Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1873
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: 405709
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
File 4 of 4
Found at i:380984 original size:92 final size:92
Alignment explanation
Indices: 380826--381191 Score: 582
Period size: 92 Copynumber: 4.0 Consensus size: 92
380816 CCTTTTCCAT
* * * *
380826 CTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTTATCTTTAAGTCCAATGTA
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCATCTTCATCTTTAAGTCCAATGTA
380891 GCTGGCCTTGAATCAGCACATTGGCAC
66 GCTGGCCTTGAATCAGCACATTGGCAC
* * *
380918 TTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGTA
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCATCTTCATCTTTAAGTCCAATGTA
*
380983 GCTGGCCTTGACTCAGCACATTGGCAC
66 GCTGGCCTTGAATCAGCACATTGGCAC
* *
381010 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGTA
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCATCTTCATCTTTAAGTCCAATGTA
381075 GCTGGCCTTGAATCAGCACATTGGCAC
66 GCTGGCCTTGAATCAGCACATTGGCAC
*
381102 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCA----C--CTTTAAGTCCAATATA
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCATCTTCATCTTTAAGTCCAATGTA
*
381161 GCTGGCCTTGAATCAGCATATTGGCAC
66 GCTGGCCTTGAATCAGCACATTGGCAC
381188 CTTT
1 CTTT
381192 TCCATCTTTA
Statistics
Matches: 260, Mismatches: 14, Indels: 6
0.93 0.05 0.02
Matches are distributed among these distances:
86 45 0.17
88 1 0.00
92 214 0.82
ACGTcount: A:0.25, C:0.25, G:0.19, T:0.31
Consensus pattern (92 bp):
CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCATCTTCATCTTTAAGTCCAATGTA
GCTGGCCTTGAATCAGCACATTGGCAC
Found at i:381104 original size:21 final size:21
Alignment explanation
Indices: 381080--381147 Score: 52
Period size: 21 Copynumber: 3.2 Consensus size: 21
381070 ATGTAGCTGG
381080 CCTTGAATCAGCACATTGGCA
1 CCTTGAATCAGCACATTGGCA
* * *
381101 CCTTTAAGTC--CA-ATATAGCTGG
1 CCTTGAA-TCAGCACAT-TGGC--A
381123 CCTTGAATCAGCACATTGGCA
1 CCTTGAATCAGCACATTGGCA
381144 CCTT
1 CCTT
381148 TAAGTCCAAT
Statistics
Matches: 34, Mismatches: 6, Indels: 14
0.63 0.11 0.26
Matches are distributed among these distances:
19 2 0.06
20 5 0.15
21 12 0.35
22 8 0.24
23 5 0.15
24 2 0.06
ACGTcount: A:0.26, C:0.28, G:0.18, T:0.28
Consensus pattern (21 bp):
CCTTGAATCAGCACATTGGCA
Found at i:381123 original size:24 final size:24
Alignment explanation
Indices: 381096--381166 Score: 62
Period size: 21 Copynumber: 3.2 Consensus size: 24
381086 ATCAGCACAT
381096 TGGCACCTTTAAGTCCAATATAGC
1 TGGCACCTTTAAGTCCAATATAGC
* ** * *
381120 TGG--CCTTGAA-T-CAGCACA-T
1 TGGCACCTTTAAGTCCAATATAGC
381139 TGGCACCTTTAAGTCCAATATAGC
1 TGGCACCTTTAAGTCCAATATAGC
381163 TGGC
1 TGGC
381167 CTTGAATCAG
Statistics
Matches: 32, Mismatches: 10, Indels: 10
0.62 0.19 0.19
Matches are distributed among these distances:
19 3 0.09
20 4 0.12
21 7 0.22
22 7 0.22
23 4 0.12
24 7 0.22
ACGTcount: A:0.27, C:0.25, G:0.20, T:0.28
Consensus pattern (24 bp):
TGGCACCTTTAAGTCCAATATAGC
Found at i:381126 original size:22 final size:22
Alignment explanation
Indices: 381101--381169 Score: 56
Period size: 22 Copynumber: 3.2 Consensus size: 22
