
* *
54163925 CTGACTAGTGCTGGGCACAACCATCGTTGGTTATCTGACTAGTGTTGGGTGTAACTTCTGTCAAT
586 CTGACTAGTGCTGGGCACAACCATCGTTGGTTATCTGACTAGTATTGGGTGCAACTTCTGTCAAT
* * * ***
54163990 TTATCTGACTA--GCTAGGCACAACCATTGTCGGTTATCTGAGTAGCACTGGGGTTAACTTCTAT
651 TTATCTGACTAGTGCTGGGCACAACCATCGTCGGTTATCCGAGTAGCACTGGGCACAACTTCTAT
* * * * * *
54164053 CAGTCTATCTGACTAGTGTTGGGCACAACCATCGTCAATTATC-CGACTAGCGTTGGGCACAACT
716 CAGTTTATCTGACTAGTGTTAGGCACAACCATCGTCAGTTATCTC-ACTACCGCTGGGCGCAACT
* *
54164117 TCTGTTAGTTTATTTGACCAGTG
780 TCTGTTAGTTTATCTGACTAGTG
54164140 TTGGGCACAC
Statistics
Matches: 1557, Mismatches: 66, Indels: 33
0.94 0.04 0.02
Matches are distributed among these distances:
824 1 0.00
825 118 0.08
827 271 0.17
828 663 0.43
829 2 0.00
834 2 0.00
835 2 0.00
838 2 0.00
840 1 0.00
842 1 0.00
846 56 0.04
848 410 0.26
849 1 0.00
850 27 0.02
ACGTcount: A:0.32, C:0.12, G:0.18, T:0.37
Consensus pattern (828 bp):
TGAACTAAATAAATATTTTCTTTAATGCTAAGTAAGTTCGTAATTCTTTAACTTGAACTATTTAA
ATATTTACTTGTGAATTTTGATATATATATATATGATACTTGTATACATTTATTAGCTATTTGGA
GATATGATAAAATGTATATTTAATCCAATGAATGGTTGATAAAATGAATAAATGAACAATTAGCC
TTAAACTAATAGTATAGAAATTTTATATATGGAGATGTATTGCCGAACTGATGAGATTGAAGTTG
AATAATGGTTAATGTATGCAGTTAAATAAAATCTTGTGTTTACATACTAGGTAAGTTCATAGTCT
TGGAACTCGAACGTTATTTACTTAACTTAATTAGTTAATTGTTAATTATTATTTAACTATGTTTT
TAATTGGGTTTGATTAAGCTCTATTGAACGGATATTGATAAAATCATATATAGATAAAACGTGGC
ATTATGGAATAAATTAATGGATGATTAATAGATAACTGAAATGAATGTGATATTGAGTTATGAAA
TGTGATATTGGGTTATGAAATGCGATTTTATGGACTAGCGTTAGGCACAACTTCTGTCAGTTTAT
CTGACTAGTGCTGGGCACAACCATCGTTGGTTATCTGACTAGTATTGGGTGCAACTTCTGTCAAT
TTATCTGACTAGTGCTGGGCACAACCATCGTCGGTTATCCGAGTAGCACTGGGCACAACTTCTAT
CAGTTTATCTGACTAGTGTTAGGCACAACCATCGTCAGTTATCTCACTACCGCTGGGCGCAACTT
CTGTTAGTTTATCTGACTAGTGCTAAGCACAACCATCGTCAATTATCT
Found at i:54163863 original size:20 final size:20
Alignment explanation
Indices: 54163838--54163881 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
54163828 AACTGAAATG
54163838 AATGTGATATTAAGTTATGA
1 AATGTGATATTAAGTTATGA
**
54163858 AATGTGATATTGGGTTATGA
1 AATGTGATATTAAGTTATGA
54163878 AATG
1 AATG
54163882 CGATTTTATG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.25, T:0.39
Consensus pattern (20 bp):
AATGTGATATTAAGTTATGA
Found at i:54163931 original size:35 final size:35
Alignment explanation
Indices: 54163892--54164190 Score: 166
Period size: 35 Copynumber: 8.5 Consensus size: 35
54163882 CGATTTTATG
*
54163892 GACTAGCGTTAGGCACAACTTCTGTCAGTTTATCT
1 GACTAGCGTTGGGCACAACTTCTGTCAGTTTATCT
* * * * *
54163927 GACTAGTGCTGGGCACAACCATC-GT-TGGTTATCT
1 GACTAGCGTTGGGCACAA-CTTCTGTCAGTTTATCT
* *** *
54163961 GACTAGTGTTGGGTGTAACTTCTGTCAATTTATCT
1 GACTAGCGTTGGGCACAACTTCTGTCAGTTTATCT
* * *
54163996 GACTAGC--TAGGCACAACCAT-TGTC-GGTTATCT
1 GACTAGCGTTGGGCACAA-CTTCTGTCAGTTTATCT
