Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold367
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: 914901
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
File 3 of 5
Found at i:443921 original size:22 final size:22
Alignment explanation
Indices: 443854--443964 Score: 58
Period size: 22 Copynumber: 5.1 Consensus size: 22
443844 GCACCTTTAT
443854 CTTTAAGTCCAATATCGCTGGC
1 CTTTAAGTCCAATATCGCTGGC
* * *
443876 CTTGAA-TCAGCACAT-TGGC--AC
1 CTTTAAGTC--CA-ATATCGCTGGC
443897 CTTTAAGTCCAATATCGCTGGC
1 CTTTAAGTCCAATATCGCTGGC
* * *
443919 CTTGAA-TCAGCACAT-TAGC--AC
1 CTTTAAGTC--CA-ATATCGCTGGC
443940 CTTTAAGTCCAATATCGCTGGC
1 CTTTAAGTCCAATATCGCTGGC
443962 CTT
1 CTT
443965 GAATCAGCAT
Statistics
Matches: 63, Mismatches: 12, Indels: 28
0.61 0.12 0.27
Matches are distributed among these distances:
19 4 0.06
20 10 0.16
21 16 0.25
22 19 0.30
23 10 0.16
24 4 0.06
ACGTcount: A:0.25, C:0.28, G:0.17, T:0.30
Consensus pattern (22 bp):
CTTTAAGTCCAATATCGCTGGC
Found at i:444019 original size:95 final size:97
Alignment explanation
Indices: 443897--444081 Score: 302
Period size: 95 Copynumber: 1.9 Consensus size: 97
443887 ACATTGGCAC
443897 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTAGCA-C-CTTTAAGTCCAATATCGCTG
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTAGCATCACTTTAAGTCCAATATCGCTG
*
443960 GCCTTGAATCAGCATATTGGCGCCTTTGTCAT
66 GCCTTGAATCAGCACATTGGCGCCTTTGTCAT
*
443992 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACTTTCATCTTTAAGTCCAATATC
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTAGCA---TCA-CTTTAAGTCCAATATC
444057 GCTGGCCTTGAATCAGCACATTGGC
62 GCTGGCCTTGAATCAGCACATTGGC
444082 ATTCTTCTCT
Statistics
Matches: 82, Mismatches: 2, Indels: 6
0.91 0.02 0.07
Matches are distributed among these distances:
95 41 0.50
99 1 0.01
101 40 0.49
ACGTcount: A:0.24, C:0.26, G:0.18, T:0.31
Consensus pattern (97 bp):
CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTAGCATCACTTTAAGTCCAATATCGCTG
GCCTTGAATCAGCACATTGGCGCCTTTGTCAT
Found at i:444123 original size:52 final size:49
Alignment explanation
Indices: 443253--444101 Score: 949
Period size: 49 Copynumber: 18.2 Consensus size: 49
443243 TGGCATCTAC
*
443253 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTT-AT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCA-CTTTCAT
* *
443302 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA----C--
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACTTTCAT
* * * *
443345 CTTTAAGTCCAATATCGCTGACCTTGAATCTGCATATTGTCACCTTT-AT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCA-CTTTCAT
* *
443394 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA----C--
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACTTTCAT
*
443437 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTT-AT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCA-CTTTCAT
* *
443486 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA----C--
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACTTTCAT
*
443529 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTT-AT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCA-CTTTCAT
* *
443578 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAC---C-T
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACTTTCAT
* *
443623 -TTT-AGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCAT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACTTTCAT
* * *
443670 CTTTAAGTCCAATGTAGCTGGCCTTGAATTAGCACATTGGCA----C--
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACTTTCAT
* *
443713 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCAT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACTTTCAT
* * *
443762 CTTTAAATCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA----C--
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACTTTCAT
* *
443805 CTTTAAGTCCAATATCGCTGGCCTTGAATCAACATATTGGCACCTTT-AT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCA-CTTTCAT
443854 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCA----C--
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACTTTCAT
*
443897 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTAGCA----C--
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACTTTCAT
* *
443940 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCAT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGC-AC-TT-TCAT
443992 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACTTTCAT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACTTTCAT
*
444041 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCATTCTTCTCTT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCA--CTT-TCAT
444093 CTTTAAGTC
1 CTTTAAGTC
444102 TAATGACGCT
Statistics
Matches: 687, Mismatches: 56, Indels: 111
0.80 0.07 0.13
Matches are distributed among these distances:
43 305 0.44
44 3 0.00
45 3 0.00
46 1 0.00
47 2 0.00
48 4 0.01
49 310 0.45
50 3 0.00
51 4 0.01
52 52 0.08
ACGTcount: A:0.25, C:0.26, G:0.17, T:0.32
Consensus pattern (49 bp):
CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACTTTCAT
Found at i:444123 original size:101 final size:101
Alignment explanation
Indices: 443897--444123 Score: 263
Period size: 101 Copynumber: 2.3 Consensus size: 101
443887 ACATTGGCAC
* * * *
443897 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTAGCA----C--CTTTAAGTCCAATATC
1 CTTTAAGTCCAATATCGCTGACCATAAATCAGCACATTGGCACTTTCATCTTTAAGTCCAATATC
* *
443956 GCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCAT
66 GCTGGCCTTGAATCAGCACATTGGCGCCTTTCTCAT
* * *
443992 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACTTTCATCTTTAAGTCCAATATC
1 CTTTAAGTCCAATATCGCTGACCATAAATCAGCACATTGGCACTTTCATCTTTAAGTCCAATATC
** *
444057 GCTGGCCTTGAATCAGCACATTGGC-ATTCTTCTCTT
66 GCTGGCCTTGAATCAGCACATTGGCGCCT-TTCTCAT
*
444093 CTTTAAGTCTAATGA-CGCTGACCATAAATCA
1 CTTTAAGTCCAAT-ATCGCTGACCATAAATCA
444124 ACGCATTGAC
Statistics
Matches: 114, Mismatches: 10, Indels: 10
0.85 0.07 0.07
Matches are distributed among these distances:
95 41 0.36
99 1 0.01
100 1 0.01
101 70 0.61
102 1 0.01
ACGTcount: A:0.25, C:0.26, G:0.16, T:0.33
Consensus pattern (101 bp):
CTTTAAGTCCAATATCGCTGACCATAAATCAGCACATTGGCACTTTCATCTTTAAGTCCAATATC
GCTGGCCTTGAATCAGCACATTGGCGCCTTTCTCAT
Found at i:444841 original size:19 final size:18
Alignment explanation
Indices: 444816--444880 Score: 68
Period size: 19 Copynumber: 3.8 Consensus size: 18
444806 ATTTCAACGA
444816 TTTGTATCGATACATAAG
1 TTTGTATCGATACATAAG
*
444834 TGTTGTATCTATAC--AA-
1 T-TTGTATCGATACATAAG
444850 --TGTATCGATACATAAG
1 TTTGTATCGATACATAAG
444866 TTTTGTATCGATACA
1 -TTTGTATCGATACA
444881 ATGTATCGCT
Statistics
Matches: 38, Mismatches: 2, Indels: 13
0.72 0.04 0.25
Matches are distributed among these distances:
13 10 0.26
15 2 0.05
17 2 0.05
18 1 0.03
19 23 0.61
ACGTcount: A:0.32, C:0.12, G:0.15, T:0.40
Consensus pattern (18 bp):
TTTGTATCGATACATAAG
Found at i:444859 original size:32 final size:32
Alignment explanation
Indices: 444818--444888 Score: 124
Period size: 32 Copynumber: 2.2 Consensus size: 32
444808 TTCAACGATT
*
444818 TGTATCGATACATAAGTGTTGTATCTATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
*
444850 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
444882 TGTATCG
1 TGTATCG
444889 CTATGAAGCT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 37 1.00
ACGTcount: A:0.32, C:0.13, G:0.17, T:0.38
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTGTATCGATACAA
Found at i:451814 original size:15 final size:15
Alignment explanation
Indices: 451775--451816 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 15
451765 TCAAAGTATA
*
451775 TATGCCAAAAGCACT
1 TATGCCAAAAGTACT
*
451790 TATACC-AAAGTACT
1 TATGCCAAAAGTACT
*
451804 TGTGCCAAAAGTA
1 TATGCCAAAAGTA
451817 TTTACATTAA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
14 11 0.50
15 11 0.50
ACGTcount: A:0.40, C:0.21, G:0.14, T:0.24
Consensus pattern (15 bp):
TATGCCAAAAGTACT
Found at i:451828 original size:29 final size:29
Alignment explanation
Indices: 451795--451874 Score: 90
Period size: 29 Copynumber: 2.8 Consensus size: 29
451785 GCACTTATAC
*
451795 CAAAGTACTTGTGCCAAAAGTATTTACAT
1 CAAAGTACTTGTACCAAAAGTATTTACAT
* * **
451824 TAAAGTATCTT-TACCAAAGGTATTTATGT
1 CAAAGTA-CTTGTACCAAAAGTATTTACAT
*
451853 CAAAGTACTTGTACTAAAAGTA
1 CAAAGTACTTGTACCAAAAGTA
451875 CCTACACTAA
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
28 3 0.07
29 35 0.85
30 3 0.07
ACGTcount: A:0.39, C:0.14, G:0.14, T:0.34
Consensus pattern (29 bp):
CAAAGTACTTGTACCAAAAGTATTTACAT
Found at i:452011 original size:14 final size:15