381091 CACATTGGCA
381101 CCTTTAAGTCCAATATAGCTGG
1 CCTTTAAGTCCAATATAGCTGG
* * *
381123 CCTTGAA-TCAGCACAT-TGGC--A
1 CCTTTAAGTC--CA-ATATAGCTGG
381144 CCTTTAAGTCCAATATAGCTGG
1 CCTTTAAGTCCAATATAGCTGG
381166 CCTT
1 CCTT
381170 GAATCAGCAT
Statistics
Matches: 34, Mismatches: 6, Indels: 14
0.63 0.11 0.26
Matches are distributed among these distances:
19 2 0.06
20 5 0.15
21 8 0.24
22 12 0.35
23 5 0.15
24 2 0.06
ACGTcount: A:0.26, C:0.26, G:0.17, T:0.30
Consensus pattern (22 bp):
CCTTTAAGTCCAATATAGCTGG
Found at i:381281 original size:56 final size:52
Alignment explanation
Indices: 381145--381283 Score: 170
Period size: 52 Copynumber: 2.6 Consensus size: 52
381135 ACATTGGCAC
* *
381145 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGACACCTTTTCCAT
* *
381197 CTTTAAGTTCAATGTAGCTGGCCTTGAATCAGCACATTGACATCCTTTTTCATCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGACA-CC-TTTTC--CAT
* * * *
381253 CTTTAAGCCCAATATCGTTGGCCGTGAATCA
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCA
381284 ACATATTGGC
Statistics
Matches: 73, Mismatches: 10, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
52 38 0.52
53 2 0.03
54 5 0.07
56 28 0.38
ACGTcount: A:0.25, C:0.24, G:0.16, T:0.35
Consensus pattern (52 bp):
CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGACACCTTTTCCAT
Found at i:381621 original size:16 final size:17
Alignment explanation
Indices: 381596--381633 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
381586 TTGTGCTATA
* *
381596 ATCATGACATC-ATGAC
1 ATCATAACATCAATAAC
381612 ATCATAACATCAATAAC
1 ATCATAACATCAATAAC
381629 ATCAT
1 ATCAT
381634 TATTTGCATC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 10 0.53
17 9 0.47
ACGTcount: A:0.45, C:0.24, G:0.05, T:0.26
Consensus pattern (17 bp):
ATCATAACATCAATAAC
Found at i:381833 original size:34 final size:34
Alignment explanation
Indices: 381794--382273 Score: 643
Period size: 34 Copynumber: 14.9 Consensus size: 34
381784 TGGCATTTTT
381794 TTTTCAAAGCCCACAACTCCGTGGCACCTTCTTC
1 TTTTCAAAGCCCACAACTCCGTGGCACCTTCTTC
381828 TTTTCAAAGCCCACAACTCCGTGGCACCTTCTTC
1 TTTTCAAAGCCCACAACTCCGTGGCACCTTCTTC
*
381862 TTTTCAAAGCCCACGACTCCGTGGCA----C-TC
1 TTTTCAAAGCCCACAACTCCGTGGCACCTTCTTC
*
381891 TTTTCAAAGCCCACGACTCCGTGGCA-C-TC-T-
1 TTTTCAAAGCCCACAACTCCGTGGCACCTTCTTC
*
381921 TTTT-AAAGCCCACGACTCCGTGGCA-C-TC-T-
1 TTTTCAAAGCCCACAACTCCGTGGCACCTTCTTC
*
381950 TTTT-AAAGCCCACAACTCTGTGGCACCTTCTTC
1 TTTTCAAAGCCCACAACTCCGTGGCACCTTCTTC
*
381983 TTTTCAAAGCCCACGACTCCGTGGCA----C-TC
1 TTTTCAAAGCCCACAACTCCGTGGCACCTTCTTC
*
382012 TTTTCAAAGCCCACGACTCCGTGGCA-C-TC-T-
1 TTTTCAAAGCCCACAACTCCGTGGCACCTTCTTC
*
382042 TTTT-AAAGCCCACGACTCCGTGGCACCTTCTTC
1 TTTTCAAAGCCCACAACTCCGTGGCACCTTCTTC
*
382075 TTTTTAAAGCCCACAACTCCGTGGCACCTTCTTC
1 TTTTCAAAGCCCACAACTCCGTGGCACCTTCTTC
*
382109 TTTTCAAAGCCCATAACTCCGTGGCACCTTCTTC
1 TTTTCAAAGCCCACAACTCCGTGGCACCTTCTTC
*
382143 TTTTCAAAGCCCACAACTCCATGGCACCTTCTTC
1 TTTTCAAAGCCCACAACTCCGTGGCACCTTCTTC
*
382177 TTTTCAAAGCCCACGACTCCGTGGCACCTTCTTC
1 TTTTCAAAGCCCACAACTCCGTGGCACCTTCTTC
*
382211 TTTTCAAAGCCCACAACTCCGTGGCACCTTTTTC
1 TTTTCAAAGCCCACAACTCCGTGGCACCTTCTTC
