Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A05
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: 100714657
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 3970000 characters in sequence are not A, C, G, or T
File 124 of 318
Found at i:38715014 original size:147 final size:147
Alignment explanation
Indices: 38714747--38715041 Score: 590
Period size: 147 Copynumber: 2.0 Consensus size: 147
38714737 ATGAGACACA
38714747 AGGTGTCAACTTATTGCTTCGAATTATCCGATGAGGTACTGGGTACCAAACTGGTGTGTTTTGGT
1 AGGTGTCAACTTATTGCTTCGAATTATCCGATGAGGTACTGGGTACCAAACTGGTGTGTTTTGGT
38714812 TGAATCCGTGTATCCGTCCAAATCTGAGTCGTGTTAATAAGGGTAATTAAAAGAAGTGATATTAT
66 TGAATCCGTGTATCCGTCCAAATCTGAGTCGTGTTAATAAGGGTAATTAAAAGAAGTGATATTAT
38714877 GAAAAGTATATGAAAAT
131 GAAAAGTATATGAAAAT
38714894 AGGTGTCAACTTATTGCTTCGAATTATCCGATGAGGTACTGGGTACCAAACTGGTGTGTTTTGGT
1 AGGTGTCAACTTATTGCTTCGAATTATCCGATGAGGTACTGGGTACCAAACTGGTGTGTTTTGGT
38714959 TGAATCCGTGTATCCGTCCAAATCTGAGTCGTGTTAATAAGGGTAATTAAAAGAAGTGATATTAT
66 TGAATCCGTGTATCCGTCCAAATCTGAGTCGTGTTAATAAGGGTAATTAAAAGAAGTGATATTAT
38715024 GAAAAGTATATGAAAAT
131 GAAAAGTATATGAAAAT
38715041 A
1 A
38715042 CTGAATGTGA
Statistics
Matches: 148, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
147 148 1.00
ACGTcount: A:0.32, C:0.12, G:0.24, T:0.33
Consensus pattern (147 bp):
AGGTGTCAACTTATTGCTTCGAATTATCCGATGAGGTACTGGGTACCAAACTGGTGTGTTTTGGT
TGAATCCGTGTATCCGTCCAAATCTGAGTCGTGTTAATAAGGGTAATTAAAAGAAGTGATATTAT
GAAAAGTATATGAAAAT
Found at i:38723583 original size:29 final size:27
Alignment explanation
Indices: 38723531--38723599 Score: 68
Period size: 28 Copynumber: 2.4 Consensus size: 27
38723521 TTTAAACACA
* * *
38723531 TTTTTAATTTTTATTTCATGTTAT-TT
1 TTTTTAATTTTTAATTAATATTATATT
38723557 TAATTTTAATTTTTAATTAATAATTATATT
1 T--TTTTAATTTTTAATTAAT-ATTATATT
38723587 TTTTTCAATTTTT
1 TTTTT-AATTTTT
38723600 TATTTTCAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
26 1 0.03
28 20 0.57
29 11 0.31
30 3 0.09
ACGTcount: A:0.28, C:0.03, G:0.01, T:0.68
Consensus pattern (27 bp):
TTTTTAATTTTTAATTAATATTATATT
Found at i:38724188 original size:16 final size:16
Alignment explanation
Indices: 38724179--38724217 Score: 55
Period size: 15 Copynumber: 2.5 Consensus size: 16
38724169 TATTATATTG
38724179 TTATTATATTATTATA
1 TTATTATATTATTATA
38724195 TTATTATA-TATTATCA
1 TTATTATATTATTAT-A
38724211 -TATTATA
1 TTATTATA
38724218 ATTAAAGTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 13 0.59
16 9 0.41
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (16 bp):
TTATTATATTATTATA
Found at i:38724190 original size:8 final size:8
Alignment explanation
Indices: 38724179--38724217 Score: 55
Period size: 8 Copynumber: 5.0 Consensus size: 8
38724169 TATTATATTG
38724179 TTATTATA
1 TTATTATA
38724187 TTATTATA
1 TTATTATA
38724195 TTATTATA
1 TTATTATA
38724203 -TATTATCA
1 TTATTAT-A
38724211 -TATTATA
1 TTATTATA
38724218 ATTAAAGTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
7 7 0.23
8 23 0.77
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (8 bp):
TTATTATA
Found at i:38726713 original size:18 final size:18
Alignment explanation
Indices: 38726692--38726746 Score: 64
Period size: 15 Copynumber: 3.3 Consensus size: 18
38726682 ATGTAAAATA
38726692 TTTCAAATATCATTGTTT
1 TTTCAAATATCATTGTTT
**
38726710 TTTCATCTA-CA-T-TTT
1 TTTCAAATATCATTGTTT
38726725 TTT-AAATATCATTGTTT
1 TTTCAAATATCATTGTTT
38726742 TTTCA
1 TTTCA
38726747 TCTACATTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 8
0.71 0.10 0.20
Matches are distributed among these distances:
14 3 0.10
15 8 0.28
16 2 0.07
17 8 0.28
18 8 0.28
ACGTcount: A:0.25, C:0.13, G:0.04, T:0.58
Consensus pattern (18 bp):
TTTCAAATATCATTGTTT
Found at i:38726727 original size:17 final size:17
Alignment explanation
Indices: 38726702--38726754 Score: 65
Period size: 16 Copynumber: 3.2 Consensus size: 17
38726692 TTTCAAATAT
38726702 CATTGTTTTTTCATCTA
1 CATTGTTTTTTCATCTA
** *
38726719 CATT-TTTTTAAATAT-
1 CATTGTTTTTTCATCTA
38726734 CATTGTTTTTTCATCTA
1 CATTGTTTTTTCATCTA
38726751 CATT
1 CATT
38726755 TACATTGTGG
Statistics
Matches: 28, Mismatches: 6, Indels: 4
0.74 0.16 0.11
Matches are distributed among these distances:
15 4 0.14
16 16 0.57
17 8 0.29
ACGTcount: A:0.23, C:0.15, G:0.04, T:0.58
Consensus pattern (17 bp):
CATTGTTTTTTCATCTA
Found at i:38727041 original size:19 final size:18
Alignment explanation
Indices: 38726990--38727041 Score: 54
Period size: 17 Copynumber: 2.9 Consensus size: 18
38726980 AATAAATGAG
38726990 TTATTAATTAAAAATATT
1 TTATTAATTAAAAATATT
* *
38727008 TTTTTGAA--AACAATATAT
1 TTATT-AATTAAAAATAT-T
38727026 TTATTAATTAAAAATA
1 TTATTAATTAAAAATA
38727042 AAAAAGCTTA
Statistics
Matches: 26, Mismatches: 4, Indels: 7
0.70 0.11 0.19
Matches are distributed among these distances:
17 9 0.35
18 9 0.35
19 8 0.31
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (18 bp):
TTATTAATTAAAAATATT
Found at i:38730386 original size:61 final size:62
Alignment explanation
Indices: 38730226--38730404 Score: 225
Period size: 62 Copynumber: 2.9 Consensus size: 62
38730216 TACGAACGGC
* * * * *
38730226 CGTGTAACTTACTGTTCATGGTATAAAACCACATGGCCAGGGACACGGGTGTGTGCCCAGGT
1 CGTGTAACTCACTGTTCATAGTATAAAACCACACGACCAGGGACACGGGCGTGTGCCCAGGT
* * * ** *
38730288 CGTGTAACTCACTTTTTATAGTGTAAAACCATGCGACCAGGGACATGGGCGTGTGCCCAGG-
1 CGTGTAACTCACTGTTCATAGTATAAAACCACACGACCAGGGACACGGGCGTGTGCCCAGGT
* * *
38730349 CGTGTAACTCACTGTTCATTGTATAAAACCACACGACCAGGGACACGAGCATGTGC
1 CGTGTAACTCACTGTTCATAGTATAAAACCACACGACCAGGGACACGGGCGTGTGC
38730405 ATCACTGTTG
Statistics
Matches: 97, Mismatches: 20, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
61 47 0.48
62 50 0.52
ACGTcount: A:0.26, C:0.24, G:0.26, T:0.23
Consensus pattern (62 bp):
CGTGTAACTCACTGTTCATAGTATAAAACCACACGACCAGGGACACGGGCGTGTGCCCAGGT
Found at i:38738133 original size:30 final size:30
Alignment explanation
Indices: 38738077--38738184 Score: 117
Period size: 30 Copynumber: 3.6 Consensus size: 30
38738067 TGGCCATGTC
** * **
38738077 TATAATGCTGGTCAATCTGATGGTTAAGTT
1 TATAATGCTGGTCAAAATGCTGGTTAAAAT
*
38738107 TATAATGCTGGTCAAAATGCTAGTTAAAAT
1 TATAATGCTGGTCAAAATGCTGGTTAAAAT
* * *
38738137 TATAATCCTGGTTAAAATGCTGGTCAAAAT
1 TATAATGCTGGTCAAAATGCTGGTTAAAAT
* *
38738167 TATCATACTGGTCAAAAT
1 TATAATGCTGGTCAAAAT
38738185 TGGTCTCTGC
Statistics
Matches: 65, Mismatches: 13, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 65 1.00
ACGTcount: A:0.35, C:0.12, G:0.18, T:0.35
Consensus pattern (30 bp):
TATAATGCTGGTCAAAATGCTGGTTAAAAT
Found at i:38742937 original size:26 final size:27
Alignment explanation
Indices: 38742900--38742969 Score: 63
Period size: 26 Copynumber: 2.5 Consensus size: 27
38742890 ATAAATATTT
38742900 AATTATCT-ATATTTAATCA-TATAATA
1 AATTAT-TAATATTTAATCATTATAATA
* *
38742926 AATTATTAATATAGTTTATCATTTTAATA
1 AATTATTAATAT--TTAATCATTATAATA
*
38742955 AATTTCTTAATATTT
1 AA-TTATTAATATTT
38742970 TAATTTTATT
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
25 1 0.03
26 10 0.28
28 8 0.22
29 8 0.22
30 9 0.25
ACGTcount: A:0.41, C:0.06, G:0.01, T:0.51
Consensus pattern (27 bp):
AATTATTAATATTTAATCATTATAATA
Found at i:38742938 original size:28 final size:30
Alignment explanation
Indices: 38742907--38742973 Score: 79
Period size: 29 Copynumber: 2.3 Consensus size: 30
38742897 TTTAATTATC
38742907 TATATTTAATCA-TATAATAAA-TTATTAA
1 TATATTTAATCATTATAATAAATTTATTAA
* *
38742935 TATAGTTT-ATCATTTTAATAAATTTCTTAA
1 TATA-TTTAATCATTATAATAAATTTATTAA
38742965 TAT-TTTAAT
1 TATATTTAAT
38742974 TTTATTTTAA
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
28 11 0.33
29 13 0.39
30 9 0.27
ACGTcount: A:0.42, C:0.04, G:0.01, T:0.52
Consensus pattern (30 bp):
TATATTTAATCATTATAATAAATTTATTAA
Found at i:38748767 original size:34 final size:34
Alignment explanation
Indices: 38748727--38748837 Score: 134
Period size: 34 Copynumber: 3.3 Consensus size: 34
38748717 GAAGTACATA
*
38748727 AATATATATGTATGGCTTGGCATAATCGAAGATG
1 AATATATATGTATGGCTTGGTATAATCGAAGATG
* * *
38748761 ATTATATATGTATAGCTTGGTATAATC-AAAAGTG
1 AATATATATGTATGGCTTGGTATAATCGAAGA-TG
* * * *
38748795 AATATATATGTATGGTTTGATATAACCGAAGGTG
1 AATATATATGTATGGCTTGGTATAATCGAAGATG
38748829 AATATATAT
1 AATATATAT
38748838 ATACATTTAT
Statistics
Matches: 64, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
33 3 0.05
34 59 0.92
35 2 0.03
ACGTcount: A:0.38, C:0.06, G:0.20, T:0.36
Consensus pattern (34 bp):
AATATATATGTATGGCTTGGTATAATCGAAGATG
Found at i:38749037 original size:59 final size:61
Alignment explanation
Indices: 38748910--38749047 Score: 167
Period size: 59 Copynumber: 2.3 Consensus size: 61
38748900 TAAGCTTGAG
* * *
38748910 ATGAGCACTAAGTGTGCGAAATGAAATTGGTACTGAGTACTAAGTGTACGAAATTGGTCAT
1 ATGAGCACTAAGTGTGCGAAATGAAATTGATACCGAGTACTAAGTGTACGAAATCGGTCAT
* * * * *
38748971 TTG-GCACTAAGGGTGC-AAATTG-AATTTATACCGAGTACTAAGTGTACGAGATCGGTTA-
1 ATGAGCACTAAGTGTGCGAAA-TGAAATTGATACCGAGTACTAAGTGTACGAAATCGGTCAT
38749029 ATGAGCACTAAGTGTGCGA
1 ATGAGCACTAAGTGTGCGA
38749048 GTTTATCTTT
Statistics
Matches: 64, Mismatches: 10, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
58 2 0.03
59 45 0.70
60 15 0.23
61 2 0.03
ACGTcount: A:0.33, C:0.13, G:0.27, T:0.28
Consensus pattern (61 bp):
ATGAGCACTAAGTGTGCGAAATGAAATTGATACCGAGTACTAAGTGTACGAAATCGGTCAT
Found at i:38763271 original size:25 final size:25
Alignment explanation
Indices: 38763243--38763291 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
38763233 ATAATTAAAC
* * *
38763243 CCTAGGGGTATAATGGTCATTTTTA
1 CCTAGGGGCAAAATAGTCATTTTTA
38763268 CCTAGGGGCAAAATAGTCATTTTT
1 CCTAGGGGCAAAATAGTCATTTTT
38763292 CATATTATAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.27, C:0.14, G:0.22, T:0.37
Consensus pattern (25 bp):
CCTAGGGGCAAAATAGTCATTTTTA
Found at i:38765743 original size:19 final size:18
Alignment explanation
Indices: 38765715--38765750 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
38765705 TATATGAAAT
*
38765715 AAAAGTAATAAAAATAAAG
1 AAAAGGAAT-AAAATAAAG
38765734 AAAAGGAATAAAATAAA
1 AAAAGGAATAAAATAAA
38765751 ACCACTTGCT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.75, C:0.00, G:0.11, T:0.14
Consensus pattern (18 bp):
AAAAGGAATAAAATAAAG
Found at i:38766502 original size:34 final size:34
Alignment explanation
Indices: 38766464--38766571 Score: 144
Period size: 34 Copynumber: 3.2 Consensus size: 34
38766454 GTACATAAAA
* * *
38766464 ATATATGTATAGCTTGGCATAATCGAAGGTGATT
1 ATATATGTATAGTTTGGTATAATCGAAGGTGAAT
* *
38766498 ATATATGTATAGTTTGGTATAATCAAAAGTGAAT
1 ATATATGTATAGTTTGGTATAATCGAAGGTGAAT
* * *
38766532 ATATATGTATGGTTTGATATAACCGAAGGTGAAT
1 ATATATGTATAGTTTGGTATAATCGAAGGTGAAT
38766566 ATATAT
1 ATATAT
38766572 ATACATTTAT
Statistics
Matches: 64, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