Alignment explanation
Indices: 451990--452030 Score: 57
Period size: 14 Copynumber: 2.8 Consensus size: 15
451980 GCATTGTTAC
*
451990 CAAAAGTACCTGTGT
1 CAAAAGTACCTATGT
*
452005 C-AAAGTATCTATGT
1 CAAAAGTACCTATGT
452019 CAAAAGTACCTA
1 CAAAAGTACCTA
452031 CACCAAAATA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
14 12 0.55
15 10 0.45
ACGTcount: A:0.39, C:0.20, G:0.15, T:0.27
Consensus pattern (15 bp):
CAAAAGTACCTATGT
Found at i:452109 original size:28 final size:29
Alignment explanation
Indices: 452078--452141 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 29
452068 ACCTCTATCA
* * * *
452078 AAAGTATCTGTG-TCAAAATACTTGTGCC
1 AAAGTACCTGTGCTAAAAATACATATGCC
452106 AAAGTACCTGTGCTAAAAATACATATGCC
1 AAAGTACCTGTGCTAAAAATACATATGCC
452135 AAAGTAC
1 AAAGTAC
452142 TTTTACCAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
28 11 0.35
29 20 0.65
ACGTcount: A:0.39, C:0.19, G:0.16, T:0.27
Consensus pattern (29 bp):
AAAGTACCTGTGCTAAAAATACATATGCC
Found at i:452143 original size:43 final size:43
Alignment explanation
Indices: 452091--452194 Score: 118
Period size: 43 Copynumber: 2.4 Consensus size: 43
452081 GTATCTGTGT
* * * *
452091 CAAAATACTTGTGCCAAAGTACCTGTGCTAAAAATACATATGC
1 CAAAGTACTTATGCCAAAGTACCTGTGCCAAAAATACATAAGC
* * * * *
452134 CAAAGTACTTTTACCAAAGTACTTGTGCCGAAAATACCTAAGC
1 CAAAGTACTTATGCCAAAGTACCTGTGCCAAAAATACATAAGC
*
452177 CAAAGCACTTATGCCAAA
1 CAAAGTACTTATGCCAAA
452195 AAAGTGCTAT
Statistics
Matches: 50, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
43 50 1.00
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.24
Consensus pattern (43 bp):
CAAAGTACTTATGCCAAAGTACCTGTGCCAAAAATACATAAGC
Found at i:452194 original size:14 final size:14
Alignment explanation
Indices: 452091--452194 Score: 64
Period size: 14 Copynumber: 7.3 Consensus size: 14
452081 GTATCTGTGT
* *
452091 CAAAATACTTGTGC
1 CAAAGTACTTATGC
* *
452105 CAAAGTACCTGTGC
1 CAAAGTACTTATGC
* * *
452119 TAAAAATACATATGC
1 -CAAAGTACTTATGC
* *
452134 CAAAGTACTTTTAC
1 CAAAGTACTTATGC
*
452148 CAAAGTACTTGTGC
1 CAAAGTACTTATGC
* * *
452162 CGAAAATACCTAAGC
1 C-AAAGTACTTATGC
*
452177 CAAAGCACTTATGC
1 CAAAGTACTTATGC
452191 CAAA
1 CAAA
452195 AAAGTGCTAT
Statistics
Matches: 67, Mismatches: 21, Indels: 4
0.73 0.23 0.04
Matches are distributed among these distances:
14 47 0.70
15 20 0.30
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.24
Consensus pattern (14 bp):
CAAAGTACTTATGC
Found at i:453288 original size:80 final size:80
Alignment explanation
Indices: 453195--453346 Score: 259
Period size: 80 Copynumber: 1.9 Consensus size: 80
453185 GGGCTAACAA
* ** * *
453195 CATGTGTAATCTCTAAACTTTAGTGCATATTTTATATTGGTTCTTAAATTTTAAAATGTATTAAT
1 CATGTATAATCTCTAAACTTTAAAGCATATTTTATATTGGTTCTCAAATTTTAAAAAGTATTAAT
453260 CAGATCTCCTAATAG
66 CAGATCTCCTAATAG
453275 CATGTATAATCTCTAAACTTTAAAGCATATTTTATATTGGTTCTCAAATTTTAAAAAGTATTAAT
1 CATGTATAATCTCTAAACTTTAAAGCATATTTTATATTGGTTCTCAAATTTTAAAAAGTATTAAT
453340 CAGATCT
66 CAGATCT
453347 TCAATCTTAA
Statistics
Matches: 67, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
80 67 1.00
ACGTcount: A:0.35, C:0.12, G:0.10, T:0.43
Consensus pattern (80 bp):
CATGTATAATCTCTAAACTTTAAAGCATATTTTATATTGGTTCTCAAATTTTAAAAAGTATTAAT
CAGATCTCCTAATAG
Found at i:454146 original size:14 final size:15
Alignment explanation
Indices: 454141--454174 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
454131 TTTCATGCAT
454141 TGCATTGC-ATTTCA
1 TGCATTGCTATTTCA
454155 TGCA-TGCTATTTCA
1 TGCATTGCTATTTCA
454169 TGCATT
1 TGCATT
454175 TCATGAAACA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 3 0.17
14 14 0.78
15 1 0.06
ACGTcount: A:0.21, C:0.21, G:0.15, T:0.44
Consensus pattern (15 bp):
TGCATTGCTATTTCA
Found at i:454170 original size:10 final size:9
Alignment explanation
Indices: 454127--454179 Score: 51
Period size: 9 Copynumber: 6.2 Consensus size: 9
454117 CATGCATATG
454127 TGCATTTCA
1 TGCATTTCA
*
454136 TGCATTGCA
1 TGCATTTCA
454145 TTGCATTTCA
1 -TGCATTTCA
*
454155 TGCA-TGC-
1 TGCATTTCA
454162 T--ATTTCA
1 TGCATTTCA
454169 TGCATTTCA
1 TGCATTTCA
454178 TG
1 TG
454180 AAACATTTCA
Statistics
Matches: 35, Mismatches: 4, Indels: 10
0.71 0.08 0.20
Matches are distributed among these distances:
5 1 0.03
6 2 0.06
7 2 0.06
8 2 0.06
9 20 0.57
10 8 0.23
ACGTcount: A:0.21, C:0.21, G:0.15, T:0.43
Consensus pattern (9 bp):
TGCATTTCA
Found at i:454739 original size:19 final size:21
Alignment explanation
Indices: 454715--454758 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 21
454705 AATCGAAAGC
*
454715 AAAAAAGA-CAAAAACAAA-A
1 AAAAAACAGCAAAAACAAATA
*
454734 AAAAAACAGTAAAAACAAATA
1 AAAAAACAGCAAAAACAAATA
454755 AAAA
1 AAAA
454759 GTAATAATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 7 0.33
20 9 0.43
21 5 0.24
ACGTcount: A:0.82, C:0.09, G:0.05, T:0.05
Consensus pattern (21 bp):
AAAAAACAGCAAAAACAAATA
Found at i:458680 original size:19 final size:20
Alignment explanation
Indices: 458644--458687 Score: 56
Period size: 19 Copynumber: 2.2 Consensus size: 20
458634 TTATAATTTA
*
458644 AATTTTTTATAAAAAT-AAT
1 AATTTATTATAAAAATAAAT
458663 AATTTATTA-AAAATATAAAT
1 AATTTATTATAAAA-ATAAAT
458683 AATTT
1 AATTT
458688 TTTCATTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 4 0.18
19 10 0.45
20 8 0.36
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
AATTTATTATAAAAATAAAT
Found at i:459106 original size:6 final size:6
Alignment explanation
Indices: 459097--459135 Score: 51
Period size: 6 Copynumber: 6.2 Consensus size: 6
459087 ATTTTTATTT
*
459097 ATAAAA ATAAAA ATAAAAA ATACAA ATAAAAA ATAAAA A
1 ATAAAA ATAAAA AT-AAAA ATAAAA AT-AAAA ATAAAA A
459136 ATGAAAGAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
6 18 0.62
7 11 0.38
ACGTcount: A:0.82, C:0.03, G:0.00, T:0.15
Consensus pattern (6 bp):
ATAAAA
Found at i:459115 original size:7 final size:7
Alignment explanation
Indices: 459099--459152 Score: 58
Period size: 7 Copynumber: 7.7 Consensus size: 7
459089 TTTTATTTAT
459099 AAAAAT-
1 AAAAATA
459105 AAAAATA
1 AAAAATA
459112 AAAAAT-
1 AAAAATA
*
459118 ACAAATA
1 AAAAATA
459125 AAAAATA
1 AAAAATA
459132 AAAAATGA
1 AAAAAT-A
*
459140 AAGAAAGA
1 AA-AAATA
459148 AAAAA
1 AAAAA
459153 ATTAAATTAA
Statistics
Matches: 41, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
6 11 0.27
7 21 0.51
8 6 0.15
9 3 0.07
ACGTcount: A:0.81, C:0.02, G:0.06, T:0.11
Consensus pattern (7 bp):
AAAAATA
Found at i:459117 original size:13 final size:13
Alignment explanation
Indices: 459099--459135 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
459089 TTTTATTTAT
459099 AAAAATAAAAATA
1 AAAAATAAAAATA
*
459112 AAAAATACAAATA
1 AAAAATAAAAATA
459125 AAAAATAAAAA
1 AAAAATAAAAA
459136 ATGAAAGAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.84, C:0.03, G:0.00, T:0.14
Consensus pattern (13 bp):
AAAAATAAAAATA
Found at i:459191 original size:18 final size:18
Alignment explanation
Indices: 459168--459212 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 18
459158 ATTAAATGAA
459168 TATTT-ATATTTTATAAAT
1 TATTTAATA-TTTATAAAT
459186 TATTTAATATTTATAAAAT
1 TATTTAATATTTAT-AAAT
459205 TAATTTAA
1 T-ATTTAA
459213 ATTATAATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
18 10 0.42
19 8 0.33
20 6 0.25
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
TATTTAATATTTATAAAT
Found at i:459197 original size:19 final size:19
Alignment explanation
Indices: 459168--459233 Score: 59
Period size: 20 Copynumber: 3.4 Consensus size: 19
459158 ATTAAATGAA
459168 TATTT-ATATTTTATAAAT
1 TATTTAATATTTTATAAAT
459186 TATTTAATA-TTTATAAAAT
1 TATTTAATATTTTAT-AAAT
459205 TAATTTAA-ATTATAATATAAAT
1 T-ATTTAATATT-T--TATAAAT
459227 T-TTTAAT
1 TATTTAAT
459234 TATGGTCTAG
Statistics
Matches: 40, Mismatches: 0, Indels: 13
0.75 0.00 0.25
Matches are distributed among these distances:
18 10 0.25
19 9 0.22
20 12 0.30
21 1 0.03
22 5 0.12
23 3 0.08
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (19 bp):
TATTTAATATTTTATAAAT
Found at i:459217 original size:18 final size:19
Alignment explanation
Indices: 459168--459233 Score: 59
Period size: 19 Copynumber: 3.4 Consensus size: 19
459158 ATTAAATGAA
459168 TATTT-ATATTT-TATAAAT
1 TATTTAATATTTATA-AAAT
459186 TATTTAATATTTATAAAAT
1 TATTTAATATTTATAAAAT
459205 TAATTTAA-ATTATAATATAAAT
1 T-ATTTAATATT-T-ATA-AAAT
459227 T-TTTAAT
1 TATTTAAT
459234 TATGGTCTAG
Statistics
Matches: 41, Mismatches: 0, Indels: 11
0.79 0.00 0.21
Matches are distributed among these distances:
18 5 0.12
19 14 0.34
20 14 0.34
21 3 0.07
22 5 0.12
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (19 bp):
TATTTAATATTTATAAAAT