* *
382245 TGTTT-AATGCCCACAACTCTGTGGCACCT
1 T-TTTCAAAGCCCACAACTCCGTGGCACCT
382274 ACAACTCCGT
Statistics
Matches: 415, Mismatches: 16, Indels: 30
0.90 0.03 0.07
Matches are distributed among these distances:
29 125 0.30
30 12 0.03
31 8 0.02
32 2 0.00
33 8 0.02
34 257 0.62
35 3 0.01
ACGTcount: A:0.20, C:0.36, G:0.14, T:0.29
Consensus pattern (34 bp):
TTTTCAAAGCCCACAACTCCGTGGCACCTTCTTC
Found at i:381902 original size:29 final size:31
Alignment explanation
Indices: 381736--382236 Score: 504
Period size: 34 Copynumber: 15.7 Consensus size: 31
381726 AAATACCTTC
* *
381736 TCAAAGCCCACGACTCAGTGGCAT-TT-TGTC
1 TCAAAGCCCACGACTCCGTGGCATCTTCT-TT
** * * *
381766 TCAAAGTTCACGACTCAGTGGCATTTTTTTT
1 TCAAAGCCCACGACTCCGTGGCATCTTCTTT
*
381797 TCAAAGCCCACAACTCCGTGGCACCTTCTTCTTT
1 TCAAAGCCCACGACTCCGTGGCA---TCTTCTTT
*
381831 TCAAAGCCCACAACTCCGTGGCACCTTCTTCTTT
1 TCAAAGCCCACGACTCCGTGGCA---TCTTCTTT
381865 TCAAAGCCCACGACTCCGTGGCA-C-TCTTT
1 TCAAAGCCCACGACTCCGTGGCATCTTCTTT
381894 TCAAAGCCCACGACTCCGTGGCA-C-TCTTT
1 TCAAAGCCCACGACTCCGTGGCATCTTCTTT
*
381923 TTAAAGCCCACGACTCCGTGGCA-C-TCTTT
1 TCAAAGCCCACGACTCCGTGGCATCTTCTTT
* * *
381952 TTAAAGCCCACAACTCTGTGGCACCTTCTTCTTT
1 TCAAAGCCCACGACTCCGTGGCA---TCTTCTTT
381986 TCAAAGCCCACGACTCCGTGGCA-C-TCTTT
1 TCAAAGCCCACGACTCCGTGGCATCTTCTTT
382015 TCAAAGCCCACGACTCCGTGGCA-C-TCTTT
1 TCAAAGCCCACGACTCCGTGGCATCTTCTTT
*
382044 TTAAAGCCCACGACTCCGTGGCACCTTCTTCTTT
1 TCAAAGCCCACGACTCCGTGGCA---TCTTCTTT
* *
382078 TTAAAGCCCACAACTCCGTGGCACCTTCTTCTTT
1 TCAAAGCCCACGACTCCGTGGCA---TCTTCTTT
**
382112 TCAAAGCCCATAACTCCGTGGCACCTTCTTCTTT
1 TCAAAGCCCACGACTCCGTGGCA---TCTTCTTT
* *
382146 TCAAAGCCCACAACTCCATGGCACCTTCTTCTTT
1 TCAAAGCCCACGACTCCGTGGCA---TCTTCTTT
382180 TCAAAGCCCACGACTCCGTGGCACCTTCTTCTTT
1 TCAAAGCCCACGACTCCGTGGCA---TCTTCTTT
*
382214 TCAAAGCCCACAACTCCGTGGCA
1 TCAAAGCCCACGACTCCGTGGCA
382237 CCTTTTTCTG
Statistics
Matches: 431, Mismatches: 25, Indels: 26
0.89 0.05 0.05
Matches are distributed among these distances:
29 139 0.32
30 24 0.06
31 22 0.05
32 1 0.00
33 2 0.00
34 243 0.56
ACGTcount: A:0.21, C:0.35, G:0.15, T:0.29
Consensus pattern (31 bp):
TCAAAGCCCACGACTCCGTGGCATCTTCTTT
Found at i:382323 original size:54 final size:51
Alignment explanation
Indices: 382223--382325 Score: 145
Period size: 54 Copynumber: 2.0 Consensus size: 51
382213 TTCAAAGCCC
* *
382223 ACAACTCCGTGGCACCTTTTTCTGTTTAATGCCCACAACTCTGTGGCACCT
1 ACAACTCCGTGGCACCTTTTTCTGTTTAAAGCCCACAACTCCGTGGCACCT
382274 ACAACTCCGTGGCACTCTTTTTCCCT-TTTCAAAGCCCACAACTCCGTGGCAC
1 ACAACTCCGTGGCAC-CTTTTT--CTGTTT-AAAGCCCACAACTCCGTGGCAC
382326 TTTTTTCTTT
Statistics
Matches: 46, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
51 15 0.33
52 6 0.13
53 3 0.07
54 22 0.48
ACGTcount: A:0.20, C:0.36, G:0.15, T:0.29
Consensus pattern (51 bp):
ACAACTCCGTGGCACCTTTTTCTGTTTAAAGCCCACAACTCCGTGGCACCT
Found at i:382346 original size:33 final size:35
Alignment explanation
Indices: 382274--382417 Score: 188
Period size: 33 Copynumber: 4.1 Consensus size: 35
382264 TGTGGCACCT
382274 ACAACTCCGTGGCACTCTTTTTCCCTTTTCAAAGCCC
1 ACAACTCCGTGGCACTCTTTTT-CCTTTT-AAAGCCC
382311 ACAACTCCGTGGCACT-TTTTT-CTTTTAAAGCCC