* ** *** * *
54164028 GAGTAGCACTGGGGTTAACTTCTATCAGTCTATCT
1 GACTAGCGTTGGGCACAACTTCTGTCAGTTTATCT
* * * *
54164063 GACTAGTGTTGGGCACAACCATC-GTCA-ATTATCC
1 GACTAGCGTTGGGCACAA-CTTCTGTCAGTTTATCT
* *
54164097 GACTAGCGTTGGGCACAACTTCTGTTAGTTTATTT
1 GACTAGCGTTGGGCACAACTTCTGTCAGTTTATCT
* * *
54164132 GACCAGTGTTGGGCAC-ACTTTTTATATCTGTCAATTTATCT
1 GACTAGCGTTGGGCACAAC------T-TCTGTCAGTTTATCT
54164173 GACTAGCGTTGGGCACAA
1 GACTAGCGTTGGGCACAA
54164191 AGTTAGATAC
Statistics
Matches: 189, Mismatches: 56, Indels: 31
0.68 0.20 0.11
Matches are distributed among these distances:
32 12 0.06
33 17 0.09
34 59 0.31
35 67 0.35
36 6 0.03
40 1 0.01
41 26 0.14
42 1 0.01
ACGTcount: A:0.23, C:0.21, G:0.22, T:0.34
Consensus pattern (35 bp):
GACTAGCGTTGGGCACAACTTCTGTCAGTTTATCT
Found at i:54164047 original size:67 final size:67
Alignment explanation
Indices: 54163908--54164102 Score: 203
Period size: 67 Copynumber: 2.9 Consensus size: 67
54163898 CGTTAGGCAC
* * ** *
54163908 AACTTCTGTCAGTTTATCTGACTAGTGCTGGGCACAACCATCGTTGGTTATCTGACTAGTGTTGG
1 AACTTCTGTCAGTTTATCTGACTA--GCTAGGCACAACCATCGTCGGTTATCTGACTAGACTGGG
54163973 GTGT
64 GTGT
* * *
54163977 AACTTCTGTCAATTTATCTGACTAGCTAGGCACAACCATTGTCGGTTATCTGAGTAGCACTGGGG
1 AACTTCTGTCAGTTTATCTGACTAGCTAGGCACAACCATCGTCGGTTATCTGACTAG-ACTGGGG
54164042 T-T
65 TGT
* * * * ** *
54164044 AACTTCTATCAGTCTATCTGACTAGTGTTGGGCACAACCATCGTCAATTATCCGACTAG
1 AACTTCTGTCAGTTTATCTGACTA--GCTAGGCACAACCATCGTCGGTTATCTGACTAG
54164103 CGTTGGGCAC
Statistics
Matches: 105, Mismatches: 18, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
67 51 0.49
68 5 0.05
69 49 0.47
ACGTcount: A:0.23, C:0.22, G:0.22, T:0.33
Consensus pattern (67 bp):
AACTTCTGTCAGTTTATCTGACTAGCTAGGCACAACCATCGTCGGTTATCTGACTAGACTGGGGT
GT
Found at i:54164117 original size:69 final size:69
Alignment explanation
Indices: 54163892--54164148 Score: 275
Period size: 69 Copynumber: 3.8 Consensus size: 69
54163882 CGATTTTATG
* *
54163892 GACTAGCGTTAGGCACAACTTCTGTCAGTTTATCTGACTAGTGCTGGGCACAACCATCGTTGGTT
1 GACTAGCGTTGGGCACAACTTCTGTCAGTTTATCTGACTAGTGCTGGGCACAACCATCGTCGGTT
54163957 ATCT
66 ATCT
* *** * * *
54163961 GACTAGTGTTGGGTGTAACTTCTGTCAATTTATCTGACTA--GCTAGGCACAACCATTGTCGGTT
1 GACTAGCGTTGGGCACAACTTCTGTCAGTTTATCTGACTAGTGCTGGGCACAACCATCGTCGGTT
54164024 ATCT
66 ATCT
* ** *** * * * **
54164028 GAGTAGCACTGGGGTTAACTTCTATCAGTCTATCTGACTAGTGTTGGGCACAACCATCGTCAATT
1 GACTAGCGTTGGGCACAACTTCTGTCAGTTTATCTGACTAGTGCTGGGCACAACCATCGTCGGTT
*
54164093 ATCC
66 ATCT
* * * *
54164097 GACTAGCGTTGGGCACAACTTCTGTTAGTTTATTTGACCAGTGTTGGGCACA
1 GACTAGCGTTGGGCACAACTTCTGTCAGTTTATCTGACTAGTGCTGGGCACA
54164149 CTTTTTATAT
Statistics
Matches: 151, Mismatches: 35, Indels: 4
0.79 0.18 0.02
Matches are distributed among these distances:
67 55 0.36