34 64 1.00
ACGTcount: A:0.37, C:0.06, G:0.20, T:0.37
Consensus pattern (34 bp):
ATATATGTATAGTTTGGTATAATCGAAGGTGAAT
Found at i:38770289 original size:18 final size:18
Alignment explanation
Indices: 38770266--38770300 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
38770256 ATGCGAATAT
*
38770266 ATAAAAACAATAAATAAC
1 ATAAAAACAACAAATAAC
*
38770284 ATAAAAATAACAAATAA
1 ATAAAAACAACAAATAA
38770301 TTTATGAGAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.74, C:0.09, G:0.00, T:0.17
Consensus pattern (18 bp):
ATAAAAACAACAAATAAC
Found at i:38770701 original size:12 final size:12
Alignment explanation
Indices: 38770686--38770744 Score: 58
Period size: 10 Copynumber: 5.4 Consensus size: 12
38770676 TAATATAAGG
38770686 AATAATATATAT
1 AATAATATATAT
38770698 AATAA-A-ATAT
1 AATAATATATAT
*
38770708 AAT-ATGTA-AT
1 AATAATATATAT
38770718 AA-AATATATA-
1 AATAATATATAT
*
38770728 AATAAAATATAT
1 AATAATATATAT
38770740 AATAA
1 AATAA
38770745 AATACAAATA
Statistics
Matches: 38, Mismatches: 3, Indels: 12
0.72 0.06 0.23
Matches are distributed among these distances:
9 1 0.03
10 17 0.45
11 10 0.26
12 10 0.26
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (12 bp):
AATAATATATAT
Found at i:38770708 original size:42 final size:42
Alignment explanation
Indices: 38770637--38770748 Score: 115
Period size: 42 Copynumber: 2.7 Consensus size: 42
38770627 ATGTACTAAT
* **
38770637 AAATA-ATAAATAATAGA-ATAATATGATATAAAATG-AAGA
1 AAATATATAAATAATATATATAATAAAATATAAAATGTAAGA
* * *
38770676 TAATATA-AGGAATAATATATATAATAAAATATAATATGTAATA
1 AAATATATA--AATAATATATATAATAAAATATAAAATGTAAGA
*
38770719 AAATATATAAATAAAATATATAATAAAATA
1 AAATATATAAATAATATATATAATAAAATA
38770749 CAAATAACCT
Statistics
Matches: 59, Mismatches: 8, Indels: 9
0.78 0.11 0.12
Matches are distributed among these distances:
39 5 0.08
40 1 0.02
41 8 0.14
42 35 0.59
43 9 0.15
44 1 0.02
ACGTcount: A:0.63, C:0.00, G:0.06, T:0.30
Consensus pattern (42 bp):
AAATATATAAATAATATATATAATAAAATATAAAATGTAAGA
Found at i:38770745 original size:12 final size:12
Alignment explanation
Indices: 38770703--38770748 Score: 65
Period size: 12 Copynumber: 3.8 Consensus size: 12
38770693 TATATAATAA
* *
38770703 AATATAATATGT
1 AATAAAATATAT
38770715 AATAAAATATAT
1 AATAAAATATAT
38770727 AAATAAAATATAT
1 -AATAAAATATAT
38770740 AATAAAATA
1 AATAAAATA
38770749 CAAATAACCT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
12 19 0.61
13 12 0.39
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (12 bp):
AATAAAATATAT
Found at i:38770771 original size:42 final size:42
Alignment explanation
Indices: 38770686--38770786 Score: 118
Period size: 42 Copynumber: 2.4 Consensus size: 42
38770676 TAATATAAGG
* * **
38770686 AATAATATATATAATAAAATATAATATGTAATAAAATATATA
1 AATAAAATATATAATAAAATAAAATACCTAATAAAATATATA
38770728 AATAAAATATATAATAAAATACAAATAACCTAAT-AAATA-ATA
1 AATAAAATATATAATAAAATA-AAAT-ACCTAATAAAATATATA
38770770 AA-AATAATATATAATAA
1 AATAA-AATATATAATAA
38770787 TTTTTACATG
Statistics
Matches: 52, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
41 2 0.04
42 37 0.71
43 8 0.15
44 5 0.10
ACGTcount: A:0.65, C:0.03, G:0.01, T:0.31
Consensus pattern (42 bp):
AATAAAATATATAATAAAATAAAATACCTAATAAAATATATA
Found at i:38770837 original size:18 final size:18
Alignment explanation
Indices: 38770810--38770852 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
38770800 AAATAATGTT
*
38770810 TATA-AAAATAATTAATA
1 TATATAAAATAATTAAAA
*
38770827 TATATAAAATATTTAAAA
1 TATATAAAATAATTAAAA
*
38770845 TAAATAAA
1 TATATAAA
38770853 TTGTATGTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
17 4 0.18
18 18 0.82
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (18 bp):
TATATAAAATAATTAAAA
Found at i:38775074 original size:12 final size:14
Alignment explanation
Indices: 38775052--38775096 Score: 58
Period size: 15 Copynumber: 3.3 Consensus size: 14
38775042 AAAAATAGTG
38775052 ATAAAAGGATAAT-
1 ATAAAAGGATAATA
38775065 ATAAAA-GATAATA
1 ATAAAAGGATAATA
*
38775078 ATAATAATGATAATA
1 ATAA-AAGGATAATA
38775093 ATAA
1 ATAA
38775097 TAATAATATA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
12 6 0.21
13 10 0.34
14 2 0.07
15 11 0.38
ACGTcount: A:0.64, C:0.00, G:0.09, T:0.27
Consensus pattern (14 bp):
ATAAAAGGATAATA
Found at i:38775080 original size:3 final size:3
Alignment explanation
Indices: 38775072--38775104 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
38775062 AATATAAAAG
*
38775072 ATA ATA ATA ATA ATG ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
38775105 TACCTATGAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:38775100 original size:15 final size:15
Alignment explanation
Indices: 38775059--38775100 Score: 63
Period size: 15 Copynumber: 3.0 Consensus size: 15
38775049 GTGATAAAAG
38775059 GATAAT-ATAA-AA-
1 GATAATAATAATAAT
38775071 GATAATAATAATAAT
1 GATAATAATAATAAT
38775086 GATAATAATAATAAT
1 GATAATAATAATAAT
38775101 AATATACCTA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
12 6 0.22
13 4 0.15
14 2 0.07
15 15 0.56
ACGTcount: A:0.62, C:0.00, G:0.07, T:0.31
Consensus pattern (15 bp):
GATAATAATAATAAT
Found at i:38775226 original size:11 final size:12
Alignment explanation
Indices: 38775208--38775234 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
38775198 GTAAATAAAA
38775208 TAAAAAAATAAC
1 TAAAAAAATAAC
38775220 TAAAAAAATAAC
1 TAAAAAAATAAC
38775232 TAA
1 TAA
38775235 TAATAATGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.74, C:0.07, G:0.00, T:0.19
Consensus pattern (12 bp):
TAAAAAAATAAC
Found at i:38775326 original size:47 final size:47
Alignment explanation
Indices: 38775220--38775331 Score: 108
Period size: 49 Copynumber: 2.4 Consensus size: 47
38775210 AAAAAATAAC
* *
38775220 TAAAAAAATA-ACTAATAATAATGATATATAAATTTATACATATATG
1 TAAAAAAATATACTAATAATAATGATATAAAAATGTATACATATATG
*
38775266 TACTAAAATATATACGTAATAATAA-GA-ATAAAAAGTGTATACATGATAT-
1 TA--AAAAAATATAC-TAATAATAATGATATAAAAA-TGTATACAT-ATATG
*
38775315 TAAAAAGATATA-TAATA
1 TAAAAAAATATACTAATA
38775332 TATATATTAG
Statistics
Matches: 56, Mismatches: 4, Indels: 13
0.77 0.05 0.18
Matches are distributed among these distances:
45 5 0.09
46 2 0.04
47 9 0.16
48 13 0.23
49 14 0.25
50 13 0.23
ACGTcount: A:0.56, C:0.04, G:0.07, T:0.32
Consensus pattern (47 bp):
TAAAAAAATATACTAATAATAATGATATAAAAATGTATACATATATG
Found at i:38775455 original size:11 final size:11
Alignment explanation
Indices: 38775407--38775510 Score: 50
Period size: 11 Copynumber: 8.9 Consensus size: 11
38775397 ATATATATTA
38775407 ATAAGTATATAC
1 ATAA-TATATAC
*
38775419 ATAATAATGATATT
1 ATAAT-AT-ATA-C
*
38775433 AAAATATATAC
1 ATAATATATAC
*
38775444 ATAATATGTAC
1 ATAATATATAC
*
38775455 ATGATATATATAA
1 AT-A-ATATATAC
* *
38775468 AGAAAAATATAC
1 A-TAATATATAC
*
38775480 ATAGTATATTA-
1 ATAATATA-TAC
*
38775491 A-AATATAGAC
1 ATAATATATAC
38775501 ATAATATATA
1 ATAATATATA
38775511 TAAAAAAAAT
Statistics
Matches: 67, Mismatches: 16, Indels: 19
0.66 0.16 0.19
Matches are distributed among these distances:
9 1 0.01
10 6 0.09
11 24 0.36
12 19 0.28
13 13 0.19
14 4 0.06
ACGTcount: A:0.55, C:0.05, G:0.07, T:0.34
Consensus pattern (11 bp):
ATAATATATAC
Found at i:38775502 original size:21 final size:21
Alignment explanation
Indices: 38775470--38775516 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
38775460 ATATATAAAG
* *
38775470 AAAAATATACATAGTATAT-T
1 AAAAATAGACATAATATATAT
38775490 AAAATATAGACATAATATATAT
1 AAAA-ATAGACATAATATATAT
38775512 AAAAA
1 AAAAA
38775517 AAATATATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
20 4 0.17
21 14 0.61
22 5 0.22
ACGTcount: A:0.62, C:0.04, G:0.04, T:0.30
Consensus pattern (21 bp):
AAAAATAGACATAATATATAT
Found at i:38775528 original size:21 final size:20
Alignment explanation
Indices: 38775458--38775529 Score: 65
Period size: 23 Copynumber: 3.4 Consensus size: 20
38775448 TATGTACATG
38775458 ATATATATAAAGAAAAATATA
1 ATATATATAAA-AAAAATATA
* *
38775479 CATAGTATATTAAAATATAGACATA
1 -ATA-TATA-TAAAA-A-AAATATA
38775504 ATATATATAAAAAAAATAT-
1 ATATATATAAAAAAAATATA
38775523 ATATATA
1 ATATATA
38775530 CATATAAGGT
Statistics
Matches: 42, Mismatches: 4, Indels: 11
0.74 0.07 0.19
Matches are distributed among these distances:
19 7 0.17
20 4 0.10
21 1 0.02
22 8 0.19
23 9 0.21
24 8 0.19
25 5 0.12
ACGTcount: A:0.61, C:0.03, G:0.04, T:0.32
Consensus pattern (20 bp):
ATATATATAAAAAAAATATA
Found at i:38775580 original size:24 final size:24
Alignment explanation
Indices: 38775553--38775632 Score: 80
Period size: 24 Copynumber: 3.5 Consensus size: 24
38775543 AAAAGAACAA
*
38775553 ATATATGTAATATAATACTAATAT
1 ATATACGTAATATAATACTAATAT
* **
38775577 ATATGCGTAATAT-GGAC-AA-AT
1 ATATACGTAATATAATACTAATAT
38775598 ATAT--GTAATATAATACTAATAT
1 ATATACGTAATATAATACTAATAT
*
38775620 ATATGCGTAATAT
1 ATATACGTAATAT
38775633 GGAGTATAAA
Statistics
Matches: 45, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
19 7 0.16
20 2 0.04
21 8 0.18
22 8 0.18
23 2 0.04
24 18 0.40
ACGTcount: A:0.46, C:0.06, G:0.10, T:0.38
Consensus pattern (24 bp):
ATATACGTAATATAATACTAATAT
Found at i:38775596 original size:43 final size:43
Alignment explanation
Indices: 38775549--38775635 Score: 174
Period size: 43 Copynumber: 2.0 Consensus size: 43
38775539 TTTAAAAAGA
38775549 ACAAATATATGTAATATAATACTAATATATATGCGTAATATGG
1 ACAAATATATGTAATATAATACTAATATATATGCGTAATATGG
38775592 ACAAATATATGTAATATAATACTAATATATATGCGTAATATGG
1 ACAAATATATGTAATATAATACTAATATATATGCGTAATATGG
38775635 A
1 A
38775636 GTATAAAGTA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.47, C:0.07, G:0.11, T:0.34
Consensus pattern (43 bp):
ACAAATATATGTAATATAATACTAATATATATGCGTAATATGG
Found at i:38775605 original size:19 final size:20
Alignment explanation
Indices: 38775549--38775621 Score: 67
Period size: 20 Copynumber: 3.5 Consensus size: 20
38775539 TTTAAAAAGA
*
38775549 ACAAATATATGTAATATAAT
1 ACAAATATATGTAATATAAG
*
38775569 ACTAATATATATGCGTAATAT-GG
1 AC-AA-ATATAT--GTAATATAAG
*
38775592 ACAAATATATGTAATATAAT
1 ACAAATATATGTAATATAAG
*
38775612 ACTAATATAT
1 ACAAATATAT
38775622 ATGCGTAATA
Statistics
Matches: 43, Mismatches: 5, Indels: 10
0.74 0.09 0.17
Matches are distributed among these distances:
19 7 0.16
20 11 0.26
21 8 0.19
22 8 0.19
23 2 0.05
24 7 0.16
ACGTcount: A:0.49, C:0.07, G:0.08, T:0.36
Consensus pattern (20 bp):
ACAAATATATGTAATATAAG
Found at i:38778036 original size:174 final size:171
Alignment explanation
Indices: 38777816--38778247 Score: 509
Period size: 174 Copynumber: 2.5 Consensus size: 171
38777806 TTCGTCGTCT
* * * * * *
38777816 TTTGATCTGCTTCCCTACTGCTTATGGTGATGAGATCTATAAATCTTCAGCCTGTTACCCTACTG
1 TTTGATCTGTTTCCCTACTGCTTAGGGGGTTAAGATCTGTAAATCTTCAGCCTGTTACCCTACTG
* * * * * *