Found at i:459289 original size:18 final size:18
Alignment explanation
Indices: 459262--459298 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
459252 TTAAGAAGAC
*
459262 AAAATGAAAGAAAGAAAA
1 AAAATGAAAGAAACAAAA
*
459280 AAAATTAAAGAAACAAAA
1 AAAATGAAAGAAACAAAA
459298 A
1 A
459299 GAATAAAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.78, C:0.03, G:0.11, T:0.08
Consensus pattern (18 bp):
AAAATGAAAGAAACAAAA
Found at i:462632 original size:16 final size:16
Alignment explanation
Indices: 462601--462653 Score: 54
Period size: 15 Copynumber: 3.2 Consensus size: 16
462591 AAATTTAAAA
462601 TTATTATATATTTATTTT
1 TTATTATATA--TATTTT
462619 TTATTATATATA-TTT
1 TTATTATATATATTTT
** *
462634 TTAAGAAATATATTTT
1 TTATTATATATATTTT
462650 TTAT
1 TTAT
462654 CTTTTTAATT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
15 12 0.40
16 8 0.27
18 10 0.33
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (16 bp):
TTATTATATATATTTT
Found at i:463649 original size:25 final size:26
Alignment explanation
Indices: 463621--463669 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
463611 AATTTGACAT
*
463621 TTTATAA-A-ATAATCATTTATAAATA
1 TTTATAATATATAATC-TATATAAATA
463646 TTTATAATATATAATCTATATAAA
1 TTTATAATATATAATCTATATAAA
463670 AGTATAAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
25 7 0.33
26 8 0.38
27 6 0.29
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (26 bp):
TTTATAATATATAATCTATATAAATA
Found at i:464494 original size:20 final size:21
Alignment explanation
Indices: 464456--464499 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
464446 ATTTTTATCA
*
464456 AATTATTTAAAATGGTTTTGT
1 AATTATTTAAAATGGTTTTAT
*
464477 AATTTTTTAAAA-GGTTTTAT
1 AATTATTTAAAATGGTTTTAT
464497 AAT
1 AAT
464500 AAATTTTTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 10 0.48
21 11 0.52
ACGTcount: A:0.36, C:0.00, G:0.11, T:0.52
Consensus pattern (21 bp):
AATTATTTAAAATGGTTTTAT
Found at i:466313 original size:2 final size:2
Alignment explanation
Indices: 466306--466335 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
466296 AGTTTAAATA
*
466306 AT AT AT AT AT AT AT AT AT AT AG AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
466336 TGTGGGCAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:468034 original size:19 final size:20
Alignment explanation
Indices: 468003--468042 Score: 73
Period size: 19 Copynumber: 2.0 Consensus size: 20
467993 TTAAGCTACT
468003 TATGAATTATTTAAATTTGA
1 TATGAATTATTTAAATTTGA
468023 TATGAA-TATTTAAATTTGA
1 TATGAATTATTTAAATTTGA
468042 T
1 T
468043 TATTTACTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 14 0.70
20 6 0.30
ACGTcount: A:0.40, C:0.00, G:0.10, T:0.50
Consensus pattern (20 bp):
TATGAATTATTTAAATTTGA
Found at i:470005 original size:30 final size:30
Alignment explanation
Indices: 469963--470019 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 30
469953 TTAATATTAT
*
469963 TTTTACATATAATAATATGTCATTATTTGAA
1 TTTTACATATAAT-ATATGTAATTATTTGAA
*
469994 TTTTA-ATATAATATATTTAATTATTT
1 TTTTACATATAATATATGTAATTATTT
470020 TATATATTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 12 0.50
30 7 0.29
31 5 0.21
ACGTcount: A:0.39, C:0.04, G:0.04, T:0.54
Consensus pattern (30 bp):
TTTTACATATAATATATGTAATTATTTGAA
Found at i:470030 original size:30 final size:30
Alignment explanation
Indices: 469969--470031 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 30
469959 TTATTTTTAC
* *
469969 ATATAATAATATGTCATTATTTGAATTTTA
1 ATATAATAATATGTAATTATTTGAATATTA
* *
469999 ATATAAT-ATATTTAATTATTTTATATATTA
1 ATATAATAATATGTAATTATTTGA-ATATTA
470029 ATA
1 ATA
470032 ATTTTTATAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 13 0.46
30 15 0.54
ACGTcount: A:0.43, C:0.02, G:0.03, T:0.52
Consensus pattern (30 bp):
ATATAATAATATGTAATTATTTGAATATTA
Found at i:470039 original size:22 final size:22
Alignment explanation
Indices: 469993--470039 Score: 53
Period size: 24 Copynumber: 2.1 Consensus size: 22
469983 CATTATTTGA
469993 ATTTTAATATAATATATTTAATT
1 ATTTTAATATAATATATTT-ATT
470016 ATTTTATATATTAATA-ATTT-TT
1 ATTTTA-ATA-TAATATATTTATT
470038 AT
1 AT
470040 AAGTGATTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
22 4 0.18
23 6 0.27
24 7 0.32
25 5 0.23
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (22 bp):
ATTTTAATATAATATATTTATT
Found at i:470040 original size:15 final size:17
Alignment explanation
Indices: 470004--470040 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
469994 TTTTAATATA
*
470004 ATATATTTAATTATTTT
1 ATATATTTAATAATTTT
470021 ATATA-TTAATAATTTT
1 ATATATTTAATAATTTT
470037 -TATA
1 ATATA
470041 AGTGATTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 4 0.21
16 10 0.53
17 5 0.26
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
ATATATTTAATAATTTT
Found at i:472261 original size:34 final size:33
Alignment explanation
Indices: 472220--472310 Score: 119
Period size: 34 Copynumber: 2.7 Consensus size: 33
472210 TTTAAATATC
* *
472220 ATTAAAATAAAAATAAAAAGTTATTTAACGAAAA
1 ATTAAAAT-AAAATAAAAAATTATTTAACCAAAA
472254 ATTAAAATTAAAATAAAAAATTATTTAACCAAAA
1 ATTAAAA-TAAAATAAAAAATTATTTAACCAAAA
* *
472288 ATTTAAATATAATAAAAATATTA
1 ATTAAAATAAAATAAAAA-ATTA
472311 AAAAGTACTT
Statistics
Matches: 51, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
33 10 0.20
34 40 0.78
35 1 0.02
ACGTcount: A:0.64, C:0.03, G:0.02, T:0.31
Consensus pattern (33 bp):
ATTAAAATAAAATAAAAAATTATTTAACCAAAA
Found at i:476235 original size:24 final size:22
Alignment explanation
Indices: 476171--476241 Score: 70
Period size: 24 Copynumber: 3.0 Consensus size: 22
476161 CTAAAGAATT
*
476171 ATTATATAATAAATCTATTTTA
1 ATTATATAATAAATTTATTTTA
* *
476193 ATGATATAATTAAAATTATTTCTA
1 ATTATATAA-TAAATTTATTT-TA
*
476217 CTTATATAATAAATTTTATTATTA
1 ATTATATAATAAA-TTTATT-TTA
476241 A
1 A
476242 AATTCAATAT
Statistics
Matches: 38, Mismatches: 7, Indels: 6
0.75 0.14 0.12
Matches are distributed among these distances:
22 8 0.21
23 13 0.34
24 16 0.42
25 1 0.03
ACGTcount: A:0.45, C:0.04, G:0.01, T:0.49
Consensus pattern (22 bp):
ATTATATAATAAATTTATTTTA
Found at i:478605 original size:26 final size:27
Alignment explanation
Indices: 478544--478607 Score: 67
Period size: 28 Copynumber: 2.4 Consensus size: 27
478534 AAGAAATGCT
* *
478544 AGTAATTATTGCTTATTTATACCGAAA
1 AGTAATTTTTGCTTATTTATACCCAAA
* * *
478571 AATATATTTTTTCTTTTTTAT-CCCAAA
1 AGTA-ATTTTTGCTTATTTATACCCAAA
478598 AGTAATTTTT
1 AGTAATTTTT
478608 AACTAATTAG
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
26 6 0.20
27 11 0.37
28 13 0.43
ACGTcount: A:0.33, C:0.11, G:0.06, T:0.50
Consensus pattern (27 bp):
AGTAATTTTTGCTTATTTATACCCAAA
Found at i:479525 original size:22 final size:22
Alignment explanation
Indices: 479497--479566 Score: 77
Period size: 22 Copynumber: 3.2 Consensus size: 22
479487 TGATTCGGCC
* *
479497 ATTTAATTATAGTCATATATAT
1 ATTTAATTATAATTATATATAT
* *
479519 ATTTAATTATAATTATATAAAC
1 ATTTAATTATAATTATATATAT
* * *
479541 ATTTAGTTATATTTATATGTAT
1 ATTTAATTATAATTATATATAT
479563 ATTT
1 ATTT
479567 GGTGATGGTG
Statistics
Matches: 39, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 39 1.00
ACGTcount: A:0.40, C:0.03, G:0.04, T:0.53
Consensus pattern (22 bp):
ATTTAATTATAATTATATATAT
Found at i:479732 original size:22 final size:22
Alignment explanation
Indices: 479697--479775 Score: 95
Period size: 22 Copynumber: 3.6 Consensus size: 22
479687 ACAGGAGTTT
* * *
479697 GTCATTTGTGCATTCAATTATA
1 GTCATATGTACATTCAATTATG
* * *
479719 ATCATATGTACATTTAGTTATG
1 GTCATATGTACATTCAATTATG
*
479741 GTCATATGTATATTCAATTATG
1 GTCATATGTACATTCAATTATG
479763 GTCATATGTACAT
1 GTCATATGTACAT
479776 CACATTTATT
Statistics
Matches: 46, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 46 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.44
Consensus pattern (22 bp):
GTCATATGTACATTCAATTATG
Found at i:480188 original size:22 final size:22
Alignment explanation
Indices: 480163--480229 Score: 89
Period size: 22 Copynumber: 3.0 Consensus size: 22
480153 TTTAGTCATG
*
480163 TGTACATTCAATTATAGTTGTA
1 TGTACATTCAATTATAGTTATA
* * *
480185 TGTACATTTAGTTATAGTTATT
1 TGTACATTCAATTATAGTTATA
*
480207 TGTACATTCAATTATAGTCATA
1 TGTACATTCAATTATAGTTATA
480229 T
1 T
480230 ATATATATAT
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 37 1.00
ACGTcount: A:0.31, C:0.09, G:0.12, T:0.48
Consensus pattern (22 bp):
TGTACATTCAATTATAGTTATA
Found at i:480432 original size:22 final size:22
Alignment explanation
Indices: 480407--480467 Score: 70
Period size: 22 Copynumber: 2.8 Consensus size: 22
480397 TGTTTTAGTC
480407 ATATGTATATTCAATTATA-CTA