1 ACAACTCCGTGGCACTCTTTTTCCTTTTAAAGCCC
*
382344 ACAACTCCGTGGCACTCTTTTTCCCTTTT-AAGTCC
1 ACAACTCCGTGGCACTCTTTTT-CCTTTTAAAGCCC
* *
382379 ACAACTCCGTGGCA-TCTTTCTCCATTCCTAAAGCCC
1 ACAACTCCGTGGCACTCTTTTTCC-TT-TTAAAGCCC
382415 ACA
1 ACA
382418 CAAGTCGGTG
Statistics
Matches: 97, Mismatches: 4, Indels: 13
0.85 0.04 0.11
Matches are distributed among these distances:
33 25 0.26
34 18 0.19
35 20 0.21
36 18 0.19
37 16 0.16
ACGTcount: A:0.21, C:0.35, G:0.11, T:0.33
Consensus pattern (35 bp):
ACAACTCCGTGGCACTCTTTTTCCTTTTAAAGCCC
Found at i:382364 original size:35 final size:35
Alignment explanation
Indices: 382274--382417 Score: 186
Period size: 35 Copynumber: 4.1 Consensus size: 35
382264 TGTGGCACCT
382274 ACAACTCCGTGGCACTCTTTTTCCCTTTTCAAAGCCC
1 ACAACTCCGTGGCA-TCTTTTTCCCTTTT-AAAGCCC
*
382311 ACAACTCCGTGGCA-CTTTTT-TCTTTTAAAGCCC
1 ACAACTCCGTGGCATCTTTTTCCCTTTTAAAGCCC
*
382344 ACAACTCCGTGGCACTCTTTTTCCCTTTT-AAGTCC
1 ACAACTCCGTGGCA-TCTTTTTCCCTTTTAAAGCCC
* * *
382379 ACAACTCCGTGGCATCTTTCTCCATTCCTAAAGCCC
1 ACAACTCCGTGGCATCTTTTTCCCTT-TTAAAGCCC
382415 ACA
1 ACA
382418 CAAGTCGGTG
Statistics
Matches: 95, Mismatches: 7, Indels: 11
0.84 0.06 0.10
Matches are distributed among these distances:
33 21 0.22
34 15 0.16
35 32 0.34
36 13 0.14
37 14 0.15
ACGTcount: A:0.21, C:0.35, G:0.11, T:0.33
Consensus pattern (35 bp):
ACAACTCCGTGGCATCTTTTTCCCTTTTAAAGCCC
Found at i:382560 original size:52 final size:51
Alignment explanation
Indices: 382471--382961 Score: 475
Period size: 52 Copynumber: 10.0 Consensus size: 51
382461 GCAACCCTTC
* * *
382471 TAAGCCCACTATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTTT-CATCTT
* *
382523 TAAGTCCAATGTAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTTT-CATCTT
* *
382575 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACC-TTT-ATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTTTCATCTT
* *
382624 TAAGTCTAATGTAGCTGGCCTTGAATCAGCACATTGGCA------C-T-TT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTTTCATCTT
* * * *
382667 TAAGTCCAATATCGCTGGCCTTGAGTCAGCATATTGGCA--TCTTCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTTTCATCTT
*
382716 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA------C--CTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTTTCATCTT
382759 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCA------C--CTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTTTCATCTT
*
382802 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTTT-CATCTT
* *
382854 TAAGTTCAATATAGCTGGCCTTGAATCAGCACATTGACATCCTTTTTCATCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCA-CC--TTT--TCATCTT
* * * * * *
382910 TAAGCCCAATATCA-TTGGCCGTGAATCAACATATTGGCATCTTTATCA-CTT
1 TAAGTCCAATAT-AGCTGGCCTTGAATCAGCACATTGGCACCTTT-TCATCTT
382961 T
1 T
382962 TCTCATCTTC
Statistics
Matches: 388, Mismatches: 29, Indels: 45
0.84 0.06 0.10
Matches are distributed among these distances:
43 119 0.31
44 1 0.00
45 1 0.00
47 1 0.00
48 1 0.00
49 79 0.20
50 1 0.00
51 7 0.02
52 131 0.34
53 5 0.01
55 4 0.01
56 36 0.09
57 2 0.01
ACGTcount: A:0.25, C:0.25, G:0.17, T:0.33
Consensus pattern (51 bp):
TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTTTCATCTT
Found at i:382684 original size:43 final size:43
Alignment explanation
Indices: 382622--382889 Score: 311
Period size: 43 Copynumber: 5.9 Consensus size: 43
382612 CACCTTTATC
* *
382622 TTTAAGTCTAATGTAGCTGGCCTTGAATCAGCACATTGGCACT
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACT
* * *
382665 TTTAAGTCCAATATCGCTGGCCTTGAGTCAGCATATTGGCATCTTCAT
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCA----C-T
* *
382713 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACC
1 -TTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACT
*
382757 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACC
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACT
*
382800 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCAT
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCA-------C-T
*
382851 CTTTAAGTTCAATATAGCTGGCCTTGAATCAGCACATTG
1 -TTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTG
382890 ACATCCTTTT
Statistics
Matches: 195, Mismatches: 15, Indels: 21
0.84 0.06 0.09
Matches are distributed among these distances:
43 118 0.61
45 1 0.01
47 1 0.01
48 1 0.01
49 37 0.19
50 1 0.01
52 36 0.18
ACGTcount: A:0.26, C:0.24, G:0.19, T:0.32
Consensus pattern (43 bp):
TTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACT
Found at i:382730 original size:92 final size:91
Alignment explanation
Indices: 382573--382889 Score: 401
Period size: 92 Copynumber: 3.4 Consensus size: 91
382563 CTTTTCCATC
* * * *
382573 TTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTTATCTTTAAGTCTAATGTAG
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCA-CTTCATCTTTAAGTCCAATGTAG
382638 CTGGCCTTGAATCAGCACATTGGCACT
65 CTGGCCTTGAATCAGCACATTGGCACT
* * *
382665 TTTAAGTCCAATATCGCTGGCCTTGAGTCAGCATATTGGCATCTTCATCTTTAAGTCCAATGTAG
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCA-CTTCATCTTTAAGTCCAATGTAG
*
382730 CTGGCCTTGAATCAGCACATTGGCACC
65 CTGGCCTTGAATCAGCACATTGGCACT
*
382757 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCA---C--CTTTAAGTCCAATATAGC
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACTTCATCTTTAAGTCCAATGTAGC
*
382817 TGGCCTTGAATCAGCATATTGGCACCTTTTCCAT
66 TGGCCTTGAATCAGCACATTGGCA-------C-T
*
382851 CTTTAAGTTCAATATAGCTGGCCTTGAATCAGCACATTG
1 -TTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTG
382890 ACATCCTTTT
Statistics
Matches: 201, Mismatches: 15, Indels: 15
0.87 0.06 0.06
Matches are distributed among these distances:
86 40 0.20
88 1 0.00
92 122 0.61
93 1 0.00
95 37 0.18
ACGTcount: A:0.25, C:0.24, G:0.19, T:0.32
Consensus pattern (91 bp):
TTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACTTCATCTTTAAGTCCAATGTAGC
TGGCCTTGAATCAGCACATTGGCACT
Found at i:382758 original size:21 final size:21
Alignment explanation
Indices: 382734--382801 Score: 52
Period size: 21 Copynumber: 3.2 Consensus size: 21
382724 ATGTAGCTGG
382734 CCTTGAATCAGCACATTGGCA
1 CCTTGAATCAGCACATTGGCA
* * *
382755 CCTTTAAGTC--CA-ATATAGCTGG
1 CCTTGAA-TCAGCACAT-TGGC--A
382777 CCTTGAATCAGCACATTGGCA
1 CCTTGAATCAGCACATTGGCA
382798 CCTT
1 CCTT
382802 TAAGTCCAAT
Statistics
Matches: 34, Mismatches: 6, Indels: 14