38777881 CTTAGGAGGTTAAGGCTTGTTACCTTTGATCTG-TTTCCCTACTGCTTAGGGGGATAAGATCTAT
66 CTTAGGAGGTTAAGGCTTGTT--CTTCGATCTGCTCT-ACTACTACTTAGGGAGATAAGATCTAC
* **
38777945 AATCTTCGGCCTGTTACCCTACTGCTTAGGGGGTTAAGGTCCATC-
128 AA--TTCGACCTGTTACCCTACTGCTTAGGGGGTTAAGACCCATCG
*
38777990 TTTGATCTGTTTCCCTACTGCTTAGGGGGTTAAGATCTGGAAATCTTCAGCCTGTTACCCTACTG
1 TTTGATCTGTTTCCCTACTGCTTAGGGGGTTAAGATCTGTAAATCTTCAGCCTGTTACCCTACTG
* *
38778055 CTTAGG-GGTTTGAGGCCCTTCG-TCTTCGATCTGCTCTACTACTACTTAGGGAGATAAGATCTG
66 CTTAGGAGG-TTAAGG--CTT-GTTCTTCGATCTGCTCTACTACTACTTAGGGAGATAAGATCTA
* * *
38778118 CAATTCGATCTGTTACCCTACTGCTTAGGGGTTTAAGACCCTTCG
127 CAATTCGACCTGTTACCCTACTGCTTAGGGGGTTAAGACCCATCG
38778163 TCTTCGATCTGTTTCCCTACTGCTTAGGGGGTTAAGATCTGTAAA--TTCAGCCTGTTACCCTAC
1 T-TT-GATCTGTTTCCCTACTGCTTAGGGGGTTAAGATCTGTAAATCTTCAGCCTGTTACCCTAC
*
38778226 TGCTTATGGA-GATAAGGCTTGT
64 TGCTTA-GGAGGTTAAGGCTTGT
38778248 GAATTCACCG
Statistics
Matches: 223, Mismatches: 24, Indels: 25
0.82 0.09 0.09
Matches are distributed among these distances:
170 1 0.00
171 3 0.01
172 35 0.16
173 31 0.14
174 107 0.48
175 41 0.18
176 4 0.02
177 1 0.00
ACGTcount: A:0.19, C:0.23, G:0.22, T:0.36
Consensus pattern (171 bp):
TTTGATCTGTTTCCCTACTGCTTAGGGGGTTAAGATCTGTAAATCTTCAGCCTGTTACCCTACTG
CTTAGGAGGTTAAGGCTTGTTCTTCGATCTGCTCTACTACTACTTAGGGAGATAAGATCTACAAT
TCGACCTGTTACCCTACTGCTTAGGGGGTTAAGACCCATCG
Found at i:38778094 original size:86 final size:86
Alignment explanation
Indices: 38777827--38778231 Score: 404
Period size: 86 Copynumber: 4.7 Consensus size: 86
38777817 TTGATCTGCT
* * * *
38777827 TCCCTACTGCTTATGGTGATGAGATCTATAAATCTTCAGCCTGTTACCCTACTGCTTAGGAGG-T
1 TCCCTACTGCTTAGGGGGATAAGATCT-GAAATCTTCAGCCTGTTACCCTACTGCTTAGG-GGTT
*
38777891 TAAGG--CTT-GTTACCTTTGATCTG
64 TAAGGCCCTTCG-T--CTTCGATCTG
* *
38777914 TTTCCCTACTGCTTAGGGGGATAAGATCT-ATAATCTTCGGCCTGTTACCCTACTGCTTAGGGGG
1 --TCCCTACTGCTTAGGGGGATAAGATCTGA-AATCTTCAGCCTGTTACCCTACTGCTTAGGGGT
* *
38777978 TTAAGGTCCATC-T-TT-GATCTG
63 TTAAGGCCCTTCGTCTTCGATCTG
*
38777999 TTTCCCTACTGCTTAGGGGGTTAAGATCTGGAAATCTTCAGCCTGTTACCCTACTGCTTAGGGGT
1 --TCCCTACTGCTTAGGGGGATAAGATCT-GAAATCTTCAGCCTGTTACCCTACTGCTTAGGGGT
*
38778064 TTGAGGCCCTTCGTCTTCGATCTG
63 TTAAGGCCCTTCGTCTTCGATCTG
* * * * *
38778088 CTCTACTACTACTTAGGGAGATAAGATCTGCAA--TTC-GATCTGTTACCCTACTGCTTAGGGGT
1 -TC-CCTACTGCTTAGGGGGATAAGATCTGAAATCTTCAG-CCTGTTACCCTACTGCTTAGGGGT
*
38778150 TTAAGACCCTTCGTCTTCGATCTG
63 TTAAGGCCCTTCGTCTTCGATCTG
*
38778174 TTTCCCTACTGCTTAGGGGGTTAAGATCTGTAAA--TTCAGCCTGTTACCCTACTGCTTA
1 --TCCCTACTGCTTAGGGGGATAAGATCTG-AAATCTTCAGCCTGTTACCCTACTGCTTA
38778232 TGGAGATAAG
Statistics
Matches: 274, Mismatches: 27, Indels: 32
0.82 0.08 0.10
Matches are distributed among these distances:
85 35 0.13
86 112 0.41
87 30 0.11
88 43 0.16
89 52 0.19
90 2 0.01
ACGTcount: A:0.20, C:0.23, G:0.22, T:0.35
Consensus pattern (86 bp):
TCCCTACTGCTTAGGGGGATAAGATCTGAAATCTTCAGCCTGTTACCCTACTGCTTAGGGGTTTA
AGGCCCTTCGTCTTCGATCTG
Found at i:38778199 original size:44 final size:43
Alignment explanation
Indices: 38777867--38778199 Score: 216
Period size: 44 Copynumber: 7.7 Consensus size: 43
38777857 AATCTTCAGC
* * * *
38777867 CTGTTACCCTACTGCTTAGGAGGTTAAG-GCTT-GTTACCTTTGAT
1 CTGTTTCCCTACTGCTTAGGGGGTTAAGACCTTCG-T--CTTCGAT
* * ** **
38777911 CTGTTTCCCTACTGCTTAGGGGGATAAGATCTATAATCTTCGGC
1 CTGTTTCCCTACTGCTTAGGGGGTTAAGACCT-TCGTCTTCGAT
* * *
38777955 CTGTTACCCTACTGCTTAGGGGGTTAAGGTCCATC-T-TT-GAT
1 CTGTTTCCCTACTGCTTAGGGGGTTAA-GACCTTCGTCTTCGAT
* * *
38777996 CTGTTTCCCTACTGCTTAGGGGGTTAAGATC-TGGAAATCTTC-AGC
1 CTGTTTCCCTACTGCTTAGGGGGTTAAGACCTTCG---TCTTCGA-T
* * * *
38778041 CTGTTACCCTACTGCTTAGGGGTTTGAGGCCCTTCGTCTTCGAT
1 CTGTTTCCCTACTGCTTAGGGGGTT-AAGACCTTCGTCTTCGAT
* * * * * * * **
38778085 CTG-CTCTACTACTACTTAGGGAGATAAGATCTGC-AATTCGAT
1 CTGTTTC-CCTACTGCTTAGGGGGTTAAGACCTTCGTCTTCGAT
* *
38778127 CTGTTACCCTACTGCTTAGGGGTTTAAGACCCTTCGTCTTCGAT
1 CTGTTTCCCTACTGCTTAGGGGGTTAAGA-CCTTCGTCTTCGAT
38778171 CTGTTTCCCTACTGCTTAGGGGGTTAAGA
1 CTGTTTCCCTACTGCTTAGGGGGTTAAGA
38778200 TCTGTAAATT
Statistics
Matches: 217, Mismatches: 54, Indels: 36
0.71 0.18 0.12
Matches are distributed among these distances:
39 1 0.00
40 2 0.01
41 27 0.12
42 28 0.13
43 12 0.06
44 112 0.52
45 28 0.13
46 5 0.02
47 2 0.01
ACGTcount: A:0.19, C:0.23, G:0.23, T:0.35
Consensus pattern (43 bp):
CTGTTTCCCTACTGCTTAGGGGGTTAAGACCTTCGTCTTCGAT
Found at i:38778254 original size:43 final size:43
Alignment explanation
Indices: 38777828--38778241 Score: 106
Period size: 44 Copynumber: 9.5 Consensus size: 43
38777818 TGATCTGCTT
* * * *
38777828 CCCTACTGCTTATGGTGATGAGATCTATAAATCTTCAGCCTGTTA
1 CCCTACTGCTTAGGGAGATAAGATCTGTAAA--TTCAGCCTGTTA
* * ** * * *
38777873 CCCTACTGCTTA-GGAGGTTAAG-GCTTGTTACCTT-TGATCTGTTT
1 CCCTACTGCTTAGGGA-GATAAGATC-TG-TAAATTCAG-CCTGTTA
* * * *
38777917 CCCTACTGCTTAGGGGGATAAGATCTATAATCTTCGGCCTGTTA
1 CCCTACTGCTTAGGGAGATAAGATCTGTAA-ATTCAGCCTGTTA
* * * ** ** * * *
38777961 CCCTACTGCTTAGGGGGTTAAGGTCCAT-CTTTGA-TCTGTTT
1 CCCTACTGCTTAGGGAGATAAGATCTGTAAATTCAGCCTGTTA
* * *
38778002 CCCTACTGCTTAGGGGGTTAAGATCTGGAAATCTTCAGCCTGTTA
1 CCCTACTGCTTAGGGAGATAAGATCTGTAAA--TTCAGCCTGTTA
* * ** * *
38778047 CCCTACTGCTTAGGG-GTTTGAGGCCCTTCGT--CTTC-GATCTGCTCTA
1 CCCTACTGCTTAGGGAG-AT-AAGATC-T-GTAAATTCAG-CCTG-T-TA
* * *
38778093 --CTACTACTTAGGGAGATAAGATCTG-CAATTC-GATCTGTTA
1 CCCTACTGCTTAGGGAGATAAGATCTGTAAATTCAG-CCTGTTA
* * * * *
38778133 CCCTACTGCTTAGGG-GTTTAAGACCCTTCGT--CTTC-GATCTGTTT
1 CCCTACTGCTTAGGGAG-ATAAGA-TC-T-GTAAATTCAG-CCTGTTA
* *
38778177 CCCTACTGCTTAGGGGGTTAAGATCTGTAAATTCAGCCTGTTA
1 CCCTACTGCTTAGGGAGATAAGATCTGTAAATTCAGCCTGTTA
*
38778220 CCCTACTGCTTATGGAGATAAG
1 CCCTACTGCTTAGGGAGATAAG
38778242 GCTTGTGAAT
Statistics
Matches: 276, Mismatches: 60, Indels: 68
0.68 0.15 0.17
Matches are distributed among these distances:
40 2 0.01
41 34 0.12
42 30 0.11
43 36 0.13
44 118 0.43
45 47 0.17
46 7 0.03
47 1 0.00
48 1 0.00
ACGTcount: A:0.20, C:0.23, G:0.22, T:0.35
Consensus pattern (43 bp):
CCCTACTGCTTAGGGAGATAAGATCTGTAAATTCAGCCTGTTA
Found at i:38778419 original size:64 final size:64
Alignment explanation
Indices: 38778318--38778441 Score: 194
Period size: 64 Copynumber: 1.9 Consensus size: 64
38778308 GTATCTATGT
*
38778318 TTATGCCAAATAATTAGGATGATATGATTGAAATGAATCAAATGCTCCTAACTAAATGTGATGC
1 TTATGCCAAATAATTAGGATGATATGATCGAAATGAATCAAATGCTCCTAACTAAATGTGATGC
* * * * *
38778382 TTATGTCAAATAATTAGGATGCTATGATCGAAATGAATCAACTGCTCCTAATTAGATGTG
1 TTATGCCAAATAATTAGGATGATATGATCGAAATGAATCAAATGCTCCTAACTAAATGTG
38778442 TTATGAATGC
Statistics
Matches: 54, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
64 54 1.00
ACGTcount: A:0.37, C:0.13, G:0.18, T:0.32
Consensus pattern (64 bp):
TTATGCCAAATAATTAGGATGATATGATCGAAATGAATCAAATGCTCCTAACTAAATGTGATGC
Found at i:38791696 original size:86 final size:86
Alignment explanation
Indices: 38791567--38791830 Score: 411
Period size: 86 Copynumber: 3.1 Consensus size: 86
38791557 AGTAAAAATT
* * * * *
38791567 GAAGATAAACCTTACCTCTCTCGGTCGTAGCAGAGCTGGTTGAAGTTATCAGATCTTGCCTTCCT
1 GAAGACAAACCTTGCCTCTCTCGTTTGTAGCAGAGCTGGTTGAAGATATCAGATCTTGCCTTCCT
38791632 GCATTGACAGCGAAGCAGATC
66 GCATTGACAGCGAAGCAGATC
* * *
38791653 GAAGACAAACCTTGCCACTCTCGTTTGTAGTAGAGCTGGTTGAAGATAGCAGATCTTGCCTTCCT
1 GAAGACAAACCTTGCCTCTCTCGTTTGTAGCAGAGCTGGTTGAAGATATCAGATCTTGCCTTCCT
*
38791718 GCACTGACAGCGAAGCAGATC
66 GCATTGACAGCGAAGCAGATC
*
38791739 GAAGACAAACCTTGCCTCTCTCGTTTGTAGCAGAGCTGGTTGAAGATATCAGATCTTGCTTTCCT
1 GAAGACAAACCTTGCCTCTCTCGTTTGTAGCAGAGCTGGTTGAAGATATCAGATCTTGCCTTCCT
* *
38791804 GTATTTGGCAGCGAAGCAGATC
66 GCA-TTGACAGCGAAGCAGATC
38791826 GAAGA
1 GAAGA
38791831 TGGCAGATTT
Statistics
Matches: 161, Mismatches: 16, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
86 140 0.87
87 21 0.13
ACGTcount: A:0.26, C:0.23, G:0.24, T:0.27
Consensus pattern (86 bp):
GAAGACAAACCTTGCCTCTCTCGTTTGTAGCAGAGCTGGTTGAAGATATCAGATCTTGCCTTCCT
GCATTGACAGCGAAGCAGATC
Found at i:38792018 original size:134 final size:134
Alignment explanation
Indices: 38791778--38792158 Score: 611
Period size: 134 Copynumber: 2.8 Consensus size: 134
38791768 GCAGAGCTGG
*
38791778 TTGAAGATAT-CAGATCTTGCTTTCCTGTATTTGGCAGCGAAGCAGATCGAAGATGGCAGATTTT
1 TTGAAGAT-TGCAGATCTTGCCTTCCTGTATTTGGCAGCGAAGCAGATCGAAGATGGCAGATTTT
*
38791842 ACCTCCCTGACTACAGAGGAGTACATTGAAGCCGATAACTCTATCTCCCTGTATTTGGCAGTGGA
65 ACCTCCCTGACTACAGTGGAGTACATTGAAGCCGATAACTCTATCTCCCTGTATTTGGCAGTGGA
38791907 ATAGA
130 ATAGA
* * *
38791912 TTGAAGATTGCAGATCTTGCCTTCTTGTATTTGGCAACGAAGCAGATCAAAGATGGCAGATTTTA
1 TTGAAGATTGCAGATCTTGCCTTCCTGTATTTGGCAGCGAAGCAGATCGAAGATGGCAGATTTTA
*
38791977 CCTCCCTGACCACAGTGGAGTACATTGAAGCCGATAACTCTATCTCCCTGTATTTGGCAGTGGAA
66 CCTCCCTGACTACAGTGGAGTACATTGAAGCCGATAACTCTATCTCCCTGTATTTGGCAGTGGAA
38792042 TAGA
131 TAGA
* * * * *
38792046 TTGAAGATTGCAGATCTTGCCTTCCTGTATTTGGCAGCAAAGCAGGTTGAAGACGGCGGATTTTA
1 TTGAAGATTGCAGATCTTGCCTTCCTGTATTTGGCAGCGAAGCAGATCGAAGATGGCAGATTTTA
* * **
38792111 CCTCCCTGATTACAGTGGAGTACATTGAAGCTGATAGTTCTATCTCCC
66 CCTCCCTGACTACAGTGGAGTACATTGAAGCCGATAACTCTATCTCCC
38792159 GGGGCAAGAA
Statistics
Matches: 227, Mismatches: 19, Indels: 2
0.92 0.08 0.01
Matches are distributed among these distances:
133 1 0.00
134 226 1.00
ACGTcount: A:0.27, C:0.21, G:0.23, T:0.30
Consensus pattern (134 bp):
TTGAAGATTGCAGATCTTGCCTTCCTGTATTTGGCAGCGAAGCAGATCGAAGATGGCAGATTTTA
CCTCCCTGACTACAGTGGAGTACATTGAAGCCGATAACTCTATCTCCCTGTATTTGGCAGTGGAA
TAGA
Found at i:38792082 original size:46 final size:46
Alignment explanation
Indices: 38791886--38792082 Score: 136
Period size: 46 Copynumber: 4.4 Consensus size: 46
38791876 ATAACTCTAT
*
38791886 CTCCCTGTATTTGGCAGTGGAATAGATTGAAGATTGCAGATCTTGC
1 CTCCCTGTATTTGGCAGTGGAATAGATTGAAGATTGCAGATCTTAC
* * ** * ** * *
38791932 CTTCTTGTATTTGGCA-ACGAAGCAGATCAAAGATGGCAGATTTTAC
1 CTCCCTGTATTTGGCAGTGGAA-TAGATTGAAGATTGCAGATCTTAC
*** * * ** * * *
38791978 CTCCCTG-A--CCACAGTGGAGTACATTGAAG-CCG-ATAACTCTAT
1 CTCCCTGTATTTGGCAGTGGAATAGATTGAAGATTGCAGATCT-TAC
*
38792020 CTCCCTGTATTTGGCAGTGGAATAGATTGAAGATTGCAGATCTTGC
1 CTCCCTGTATTTGGCAGTGGAATAGATTGAAGATTGCAGATCTTAC
*
38792066 CTTCCTGTATTTGGCAG
1 CTCCCTGTATTTGGCAG
38792083 CAAAGCAGGT
Statistics
Matches: 103, Mismatches: 40, Indels: 16
0.65 0.25 0.10
Matches are distributed among these distances:
41 3 0.03
42 10 0.10
43 9 0.09
44 2 0.02
45 20 0.19
46 55 0.53
47 4 0.04
ACGTcount: A:0.25, C:0.20, G:0.23, T:0.31
Consensus pattern (46 bp):
CTCCCTGTATTTGGCAGTGGAATAGATTGAAGATTGCAGATCTTAC
Found at i:38792222 original size:44 final size:44
Alignment explanation
Indices: 38792170--38792622 Score: 236
Period size: 44 Copynumber: 10.2 Consensus size: 44
38792160 GGGCAAGAAG
*
38792170 TAGATCGAAGAGAGCTGATCCTATCTTCCTATATTGGTAG-GAAA
1 TAGATCGAAGA-AGCAGATCCTATCTTCCTATATTGGTAGCGAAA
* * * * * * *