1 ATATGTATATTCAATTATAGC-A
* * *
480429 ATATGTATATTTAGTTATAGCC
1 ATATGTATATTCAATTATAGCA
*
480451 ATATGTACATTCAATTA
1 ATATGTATATTCAATTA
480468 CAGTCACATG
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
22 31 0.97
23 1 0.03
ACGTcount: A:0.38, C:0.10, G:0.08, T:0.44
Consensus pattern (22 bp):
ATATGTATATTCAATTATAGCA
Found at i:486540 original size:2 final size:2
Alignment explanation
Indices: 486533--486562 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
486523 CAATTGTAAA
486533 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
486563 CCTTTGTAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:493117 original size:24 final size:22
Alignment explanation
Indices: 493090--493136 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 22
493080 ATACTAATTT
493090 ATTAAAAAAATTACAAAAAATAAA
1 ATTAAAAAAA-TA-AAAAAATAAA
*
493114 ATTAATAAAATAAAAAAATAAA
1 ATTAAAAAAATAAAAAAATAAA
493136 A
1 A
493137 GTGTCTCAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 11 0.50
23 2 0.09
24 9 0.41
ACGTcount: A:0.77, C:0.02, G:0.00, T:0.21
Consensus pattern (22 bp):
ATTAAAAAAATAAAAAAATAAA
Found at i:493125 original size:14 final size:15
Alignment explanation
Indices: 493096--493128 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
493086 ATTTATTAAA
493096 AAAATTACAAAAAAT
1 AAAATTACAAAAAAT
*
493111 AAAATTA-ATAAAAT
1 AAAATTACAAAAAAT
493125 AAAA
1 AAAA
493129 AAATAAAAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 10 0.59
15 7 0.41
ACGTcount: A:0.76, C:0.03, G:0.00, T:0.21
Consensus pattern (15 bp):
AAAATTACAAAAAAT
Found at i:494155 original size:27 final size:27
Alignment explanation
Indices: 494125--494187 Score: 74
Period size: 27 Copynumber: 2.3 Consensus size: 27
494115 ACTGCACCAT
*
494125 AAATAAAATTAATTAAATTATAA-AAAA
1 AAATAAAATTAATT-AATTAAAAGAAAA
* * *
494152 AAATTAAATTTATTATTTAAAAGAAAA
1 AAATAAAATTAATTAATTAAAAGAAAA
494179 AAATAAAAT
1 AAATAAAAT
494188 AAAATCAAGT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
26 6 0.20
27 24 0.80
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.32
Consensus pattern (27 bp):
AAATAAAATTAATTAATTAAAAGAAAA
Found at i:498636 original size:36 final size:36
Alignment explanation
Indices: 498589--498662 Score: 139
Period size: 36 Copynumber: 2.1 Consensus size: 36
498579 ATTTTTCCAG
498589 CAACAAGTCTTGATTTACATCTTTCAACTGAACCAT
1 CAACAAGTCTTGATTTACATCTTTCAACTGAACCAT
*
498625 CAACAAGTCTTGATTTACGTCTTTCAACTGAACCAT
1 CAACAAGTCTTGATTTACATCTTTCAACTGAACCAT
498661 CA
1 CA
498663 GCTTTTCTTT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.32, C:0.26, G:0.09, T:0.32
Consensus pattern (36 bp):
CAACAAGTCTTGATTTACATCTTTCAACTGAACCAT
Found at i:499968 original size:20 final size:20
Alignment explanation
Indices: 499935--499978 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
499925 GTACCTTGAT
* *
499935 GAAGTTTTACAAAATGTAAA
1 GAAGTTTCACAAAAGGTAAA
* *
499955 GAAGTTTCAGAAAAGGTGAA
1 GAAGTTTCACAAAAGGTAAA
499975 GAAG
1 GAAG
499979 AATCTCACCC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.48, C:0.05, G:0.25, T:0.23
Consensus pattern (20 bp):
GAAGTTTCACAAAAGGTAAA
Found at i:502019 original size:11 final size:10
Alignment explanation
Indices: 502000--502069 Score: 54
Period size: 10 Copynumber: 6.9 Consensus size: 10
501990 CATATACAGA
502000 AAAAT-TAATT
1 AAAATATAA-T
502010 AAAATATAAT
1 AAAATATAAT
* *
502020 ATAATAAAAT
1 AAAATATAAT
502030 ATAAATATAAT
1 A-AAATATAAT
*
502041 ATAAATATATT
1 A-AAATATAAT
*
502052 AAAAT-TTAT
1 AAAATATAAT
*
502061 ATAATATAA
1 AAAATATAA
502070 ATTACTAACT
Statistics
Matches: 48, Mismatches: 9, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
9 6 0.12
10 21 0.44
11 21 0.44
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (10 bp):
AAAATATAAT
Found at i:502022 original size:5 final size:5
Alignment explanation
Indices: 502012--502069 Score: 55
Period size: 5 Copynumber: 11.4 Consensus size: 5
502002 AATTAATTAA
* * * *
502012 AATAT AATAT AATAA AATAT AAATAT AATAT AAATAT ATTAA AAT-T TATAT
1 AATAT AATAT AATAT AATAT -AATAT AATAT -AATAT AATAT AATAT AATAT
502063 AATAT AA
1 AATAT AA
502070 ATTACTAACT
Statistics
Matches: 42, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
4 2 0.05
5 30 0.71
6 10 0.24
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (5 bp):
AATAT
Found at i:502073 original size:21 final size:22
Alignment explanation
Indices: 502006--502073 Score: 81
Period size: 21 Copynumber: 3.2 Consensus size: 22
501996 CAGAAAAATT
502006 AATTAAAATATAATATAATA-A
1 AATTAAAATATAATATAATATA
502027 AA-TATAAATATAATATAA-ATA
1 AATTA-AAATATAATATAATATA
* *
502048 TATTAAAAT-TTATATAATATA
1 AATTAAAATATAATATAATATA
502069 AATTA
1 AATTA
502074 CTAACTTATT
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
20 10 0.25
21 28 0.70
22 2 0.05
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (22 bp):
AATTAAAATATAATATAATATA
Found at i:502382 original size:16 final size:16
Alignment explanation
Indices: 502358--502440 Score: 71
Period size: 16 Copynumber: 5.1 Consensus size: 16
502348 GTTGGGTTAA
*
502358 TTTAAATTTAAATTAT
1 TTTAGATTTAAATTAT
*
502374 TTTAGATTTAAATTAC
1 TTTAGATTTAAATTAT
* *
502390 TTTAGATTTGATATCAT
1 TTTAGATTT-AAATTAT
*
502407 TTT-GTATTTATATTAT
1 TTTAG-ATTTAAATTAT
*
502423 TTTA-AGTTTAAATAAT
1 TTTAGA-TTTAAATTAT
502439 TT
1 TT
502441 AAATTTGAAA
Statistics
Matches: 55, Mismatches: 8, Indels: 8
0.77 0.11 0.11
Matches are distributed among these distances:
15 1 0.02
16 43 0.78
17 11 0.20
ACGTcount: A:0.35, C:0.02, G:0.06, T:0.57
Consensus pattern (16 bp):
TTTAGATTTAAATTAT
Found at i:502495 original size:14 final size:14
Alignment explanation
Indices: 502472--502523 Score: 52
Period size: 14 Copynumber: 3.7 Consensus size: 14
502462 GAGTTTATTT
*
502472 TTAAAGTTTAAAGA
1 TTAAAATTTAAAGA
*
502486 TTAAAATTTAAAGT
1 TTAAAATTTAAAGA
* *
502500 TTAAGATTT-ATGA
1 TTAAAATTTAAAGA
502513 TTTAAAATTTA
1 -TTAAAATTTA
502524 CGAATTAGAA
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
13 2 0.07
14 28 0.93
ACGTcount: A:0.46, C:0.00, G:0.10, T:0.44
Consensus pattern (14 bp):
TTAAAATTTAAAGA
Found at i:502536 original size:21 final size:21
Alignment explanation
Indices: 502471--502538 Score: 59
Period size: 21 Copynumber: 3.2 Consensus size: 21
502461 TGAGTTTATT
* *
502471 TTTAAAGTTTAA-AGATTAAAA
1 TTTAAAATTTAAGA-ATTAGAA
* *
502492 TTTAAAGTTTAAGATTTATG-A
1 TTTAAAATTTAAGAATTA-GAA
*
502513 TTTAAAATTTACGAATTAGAA
1 TTTAAAATTTAAGAATTAGAA
502534 TTTAA
1 TTTAA
502539 TATCTTTAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
20 1 0.03
21 37 0.95
22 1 0.03
ACGTcount: A:0.46, C:0.01, G:0.10, T:0.43
Consensus pattern (21 bp):
TTTAAAATTTAAGAATTAGAA
Found at i:502972 original size:21 final size:21
Alignment explanation
Indices: 502948--502997 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
502938 TAAAATTAAC
502948 TTTTACTAATTTAATAT-ATTT
1 TTTTACTAATTTAATATGA-TT
* *
502969 TTTTACTATTTTAATTTGATT
1 TTTTACTAATTTAATATGATT
502990 TTTTACTA
1 TTTTACTA
502998 GTATGATGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
21 25 0.96
22 1 0.04
ACGTcount: A:0.28, C:0.06, G:0.02, T:0.64
Consensus pattern (21 bp):
TTTTACTAATTTAATATGATT
Found at i:504052 original size:20 final size:18
Alignment explanation
Indices: 504029--504076 Score: 69
Period size: 20 Copynumber: 2.5 Consensus size: 18
504019 CTGTGAGGAA
504029 TTAAAATATAAAAAATATAT
1 TTAAAATATAAAAAA-AT-T
504049 TTAAAATAATAAAAAAATT
1 TTAAAAT-ATAAAAAAATT
504068 TTAAAATAT
1 TTAAAATAT
504077 GAGGATAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
18 2 0.07
19 8 0.30
20 9 0.33
21 8 0.30
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (18 bp):
TTAAAATATAAAAAAATT
Found at i:504070 original size:19 final size:21
Alignment explanation
Indices: 504029--504075 Score: 73
Period size: 19 Copynumber: 2.4 Consensus size: 21
504019 CTGTGAGGAA
504029 TTAAAAT-ATAAAAAATATAT
1 TTAAAATAATAAAAAATATAT
504049 TTAAAATAATAAAAAA-AT-T
1 TTAAAATAATAAAAAATATAT
504068 TTAAAATA
1 TTAAAATA
504076 TGAGGATAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 9 0.35
20 9 0.35
21 8 0.31
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (21 bp):
TTAAAATAATAAAAAATATAT
Found at i:505477 original size:129 final size:132
Alignment explanation
Indices: 505334--505591 Score: 441
Period size: 131 Copynumber: 2.0 Consensus size: 132
505324 TTTATTTTTT
* *
505334 AATATATTATTATGTATATTAATCTT-AAAAAA-TGTTTTAAAATCAACTAAATTTCATCAATTA
1 AATATATTATTATGTATATTAATCTTAAAAAAAGTGTTTTAAAATCAACAAAATTCCATCAATTA
*
505397 AAATTCAATAAATATAGAT-AAAAAATAAAATTCATCAAATTAATCATTTTCACATATAATAATT