69 96 0.64
ACGTcount: A:0.23, C:0.21, G:0.23, T:0.33
Consensus pattern (69 bp):
GACTAGCGTTGGGCACAACTTCTGTCAGTTTATCTGACTAGTGCTGGGCACAACCATCGTCGGTT
ATCT
Found at i:54165232 original size:23 final size:23
Alignment explanation
Indices: 54165206--54165249 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
54165196 ATTTTTCCCA
*
54165206 ACTGTAAAAAAT-GATTTGTAATT
1 ACTGGAAAAAATAG-TTTGTAATT
*
54165229 ACTGGAAATAATAGTTTGTAA
1 ACTGGAAAAAATAGTTTGTAA
54165250 CTGTTGGAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
23 17 0.94
24 1 0.06
ACGTcount: A:0.43, C:0.05, G:0.16, T:0.36
Consensus pattern (23 bp):
ACTGGAAAAAATAGTTTGTAATT
Found at i:54166944 original size:18 final size:19
Alignment explanation
Indices: 54166923--54166966 Score: 65
Period size: 18 Copynumber: 2.4 Consensus size: 19
54166913 TACCTAAATA
54166923 CATTTTATTTTA-TTATAT
1 CATTTTATTTTATTTATAT
54166941 CATTTTA-TTTATTTATAT
1 CATTTTATTTTATTTATAT
*
54166959 CCTTTTAT
1 CATTTTAT
54166967 ATAATTTTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 4 0.17
18 19 0.83
ACGTcount: A:0.25, C:0.09, G:0.00, T:0.66
Consensus pattern (19 bp):
CATTTTATTTTATTTATAT
Found at i:54172692 original size:25 final size:23
Alignment explanation
Indices: 54172650--54172717 Score: 82
Period size: 25 Copynumber: 2.9 Consensus size: 23
54172640 CGGCCCGAAT
*
54172650 TATATATTAAATATATATTTTCTA
1 TATATATCAAATATATATTTT-TA
* *
54172674 TTTTTAATCAAATATATATTTTTA
1 TATAT-ATCAAATATATATTTTTA
*
54172698 TATATATTAAATATATATTT
1 TATATATCAAATATATATTT
54172718 AATATGGGCA
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
23 14 0.38
24 8 0.22
25 15 0.41
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (23 bp):
TATATATCAAATATATATTTTTA
Found at i:54172707 original size:27 final size:25
Alignment explanation
Indices: 54172658--54172717 Score: 79
Period size: 23 Copynumber: 2.5 Consensus size: 25
54172648 ATTATATATT
54172658 AAATATATATTTTCTATTTTTAATC
1 AAATATATATTTTCTATTTTTAATC
* * *
54172683 AAATATATATTTT-TATATAT-ATT
1 AAATATATATTTTCTATTTTTAATC
54172706 AAATATATATTT
1 AAATATATATTT
54172718 AATATGGGCA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
23 14 0.44
24 5 0.16
25 13 0.41
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (25 bp):
AAATATATATTTTCTATTTTTAATC
Found at i:54178006 original size:19 final size:20
Alignment explanation
Indices: 54177968--54178003 Score: 58
Period size: 18 Copynumber: 1.9 Consensus size: 20
54177958 TAGTTTACAG
54177968 ATTTATAAAGAGAAATAATC
1 ATTTATAAAGAGAAATAATC
54177988 ATTT-TAAAG-GAAATAA
1 ATTTATAAAGAGAAATAA
54178004 ATCCTAATTC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.44
19 5 0.31
20 4 0.25
ACGTcount: A:0.56, C:0.03, G:0.11, T:0.31
Consensus pattern (20 bp):
ATTTATAAAGAGAAATAATC
Done.