38792214 TGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAG
1 TAGATCGAAGAAGCAGATCCTATCTTCCTATATTGGTAGCGAAA
* * * * * * *
38792258 TAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGG-CGTGAAG
1 TAGATCGAAG-AAGCAGATCCTATCTTCCTATATTGGTAGCGAAA
*
38792302 TAGATCGAAGATAGCTGATCCTATCTTCCTATATTGGTAG-GAAA
1 TAGATCGAAGA-AGCAGATCCTATCTTCCTATATTGGTAGCGAAA
* * * * * * * * *
38792346 TGGATCGAAGATGCAGATCTTGTCTTCCCAAACTGGTGGCGAAG
1 TAGATCGAAGAAGCAGATCCTATCTTCCTATATTGGTAGCGAAA
* * * * * * * * *
38792390 TAGATCGCAGAAAACAGATCTTGTCTTCATGTATTGG-CGTGAAG
1 TAGATCGAAG-AAGCAGATCCTATCTTCCTATATTGGTAGCGAAA
* *
38792434 TAGATCGAAGATAGCAGGTCCTATCTTCCTATATTGGTAG-GAAG
1 TAGATCGAAGA-AGCAGATCCTATCTTCCTATATTGGTAGCGAAA
** * * * * * * *
38792478 GGGATCGAAGATGCAGATCTTGTCTTCCCATACTGGTGGCGAAG
1 TAGATCGAAGAAGCAGATCCTATCTTCCTATATTGGTAGCGAAA
** * * * * *
38792522 TAGATC-ACAGAAAGCAGATATTATCTTCATGTATTGG-CGTGAAG
1 TAGATCGA-AG-AAGCAGATCCTATCTTCCTATATTGGTAGCGAAA
* * ** * * *
38792566 TAGATCGAAGATTGCAGATCTTGCCTTCCTGTATTTGGCAGCGAAG
1 TAGATCGAAGA-AGCAGATCCTATCTTCCTATA-TTGGTAGCGAAA
*
38792612 CAGATCGAAGA
1 TAGATCGAAGA
38792623 TGGCAGATTT
Statistics
Matches: 315, Mismatches: 79, Indels: 28
0.75 0.19 0.07
Matches are distributed among these distances:
43 67 0.21
44 166 0.53
45 67 0.21
46 15 0.05
ACGTcount: A:0.28, C:0.17, G:0.26, T:0.28
Consensus pattern (44 bp):
TAGATCGAAGAAGCAGATCCTATCTTCCTATATTGGTAGCGAAA
Found at i:38792352 original size:88 final size:89
Alignment explanation
Indices: 38792166--38792622 Score: 381
Period size: 88 Copynumber: 5.2 Consensus size: 89
38792156 CCCGGGGCAA
* * * * * * *
38792166 GAAGTAGATCGAAGAGAGCTGATCCTATCTTCCTATATTGGTAG-GAAATGGATCGAAGATGCAG
1 GAAGTAGATCGAAGAAAGCAGATCTTATCTTCATATATTGGTCGTGAAGTAGATCGAAGATGCAG
38792230 ATCTTGTCTTCCCATATTGGTGGC
66 ATCTTGTCTTCCCATATTGGTGGC
* * *
38792254 GAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGG-CGTGAAGTAGATCGAAGATAGCT
1 GAAGTAGATCGAAGAAAGCAGATCTTATCTTCATATATTGGTCGTGAAGTAGATCGAAGAT-GCA
* * * *
38792318 GATCCTATCTTCCTATATTGGTAG-
65 GATCTTGTCTTCCCATATTGGTGGC
* * * * ** * * * * * **
38792342 GAAATGGATCGAAG-ATGCAGATCTTGTCTTCCCAAACTGGTGGCGAAGTAGATCGCAGAAAACA
1 GAAGTAGATCGAAGAAAGCAGATCTTATCTTCATATATTGGTCGTGAAGTAGATCGAAG-ATGCA
*** * *
38792406 GATCTTGTCTTCATGTATTGG-CGT
65 GATCTTGTCTTCCCATATTGGTGGC
* * * * * **
38792430 GAAGTAGATCGAAGATAGCAGGTCCTATCTTCCTATATTGGTAG-GAAGGGGATCGAAGATGCAG
1 GAAGTAGATCGAAGAAAGCAGATCTTATCTTCATATATTGGTCGTGAAGTAGATCGAAGATGCAG
*
38792494 ATCTTGTCTTCCCATACTGGTGGC
66 ATCTTGTCTTCCCATATTGGTGGC
* *
38792518 GAAGTAGATC-ACAGAAAGCAGATATTATCTTCATGTATTGG-CGTGAAGTAGATCGAAGATTGC
1 GAAGTAGATCGA-AGAAAGCAGATCTTATCTTCATATATTGGTCGTGAAGTAGATCGAAGA-TGC
* ** **
38792581 AGATCTTGCCTTCCTGTATTTGGCAGC
64 AGATCTTGTCTTCCCATA-TTGGTGGC
*
38792608 GAAGCAGATCGAAGA
1 GAAGTAGATCGAAGA
38792623 TGGCAGATTT
Statistics
Matches: 286, Mismatches: 71, Indels: 22
0.75 0.19 0.06
Matches are distributed among these distances:
87 44 0.15
88 163 0.57
89 61 0.21
90 17 0.06
91 1 0.00
ACGTcount: A:0.29, C:0.17, G:0.26, T:0.28
Consensus pattern (89 bp):
GAAGTAGATCGAAGAAAGCAGATCTTATCTTCATATATTGGTCGTGAAGTAGATCGAAGATGCAG
ATCTTGTCTTCCCATATTGGTGGC
Found at i:38792408 original size:132 final size:132
Alignment explanation
Indices: 38792166--38792577 Score: 716
Period size: 132 Copynumber: 3.1 Consensus size: 132
38792156 CCCGGGGCAA
*
38792166 GAAGTAGATCGAAGAGAGCTGATCCTATCTTCCTATATTGGTAGGAAATGGATCGAAGATGCAGA
1 GAAGTAGATCGAAGATAGCTGATCCTATCTTCCTATATTGGTAGGAAATGGATCGAAGATGCAGA
* *
38792231 TCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGC
66 TCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGCAGAAAGCAGATCTTGTCTTCATGTATTGGC
38792296 GT
131 GT
38792298 GAAGTAGATCGAAGATAGCTGATCCTATCTTCCTATATTGGTAGGAAATGGATCGAAGATGCAGA
1 GAAGTAGATCGAAGATAGCTGATCCTATCTTCCTATATTGGTAGGAAATGGATCGAAGATGCAGA
* *
38792363 TCTTGTCTTCCCAAACTGGTGGCGAAGTAGATCGCAGAAAACAGATCTTGTCTTCATGTATTGGC
66 TCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGCAGAAAGCAGATCTTGTCTTCATGTATTGGC
38792428 GT
131 GT
* * **
38792430 GAAGTAGATCGAAGATAGCAGGTCCTATCTTCCTATATTGGTAGGAAGGGGATCGAAGATGCAGA
1 GAAGTAGATCGAAGATAGCTGATCCTATCTTCCTATATTGGTAGGAAATGGATCGAAGATGCAGA
* * *
38792495 TCTTGTCTTCCCATACTGGTGGCGAAGTAGATCACAGAAAGCAGATATTATCTTCATGTATTGGC
66 TCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGCAGAAAGCAGATCTTGTCTTCATGTATTGGC
38792560 GT
131 GT
38792562 GAAGTAGATCGAAGAT
1 GAAGTAGATCGAAGAT
38792578 TGCAGATCTT
Statistics
Matches: 266, Mismatches: 14, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
132 266 1.00
ACGTcount: A:0.29, C:0.16, G:0.26, T:0.28
Consensus pattern (132 bp):
GAAGTAGATCGAAGATAGCTGATCCTATCTTCCTATATTGGTAGGAAATGGATCGAAGATGCAGA
TCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGCAGAAAGCAGATCTTGTCTTCATGTATTGGC
GT
Found at i:38801163 original size:18 final size:17
Alignment explanation
Indices: 38801142--38801179 Score: 58
Period size: 18 Copynumber: 2.2 Consensus size: 17
38801132 TAAAAAACCT
*
38801142 ATAAAAATATACAAAAAA
1 ATAAAAAAATA-AAAAAA
38801160 ATAAAAAAATAAAAAAA
1 ATAAAAAAATAAAAAAA
38801177 ATA
1 ATA
38801180 CCTTTTTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 9 0.47
18 10 0.53
ACGTcount: A:0.82, C:0.03, G:0.00, T:0.16
Consensus pattern (17 bp):
ATAAAAAAATAAAAAAA
Found at i:38801791 original size:27 final size:27
Alignment explanation
Indices: 38801758--38801820 Score: 74
Period size: 27 Copynumber: 2.4 Consensus size: 27
38801748 ATATTTTAAA
* *
38801758 TATTATTTATATTATCCTTATGACTAT
1 TATTATTTATATTATCATTATCACTAT
* * *
38801785 TATTATTAATATTCTTATTATCACTAT
1 TATTATTTATATTATCATTATCACTAT
38801812 TATT-TTTAT
1 TATTATTTAT
38801821 TCATTTTATC
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
26 4 0.13
27 26 0.87
ACGTcount: A:0.30, C:0.10, G:0.02, T:0.59
Consensus pattern (27 bp):
TATTATTTATATTATCATTATCACTAT
Found at i:38801821 original size:24 final size:26
Alignment explanation
Indices: 38801758--38801842 Score: 72
Period size: 27 Copynumber: 3.3 Consensus size: 26
38801748 ATATTTTAAA
* *
38801758 TATTATTTATATT-ATCCTTATGACTAT
1 TATTA-TTATATTCAT-TTTATCACTAT
38801785 TATTATTAATATTC-TTATTATCACTAT
1 TATTATT-ATATTCATT-TTATCACTAT
*
38801812 TATT-TT-TATTCATTTTATCAATA-
1 TATTATTATATTCATTTTATCACTAT
38801835 TATTATTA
1 TATTATTA
38801843 CTACAGTTAC
Statistics
Matches: 49, Mismatches: 3, Indels: 14
0.74 0.05 0.21
Matches are distributed among these distances:
23 4 0.08
24 15 0.31
25 2 0.04
26 4 0.08
27 24 0.49
ACGTcount: A:0.32, C:0.09, G:0.01, T:0.58
Consensus pattern (26 bp):
TATTATTATATTCATTTTATCACTAT
Found at i:38801829 original size:27 final size:27
Alignment explanation
Indices: 38801775--38801842 Score: 74
Period size: 24 Copynumber: 2.7 Consensus size: 27
38801765 TATATTATCC
*
38801775 TTATGACTATTATTATTAATATTCTTA
1 TTATCACTATTATTATTAATATTCTTA
38801802 TTATCACTATTATT-TT--TATTCATT-
1 TTATCACTATTATTATTAATATTC-TTA
*
38801826 TTATCAATA-TATTATTA
1 TTATCACTATTATTATTA
38801843 CTACAGTTAC
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
23 4 0.11
24 15 0.42
25 2 0.06
26 2 0.06
27 13 0.36
ACGTcount: A:0.32, C:0.09, G:0.01, T:0.57
Consensus pattern (27 bp):
TTATCACTATTATTATTAATATTCTTA
Found at i:38802027 original size:3 final size:3
Alignment explanation
Indices: 38802021--38802154 Score: 51
Period size: 3 Copynumber: 44.0 Consensus size: 3
38802011 TTTTTGTTTT
* * * **
38802021 TTA TTA TCA TTA TTA -TA TCA TTA TTA TTT TTCA TGTA CACA TTA TTCA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A T-TA -TTA TTA TT-A
* * * * * *
38802069 -TA TTA TTT TTA TAA TTA TTA TTA TT- GTA TTTA TTT TTA CTA CTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA
* * * *
38802113 TTA -TA TTTA TTA TTA GTA TTA ATA TTA TAA TTA CTA TTA TTA
1 TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
38802155 CACTTATATG
Statistics
Matches: 93, Mismatches: 28, Indels: 20
0.66 0.20 0.14
Matches are distributed among these distances:
2 6 0.06
3 78 0.84
4 8 0.09
5 1 0.01
ACGTcount: A:0.33, C:0.07, G:0.02, T:0.58
Consensus pattern (3 bp):
TTA
Found at i:38802093 original size:21 final size:21
Alignment explanation
Indices: 38802021--38802154 Score: 64
Period size: 21 Copynumber: 6.4 Consensus size: 21
38802011 TTTTTGTTTT
* *
38802021 TTATTATCATTATTAT-ATCA
1 TTATTATTATTATTATAATTA
* *
38802041 TTATTATTTTTCATGTACACATTA
1 TTATTATTATT-AT-TATA-ATTA
*
38802065 TTCA-TATTATTTTTATAATTA
1 TT-ATTATTATTATTATAATTA
* *
38802086 TTATTATT-GTATT-T-ATTT
1 TTATTATTATTATTATAATTA
* * *
38802104 TTACTACTATTA-TATTTATTA
1 TTATTATTATTATTA-TAATTA
* *
38802125 TTAGTATTAATATTATAATTA
1 TTATTATTATTATTATAATTA
*
38802146 CTATTATTA
1 TTATTATTA
38802155 CACTTATATG
Statistics
Matches: 83, Mismatches: 20, Indels: 21
0.67 0.16 0.17
Matches are distributed among these distances:
18 10 0.12
19 3 0.04
20 14 0.17
21 36 0.43
22 7 0.08
23 1 0.01
24 11 0.13
25 1 0.01
ACGTcount: A:0.33, C:0.07, G:0.02, T:0.58
Consensus pattern (21 bp):
TTATTATTATTATTATAATTA
Found at i:38802101 original size:15 final size:15
Alignment explanation
Indices: 38802069--38802154 Score: 59
Period size: 15 Copynumber: 5.7 Consensus size: 15
38802059 ACATTATTCA
*
38802069 TATTATTTTTATAAT
1 TATTATTATTATAAT
* *
38802084 TATTATTATTGTATT
1 TATTATTATTATAAT
* *
38802099 TATTTTTACTACT-AT
1 TATTATTATTA-TAAT
* *
38802114 TA-TATTTATTATTAG
1 TATTA-TTATTATAAT
*
38802129 TATTAATATTATAAT
1 TATTATTATTATAAT
*
38802144 TACTATTATTA
1 TATTATTATTA
38802155 CACTTATATG
Statistics
Matches: 52, Mismatches: 15, Indels: 8
0.69 0.20 0.11
Matches are distributed among these distances:
14 2 0.04
15 47 0.90
16 3 0.06
ACGTcount: A:0.34, C:0.03, G:0.02, T:0.60
Consensus pattern (15 bp):
TATTATTATTATAAT
Found at i:38802283 original size:20 final size:20
Alignment explanation
Indices: 38802258--38802303 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
38802248 ATGTATGTAT
*
38802258 ATATTTATGTAATATTATTA
1 ATATTTATGTAACATTATTA
* *
38802278 ATATTTTTTTAACATTATTA
1 ATATTTATGTAACATTATTA
*
38802298 TTATTT
1 ATATTT
38802304 CTTAGATGTA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.61
Consensus pattern (20 bp):
ATATTTATGTAACATTATTA
Found at i:38802343 original size:14 final size:14
Alignment explanation
Indices: 38802324--38802353 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
38802314 TACATCATGT
38802324 TTTTTAATACTATA
1 TTTTTAATACTATA
38802338 TTTTTAATACTATA
1 TTTTTAATACTATA
38802352 TT
1 TT
38802354 ATGTATATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.60
Consensus pattern (14 bp):
TTTTTAATACTATA
Found at i:38802443 original size:23 final size:23
Alignment explanation
Indices: 38802411--38802466 Score: 64
Period size: 23 Copynumber: 2.6 Consensus size: 23
38802401 TCATATGTAT