66 AAATTCAATAAATATAAATAAAAAAATAAAATTCATCAAATTAATCATTTTCACATATAATAATT
505461 TG
131 TG
505463 AATATATTATTATGTATATTAATCTTAAAAAAAGTGTTTTAAAATCAACAAAATTCCATCAATTA
1 AATATATTATTATGTATATTAATCTTAAAAAAAGTGTTTTAAAATCAACAAAATTCCATCAATTA
* * *
505528 AAATTCAATTAATATAAATAAAAAAATAAAATTTATCAAATTAATTATTTTCACATATAATAAT
66 AAATTCAATAAATATAAATAAAAAAATAAAATTCATCAAATTAATCATTTTCACATATAATAAT
505592 CATAACTAGC
Statistics
Matches: 120, Mismatches: 6, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
129 26 0.22
130 6 0.05
131 46 0.38
132 42 0.35
ACGTcount: A:0.51, C:0.08, G:0.03, T:0.38
Consensus pattern (132 bp):
AATATATTATTATGTATATTAATCTTAAAAAAAGTGTTTTAAAATCAACAAAATTCCATCAATTA
AAATTCAATAAATATAAATAAAAAAATAAAATTCATCAAATTAATCATTTTCACATATAATAATT
TG
Found at i:507508 original size:26 final size:27
Alignment explanation
Indices: 507456--507513 Score: 70
Period size: 27 Copynumber: 2.3 Consensus size: 27
507446 ATTTTACCAT
*
507456 TATA-TTTTAATTTTATTAAATATTAA
1 TATATTTTTAATTTTATTAAATAATAA
507482 TATATTTTTAATTTT-TATAAA-AATAA
1 TATATTTTTAATTTTAT-TAAATAATAA
507508 T-TATTT
1 TATATTT
507514 CATATATTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
25 5 0.17
26 10 0.34
27 14 0.48
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (27 bp):
TATATTTTTAATTTTATTAAATAATAA
Found at i:507711 original size:13 final size:13
Alignment explanation
Indices: 507693--507717 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
507683 CACTTCCTTA
507693 ATAAAATATTTTC
1 ATAAAATATTTTC
507706 ATAAAATATTTT
1 ATAAAATATTTT
507718 TAATATGAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (13 bp):
ATAAAATATTTTC
Found at i:508609 original size:4 final size:4
Alignment explanation
Indices: 508600--508655 Score: 50
Period size: 4 Copynumber: 14.8 Consensus size: 4
508590 GTTAGGTAAA
508600 AAAG AAAG AAAG -AAG ATGAAG -AAG AAAG AAAG AAAG -AA- AAAG AAA-
1 AAAG AAAG AAAG AAAG A--AAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG
*
508645 AAAA AAAG AAA
1 AAAG AAAG AAA
508656 AAAATATGAA
Statistics
Matches: 44, Mismatches: 1, Indels: 14
0.75 0.02 0.24
Matches are distributed among these distances:
3 13 0.30
4 28 0.64
6 3 0.07
ACGTcount: A:0.77, C:0.00, G:0.21, T:0.02
Consensus pattern (4 bp):
AAAG
Found at i:508666 original size:11 final size:11
Alignment explanation
Indices: 508618--508659 Score: 50
Period size: 11 Copynumber: 3.9 Consensus size: 11
508608 AAAGAAGATG
* *
508618 AAGAAGAAAGA
1 AAGAAAAAAAA
*
508629 AAG-AAAGAAA
1 AAGAAAAAAAA
508639 AAGAAAAAAAA
1 AAGAAAAAAAA
508650 AAGAAAAAAA
1 AAGAAAAAAA
508660 TATGAAATGG
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
10 7 0.27
11 19 0.73
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (11 bp):
AAGAAAAAAAA
Found at i:509017 original size:13 final size:15
Alignment explanation
Indices: 508987--509036 Score: 50
Period size: 16 Copynumber: 3.3 Consensus size: 15
508977 TTTGCATTTG
508987 TTTTTTTATTATCATA
1 TTTTTTTATTAT-ATA
509003 TTTTTTTATT-T-TA
1 TTTTTTTATTATATA
* *
509016 TTTATATATATATATA
1 TTTTTTTAT-TATATA
509032 TTTTT
1 TTTTT
509037 GAAAATCTCC
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
13 9 0.32
14 1 0.04
15 2 0.07
16 16 0.57
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (15 bp):
TTTTTTTATTATATA
Found at i:511721 original size:2 final size:2
Alignment explanation
Indices: 511716--511751 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
511706 CATGAGAGAG
511716 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
511752 AAGAAAATTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:513810 original size:62 final size:62
Alignment explanation
Indices: 513716--513836 Score: 188
Period size: 62 Copynumber: 2.0 Consensus size: 62
513706 CCTTTCCTTC
* * *
513716 CCATTCCTTTCCTTTGCATAGCCTTAGCTGATCTTGTGGCTAGGGTTAATATATAACTTATT
1 CCATTCCTTTCCTTTGCATAGCCTTAACTGATCTTGTGGCTAGGGATAACATATAACTTATT
* * *
513778 CCATTCCTTTCCTTTGCATAGCCTTAATTGATCTTGTTGTTAGGGATAACATATAACTT
1 CCATTCCTTTCCTTTGCATAGCCTTAACTGATCTTGTGGCTAGGGATAACATATAACTT
513837 TTAAGTTTAA
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
62 53 1.00
ACGTcount: A:0.22, C:0.21, G:0.15, T:0.42
Consensus pattern (62 bp):
CCATTCCTTTCCTTTGCATAGCCTTAACTGATCTTGTGGCTAGGGATAACATATAACTTATT
Found at i:514091 original size:16 final size:16
Alignment explanation
Indices: 514070--514100 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
514060 TTCTAAGCGA
514070 AATTCAAAAAAATTCG
1 AATTCAAAAAAATTCG
*
514086 AATTCAAAATAATTC
1 AATTCAAAAAAATTC
514101 AAATAAAAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.13, G:0.03, T:0.29
Consensus pattern (16 bp):
AATTCAAAAAAATTCG
Found at i:514248 original size:2 final size:2
Alignment explanation
Indices: 514241--514269 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
514231 CAAAATTAAA
514241 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
514270 AAGGAAAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:516582 original size:24 final size:25
Alignment explanation
Indices: 516541--516605 Score: 64
Period size: 23 Copynumber: 2.6 Consensus size: 25
516531 TTGAATTTAG
* *
516541 TATT-AATTTTTATATAAATTATAAAT
1 TATTGAATTTCTAT-TAAA-TAAAAAT
*
516567 TTTTG-ATTTC-ATTAAATAAAAAT
1 TATTGAATTTCTATTAAATAAAAAT
516590 TATTGAATTTCTATTA
1 TATTGAATTTCTATTA
516606 TTAATAAATT
Statistics
Matches: 32, Mismatches: 4, Indels: 7
0.74 0.09 0.16
Matches are distributed among these distances:
23 10 0.31
24 9 0.28
25 6 0.19
26 7 0.22
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.52
Consensus pattern (25 bp):
TATTGAATTTCTATTAAATAAAAAT
Found at i:516614 original size:25 final size:24
Alignment explanation
Indices: 516555--516616 Score: 65
Period size: 24 Copynumber: 2.6 Consensus size: 24
516545 AATTTTTATA
* *
516555 TAAATTATAAATTTTTGATTTCAT
1 TAAATAATAAATTATTGATTTCAT
516579 TAAATAA-AAATTATTGAATTTCTAT
1 TAAATAATAAATTATTG-ATTTC-AT
*
516604 T-ATTAATAAATTA
1 TAAATAATAAATTA
516617 AATTATCTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
23 8 0.25
24 15 0.47
25 9 0.28
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.48
Consensus pattern (24 bp):
TAAATAATAAATTATTGATTTCAT
Found at i:517892 original size:3 final size:3
Alignment explanation
Indices: 517884--517923 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
517874 TTGAGAGTTC
517884 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
517924 ATAAATAAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:517928 original size:4 final size:4
Alignment explanation
Indices: 517919--517944 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
517909 TAATAATAAT
517919 AATA AATA AATA AATA AATA AATA AA
1 AATA AATA AATA AATA AATA AATA AA
517945 GATCAAGATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AATA
Found at i:518556 original size:32 final size:31
Alignment explanation
Indices: 518474--518588 Score: 108
Period size: 32 Copynumber: 3.7 Consensus size: 31
518464 AAATTAAACA
* * *
518474 TTTTTAATAGTTGTTAAATTTACAAATAATT
1 TTTTTAATATTTATTAAATTTACAAGTAATT
* * * * *
518505 ATGTCAATATTCATCAAATTTACAAGTAATT
1 TTTTTAATATTTATTAAATTTACAAGTAATT
*
518536 TCTTTTAATATTTATTAAATTTATAAGTAATT
1 T-TTTTAATATTTATTAAATTTACAAGTAATT
*
518568 ATATTT-A-ATTTATTAAATTTA
1 -TTTTTAATATTTATTAAATTTA
518589 TGATCAAAAT
Statistics
Matches: 67, Mismatches: 15, Indels: 5
0.77 0.17 0.06
Matches are distributed among these distances:
30 14 0.21
31 24 0.36
32 28 0.42
33 1 0.01
ACGTcount: A:0.40, C:0.05, G:0.04, T:0.50
Consensus pattern (31 bp):
TTTTTAATATTTATTAAATTTACAAGTAATT
Found at i:527170 original size:26 final size:25
Alignment explanation
Indices: 527108--527171 Score: 60
Period size: 27 Copynumber: 2.4 Consensus size: 25
527098 AATTTTTGAG
527108 TTAATATTTATTAATATATTATTATT
1 TTAATATTT-TTAATATATTATTATT
*
527134 TTAA-ATTTTTTTATATAGGTTA-TATT
1 TTAATA-TTTTTAATATA--TTATTATT
527160 ATTAATATTTTT
1 -TTAATATTTTT
527172 TCATTTTTGA
Statistics
Matches: 32, Mismatches: 1, Indels: 9
0.76 0.02 0.21
Matches are distributed among these distances:
25 8 0.25
26 11 0.34
27 12 0.38
28 1 0.03
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.62
Consensus pattern (25 bp):
TTAATATTTTTAATATATTATTATT
Found at i:531692 original size:79 final size:78
Alignment explanation
Indices: 531524--531728 Score: 216
Period size: 79 Copynumber: 2.6 Consensus size: 78
531514 AGAAATAATA
* * * * ** * *
531524 ACGGGGTTGGAGTGTCCCCTTGAAAATGACGGGGCTGGAGTATCCCCGGTTGTGAGAAATCGATG
1 ACGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAATG
531589 ATTAGAAAAAAAC
66 ATTAGAAAAAAAC
*
531602 ATCGGGATTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAAT
1 A-CGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAAT
* * *
531667 -ATTTTGGGAATAAAGC
65 GA--TT-AGAAAAAAAC
* ***
531683 -CGGGGTTGGAGTATCCCCTCGGAGGCAACGGGGTTGGAGTATCCCC
1 ACGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCC
531729 GATGAAATAA
Statistics
Matches: 106, Mismatches: 17, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
78 2 0.02
79 95 0.90
80 2 0.02
81 7 0.07
ACGTcount: A:0.28, C:0.19, G:0.31, T:0.23
Consensus pattern (78 bp):
ACGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAATG
ATTAGAAAAAAAC
Found at i:531843 original size:51 final size:53
Alignment explanation
Indices: 531745--531864 Score: 145
Period size: 51 Copynumber: 2.3 Consensus size: 53
531735 ATAACGAGGT
* * * * ** *
531745 TGGAGTATCCTCGATTGTGAAAAAATTGGTGTTTTTGGAAATAAAATCGGAGC
1 TGGAGTATCCCCGATTATGAAAAAATTAGTGTTTTTGAAAATAAAATCAAAGA
*
531798 TGGAGTATCCCCGATTAT-AGAAAATTAGTG-TTTTGAAAATAAAATCAAAGA
1 TGGAGTATCCCCGATTATGAAAAAATTAGTGTTTTTGAAAATAAAATCAAAGA
*
531849 TGGAATATCCCCGATT
1 TGGAGTATCCCCGATT
531865 GCGGAGAATT
Statistics
Matches: 58, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
51 32 0.55
52 10 0.17
53 16 0.28
ACGTcount: A:0.36, C:0.12, G:0.22, T:0.31
Consensus pattern (53 bp):
TGGAGTATCCCCGATTATGAAAAAATTAGTGTTTTTGAAAATAAAATCAAAGA
Found at i:534256 original size:20 final size:21
Alignment explanation
Indices: 534210--534263 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
534200 AACTTCCTAG
*
534210 ATGTATCGATACAAAGAATAC
1 ATGTATCGATACAAAGAATAA
*
534231 ATGTATCGATACACAGAA-AA
1 ATGTATCGATACAAAGAATAA
*
534251 ATGTATTGATACA
1 ATGTATCGATACA
534264 TTTCCTTGGC
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 13 0.43
21 17 0.57
ACGTcount: A:0.46, C:0.13, G:0.15, T:0.26
Consensus pattern (21 bp):
ATGTATCGATACAAAGAATAA
Found at i:534307 original size:19 final size:18
Alignment explanation
Indices: 534283--534350 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
534273 CAGTAGCTAA
534283 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
534302 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
534317 -T-TGTATCGATACAACAC
1 TTATGTATCGATACAA-AC
534334 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
534351 TTGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 2 0.05
19 27 0.63
ACGTcount: A:0.37, C:0.16, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:534323 original size:13 final size:13
Alignment explanation
Indices: 534305--534329 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
534295 ACAATACTTA
534305 TGTATCGATACAT
1 TGTATCGATACAT
534318 TGTATCGATACA
1 TGTATCGATACA
534330 ACACTTATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:534324 original size:32 final size:32
Alignment explanation
Indices: 534286--534348 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
534276 TAGCTAATTA
*
534286 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAACACTTATGTATCGATACAT
534318 TGTATCGATACAACACTTATGTATCGATACA
1 TGTATCGATACAACACTTATGTATCGATACA
534349 AATTGTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.17, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAACACTTATGTATCGATACAT
Found at i:539073 original size:21 final size:22
Alignment explanation
Indices: 539027--539078 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 22
539017 CAACATGATC
* * *
539027 TTGTATCGATACATTTGAGTGA
1 TTGTATCGATACATTTCACTAA
539049 -TGTATCGATACA-TTCACTAA
1 TTGTATCGATACATTTCACTAA
539069 TTGTATCGAT
1 TTGTATCGAT
539079 GCAAATCATA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
20 5 0.19
21 21 0.81
ACGTcount: A:0.29, C:0.13, G:0.17, T:0.40
Consensus pattern (22 bp):
TTGTATCGATACATTTCACTAA
Found at i:541984 original size:2 final size:2
Alignment explanation
Indices: 541977--542001 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
541967 TTAAAGACAT
541977 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
542002 TCTAAAAACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:544169 original size:40 final size:40
Alignment explanation
Indices: 544114--544207 Score: 143
Period size: 40 Copynumber: 2.4 Consensus size: 40
544104 ATGACTTACA
*
544114 TGTATCGATACATTGAAGAATCTATCAATGCAAAGCAAAT
1 TGTATCGATACATTGAAGAATCTATCAATACAAAGCAAAT
* * **
544154 TGTATCAATACATTGAAGAATGTATTGATACAAAGCAAAT
1 TGTATCGATACATTGAAGAATCTATCAATACAAAGCAAAT
544194 TGTATCGATACATT
1 TGTATCGATACATT
544208 TACTTATGTA
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 48 1.00
ACGTcount: A:0.41, C:0.13, G:0.15, T:0.31
Consensus pattern (40 bp):
TGTATCGATACATTGAAGAATCTATCAATACAAAGCAAAT
Found at i:544177 original size:20 final size:20
Alignment explanation
Indices: 544113--544178 Score: 62
Period size: 20 Copynumber: 3.3 Consensus size: 20
544103 AATGACTTAC
*
544113 ATGTATCGATACATTGAAGA
1 ATGTATCAATACATTGAAGA
* * **
544133 ATCTATCAATGCAAAGCAA-A
1 ATGTATCAATACATTG-AAGA
*
544153 TTGTATCAATACATTGAAGA
1 ATGTATCAATACATTGAAGA
544173 ATGTAT
1 ATGTAT
544179 TGATACAAAG
Statistics
Matches: 33, Mismatches: 11, Indels: 4
0.69 0.23 0.08
Matches are distributed among these distances:
19 2 0.06
20 29 0.88
21 2 0.06
ACGTcount: A:0.42, C:0.12, G:0.15, T:0.30
Consensus pattern (20 bp):
ATGTATCAATACATTGAAGA
Found at i:547949 original size:18 final size:17
Alignment explanation
Indices: 547903--547951 Score: 64
Period size: 17 Copynumber: 2.8 Consensus size: 17
547893 TTTATTTTTA
547903 ATTATATAATTTATGTT
1 ATTATATAATTTATGTT
*
547920 ATT-TTTATATTTATGTGT
1 ATTATATA-ATTTATGT-T
547938 ATTATATAATTTAT
1 ATTATATAATTTAT
547952 ATTAAATAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
16 3 0.11
17 11 0.41
18 10 0.37
19 3 0.11
ACGTcount: A:0.33, C:0.00, G:0.06, T:0.61
Consensus pattern (17 bp):
ATTATATAATTTATGTT
Found at i:548234 original size:21 final size:20
Alignment explanation
Indices: 548195--548238 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 20
548185 AAATATAAAT
548195 AATATTTTAGATCGAACAATA
1 AATATTTTAGATCGAACAA-A
548216 AATATTTTAGATC-ATACAAA
1 AATATTTTAGATCGA-ACAAA
548236 AAT
1 AAT
548239 TTAAATAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 5 0.23
21 17 0.77
ACGTcount: A:0.50, C:0.09, G:0.07, T:0.34
Consensus pattern (20 bp):
AATATTTTAGATCGAACAAA
Found at i:548492 original size:16 final size:16
Alignment explanation
Indices: 548455--548506 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 16
548445 TTTTAAAATT
* *
548455 TTCGAGTTATTTTCGAG
1 TTCGAGTCATTTT-GGG
548472 TTCGAGTCATTTTGGG
1 TTCGAGTCATTTTGGG
* *
548488 TTCGAATCATTTTAGG
1 TTCGAGTCATTTTGGG
548504 TTC
1 TTC
548507 AAGTAATTTC
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
16 19 0.61
17 12 0.39
ACGTcount: A:0.17, C:0.13, G:0.23, T:0.46
Consensus pattern (16 bp):
TTCGAGTCATTTTGGG
Found at i:548845 original size:7 final size:7
Alignment explanation
Indices: 548830--548864 Score: 52
Period size: 7 Copynumber: 5.0 Consensus size: 7
548820 ATTTACCTAG
548830 TTGAATT
1 TTGAATT
*
548837 TTAAATT
1 TTGAATT
548844 TTGAATT
1 TTGAATT
548851 TTGAATT
1 TTGAATT
*
548858 TTCAATT
1 TTGAATT
548865 GATCACAACT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.31, C:0.03, G:0.09, T:0.57
Consensus pattern (7 bp):
TTGAATT
Found at i:549427 original size:16 final size:17
Alignment explanation
Indices: 549408--549453 Score: 58
Period size: 16 Copynumber: 2.8 Consensus size: 17
549398 GGTTCGGATG
*
549408 ATTTTGAGTTTAAG-TC
1 ATTTTGAGTTTAAGTTA
*
549424 ATTTCGAGTTTAAGTTA
1 ATTTTGAGTTTAAGTTA
*
549441 ATTTTAAGTTTAA
1 ATTTTGAGTTTAA
549454 ATAGATCGAT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
16 13 0.52
17 12 0.48
ACGTcount: A:0.30, C:0.04, G:0.15, T:0.50
Consensus pattern (17 bp):
ATTTTGAGTTTAAGTTA
Found at i:550046 original size:39 final size:39
Alignment explanation
Indices: 550002--550082 Score: 153
Period size: 39 Copynumber: 2.1 Consensus size: 39
549992 CTAATTCAAA
550002 CTTTAACTCGACTAAAACTGGGGGAAATTATTATTAATC
1 CTTTAACTCGACTAAAACTGGGGGAAATTATTATTAATC
*
550041 CTTTAACTGGACTAAAACTGGGGGAAATTATTATTAATC
1 CTTTAACTCGACTAAAACTGGGGGAAATTATTATTAATC
550080 CTT
1 CTT
550083 GAGCTATAAT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.35
Consensus pattern (39 bp):
CTTTAACTCGACTAAAACTGGGGGAAATTATTATTAATC
Found at i:551221 original size:29 final size:29
Alignment explanation
Indices: 551188--551248 Score: 122
Period size: 29 Copynumber: 2.1 Consensus size: 29
551178 ATGTACTCAG
551188 ATTTTAAATAGAATTAATTATTATTTTTT
1 ATTTTAAATAGAATTAATTATTATTTTTT
551217 ATTTTAAATAGAATTAATTATTATTTTTT
1 ATTTTAAATAGAATTAATTATTATTTTTT
551246 ATT
1 ATT