0.63 0.11 0.26
Matches are distributed among these distances:
19 2 0.06
20 5 0.15
21 12 0.35
22 8 0.24
23 5 0.15
24 2 0.06
ACGTcount: A:0.26, C:0.28, G:0.18, T:0.28
Consensus pattern (21 bp):
CCTTGAATCAGCACATTGGCA
Found at i:382777 original size:24 final size:24
Alignment explanation
Indices: 382750--382820 Score: 62
Period size: 21 Copynumber: 3.2 Consensus size: 24
382740 ATCAGCACAT
382750 TGGCACCTTTAAGTCCAATATAGC
1 TGGCACCTTTAAGTCCAATATAGC
* ** * *
382774 TGG--CCTTGAA-T-CAGCACA-T
1 TGGCACCTTTAAGTCCAATATAGC
382793 TGGCACCTTTAAGTCCAATATAGC
1 TGGCACCTTTAAGTCCAATATAGC
382817 TGGC
1 TGGC
382821 CTTGAATCAG
Statistics
Matches: 32, Mismatches: 10, Indels: 10
0.62 0.19 0.19
Matches are distributed among these distances:
19 3 0.09
20 4 0.12
21 7 0.22
22 7 0.22
23 4 0.12
24 7 0.22
ACGTcount: A:0.27, C:0.25, G:0.20, T:0.28
Consensus pattern (24 bp):
TGGCACCTTTAAGTCCAATATAGC
Found at i:382780 original size:22 final size:22
Alignment explanation
Indices: 382755--382823 Score: 56
Period size: 22 Copynumber: 3.2 Consensus size: 22
382745 CACATTGGCA
382755 CCTTTAAGTCCAATATAGCTGG
1 CCTTTAAGTCCAATATAGCTGG
* * *
382777 CCTTGAA-TCAGCACAT-TGGC--A
1 CCTTTAAGTC--CA-ATATAGCTGG
382798 CCTTTAAGTCCAATATAGCTGG
1 CCTTTAAGTCCAATATAGCTGG
382820 CCTT
1 CCTT
382824 GAATCAGCAT
Statistics
Matches: 34, Mismatches: 6, Indels: 14
0.63 0.11 0.26
Matches are distributed among these distances:
19 2 0.06
20 5 0.15
21 8 0.24
22 12 0.35
23 5 0.15
24 2 0.06
ACGTcount: A:0.26, C:0.26, G:0.17, T:0.30
Consensus pattern (22 bp):
CCTTTAAGTCCAATATAGCTGG
Found at i:383764 original size:20 final size:20
Alignment explanation
Indices: 383720--383777 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
383710 ATTTCAACGA
***
383720 TTTGTATCGATACATAAAAT
1 TTTGTATCGATACATATTTT
*
383740 GTTGTATCGATACATATTTT
1 TTTGTATCGATACATATTTT
383760 TTTGTATCGATACA-ATTT
1 TTTGTATCGATACATATTT
383778 AAGCTACTGC
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
19 4 0.12
20 29 0.88
ACGTcount: A:0.31, C:0.10, G:0.12, T:0.47
Consensus pattern (20 bp):
TTTGTATCGATACATATTTT
Found at i:383834 original size:13 final size:13
Alignment explanation
Indices: 383816--383840 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
383806 ATTACTCAAA
383816 TGTATCGATACAT
1 TGTATCGATACAT
383829 TGTATCGATACA
1 TGTATCGATACA
383841 CTGATCTTTG
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:383905 original size:52 final size:52
Alignment explanation
Indices: 383849--383973 Score: 223
Period size: 52 Copynumber: 2.4 Consensus size: 52
383839 CACTGATCTT
*
383849 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
383901 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
383953 TGTATCGATACATGCAAGCAA
1 TGTATCGATACATGCAGGCAA
383974 GTTTTCATAT
Statistics
Matches: 70, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 70 1.00
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.28
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:390682 original size:15 final size:15
Alignment explanation
Indices: 390662--390690 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