38802411 ATATT-TTATGTACATACTTTTA
1 ATATTATTATGTACATACTTTTA
** *
38802433 ATATTATTATGTATTTATTTTTA
1 ATATTATTATGTACATACTTTTA
38802456 ATA-TA-TATGTA
1 ATATTATTATGTA
38802467 TATATTTATG
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
21 6 0.20
22 7 0.23
23 17 0.57
ACGTcount: A:0.34, C:0.04, G:0.05, T:0.57
Consensus pattern (23 bp):
ATATTATTATGTACATACTTTTA
Found at i:38802461 original size:25 final size:24
Alignment explanation
Indices: 38802408--38802487 Score: 62
Period size: 23 Copynumber: 3.5 Consensus size: 24
38802398 ATATCATATG
** *
38802408 TATATATT-TTATGTACATACTTT
1 TATATATTATTATGTATTTATTTT
38802431 TA-ATATTATTATGTATTTATTTT
1 TATATATTATTATGTATTTATTTT
* *
38802454 TA-ATA-TA-TATGTATATATTTA
1 TATATATTATTATGTATTTATTTT
*
38802475 TGTAGTATTATTA
1 TATA-TATTATTA
38802488 ATAGTCGTTT
Statistics
Matches: 46, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
21 13 0.28
22 8 0.17
23 21 0.46
24 2 0.04
25 2 0.04
ACGTcount: A:0.34, C:0.03, G:0.06, T:0.57
Consensus pattern (24 bp):
TATATATTATTATGTATTTATTTT
Found at i:38802473 original size:21 final size:23
Alignment explanation
Indices: 38802334--38802417 Score: 53
Period size: 23 Copynumber: 3.3 Consensus size: 23
38802324 TTTTTAATAC
38802334 TATATTTTTAATACTATATTATGTA
1 TATATTTTTAATA-T-TATTATGTA
**
38802359 TATATTTTTACAT-GCATTATGTA
1 TATATTTTTA-ATATTATTATGTA
* *
38802382 CATATTTTCAATAACTATATCATATGTA
1 TATATTTTTAAT-A-T-TAT--TATGTA
38802410 TATATTTT
1 TATATTTT
38802418 ATGTACATAC
Statistics
Matches: 45, Mismatches: 7, Indels: 11
0.71 0.11 0.17
Matches are distributed among these distances:
22 2 0.04
23 16 0.36
25 10 0.22
26 4 0.09
28 13 0.29
ACGTcount: A:0.35, C:0.08, G:0.05, T:0.52
Consensus pattern (23 bp):
TATATTTTTAATATTATTATGTA
Found at i:38802559 original size:24 final size:22
Alignment explanation
Indices: 38802516--38802576 Score: 59
Period size: 24 Copynumber: 2.7 Consensus size: 22
38802506 TTCTAATATG
* * *
38802516 TATATACTATGTAAATATTTTAA
1 TATATATTATGTATACATTTT-A
*
38802539 TACTATATTATGTATACATTTTT
1 TA-TATATTATGTATACATTTTA
*
38802562 TATATATTACGTATA
1 TATATATTATGTATA
38802577 TATATATCTT
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
22 12 0.38
23 4 0.12
24 16 0.50
ACGTcount: A:0.38, C:0.07, G:0.05, T:0.51
Consensus pattern (22 bp):
TATATATTATGTATACATTTTA
Found at i:38802733 original size:25 final size:25
Alignment explanation
Indices: 38802642--38802733 Score: 94
Period size: 25 Copynumber: 3.5 Consensus size: 25
38802632 TATATTACTT
* *
38802642 TTTTTACATATTATCTTATGTATATA
1 TTTTTA-ATACTATATTATGTATATA
*
38802668 TTTTTTTAATAACTATATTATGTATGTA
1 --TTTTTAAT-ACTATATTATGTATATA
** *
38802696 TTTTTAACGCTATATTATGTACATA
1 TTTTTAATACTATATTATGTATATA
38802721 TTTTTAATACTAT
1 TTTTTAATACTAT
38802734 GTATATACCT
Statistics
Matches: 54, Mismatches: 9, Indels: 5
0.79 0.13 0.07
Matches are distributed among these distances:
25 25 0.46
26 7 0.13
27 2 0.04
28 20 0.37
ACGTcount: A:0.32, C:0.08, G:0.05, T:0.55
Consensus pattern (25 bp):
TTTTTAATACTATATTATGTATATA
Found at i:38821150 original size:86 final size:85
Alignment explanation
Indices: 38820957--38821335 Score: 356
Period size: 86 Copynumber: 4.5 Consensus size: 85
38820947 TGTTCATCAA
*
38820957 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGCTCACATGCTGAGGTATTTTCAATT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGG---ACACGCTGAGGTATTTTCAATT
*
38821022 TCTGTTTTTCAATTCCTATTCGTT
63 TCTGTTTTTCAATT-CTATGCGTT
38821046 -AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTTCAATTT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-GGACACGCTGAGGTA-TTTTCAATTT
*
38821110 CCGTTTTTCAATT-TATGC-TT
64 CTGTTTTTCAATTCTATGCGTT
* * * *
38821130 CAAAAATCAACTCATATTGCGAGAGATGAATTGGGCCTCGGGACACACTGAGGTATTTTCAATTT
1 -AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-GGACACGCTGAGGTATTTTCAATTT
38821195 CTGTTTTTC-A----A------
64 CTGTTTTTCAATTCTATGCGTT
* * * * * * *
38821206 AAAAATCAAGCTTATATTGCGAGAGGTGAGATGAACCTTGGGACACGTTGAGGTATTTTTAGTTT
1 AAAAATCAA-CTCATATTGCGAGAGGTGAGTTGAGCC-TCGGACACGCTGAGGTATTTTCAATTT
* **
38821271 CTGTTTTTCGAATTCTGT-TTTT
64 CTGTTTTTC-AATTCTATGCGTT
* *
38821293 ATCAAAAGTCAGCTCATATCGCGAGAGGTGAGTTGAGCCTCGG
1 A--AAAA-TCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGG
38821336 GTCACATGCC
Statistics
Matches: 243, Mismatches: 27, Indels: 41
0.78 0.09 0.13
Matches are distributed among these distances:
75 9 0.04
76 51 0.21
77 1 0.00
78 1 0.00
81 1 0.00
84 3 0.01
85 22 0.09
86 60 0.25
87 23 0.09
88 40 0.16
89 29 0.12
90 3 0.01
ACGTcount: A:0.27, C:0.17, G:0.22, T:0.35
Consensus pattern (85 bp):
AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGACACGCTGAGGTATTTTCAATTTCT
GTTTTTCAATTCTATGCGTT
Found at i:38821249 original size:76 final size:75
Alignment explanation
Indices: 38821131--38821279 Score: 192
Period size: 76 Copynumber: 2.0 Consensus size: 75
38821121 TTTATGCTTC
**
38821131 AAAAATCAACTCATATTGCGAGAGATGAATTGGGCCTCGGGACACACTGAGGTATTTTCAATTTC
1 AAAAATCAACTCATATTGCGAGAGATGAATTGAACCTCGGGACACACTGAGGTATTTTCAATTTC
38821196 TGTTTTTCAA
66 TGTTTTTCAA
* * * ** * *
38821206 AAAAATCAAGCTTATATTGCGAGAGGTGAGA-TGAACCTTGGGACACGTTGAGGTATTTTTAGTT
1 AAAAATCAA-CTCATATTGCGAGAGATGA-ATTGAACCTCGGGACACACTGAGGTATTTTCAATT
38821270 TCTGTTTTTC
64 TCTGTTTTTC
38821280 GAATTCTGTT
Statistics
Matches: 63, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
75 9 0.14
76 53 0.84
77 1 0.02
ACGTcount: A:0.29, C:0.15, G:0.22, T:0.34
Consensus pattern (75 bp):
AAAAATCAACTCATATTGCGAGAGATGAATTGAACCTCGGGACACACTGAGGTATTTTCAATTTC
TGTTTTTCAA
Found at i:38823035 original size:24 final size:26
Alignment explanation
Indices: 38822972--38823056 Score: 72
Period size: 27 Copynumber: 3.3 Consensus size: 26
38822962 ATATTTTAAA
* *
38822972 TATTATTTATATT-ATCCTTATGACTAT
1 TATTA-TTATATTCAT-TTTATCACTAT
38822999 TATTATTAATATTC-TTATTATCACTAT
1 TATTATT-ATATTCATT-TTATCACTAT
*
38823026 TATT-TT-TATTCATTTTATCAATA-
1 TATTATTATATTCATTTTATCACTAT
38823049 TATTATTA
1 TATTATTA
38823057 CTACAGTTAC
Statistics
Matches: 49, Mismatches: 3, Indels: 14
0.74 0.05 0.21
Matches are distributed among these distances:
23 4 0.08
24 15 0.31
25 2 0.04
26 4 0.08
27 24 0.49
ACGTcount: A:0.32, C:0.09, G:0.01, T:0.58
Consensus pattern (26 bp):
TATTATTATATTCATTTTATCACTAT
Found at i:38823043 original size:27 final size:27
Alignment explanation
Indices: 38822989--38823056 Score: 74
Period size: 24 Copynumber: 2.7 Consensus size: 27
38822979 TATATTATCC
*
38822989 TTATGACTATTATTATTAATATTCTTA
1 TTATCACTATTATTATTAATATTCTTA
38823016 TTATCACTATTATT-TT--TATTCATT-
1 TTATCACTATTATTATTAATATTC-TTA
*
38823040 TTATCAATA-TATTATTA
1 TTATCACTATTATTATTA
38823057 CTACAGTTAC
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
23 4 0.11
24 15 0.42
25 2 0.06
26 2 0.06
27 13 0.36
ACGTcount: A:0.32, C:0.09, G:0.01, T:0.57
Consensus pattern (27 bp):
TTATCACTATTATTATTAATATTCTTA
Found at i:38823303 original size:24 final size:24
Alignment explanation
Indices: 38823239--38823318 Score: 63
Period size: 24 Copynumber: 3.1 Consensus size: 24
38823229 TGTTTTTTTA
*
38823239 TTATCATTATTATATCATTATTATTT
1 TTATGATTATTAT-TCA-TATTATTT
**
38823265 TTCATGTACACATTATTCATATTATTT
1 TT-ATG-A-TTATTATTCATATTATTT
*
38823292 TTATGATTATTATT-GTATTTATTT
1 TTATGATTATTATTCATA-TTATTT
38823316 TTA
1 TTA
38823319 CTACTATTAT
Statistics
Matches: 44, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
23 2 0.05
24 15 0.34
25 1 0.02
26 5 0.11
27 12 0.27
28 4 0.09
29 5 0.11
ACGTcount: A:0.29, C:0.07, G:0.04, T:0.60
Consensus pattern (24 bp):
TTATGATTATTATTCATATTATTT
Found at i:38823337 original size:24 final size:23
Alignment explanation
Indices: 38823257--38823338 Score: 58
Period size: 24 Copynumber: 3.3 Consensus size: 23
38823247 ATTATATCAT
* *
38823257 TATTATTTTTCATGTACACATTATTCA
1 TATTATTTTT-ATG-AC-TATTATT-G
*
38823284 TATTATTTTTATGATTATTATTG
1 TATTATTTTTATGACTATTATTG
*
38823307 TATTTATTTTTACT-ACTATTATATT
1 TA-TTATTTTTA-TGACTATTAT-TG
38823332 TATTATT
1 TATTATT
38823339 AGTATTAATA
Statistics
Matches: 47, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
23 2 0.04
24 27 0.57
25 5 0.11
26 3 0.06
27 10 0.21
ACGTcount: A:0.28, C:0.07, G:0.04, T:0.61
Consensus pattern (23 bp):
TATTATTTTTATGACTATTATTG
Found at i:38823559 original size:14 final size:14
Alignment explanation
Indices: 38823540--38823569 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
38823530 TACATCATGT
38823540 TTTTTAATACTATA
1 TTTTTAATACTATA
38823554 TTTTTAATACTATA
1 TTTTTAATACTATA
38823568 TT
1 TT
38823570 ATGTATATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.60
Consensus pattern (14 bp):
TTTTTAATACTATA
Found at i:38823648 original size:64 final size:58
Alignment explanation
Indices: 38823540--38823696 Score: 136
Period size: 64 Copynumber: 2.5 Consensus size: 58
38823530 TACATCATGT
* * * *
38823540 TTTTTAATACTATATTTTTAATACTATATTATGTATATATTTTTACAT-GCATTATGTACATA
1 TTTTTAATA-TATATATGT-ATA-TAT-TTATGTACATACTTTTA-ATAGCATTATGTACATA
** **
38823602 TTTTCAATAACTATATCATATGTATATATTTTATGTACATACTTTTAATATTATTATGTATTTA
1 TTTT---TAA-TATAT-ATATGTATATA-TTTATGTACATACTTTTAATAGCATTATGTACATA
38823666 TTTTTAATATATATATGTATATATTTATGTA
1 TTTTTAATATATATATGTATATATTTATGTA
38823697 GTATTATTAA
Statistics
Matches: 80, Mismatches: 8, Indels: 18
0.75 0.08 0.17
Matches are distributed among these distances:
58 8 0.10
59 11 0.14
60 5 0.06
61 3 0.04
62 4 0.05
63 2 0.03
64 31 0.39
65 10 0.12
66 6 0.08
ACGTcount: A:0.34, C:0.06, G:0.05, T:0.54
Consensus pattern (58 bp):
TTTTTAATATATATATGTATATATTTATGTACATACTTTTAATAGCATTATGTACATA
Found at i:38823659 original size:23 final size:23
Alignment explanation
Indices: 38823627--38823684 Score: 66
Period size: 23 Copynumber: 2.6 Consensus size: 23
38823617 TCATATGTAT
38823627 ATATT-TTATGTACATACTTTTA
1 ATATTATTATGTACATACTTTTA
** *
38823649 ATATTATTATGTATTTATTTTTA
1 ATATTATTATGTACATACTTTTA
38823672 ATA-TATATATGTA
1 ATATTAT-TATGTA
38823685 TATATTTATG
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
22 8 0.26
23 23 0.74
ACGTcount: A:0.34, C:0.03, G:0.05, T:0.57
Consensus pattern (23 bp):
ATATTATTATGTACATACTTTTA
Found at i:38823691 original size:23 final size:23
Alignment explanation
Indices: 38823550--38823633 Score: 62
Period size: 23 Copynumber: 3.3 Consensus size: 23
38823540 TTTTTAATAC
38823550 TATATTTTTAATACTATATTATGTA
1 TATATTTTTAATA-TATA-TATGTA
**
38823575 TATATTTTTACATGCAT-TATGTA
1 TATATTTTTA-ATATATATATGTA
*
38823598 CATATTTTCAATAACTATATCATATGTA
1 TATATTTT---TAA-TATAT-ATATGTA
38823626 TATATTTT
1 TATATTTT
38823634 ATGTACATAC
Statistics
Matches: 46, Mismatches: 6, Indels: 11
0.73 0.10 0.17
Matches are distributed among these distances:
23 13 0.28
25 13 0.28
26 7 0.15
28 13 0.28