551249 GTAGAAAATA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (29 bp):
ATTTTAAATAGAATTAATTATTATTTTTT
Found at i:551267 original size:32 final size:29
Alignment explanation
Indices: 551192--551261 Score: 95
Period size: 29 Copynumber: 2.4 Consensus size: 29
551182 ACTCAGATTT
* *
551192 TAAATAGAATTAATTATTATTTTTTATTT
1 TAAAAAGAATTAATTATTATTTTTTATTG
*
551221 TAAATAGAATTAATTATTATTTTTTATTG
1 TAAAAAGAATTAATTATTATTTTTTATTG
*
551250 TAGAAAATAATT
1 TA-AAAAGAATT
551262 TTAATTTAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
29 30 0.81
30 7 0.19
ACGTcount: A:0.41, C:0.00, G:0.06, T:0.53
Consensus pattern (29 bp):
TAAAAAGAATTAATTATTATTTTTTATTG
Found at i:554257 original size:2 final size:2
Alignment explanation
Indices: 554250--554290 Score: 55
Period size: 2 Copynumber: 20.5 Consensus size: 2
554240 GCCGATTGTT
* * *
554250 TC TC TC TC TC TC TT TC TC TC TC TC TC AC AC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
554291 ATACATGACA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.05, C:0.46, G:0.00, T:0.49
Consensus pattern (2 bp):
TC
Found at i:558051 original size:20 final size:20
Alignment explanation
Indices: 558026--558079 Score: 108
Period size: 20 Copynumber: 2.7 Consensus size: 20
558016 AAAATTCCTA
558026 AATGTATCGATACAAAGATC
1 AATGTATCGATACAAAGATC
558046 AATGTATCGATACAAAGATC
1 AATGTATCGATACAAAGATC
558066 AATGTATCGATACA
1 AATGTATCGATACA
558080 TTTCCTTGGC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.44, C:0.15, G:0.15, T:0.26
Consensus pattern (20 bp):
AATGTATCGATACAAAGATC
Found at i:558478 original size:19 final size:19
Alignment explanation
Indices: 558454--558521 Score: 85
Period size: 19 Copynumber: 3.9 Consensus size: 19
558444 AATTCAACAA
558454 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
558473 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
558488 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
558505 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
558522 TTAGCTACTG
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 28 0.65
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:558493 original size:13 final size:13
Alignment explanation
Indices: 558475--558499 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
558465 ACATAAGTTT
558475 TGTATCGATACAA
1 TGTATCGATACAA
558488 TGTATCGATACA
1 TGTATCGATACA
558500 TAAGTATTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:558497 original size:32 final size:32
Alignment explanation
Indices: 558456--558518 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
558446 TTCAACAATT
*
558456 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
558488 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
558519 TAATTAGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:558598 original size:33 final size:33
Alignment explanation
Indices: 558541--558607 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
558531 GCCAAGGAAA
***
558541 TGTATCGATACATTTTTCTGTGTATCAATACAT
1 TGTATCGATACATGGATCTGTGTATCAATACAT
* *
558574 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCAATACAT
558607 T
1 T
558608 TGGAAATTTT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.27, C:0.15, G:0.15, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCAATACAT
Found at i:559139 original size:11 final size:11
Alignment explanation
Indices: 559123--559149 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
559113 CTTTAGCAAC
559123 AAAAAAACAAA
1 AAAAAAACAAA
559134 AAAAAAACAAA
1 AAAAAAACAAA
559145 AAAAA
1 AAAAA
559150 CACTATTCCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.93, C:0.07, G:0.00, T:0.00
Consensus pattern (11 bp):
AAAAAAACAAA
Found at i:561023 original size:51 final size:53
Alignment explanation
Indices: 560958--561088 Score: 178
Period size: 51 Copynumber: 2.5 Consensus size: 53
560948 AGTTTCTCAA
* * * *
560958 TTCTCCACAATCGGGGATATTCCAACTCCGATTTTATTTTC-AAAACACTAA-
1 TTCTTCACAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAAT
*
561009 TT-TTCTATAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAAACACCAAT
1 TTCTTC-ACAATCGGGGATACTCCAACTCCGATTTTATTTCC-AAAAACACCAAT
561063 TTCTTCACAATCGGGGATACTCCAAC
1 TTCTTCACAATCGGGGATACTCCAAC
561089 CCCGTTAATC
Statistics
Matches: 69, Mismatches: 6, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
50 2 0.03
51 34 0.49
53 9 0.13
54 21 0.30
55 3 0.04
ACGTcount: A:0.31, C:0.26, G:0.11, T:0.32
Consensus pattern (53 bp):
TTCTTCACAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAAT
Found at i:561216 original size:52 final size:51
Alignment explanation
Indices: 561139--561322 Score: 224
Period size: 52 Copynumber: 3.5 Consensus size: 51
561129 CCAAATATTG
* * *
561139 ATTTTTCATAATCGGGGATACTCCAACCCCGATTTTATTGCTAAAACACTA
1 ATTTTTCACAATCGGGGATACTCCAACCCCGATTTTATTCCTAAAACACCA
* **
561190 ATTTTTCCACAATCGGGGATACTCCAACCCCGGTTTTATTTTTAAAACACCA
1 ATTTTT-CACAATCGGGGATACTCCAACCCCGATTTTATTCCTAAAACACCA
* ** * *
561242 ATTTTCCTTTAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCA
1 ATTTTTC-ACAATCGGGGATACTCCAACCCCGATTTTA-TTCCTAAAACACCA
* *
561295 ATTTTTCACAATTGAGGATACTCCAACC
1 ATTTTTCACAATCGGGGATACTCCAACC
561323 TCGTTATTTC
Statistics
Matches: 111, Mismatches: 19, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
51 7 0.06
52 87 0.78
53 17 0.15
ACGTcount: A:0.30, C:0.26, G:0.11, T:0.33
Consensus pattern (51 bp):
ATTTTTCACAATCGGGGATACTCCAACCCCGATTTTATTCCTAAAACACCA
Found at i:561375 original size:27 final size:27
Alignment explanation
Indices: 561310--561380 Score: 90
Period size: 28 Copynumber: 2.6 Consensus size: 27
561300 TCACAATTGA
* **
561310 GGATACTCCAACCTCGTTATTTCATCGG
1 GGATACTCCAACCCCGTTACCTCA-CGG
561338 GGATACTCCAACCCCGTTACCTC-CGAG
1 GGATACTCCAACCCCGTTACCTCACG-G
561365 GGATACTCCAACCCCG
1 GGATACTCCAACCCCG
561381 GCTTTATTCC
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
26 2 0.05
27 17 0.44
28 20 0.51
ACGTcount: A:0.23, C:0.37, G:0.18, T:0.23
Consensus pattern (27 bp):
GGATACTCCAACCCCGTTACCTCACGG
Found at i:561446 original size:106 final size:107
Alignment explanation
Indices: 561257--561459 Score: 259
Period size: 106 Copynumber: 1.9 Consensus size: 107
561247 CCTTTAATCG
* * *
561257 GGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAATTTTTCACAATTGAGGATACTCCAAC
1 GGGATACTCCAACCCCGACTTTATTTCCAAAAACACCAATTTCTCACAATTGAGGATACTCCAAC
* *
561322 CTCGTTATTTCATCGGGGATACTCCAACCCCGTTACCTCCGA
66 CCCGTTATTTCATAGGGGATACTCCAACCCCGTTACCTCCGA
* * * * * *
561364 GGGATACTCCAACCCCGGCTTTA-TTCCCAAAATATCGATTTCTCATAATT-AGGGATACTCCAA
1 GGGATACTCCAACCCCGACTTTATTTCCAAAAACACCAATTTCTCACAATTGA-GGATACTCCAA
*
561427 CCCCGTTATTTC-TGAGGGGATACTCCAATCCCG
65 CCCCGTTATTTCAT-AGGGGATACTCCAACCCCG
561460 ATGTTTTTTC
Statistics
Matches: 82, Mismatches: 12, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
105 2 0.02
106 60 0.73
107 20 0.24
ACGTcount: A:0.27, C:0.30, G:0.15, T:0.29
Consensus pattern (107 bp):
GGGATACTCCAACCCCGACTTTATTTCCAAAAACACCAATTTCTCACAATTGAGGATACTCCAAC
CCCGTTATTTCATAGGGGATACTCCAACCCCGTTACCTCCGA
Found at i:561497 original size:78 final size:78
Alignment explanation
Indices: 561335--561503 Score: 184
Period size: 78 Copynumber: 2.2 Consensus size: 78
561325 GTTATTTCAT
561335 CGGGGATACTCCAACCCCGTTACCTCCGAGGGATACTCCAACCCCGGCTTTATTCCCAAAATATC
1 CGGGGATACTCCAACCCCGTTACCTCCGAGGGATACTCCAACCCCGGCTTTATTCCCAAAATATC
* *
561400 GATTTCTCATAAT
66 GATTTCTCACAAC
** ** * * * *
561413 TAGGGATACTCCAACCCCGTTATTTCTGAGGGGATACTCCAATCCCGATG-TTT-TT-TC-TAAT
1 CGGGGATACTCCAACCCCGTTACCTCCGA-GGGATACTCCAACCCCG--GCTTTATTCCCAAAAT
561474 CATCGATTTCTCACAAC
63 -ATCGATTTCTCACAAC
561491 CGGGGATACTCCA
1 CGGGGATACTCCA
561504 GCCCTGTCAT
Statistics
Matches: 75, Mismatches: 12, Indels: 8
0.79 0.13 0.08
Matches are distributed among these distances:
77 3 0.04
78 50 0.67
79 18 0.24
80 3 0.04
81 1 0.01
ACGTcount: A:0.25, C:0.30, G:0.17, T:0.28
Consensus pattern (78 bp):
CGGGGATACTCCAACCCCGTTACCTCCGAGGGATACTCCAACCCCGGCTTTATTCCCAAAATATC
GATTTCTCACAAC
Found at i:563360 original size:15 final size:14
Alignment explanation
Indices: 563342--563395 Score: 51
Period size: 13 Copynumber: 3.9 Consensus size: 14
563332 AATAAAGAAG
563342 AAAAAGAGAAATAAA
1 AAAAAGAGAAA-AAA
* *
563357 AAAAAAAG-GAAAA
1 AAAAAGAGAAAAAA
563370 AAAAAGA-AAAACAA
1 AAAAAGAGAAAA-AA
563384 AAAAA-AGAAAAA
1 AAAAAGAGAAAAA
563396 GTTTCTTCAA
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
13 13 0.41
14 12 0.38
15 7 0.22
ACGTcount: A:0.85, C:0.02, G:0.11, T:0.02
Consensus pattern (14 bp):
AAAAAGAGAAAAAA
Found at i:563361 original size:16 final size:15
Alignment explanation