390652 AACAGTCAAA
390662 AGTAAAAAAAAAAAG
1 AGTAAAAAAAAAAAG
390677 AGTAAAAAAAAAAA
1 AGTAAAAAAAAAAA
390691 CGCGAAGGCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.83, C:0.00, G:0.10, T:0.07
Consensus pattern (15 bp):
AGTAAAAAAAAAAAG
Found at i:390954 original size:12 final size:11
Alignment explanation
Indices: 390939--390993 Score: 74
Period size: 12 Copynumber: 4.7 Consensus size: 11
390929 AAAACGAAAC
390939 AAAACAAAAAAG
1 AAAA-AAAAAAG
*
390951 AAAAAAAGAAG
1 AAAAAAAAAAG
390962 AAACAAAAAAAG
1 AAA-AAAAAAAG
390974 ACAAAAAAAAAG
1 A-AAAAAAAAAG
390986 AAAAAAAA
1 AAAAAAAA
390994 CAAAAAACCC
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
11 16 0.41
12 21 0.54
13 2 0.05
ACGTcount: A:0.85, C:0.05, G:0.09, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAAG
Found at i:390964 original size:27 final size:26
Alignment explanation
Indices: 390927--391001 Score: 91
Period size: 25 Copynumber: 2.9 Consensus size: 26
390917 GTTTTTTTCC
* *
390927 AAAAAACGAAACAAAACAAAAAAGAA
1 AAAAAAAGAAACAAAACAAAAAACAA
*
390953 AAAAAGAAGAAAC-AAA-AAAAGACAA
1 AAAAA-AAGAAACAAAACAAAAAACAA
*
390978 AAAAAAAGAAAAAAAACAAAAAAC
1 AAAAAAAGAAACAAAACAAAAAAC
391002 CCCTTTTCAC
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
24 6 0.15
25 15 0.37
26 14 0.34
27 6 0.15
ACGTcount: A:0.83, C:0.09, G:0.08, T:0.00
Consensus pattern (26 bp):
AAAAAAAGAAACAAAACAAAAAACAA
Found at i:390971 original size:24 final size:23
Alignment explanation
Indices: 390939--390993 Score: 76
Period size: 23 Copynumber: 2.3 Consensus size: 23
390929 AAAACGAAAC
*
390939 AAAACAAAAAAGA-AAAAAAGAAG
1 AAAA-AAAAAAGACAAAAAAAAAG
390962 AAACAAAAAAAGACAAAAAAAAAG
1 AAA-AAAAAAAGACAAAAAAAAAG
390986 AAAAAAAA
1 AAAAAAAA
390994 CAAAAAACCC
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
23 16 0.55
24 13 0.45
ACGTcount: A:0.85, C:0.05, G:0.09, T:0.00
Consensus pattern (23 bp):
AAAAAAAAAAGACAAAAAAAAAG
Found at i:391831 original size:16 final size:17
Alignment explanation
Indices: 391806--391843 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
391796 TTGTGCTATA
* *
391806 ATCATGACATC-ATGAC
1 ATCATAACATCAATAAC
391822 ATCATAACATCAATAAC
1 ATCATAACATCAATAAC
391839 ATCAT
1 ATCAT
391844 TATTTGCATC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 10 0.53
17 9 0.47
ACGTcount: A:0.45, C:0.24, G:0.05, T:0.26
Consensus pattern (17 bp):
ATCATAACATCAATAAC
Found at i:392043 original size:34 final size:34
Alignment explanation
Indices: 391946--392633 Score: 780
Period size: 34 Copynumber: 21.8 Consensus size: 34
391936 AAATACCTTC
* * *
391946 TCAAAGCCCACGACTCAGTGGCA--TT-TT-GTC
1 TCAAAGCCCACGACTCCGTGGCACCTTCTTCTTT
** * *
391976 TCAAAGTTCACGACTCAGTGGCA--TT-TTTTTT
1 TCAAAGCCCACGACTCCGTGGCACCTTCTTCTTT
* *
392007 TCAAAGCCCACAACTCCATGGCACCTTCTTCTTT
1 TCAAAGCCCACGACTCCGTGGCACCTTCTTCTTT
*
392041 TCAAAGCCCACAACTCCGTGGCACCTTCTTCTTT
1 TCAAAGCCCACGACTCCGTGGCACCTTCTTCTTT
*
392075 TCAAAGCCCATGACTCCGTGGCA----C-TCTTT
1 TCAAAGCCCACGACTCCGTGGCACCTTCTTCTTT
*
392104 TCAAAGCCCACGACTCTGTGGCA-C-TC-T-TTT
1 TCAAAGCCCACGACTCCGTGGCACCTTCTTCTTT
392134 T-AAAGCCCACGACTCCGTGGCA-C-TC-T-TTT
1 TCAAAGCCCACGACTCCGTGGCACCTTCTTCTTT
*