ACGTcount: A:0.35, C:0.08, G:0.05, T:0.52
Consensus pattern (23 bp):
TATATTTTTAATATATATATGTA
Found at i:38823948 original size:25 final size:25
Alignment explanation
Indices: 38823812--38824006 Score: 105
Period size: 25 Copynumber: 8.2 Consensus size: 25
38823802 TTTAATATTG
* *
38823812 TATTTTT-ATA-TATGTCATGTATA
1 TATTTTTAATACTATATTATGTATA
* *
38823835 TATTTCTAATACTATATTA---CT-
1 TATTTTTAATACTATATTATGTATA
* *
38823856 T-TTTTTACATATTATCTTATGTATA
1 TATTTTTA-ATACTATATTATGTATA
*
38823881 TATTTTTTTAATAACTATATTATGTATG
1 TA--TTTTTAAT-ACTATATTATGTATA
** *
38823909 TATTTTTAACGCTATATTATGTACA
1 TATTTTTAATACTATATTATGTATA
38823934 TATTTTTAATAC-----TATGTATA
1 TATTTTTAATACTATATTATGTATA
* * * *
38823954 TACCTTTTATTCCTATTATTACGTATA
1 TA-TTTTTAATACTA-TATTATGTATA
38823981 TA-TTTTAATAC-ATA-TATGTATA
1 TATTTTTAATACTATATTATGTATA
38824003 TATT
1 TATT
38824007 CATATATCGT
Statistics
Matches: 128, Mismatches: 25, Indels: 38
0.67 0.13 0.20
Matches are distributed among these distances:
20 14 0.11
21 17 0.13
22 10 0.08
23 9 0.07
24 5 0.04
25 35 0.27
26 7 0.05
27 11 0.09
28 20 0.16
ACGTcount: A:0.32, C:0.09, G:0.05, T:0.54
Consensus pattern (25 bp):
TATTTTTAATACTATATTATGTATA
Found at i:38827330 original size:20 final size:20
Alignment explanation
Indices: 38827291--38827338 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
38827281 TAAATTCTAA
* **
38827291 AAAGATAAATACATTTAATT
1 AAAGATAAATAAATAAAATT
38827311 AAAGATAAATAAATAAAATT
1 AAAGATAAATAAATAAAATT
38827331 AAA-ATAAA
1 AAAGATAAA
38827339 ATTCTAAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
19 5 0.20
20 20 0.80
ACGTcount: A:0.67, C:0.02, G:0.04, T:0.27
Consensus pattern (20 bp):
AAAGATAAATAAATAAAATT
Found at i:38828279 original size:23 final size:23
Alignment explanation
Indices: 38828248--38828301 Score: 99
Period size: 23 Copynumber: 2.3 Consensus size: 23
38828238 AATTAATTAC
38828248 TAACTAATGCCACCTTTATTGACT
1 TAAC-AATGCCACCTTTATTGACT
38828272 TAACAATGCCACCTTTATTGACT
1 TAACAATGCCACCTTTATTGACT
38828295 TAACAAT
1 TAACAAT
38828302 CTCTTGTTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
23 26 0.87
24 4 0.13
ACGTcount: A:0.33, C:0.24, G:0.07, T:0.35
Consensus pattern (23 bp):
TAACAATGCCACCTTTATTGACT
Found at i:38829911 original size:16 final size:16
Alignment explanation
Indices: 38829879--38829929 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 16
38829869 GGTTGAGGTG
38829879 AATGGAATA-AGACTGT
1 AATGGAATAGAGA-TGT
* *
38829895 AATGTAATTGAGATGT
1 AATGGAATAGAGATGT
*
38829911 AATGGAATAGAGTTGT
1 AATGGAATAGAGATGT
38829927 AAT
1 AAT
38829930 AAATAACTCA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
16 26 0.90
17 3 0.10
ACGTcount: A:0.41, C:0.02, G:0.25, T:0.31
Consensus pattern (16 bp):
AATGGAATAGAGATGT
Found at i:38830174 original size:60 final size:57
Alignment explanation
Indices: 38830094--38830214 Score: 170
Period size: 60 Copynumber: 2.1 Consensus size: 57
38830084 TTGTTATTAA
* *
38830094 ATTTTAATAAAATTATTATTAAGTATAATTTAATAAAAATAAAATAAATAATTTAATCAT
1 ATTTTAACAAAATTATTATTAAATATAATTTAAT-AAAAT--AATAAATAATTTAATCAT
* * *
38830154 ATTTTAACATAATTTTTATTAAATATAATTTAATAAAATAATATATAATTTAATCAT
1 ATTTTAACAAAATTATTATTAAATATAATTTAATAAAATAATAAATAATTTAATCAT
38830211 ATTT
1 ATTT
38830215 CAATTTATTT
Statistics
Matches: 56, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
57 21 0.38
59 5 0.09
60 30 0.54
ACGTcount: A:0.51, C:0.02, G:0.01, T:0.45
Consensus pattern (57 bp):
ATTTTAACAAAATTATTATTAAATATAATTTAATAAAATAATAAATAATTTAATCAT
Found at i:38837284 original size:19 final size:19
Alignment explanation
Indices: 38837247--38837284 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
38837237 ACCTGTCAGA
*
38837247 AGAAAATAAATGAAGAATT
1 AGAAAATAAATGAAAAATT
38837266 AGAAAATAAAAT-AAAAATT
1 AGAAAAT-AAATGAAAAATT
38837285 TAAATTGCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.68, C:0.00, G:0.11, T:0.21
Consensus pattern (19 bp):
AGAAAATAAATGAAAAATT
Found at i:38839151 original size:19 final size:19
Alignment explanation
Indices: 38839127--38839165 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
38839117 TTAGAGTACA
38839127 TTTTAACCAGTGGCGAATC
1 TTTTAACCAGTGGCGAATC
38839146 TTTTAACCAGTGGCGAATC
1 TTTTAACCAGTGGCGAATC
38839165 T
1 T
38839166 AGGGGGCTAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.33
Consensus pattern (19 bp):
TTTTAACCAGTGGCGAATC
Found at i:38840308 original size:16 final size:16
Alignment explanation
Indices: 38840287--38840354 Score: 127
Period size: 16 Copynumber: 4.2 Consensus size: 16
38840277 TTTGGTTCGC
38840287 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
*
38840303 TGTATTGGATTAGAGA
1 TGTATTGGATTAGAGG
38840319 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
38840335 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
38840351 TGTA
1 TGTA
38840355 ATAGCAAATC
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 50 1.00
ACGTcount: A:0.26, C:0.00, G:0.35, T:0.38
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:38840611 original size:18 final size:17
Alignment explanation
Indices: 38840590--38840624 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
38840580 TTATTATTAA
*
38840590 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
38840608 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
38840625 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:38840731 original size:18 final size:17
Alignment explanation
Indices: 38840710--38840744 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
38840700 TTATTATTAA
*
38840710 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
38840728 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
38840745 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:38840831 original size:120 final size:120
Alignment explanation
Indices: 38840573--38840820 Score: 496
Period size: 120 Copynumber: 2.1 Consensus size: 120
38840563 ATCATATTTA
38840573 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
38840638 TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
66 TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
38840693 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
38840758 TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
66 TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
38840813 AACATAAT
1 AACATAAT
38840821 AATATATAAA
Statistics
Matches: 128, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
120 128 1.00
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.44
Consensus pattern (120 bp):
AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
Found at i:38857860 original size:20 final size:20
Alignment explanation
Indices: 38857826--38857876 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
38857816 AACAAGTCAT
38857826 TATAGAAAA-TTTTTAAAAAA
1 TATA-AAAATTTTTTAAAAAA
* * *
38857846 TGTATAAATTTTTTAAAGAA
1 TATAAAAATTTTTTAAAAAA
38857866 TATAAAAATTT
1 TATAAAAATTT
38857877 CAAAAGAAAT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
19 3 0.12
20 22 0.88
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.41
Consensus pattern (20 bp):
TATAAAAATTTTTTAAAAAA
Found at i:38860869 original size:17 final size:17
Alignment explanation
Indices: 38860841--38860883 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 17
38860831 TAAAAAATTC
38860841 AAATATTAAAAATTAGAAA
1 AAATA-TAAAAA-TAGAAA
* *
38860860 AAATATAAAAATCGTAA
1 AAATATAAAAATAGAAA
38860877 AAATATA
1 AAATATA
38860884 TATAATTTGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 11 0.50
18 6 0.27
19 5 0.23
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.26
Consensus pattern (17 bp):
AAATATAAAAATAGAAA
Found at i:38860879 original size:19 final size:19
Alignment explanation
Indices: 38860857--38860944 Score: 65
Period size: 19 Copynumber: 4.7 Consensus size: 19
38860847 TAAAAATTAG
38860857 AAAAAATATAAAAATCGTA
1 AAAAAATATAAAAATCGTA
* * * *
38860876 AAAATATATATAATTTGTA
1 AAAAAATATAAAAATCGTA
***
38860895 AAATTTTATAAAAATCGTA
1 AAAAAATATAAAAATCGTA
* *
38860914 AAACAAT-TATAAAAT-AT-
1 AAAAAATATA-AAAATCGTA
38860931 AAAAAATATAAAAA
1 AAAAAATATAAAAA
38860945 AAATTATAAA
Statistics
Matches: 53, Mismatches: 14, Indels: 6
0.73 0.19 0.08
Matches are distributed among these distances:
17 10 0.19
18 5 0.09
19 38 0.72
ACGTcount: A:0.64, C:0.03, G:0.03, T:0.30
Consensus pattern (19 bp):
AAAAAATATAAAAATCGTA
Found at i:38861380 original size:85 final size:86
Alignment explanation
Indices: 38861281--38861445 Score: 208
Period size: 86 Copynumber: 1.9 Consensus size: 86
38861271 AAGAGTAGGA
* * *
38861281 GTTTAATTGCTTTTTTGAAA-AATTTTAAGGGTCTTTTTT-ATGCATTTTGAAAGTTCAAGAGCC
1 GTTTAATTGCTTTTTTGAAAGAAATTTAAGAG-CTTTTTTGATGCATTCTGAAAGTTCAAGAGCC
*
38861344 CAATTGAGTGAAAAAATCAAGG
65 CAATTAAGTGAAAAAATCAAGG
* * * * ** *
38861366 GTTTAATTGTTTTTTTTAAAGAAATTTGAGAGCTTTTTTGATGCATTCTGAAAGTTTAATTGCTC
1 GTTTAATTGCTTTTTTGAAAGAAATTTAAGAGCTTTTTTGATGCATTCTGAAAGTTCAAGAGCCC
38861431 AATTAAGTGAAAAAA
66 AATTAAGTGAAAAAA
38861446 AAAAAGAGAG
Statistics
Matches: 67, Mismatches: 11, Indels: 3
0.83 0.14 0.04
Matches are distributed among these distances:
85 25 0.37
86 42 0.63
ACGTcount: A:0.33, C:0.08, G:0.18, T:0.41
Consensus pattern (86 bp):
GTTTAATTGCTTTTTTGAAAGAAATTTAAGAGCTTTTTTGATGCATTCTGAAAGTTCAAGAGCCC
AATTAAGTGAAAAAATCAAGG
Found at i:38863977 original size:31 final size:31
Alignment explanation
Indices: 38863930--38864004 Score: 116
Period size: 31 Copynumber: 2.5 Consensus size: 31
38863920 TTTTAATGAT
* *
38863930 AGAGTTACT-AAATTGACAACTTATCTAATA
1 AGAGTGACTAAAATTGACAACTTATCTAACA
38863960 AGAGTGACTAAAATTGACAACTTATCTAACA
1 AGAGTGACTAAAATTGACAACTTATCTAACA
*
38863991 TGAGTGACTAAAAT
1 AGAGTGACTAAAAT
38864005 AGTAAATTTT
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
30 8 0.20
31 33 0.80
ACGTcount: A:0.44, C:0.13, G:0.13, T:0.29
Consensus pattern (31 bp):
AGAGTGACTAAAATTGACAACTTATCTAACA
Found at i:38869105 original size:24 final size:25
Alignment explanation
Indices: 38869077--38869128 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 25
38869067 ACTATCTTAA
*
38869077 AATAAAAAT-ATATATT-AAAATGTG
1 AATAAAAATGAAAT-TTAAAAATGTG
38869101 AAT-AAAATGAAATTTAAAAATGTG
1 AATAAAAATGAAATTTAAAAATGTG
38869125 AATA
1 AATA
38869129 CATTATATTA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
23 7 0.29
24 17 0.71
ACGTcount: A:0.60, C:0.00, G:0.10, T:0.31
Consensus pattern (25 bp):
AATAAAAATGAAATTTAAAAATGTG
Found at i:38873537 original size:3 final size:3
Alignment explanation
Indices: 38873517--38873564 Score: 64
Period size: 3 Copynumber: 16.3 Consensus size: 3
38873507 CTGAAGGAAG
*
38873517 GAA GAAA GAA GGA GAA GAA GAA -AA GAA G-A GAA GAA GAA GAA GAA
1 GAA G-AA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