Indices: 563342--563396 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 15
563332 AATAAAGAAG
563342 AAAAAGAGAAATAAAAA
1 AAAAAG-GAAA-AAAAA
563359 AAAAAGGAAAAAAAA
1 AAAAAGGAAAAAAAA
**
563374 AGAAAAACAAAAAAAA
1 A-AAAAGGAAAAAAAA
563390 GAAAAAG
1 -AAAAAG
563397 TTTCTTCAAG
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
15 6 0.18
16 20 0.61
17 7 0.21
ACGTcount: A:0.84, C:0.02, G:0.13, T:0.02
Consensus pattern (15 bp):
AAAAAGGAAAAAAAA
Found at i:563364 original size:26 final size:24
Alignment explanation
Indices: 563326--563395 Score: 86
Period size: 26 Copynumber: 2.8 Consensus size: 24
563316 GTTCTCAGCC
* *
563326 AAAAAAAATAAAGAAGAAAAAGAGA
1 AAAAAAAAAAAAGAA-AAAAAAAGA
563351 AATAAAAAAAAAAGGAAAAAAAAAGA
1 AA-AAAAAAAAAA-GAAAAAAAAAGA
563377 AAAACAAAAAAAAGAAAAA
1 AAAA-AAAAAAAAGAAAAA
563396 GTTTCTTCAA
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
25 10 0.25
26 27 0.68
27 3 0.08
ACGTcount: A:0.84, C:0.01, G:0.11, T:0.03
Consensus pattern (24 bp):
AAAAAAAAAAAAGAAAAAAAAAGA
Found at i:563369 original size:12 final size:11
Alignment explanation
Indices: 563329--563396 Score: 57
Period size: 11 Copynumber: 6.0 Consensus size: 11
563319 CTCAGCCAAA
563329 AAAAATAAAGAAG
1 AAAAA-AAA-AAG
* *
563342 AAAAAGAGAAAT
1 AAAAA-AAAAAG
563354 AAAAAAAAAAG
1 AAAAAAAAAAG
*
563365 GAAAAAAAAAG
1 AAAAAAAAAAG
*
563376 AAAAACAAAA-
1 AAAAAAAAAAG
*
563386 AAAAGAAAAAG
1 AAAAAAAAAAG
563397 TTTCTTCAAG
Statistics
Matches: 44, Mismatches: 10, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
10 8 0.18
11 22 0.50
12 7 0.16
13 7 0.16
ACGTcount: A:0.82, C:0.01, G:0.13, T:0.03
Consensus pattern (11 bp):
AAAAAAAAAAG
Found at i:563371 original size:10 final size:10
Alignment explanation
Indices: 563355--563396 Score: 50
Period size: 10 Copynumber: 4.0 Consensus size: 10
563345 AAGAGAAATA
563355 AAAAAAAAAGG
1 AAAAAAAAA-G
563366 AAAAAAAAAG
1 AAAAAAAAAG
563376 AAAAACAAAA-
1 AAAAA-AAAAG
563386 AAAAGAAAAAG
1 AAAA-AAAAAG
563397 TTTCTTCAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
10 14 0.50
11 14 0.50
ACGTcount: A:0.86, C:0.02, G:0.12, T:0.00
Consensus pattern (10 bp):
AAAAAAAAAG
Found at i:566989 original size:11 final size:10
Alignment explanation
Indices: 566965--566998 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
566955 GATGTAACAA
*
566965 TTTTATAAAT
1 TTTTATATAT
566975 TTTTATCATAT
1 TTTTAT-ATAT
566986 TTTTATATAT
1 TTTTATATAT
566996 TTT
1 TTT
566999 ATTATATTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 13 0.59
11 9 0.41
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (10 bp):
TTTTATATAT
Found at i:566998 original size:20 final size:21
Alignment explanation
Indices: 566965--567006 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
566955 GATGTAACAA
566965 TTTTATAAATTTTTATCATAT
1 TTTTATAAATTTTTATCATAT
* *
566986 TTTTATATA-TTTTATTATAT
1 TTTTATAAATTTTTATCATAT
567006 T
1 T
567007 ATAATTATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (21 bp):
TTTTATAAATTTTTATCATAT
Found at i:567128 original size:19 final size:20
Alignment explanation
Indices: 567106--567151 Score: 51
Period size: 20 Copynumber: 2.3 Consensus size: 20
567096 CATCTTTTTA
*
567106 TTATTTTATAAA-TA-TATAT
1 TTATTTTA-AAATTATTAAAT
567125 TTATATTTAAAATTATTAAAT
1 TTAT-TTTAAAATTATTAAAT
567146 TTATTT
1 TTATTT
567152 ATTTTTTTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
19 7 0.30
20 8 0.35
21 8 0.35
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (20 bp):
TTATTTTAAAATTATTAAAT
Found at i:567131 original size:24 final size:24
Alignment explanation
Indices: 567086--567131 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
567076 CAAATATAAA
* *
567086 TTTATAATATCATCTTTTTATTAT
1 TTTATAATATCATATTTATATTAT
567110 TTTATAAATAT-ATATTTATATT
1 TTTAT-AATATCATATTTATATT
567132 TAAAATTATT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 14 0.74
25 5 0.26
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (24 bp):
TTTATAATATCATATTTATATTAT
Found at i:568243 original size:2 final size:2
Alignment explanation
Indices: 568236--568265 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
568226 TTTCTTTAAG
568236 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
568266 TGCTTTTATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:569645 original size:14 final size:12
Alignment explanation
Indices: 569613--569637 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
569603 CTTAATTTTT
569613 TTCTTTTGAATA
1 TTCTTTTGAATA
569625 TTCTTTTGAATA
1 TTCTTTTGAATA
569637 T
1 T
569638 ATGCTTTTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.08, G:0.08, T:0.60
Consensus pattern (12 bp):
TTCTTTTGAATA
Found at i:583617 original size:14 final size:14
Alignment explanation
Indices: 583600--583626 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
583590 AAAATTTGAG
583600 TTTTTTTATTTTAT
1 TTTTTTTATTTTAT
583614 TTTTTTTATTTTA
1 TTTTTTTATTTTA
583627 ATTAAATTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (14 bp):
TTTTTTTATTTTAT
Found at i:583693 original size:22 final size:23
Alignment explanation
Indices: 583643--583694 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 23
583633 TTTACGTAGA
*
583643 TTTTTAAGTTTAGATGAATATGAG
1 TTTTT-AGTTAAGATGAATATGAG
* *
583667 CTTTTAGTTAAGATTAA-ATGAG
1 TTTTTAGTTAAGATGAATATGAG
583689 TTTTTA
1 TTTTTA
583695 AATATTTTAT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
22 10 0.42
23 10 0.42
24 4 0.17
ACGTcount: A:0.33, C:0.02, G:0.17, T:0.48
Consensus pattern (23 bp):
TTTTTAGTTAAGATGAATATGAG
Found at i:583733 original size:23 final size:22
Alignment explanation
Indices: 583690--583737 Score: 53
Period size: 23 Copynumber: 2.1 Consensus size: 22
583680 TTAAATGAGT
*
583690 TTTTAAATATTTTATTAATTATA
1 TTTTAAATATTTTAATAATTA-A
*
583713 TTTTAAATTTTTTAA-ATATTAA
1 TTTTAAATATTTTAATA-ATTAA
583735 TTT
1 TTT
583738 AGTTAATTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
22 5 0.23
23 17 0.77
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (22 bp):
TTTTAAATATTTTAATAATTAA
Found at i:583893 original size:18 final size:18
Alignment explanation
Indices: 583870--583905 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
583860 TAATAATAAA
583870 TTATTTAAAAAATTAATT
1 TTATTTAAAAAATTAATT
*
583888 TTATTTAACAAATTAATT
1 TTATTTAAAAAATTAATT
583906 ATATATATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (18 bp):
TTATTTAAAAAATTAATT
Found at i:583997 original size:19 final size:18
Alignment explanation
Indices: 583930--584010 Score: 62
Period size: 19 Copynumber: 4.5 Consensus size: 18
583920 AAATTTCAAT
583930 AAATAAATAA-TTAA-AA
1 AAATAAATAATTTAATAA
* *
583946 ATATTAAA-AATATAATAA
1 A-AATAAATAATTTAATAA
*
583964 TATAATAAA-AATTTACTTAA
1 -A-AATAAATAATTTA-ATAA
*
583984 AAATTAATAATTTAATAA
1 AAATAAATAATTTAATAA
584002 AAATAAATA
1 AAATAAATA
584011 TTAAATTATA
Statistics
Matches: 51, Mismatches: 8, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
16 3 0.06
17 8 0.16
18 18 0.35
19 19 0.37
20 3 0.06
ACGTcount: A:0.65, C:0.01, G:0.00, T:0.33
Consensus pattern (18 bp):
AAATAAATAATTTAATAA
Found at i:585330 original size:22 final size:22
Alignment explanation
Indices: 585288--585331 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
585278 GAAGTAAAAC
* *
585288 TTTAAATATTAAAATTGATATT
1 TTTAAATATAAAAATTAATATT
585310 TTTAAA-ATAAAAATATAATATT
1 TTTAAATATAAAAAT-TAATATT
585332 AACACATTTG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (22 bp):
TTTAAATATAAAAATTAATATT
Found at i:586945 original size:22 final size:21
Alignment explanation
Indices: 586917--586958 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
586907 TAGACAGTGT
586917 TATGAT-AATACATATTCATAAC
1 TATGATAAAT-CATATT-ATAAC
586939 TATGATAAATCATATTATAA
1 TATGATAAATCATATTATAA
586959 GTGTAAGAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 4 0.21
22 12 0.63
23 3 0.16
ACGTcount: A:0.48, C:0.10, G:0.05, T:0.38
Consensus pattern (21 bp):
TATGATAAATCATATTATAAC
Found at i:590325 original size:52 final size:52
Alignment explanation
Indices: 590177--590305 Score: 222
Period size: 52 Copynumber: 2.5 Consensus size: 52
590167 CGAAATATGA
* *
590177 AAATTTGCTTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTAGGC
*
590229 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTAGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTAGGC
*
590281 AATTTTGCCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
590306 AAGATCAGTG
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 73 1.00
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.36
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTAGGC
Done.