38873561 GAA G
1 GAA G
38873565 GAGGAGGAGG
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
2 4 0.10
3 33 0.82
4 3 0.08
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:38873554 original size:22 final size:21
Alignment explanation
Indices: 38873518--38873560 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 21
38873508 TGAAGGAAGG
*
38873518 AAGAAAGAAGGAGAAGAAGAA
1 AAGAAAGAAGAAGAAGAAGAA
38873539 AAGAAGAGAAGAAGAAGAAGAA
1 AAGAA-AGAAGAAGAAGAAGAA
38873561 GAAGGAGGAG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 5 0.25
22 15 0.75
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (21 bp):
AAGAAAGAAGAAGAAGAAGAA
Found at i:38873557 original size:25 final size:24
Alignment explanation
Indices: 38873517--38873563 Score: 76
Period size: 25 Copynumber: 1.9 Consensus size: 24
38873507 CTGAAGGAAG
*
38873517 GAAGAAAGAAGGAGAAGAAGAAAA
1 GAAGAAAGAAGAAGAAGAAGAAAA
38873541 GAAGAGAAGAAGAAGAAGAAGAA
1 GAAGA-AAGAAGAAGAAGAAGAA
38873564 GGAGGAGGAG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 5 0.24
25 16 0.76
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (24 bp):
GAAGAAAGAAGAAGAAGAAGAAAA
Found at i:38874062 original size:17 final size:16
Alignment explanation
Indices: 38874032--38874114 Score: 60
Period size: 16 Copynumber: 5.1 Consensus size: 16
38874022 TTTTTTTACA
* *
38874032 AAAATAGTATAAAATAT
1 AAAATACTA-AAAAAAT
38874049 AAAATACTAAAAAAAT
1 AAAATACTAAAAAAAT
*** * *
38874065 ATCTTAATGAAAAAAT
1 AAAATACTAAAAAAAT
*
38874081 AAAATACGAAAAGAAAT
1 AAAATACTAAAA-AAAT
*
38874098 AAAATA-TGAAAAAAT
1 AAAATACTAAAAAAAT
38874113 AA
1 AA
38874115 CTTTTTGGGA
Statistics
Matches: 50, Mismatches: 15, Indels: 4
0.72 0.22 0.06
Matches are distributed among these distances:
15 6 0.12
16 26 0.52
17 18 0.36
ACGTcount: A:0.69, C:0.04, G:0.06, T:0.22
Consensus pattern (16 bp):
AAAATACTAAAAAAAT
Found at i:38876666 original size:32 final size:32
Alignment explanation
Indices: 38876585--38876699 Score: 133
Period size: 33 Copynumber: 3.5 Consensus size: 32
38876575 ATCTTTAGAT
*
38876585 CGTATCCACTGCAGTACAGCACTA-CCCTCGACC
1 CGTATCCACCGCAGTACAGCACTACCCCT-G-CC
* *
38876618 CGTATCCATCGTAGTACAGCACTACCCCTGCC
1 CGTATCCACCGCAGTACAGCACTACCCCTGCC
* * *
38876650 CGAATCCACCACAGTACAGCACTACTCCCGGCC
1 CGTATCCACCGCAGTACAGCACTAC-CCCTGCC
*
38876683 CGTATCAACCGCAGTAC
1 CGTATCCACCGCAGTAC
38876700 TCCACTCCTT
Statistics
Matches: 69, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
32 23 0.33
33 42 0.61
34 4 0.06
ACGTcount: A:0.25, C:0.42, G:0.16, T:0.17
Consensus pattern (32 bp):
CGTATCCACCGCAGTACAGCACTACCCCTGCC
Found at i:38882648 original size:45 final size:42
Alignment explanation
Indices: 38882563--38882648 Score: 109
Period size: 45 Copynumber: 2.0 Consensus size: 42
38882553 TACAACATAA
* *
38882563 ACCCAATAACCCAAAGCCCAAATACTTAAAATTAAACCCAAG
1 ACCCAATAACCCAAAACCCAAATACTTAAAACTAAACCCAAG
* *
38882605 ACCCACTAACACCTAAAACCCAAATACATTATAACTAAACCCAA
1 ACCCAATAAC-CC-AAAACCCAAATAC-TTAAAACTAAACCCAA
38882649 CACTCATTAA
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
42 9 0.24
43 2 0.05
44 12 0.32
45 14 0.38
ACGTcount: A:0.50, C:0.33, G:0.02, T:0.15
Consensus pattern (42 bp):
ACCCAATAACCCAAAACCCAAATACTTAAAACTAAACCCAAG
Found at i:38899538 original size:11 final size:11
Alignment explanation
Indices: 38899522--38899549 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
38899512 TTCCACCATT
38899522 TTCTTCCAAAC
1 TTCTTCCAAAC
38899533 TTCTTCCAAAC
1 TTCTTCCAAAC
38899544 TTCTTC
1 TTCTTC
38899550 TAACGGGCTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.21, C:0.36, G:0.00, T:0.43
Consensus pattern (11 bp):
TTCTTCCAAAC
Found at i:38905015 original size:4 final size:4
Alignment explanation
Indices: 38905008--38905037 Score: 51
Period size: 4 Copynumber: 7.5 Consensus size: 4
38904998 ACACGCAAGC
*
38905008 AAAT AAAT AAAT GAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA
38905038 TGGTAGAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.73, C:0.00, G:0.03, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:38905519 original size:19 final size:19
Alignment explanation
Indices: 38905495--38905533 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
38905485 AAAATAGACA
38905495 TAACAATA-ATATGATATAT
1 TAACAATATATAT-ATATAT
38905514 TAACAATATATATATATAT
1 TAACAATATATATATATAT
38905533 T
1 T
38905534 TATATGATGT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 15 0.79
20 4 0.21
ACGTcount: A:0.51, C:0.05, G:0.03, T:0.41
Consensus pattern (19 bp):
TAACAATATATATATATAT
Found at i:38905756 original size:21 final size:23
Alignment explanation
Indices: 38905730--38905778 Score: 66
Period size: 21 Copynumber: 2.2 Consensus size: 23
38905720 AGGTATTACA
*
38905730 TAAAAATATATACAT-AT-ATAT
1 TAAAAATAAATACATGATAATAT
*
38905751 TAAAAATAAATATATGATAATAT
1 TAAAAATAAATACATGATAATAT
38905774 TAAAA
1 TAAAA
38905779 GTATGTGCAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 13 0.54
22 2 0.08
23 9 0.38
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.35
Consensus pattern (23 bp):
TAAAAATAAATACATGATAATAT
Found at i:38906830 original size:32 final size:32
Alignment explanation
Indices: 38906760--38906830 Score: 79
Period size: 32 Copynumber: 2.2 Consensus size: 32
38906750 TTTGTTTGAA
* * * * *
38906760 CTGTTTTTTGCCTTTTGATTTTGCTGAGATTT
1 CTGTTTTTTACCTTTTGATGTTGATGAAATCT
* *
38906792 CAGTTTTTTACTTTTTGATGTTGATGAAATCT
1 CTGTTTTTTACCTTTTGATGTTGATGAAATCT
38906824 CTGTTTT
1 CTGTTTT
38906831 GTATTCTTTA
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.14, C:0.11, G:0.17, T:0.58
Consensus pattern (32 bp):
CTGTTTTTTACCTTTTGATGTTGATGAAATCT
Found at i:38909215 original size:26 final size:26
Alignment explanation
Indices: 38909186--38909295 Score: 177
Period size: 26 Copynumber: 4.2 Consensus size: 26
38909176 TGGTACAAAT
38909186 TGATAATAGGTTAGGTAAATG-TTCGA
1 TGATAATAGGTTAGGTAAATGTTTC-A
*
38909212 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTTCA
*
38909238 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTTCA
*
38909264 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTTCA
38909290 TGATAA
1 TGATAA
38909296 GAATTTCATG
Statistics
Matches: 80, Mismatches: 3, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
26 78 0.98
27 2 0.03
ACGTcount: A:0.34, C:0.05, G:0.25, T:0.36
Consensus pattern (26 bp):
TGATAATAGGTTAGGTAAATGTTTCA
Found at i:38910492 original size:15 final size:15
Alignment explanation
Indices: 38910469--38910499 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
38910459 ACTAGATTGG
38910469 CAAAAGCCGAAAAGT
1 CAAAAGCCGAAAAGT
*
38910484 CAAATGCCGAAAAGT
1 CAAAAGCCGAAAAGT
38910499 C
1 C
38910500 GGTATTTTGG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.23, G:0.19, T:0.10
Consensus pattern (15 bp):
CAAAAGCCGAAAAGT
Found at i:38910776 original size:28 final size:26
Alignment explanation
Indices: 38910745--38910804 Score: 66
Period size: 26 Copynumber: 2.2 Consensus size: 26
38910735 AATAACTATA
* *
38910745 ATACCCCTATGTATGGAAAATTACTGTT
1 ATACCCCTA-G-ATGCAAAATTACCGTT
* *
38910773 ATACCCTTAGGTGCAAAATTACCGTT
1 ATACCCCTAGATGCAAAATTACCGTT
38910799 ATACCC
1 ATACCC
38910805 GTAGGGTTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
26 19 0.68
27 1 0.04
28 8 0.29
ACGTcount: A:0.32, C:0.23, G:0.13, T:0.32
Consensus pattern (26 bp):
ATACCCCTAGATGCAAAATTACCGTT
Found at i:38910974 original size:27 final size:27
Alignment explanation
Indices: 38910912--38910978 Score: 80
Period size: 27 Copynumber: 2.5 Consensus size: 27
38910902 GAGGAAGCGT
* *
38910912 TCTGGTGGCTATGCCACAAATATTTGA
1 TCTGGTGGCTCTGCCACAAATATCTGA
* * *
38910939 TCTGATGGCTCTGCCACATATATCTGT
1 TCTGGTGGCTCTGCCACAAATATCTGA
*
38910966 TTTGGTGGCTCTG
1 TCTGGTGGCTCTG
38910979 TCACGATGAT
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.18, C:0.21, G:0.24, T:0.37
Consensus pattern (27 bp):
TCTGGTGGCTCTGCCACAAATATCTGA
Found at i:38915011 original size:26 final size:26
Alignment explanation
Indices: 38914982--38915091 Score: 150
Period size: 26 Copynumber: 4.2 Consensus size: 26
38914972 TGGTACAAAT
*
38914982 TGATAATAGGTTAGGGAAATG-TTCAA
1 TGATAATAGGTTAGGTAAATGTTTC-A
* *
38915008 TGATAATAAGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTTCA
*
38915034 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTTCA
* *
38915060 TGATAATGGGTTAGGTAAACGTTTCA
1 TGATAATAGGTTAGGTAAATGTTTCA
38915086 TGATAA
1 TGATAA
38915092 GAATTTCATG
Statistics
Matches: 76, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
26 74 0.97
27 2 0.03
ACGTcount: A:0.35, C:0.05, G:0.25, T:0.35
Consensus pattern (26 bp):
TGATAATAGGTTAGGTAAATGTTTCA
Found at i:38916726 original size:27 final size:27
Alignment explanation
Indices: 38916695--38916796 Score: 98
Period size: 27 Copynumber: 3.8 Consensus size: 27
38916685 CTAGTGGCTA
*
38916695 TGCCACAAATATCTGATCTGGTGGCTC
1 TGCCACAAATATCTGATCTGGTGACTC
* *
38916722 TGCCACATATATCTGTTCTGGTGACTC
1 TGCCACAAATATCTGATCTGGTGACTC
* * * *
38916749 CGTCACGATTATCTGTATCTGGTGACTC
1 TGCCACAAATATCTG-ATCTGGTGACTC
* * *
38916777 TGTCAC-ATTATCTGTTCTGG
1 TGCCACAAATATCTGATCTGG
38916797 CAGCTATGCT
Statistics
Matches: 63, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
26 5 0.08
27 42 0.67
28 16 0.25
ACGTcount: A:0.19, C:0.25, G:0.21, T:0.36
Consensus pattern (27 bp):
TGCCACAAATATCTGATCTGGTGACTC
Found at i:38919449 original size:20 final size:18
Alignment explanation
Indices: 38919417--38919471 Score: 56
Period size: 19 Copynumber: 2.9 Consensus size: 18
38919407 ACTTTAATTC
*
38919417 ATTAATTTTTTAAAAAAA
1 ATTAATATTTTAAAAAAA
*
38919435 TATTAATAATTTTAAATATAA
1 -ATTAAT-ATTTTAAA-AAAA
*
38919456 ATTAATATTATAAAAA
1 ATTAATATTTTAAAAA
38919472 TGTTATAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
18 1 0.03
19 13 0.43
20 13 0.43
21 3 0.10
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
ATTAATATTTTAAAAAAA
Found at i:38926320 original size:43 final size:43
Alignment explanation
Indices: 38926272--38926360 Score: 151
Period size: 43 Copynumber: 2.1 Consensus size: 43
38926262 CAATGAAAAG
*
38926272 TATGATTTGGAACTAATTAATAGTAATACATGAGTATATACCA
1 TATGATTTGGAACTAATTAATAGTAATACATGAATATATACCA
* *
38926315 TATGATTTGGAACTAATTAATAGTAATCCATGAATATATACTA
1 TATGATTTGGAACTAATTAATAGTAATACATGAATATATACCA
38926358 TAT
1 TAT
38926361 TAAAATAAAA
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.42, C:0.09, G:0.12, T:0.37
Consensus pattern (43 bp):
TATGATTTGGAACTAATTAATAGTAATACATGAATATATACCA
Found at i:38928142 original size:40 final size:39
Alignment explanation
Indices: 38928075--38928211 Score: 104
Period size: 37 Copynumber: 3.5 Consensus size: 39
38928065 ACTAGAATGG
38928075 CACCCAGTGCCTCATCGGA--TAGTTCGAAGCAATATAGTGA
1 CACCCAGTGCCTCATC-GACCTAG-TCGAAG-AATATAGTGA
* * *
38928115 CACCCAGTGTCTCATCGACCTAGTCGAAG--TAAAGTGG
1 CACCCAGTGCCTCATCGACCTAGTCGAAGAATATAGTGA
* * * * *
38928152 TACCCAGTACCTCATCGAATCTA-TCTGAAAAAATATAGTAA
1 CACCCAGTGCCTCATCG-ACCTAGTC-G-AAGAATATAGTGA
*
38928193 CACCCAGTGTCTCATCGAC
1 CACCCAGTGCCTCATCGAC
38928212 TTGAGGTCGA
Statistics
Matches: 75, Mismatches: 15, Indels: 14
0.72 0.14 0.13
Matches are distributed among these distances:
37 22 0.29
38 5 0.07
39 4 0.05
40 22 0.29
41 22 0.29
ACGTcount: A:0.31, C:0.27, G:0.18, T:0.23
Consensus pattern (39 bp):
CACCCAGTGCCTCATCGACCTAGTCGAAGAATATAGTGA
Found at i:38928830 original size:42 final size:41
Alignment explanation
Indices: 38928784--38928913 Score: 123
Period size: 42 Copynumber: 3.3 Consensus size: 41
38928774 TTGAATTTCT
38928784 ATTCAATTTACACCTTATTTTCAATTAGGTCCTAGCTGATTC
1 ATTCAATTTACACCTTATTTTCAATTAGGTCCTA-CTGATTC
* * * *
38928826 ATTCACTTTACTAACTTA-ATTC-A-TA-CT-CTA-T--TTC
1 ATTCAATTTAC-ACCTTATTTTCAATTAGGTCCTACTGATTC
38928860 TATTCAATTTACACCTTATTTTCAATTAGGTCCTAACTGATTC
1 -ATTCAATTTACACCTTATTTTCAATTAGGTCCT-ACTGATTC
*
38928903 ATTCACTTTAC
1 ATTCAATTTAC
38928914 TAACTTAATT
Statistics
Matches: 68, Mismatches: 9, Indels: 22
0.69 0.09 0.22
Matches are distributed among these distances:
34 8 0.12
35 13 0.19
36 2 0.03
37 2 0.03
38 4 0.06
39 3 0.04
40 3 0.04
41 2 0.03
42 23 0.34
43 8 0.12
ACGTcount: A:0.28, C:0.22, G:0.05, T:0.45
Consensus pattern (41 bp):
ATTCAATTTACACCTTATTTTCAATTAGGTCCTACTGATTC
Found at i:38928865 original size:77 final size:77
Alignment explanation
Indices: 38928778--38928943 Score: 323
Period size: 77 Copynumber: 2.2 Consensus size: 77
38928768 AAATAATTGA
*
38928778 ATTTCTATTCAATTTACACCTTATTTTCAATTAGGTCCTAGCTGATTCATTCACTTTACTAACTT
1 ATTTCTATTCAATTTACACCTTATTTTCAATTAGGTCCTAACTGATTCATTCACTTTACTAACTT
38928843 AATTCATACTCT
66 AATTCATACTCT
38928855 ATTTCTATTCAATTTACACCTTATTTTCAATTAGGTCCTAACTGATTCATTCACTTTACTAACTT
1 ATTTCTATTCAATTTACACCTTATTTTCAATTAGGTCCTAACTGATTCATTCACTTTACTAACTT
38928920 AATTCATACTCT
66 AATTCATACTCT
38928932 ATTTCTATTCAA
1 ATTTCTATTCAA
38928944 GTTCCATCCA
Statistics
Matches: 88, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
77 88 1.00
ACGTcount: A:0.28, C:0.22, G:0.04, T:0.46
Consensus pattern (77 bp):
ATTTCTATTCAATTTACACCTTATTTTCAATTAGGTCCTAACTGATTCATTCACTTTACTAACTT
AATTCATACTCT
Found at i:38930258 original size:26 final size:26
Alignment explanation
Indices: 38930229--38930278 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
38930219 TGTGAGACCT
*
38930229 TAGTGT-TAGAACCCTTAAGTGCGAGC
1 TAGTGTGT-GAACCCCTAAGTGCGAGC
*
38930255 TAGTGTGTGAACCCCTATGTGCGA
1 TAGTGTGTGAACCCCTAAGTGCGA
38930279 ACCCTTATGC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
26 20 0.95
27 1 0.05
ACGTcount: A:0.24, C:0.20, G:0.28, T:0.28
Consensus pattern (26 bp):
TAGTGTGTGAACCCCTAAGTGCGAGC
Found at i:38930420 original size:28 final size:28
Alignment explanation
Indices: 38930317--38930420 Score: 86
Period size: 28 Copynumber: 3.7 Consensus size: 28
38930307 TCCTACGTGT
* *
38930317 AAACCCTTATGTGTGAACTTGTATCTGC
1 AAACCCTTATGTGTGAACCTGTATGTGC
* * *
38930345 AAACCCCTATGTGTGAGCTCTAGGTGTGTG-
1 AAACCCTTATGTGTGAAC-CT--GTATGTGC
** *
38930375 -AACCCTTATACGTAAACCTGTATGTGC
1 AAACCCTTATGTGTGAACCTGTATGTGC
*
38930402 AAACCCTTATGTGTCAACC
1 AAACCCTTATGTGTGAACC
38930421 CTATAGTTTA
Statistics
Matches: 57, Mismatches: 14, Indels: 10
0.70 0.17 0.12
Matches are distributed among these distances:
26 6 0.11
28 33 0.58
29 13 0.23
31 5 0.09
ACGTcount: A:0.26, C:0.24, G:0.19, T:0.31
Consensus pattern (28 bp):
AAACCCTTATGTGTGAACCTGTATGTGC
Found at i:38930536 original size:36 final size:36
Alignment explanation
Indices: 38930451--38930528 Score: 104
Period size: 36 Copynumber: 2.2 Consensus size: 36
38930441 ACCCTAGGTT
* *
38930451 ATGTTATGTGAACCTTGTATGTGTCATATGCAAGCC
1 ATGTTATGTGAACCTAGTATGTGTCATATACAAGCC
* *
38930487 ATGATATCTGAACCTAGTATGTGTCATATACGAA-CC
1 ATGTTATGTGAACCTAGTATGTGTCATATAC-AAGCC
38930523 ATGTTA
1 ATGTTA
38930529 GGAGAACCCT
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
36 34 0.94
37 2 0.06
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.35
Consensus pattern (36 bp):
ATGTTATGTGAACCTAGTATGTGTCATATACAAGCC
Found at i:38932412 original size:17 final size:19
Alignment explanation
Indices: 38932377--38932420 Score: 65
Period size: 17 Copynumber: 2.4 Consensus size: 19
38932367 TATTATTTTT
38932377 ATATTTTATATTATTAATA
1 ATATTTTATATTATTAATA
38932396 ATATTTTATA-T-TTAATA
1 ATATTTTATATTATTAATA
*
38932413 ATTTTTTA
1 ATATTTTA
38932421 ATAACTTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 13 0.54
18 1 0.04
19 10 0.42
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (19 bp):
ATATTTTATATTATTAATA
Found at i:38934914 original size:226 final size:217
Alignment explanation
Indices: 38934519--38934922 Score: 504
Period size: 226 Copynumber: 1.8 Consensus size: 217
38934509 GAAGTTGTCG
* * * * * *
38934519 AAATTATGATATAATGTTGAAAATTTTAAATTTTTTTGGTTAAAGAACTGGTTTTAGGTGAGGAA
1 AAATTATGATATAAGGTTCAAAAATTTAAATTTTTTTGGTTAAAGAACTGATATTAGGTGAAGAA
* * * *
38934584 TTTATTTGAATTTATATTTTAAAAGCTCCAATTTTAAAGAAAATGTAAGATGCTTGATCTCAATA
66 TTTATATGAATTTAGATTATAAAAGCTCCAATTTTAAAGAAAATGCAAGATGCTTGATCTCAATA
* * *
38934649 TTTTAATTTTATTTTGTTTGATTTGGATTCTTGTGAGCTTGTTTATTTAAATTTTTTTTCTTTTG
131 TTTTAATTTTATTTTGTTTAATTTGGATTATTGTGAGCTTATTTATTTAAATTTTTTTTCTTTTG
38934714 GGTTAAATTGGCTTCTTTTGTT
196 GGTTAAATTGGCTTCTTTTGTT
** *
38934736 AAATTATGATATGCGGTTCAAAAATTTAAGTTTTTTTGGGTTAAAGAACTGATATTAGGT-AAGA
1 AAATTATGATATAAGGTTCAAAAATTTAAATTTTTTT-GGTTAAAGAACTGATATTAGGTGAAGA
* *
38934800 ATATATATATGAGTTTAGATTATAAAAGCTCCTATTGTTTAAAAAAGAAAAGTTGCAAGATGCTT
65 AT-T-TATATGAATTTAGATTATAAAAGCTCC-AAT-TTT---AAAGAAAA--TGCAAGATGCTT
* * * * *
38934865 GATCTTAATATTTTTATTTTGTTTTGTTTAATTTGGCTTATTTTGAGCTTATTTATTT
121 GATCTCAATATTTTAATTTTATTTTGTTTAATTTGGATTATTGTGAGCTTATTTATTT
38934923 GGATTTATTT
Statistics
Matches: 154, Mismatches: 23, Indels: 11
0.82 0.12 0.06
Matches are distributed among these distances:
217 36 0.23
218 21 0.14
219 23 0.15
220 2 0.01
221 3 0.02
224 8 0.05
226 61 0.40
ACGTcount: A:0.31, C:0.06, G:0.16, T:0.48
Consensus pattern (217 bp):
AAATTATGATATAAGGTTCAAAAATTTAAATTTTTTTGGTTAAAGAACTGATATTAGGTGAAGAA
TTTATATGAATTTAGATTATAAAAGCTCCAATTTTAAAGAAAATGCAAGATGCTTGATCTCAATA
TTTTAATTTTATTTTGTTTAATTTGGATTATTGTGAGCTTATTTATTTAAATTTTTTTTCTTTTG
GGTTAAATTGGCTTCTTTTGTT
Found at i:38945976 original size:41 final size:40
Alignment explanation
Indices: 38945908--38946009 Score: 127
Period size: 41 Copynumber: 2.5 Consensus size: 40
38945898 CACCCATTTC
** *
38945908 CTCATTGGGTAATTCGAAGTAATAAATTGACAC-CTAGTGT
1 CTCATTGAATAATTCGAAGTAATAAATTAACACAC-AGTGT
38945948 CTCATTGAATAATTCTGAAGTAATAAATTAACACACAGTGT
1 CTCATTGAATAATTC-GAAGTAATAAATTAACACACAGTGT
* *
38945989 CTCATTG-GTAAATCGAAGTAA
1 CTCATTGAATAATTCGAAGTAA
38946010 ATTGGAACCC
Statistics
Matches: 55, Mismatches: 5, Indels: 5
0.85 0.08 0.08
Matches are distributed among these distances:
39 7 0.13
40 18 0.33
41 29 0.53
42 1 0.02
ACGTcount: A:0.37, C:0.15, G:0.17, T:0.31
Consensus pattern (40 bp):
CTCATTGAATAATTCGAAGTAATAAATTAACACACAGTGT
Found at i:38946368 original size:5 final size:5
Alignment explanation
Indices: 38946358--38946395 Score: 76
Period size: 5 Copynumber: 7.6 Consensus size: 5
38946348 TAAAATTCAT
38946358 CAACA CAACA CAACA CAACA CAACA CAACA CAACA CAA
1 CAACA CAACA CAACA CAACA CAACA CAACA CAACA CAA
38946396 TTCAATTGCA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 33 1.00
ACGTcount: A:0.61, C:0.39, G:0.00, T:0.00
Consensus pattern (5 bp):
CAACA
Found at i:38946475 original size:19 final size:19
Alignment explanation
Indices: 38946453--38946491 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
38946443 TTTTCAATTT
*
38946453 AGTCCCTAAATCGAGACTA
1 AGTCCCTAAACCGAGACTA
38946472 AGTCCCTAAACCGAGACTA
1 AGTCCCTAAACCGAGACTA
38946491 A
1 A
38946492 CTTTTTTCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.38, C:0.28, G:0.15, T:0.18
Consensus pattern (19 bp):
AGTCCCTAAACCGAGACTA
Found at i:38947049 original size:19 final size:20
Alignment explanation
Indices: 38947017--38947055 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
38947007 AAACATATTT
*
38947017 TATTAATATATACATATGTA
1 TATTAATATATACACATGTA
*
38947037 TATTAA-ATTTACACATGTA
1 TATTAATATATACACATGTA
38947056 ATCAGTAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.44, C:0.08, G:0.05, T:0.44
Consensus pattern (20 bp):
TATTAATATATACACATGTA
Found at i:38950672 original size:24 final size:24
Alignment explanation
Indices: 38950645--38950756 Score: 100
Period size: 24 Copynumber: 4.6 Consensus size: 24
38950635 AGAAATTTCA
* *
38950645 GCACTATGTGTGCGAGGTTATGCG
1 GCACTATGTGTGCGAGATTATACG
* * * * *
38950669 GCACTATGTGTGCAAAAACTACATG
1 GCACTATGTGTGC-GAGATTATACG
**
38950694 GCACTATGTGTGCGAGATTATATA
1 GCACTATGTGTGCGAGATTATACG
* *
38950718 GCACTATGTGTGCGAGGA-AATGCG
1 GCACTATGTGTGCGA-GATTATACG
38950742 GCACTATGTGTGCGA
1 GCACTATGTGTGCGA
38950757 ATGAGTAAGA
Statistics
Matches: 70, Mismatches: 16, Indels: 4
0.78 0.18 0.04
Matches are distributed among these distances:
24 51 0.73
25 19 0.27
ACGTcount: A:0.26, C:0.17, G:0.30, T:0.27
Consensus pattern (24 bp):
GCACTATGTGTGCGAGATTATACG
Found at i:38956099 original size:14 final size:14
Alignment explanation
Indices: 38956080--38956117 Score: 67
Period size: 14 Copynumber: 2.7 Consensus size: 14
38956070 CATATCTTCC
*
38956080 AATTTTGAACTCAA
1 AATTTTAAACTCAA
38956094 AATTTTAAACTCAA
1 AATTTTAAACTCAA
38956108 AATTTTAAAC
1 AATTTTAAAC
38956118 AGACTTCAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.47, C:0.13, G:0.03, T:0.37
Consensus pattern (14 bp):
AATTTTAAACTCAA
Found at i:38958016 original size:20 final size:20
Alignment explanation
Indices: 38957991--38958035 Score: 58
Period size: 19 Copynumber: 2.3 Consensus size: 20
38957981 CCATATATAA
*
38957991 TTTGAAATTTTTATAAA-TAT
1 TTTGAAATTTTCA-AAATTAT
38958011 TTTG-AATTTTCAAAATTAT
1 TTTGAAATTTTCAAAATTAT
38958030 TTTGAA
1 TTTGAA
38958036 TTATTTTGTA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
18 3 0.14
19 14 0.64
20 5 0.23
ACGTcount: A:0.38, C:0.02, G:0.07, T:0.53
Consensus pattern (20 bp):
TTTGAAATTTTCAAAATTAT
Found at i:38959840 original size:18 final size:16
Alignment explanation
Indices: 38959817--38959852 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 16
38959807 TTAATGAATG
38959817 TTTTTATTATTTATGTAA
1 TTTTTATT-TTTAT-TAA
38959835 TTTTTATTTTTATTAA
1 TTTTTATTTTTATTAA
38959851 TT
1 TT
38959853 AATGCTAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 5 0.28
17 5 0.28
18 8 0.44
ACGTcount: A:0.25, C:0.00, G:0.03, T:0.72
Consensus pattern (16 bp):
TTTTTATTTTTATTAA
Done.