392163 T-AAAGCCCACAACTCCGTGGCACCTTCTTCTTT
1 TCAAAGCCCACGACTCCGTGGCACCTTCTTCTTT
392196 TCAAAGCCCACGACTCCGTGGCA----C-TCTTT
1 TCAAAGCCCACGACTCCGTGGCACCTTCTTCTTT
392225 TCAAAGCCCACGACTCCGTGGCA-C-TC-T-TTT
1 TCAAAGCCCACGACTCCGTGGCACCTTCTTCTTT
392255 T-AAAGCCCACGACTCCGTGGCA-C-TC-T-TTT
1 TCAAAGCCCACGACTCCGTGGCACCTTCTTCTTT
*
392284 T-AAAGCCCACGACTCCGTGGCACCTTTTTCTTT
1 TCAAAGCCCACGACTCCGTGGCACCTTCTTCTTT
*
392317 TTAAAGCCCACGACTCCGTGGCA----C-TCTTT
1 TCAAAGCCCACGACTCCGTGGCACCTTCTTCTTT
392346 TCAAAGCCCACGACTCCGTGGCA-C-TC-T-TTT
1 TCAAAGCCCACGACTCCGTGGCACCTTCTTCTTT
392376 T-AAAGCCCACGACTCCGTGGCA-C-TC-T-TTT
1 TCAAAGCCCACGACTCCGTGGCACCTTCTTCTTT
392405 T-AAAGCCCACGACTCCGTGGCACCTTCTTCTTT
1 TCAAAGCCCACGACTCCGTGGCACCTTCTTCTTT
* *
392438 TTAAAGCCCACAACTCCGTGGCACCTTCTTCTTT
1 TCAAAGCCCACGACTCCGTGGCACCTTCTTCTTT
* *
392472 TCAAAGCCCACAACTCCATGGCACCTTCTTCTTT
1 TCAAAGCCCACGACTCCGTGGCACCTTCTTCTTT
*
392506 TCAAAGCCCACAACTCCGTGGCACCTTCTTCTTT
1 TCAAAGCCCACGACTCCGTGGCACCTTCTTCTTT
392540 TCAAAGCCCACGACTCCGTGGCACCTTCTTCTTT
1 TCAAAGCCCACGACTCCGTGGCACCTTCTTCTTT
* *
392574 TCAAAGCCCACAACTCCGTGGCACCTTTTTCTGTT
1 TCAAAGCCCACGACTCCGTGGCACCTTCTTCT-TT
* *
392609 T-AAAGCCCACAACTCTGTGGCACCT
1 TCAAAGCCCACGACTCCGTGGCACCT
392634 ACAACTCCGT
Statistics
Matches: 603, Mismatches: 29, Indels: 48
0.89 0.04 0.07
Matches are distributed among these distances:
29 229 0.38
30 42 0.07
31 30 0.05
32 3 0.00
33 14 0.02
34 282 0.47
35 3 0.00
ACGTcount: A:0.21, C:0.35, G:0.15, T:0.29
Consensus pattern (34 bp):
TCAAAGCCCACGACTCCGTGGCACCTTCTTCTTT
Found at i:392183 original size:121 final size:121
Alignment explanation
Indices: 391946--392602 Score: 895
Period size: 121 Copynumber: 5.2 Consensus size: 121
391936 AAATACCTTC
* * ** * * *
391946 TCAAAGCCCACGACTCAGTGGCA-TTTTGTCTCAAAGTTCACGACTCAGTGGCATTTTTTTTTCA
1 TCAAAGCCCACGACTCCGTGGCACTCTT-T-TCAAAGCCCACGACTCCGTGGCA-CTCTTTTT-A
* * *
392010 AAGCCCACAACTCCATGGCACCTTCTTCTTTTCAAAGCCCACAACTCCGTGGCACCTTCTTCTTT
62 AAGCCCACGACTCCGTGGCA-C-TC-T-TTTT-AAAGCCCACGACTCCGTGGCACCTTCTTCTTT
* *
392075 TCAAAGCCCATGACTCCGTGGCACTCTTTTCAAAGCCCACGACTCTGTGGCACTCTTTTTAAAGC
1 TCAAAGCCCACGACTCCGTGGCACTCTTTTCAAAGCCCACGACTCCGTGGCACTCTTTTTAAAGC
*
392140 CCACGACTCCGTGGCACTCTTTTTAAAGCCCACAACTCCGTGGCACCTTCTTCTTT
66 CCACGACTCCGTGGCACTCTTTTTAAAGCCCACGACTCCGTGGCACCTTCTTCTTT
392196 TCAAAGCCCACGACTCCGTGGCACTCTTTTCAAAGCCCACGACTCCGTGGCACTCTTTTTAAAGC
1 TCAAAGCCCACGACTCCGTGGCACTCTTTTCAAAGCCCACGACTCCGTGGCACTCTTTTTAAAGC
*
392261 CCACGACTCCGTGGCACTCTTTTTAAAGCCCACGACTCCGTGGCACCTTTTTCTTT
66 CCACGACTCCGTGGCACTCTTTTTAAAGCCCACGACTCCGTGGCACCTTCTTCTTT
*
392317 TTAAAGCCCACGACTCCGTGGCACTCTTTTCAAAGCCCACGACTCCGTGGCACTCTTTTTAAAGC
1 TCAAAGCCCACGACTCCGTGGCACTCTTTTCAAAGCCCACGACTCCGTGGCACTCTTTTTAAAGC
392382 CCACGACTCCGTGGCACTCTTTTTAAAGCCCACGACTCCGTGGCACCTTCTTCTTT
66 CCACGACTCCGTGGCACTCTTTTTAAAGCCCACGACTCCGTGGCACCTTCTTCTTT
* * * *
392438 TTAAAGCCCACAACTCCGTGGCACCTTCTTCTTTTCAAAGCCCACAACTCCATGGCACCTTCTTC
1 TCAAAGCCCACGACTCCGTGGCA----C-TCTTTTCAAAGCCCACGACTCCGTGGCA-C-TC-T-
*
392503 TTTTCAAAGCCCACAACTCCGTGGCACCTTCTTCTTTTCAAAGCCCACGACTCCGTGGCACCTTC
57 TTTT-AAAGCCCACGACTCCGTGGCA-C-TC-T-TTTT-AAAGCCCACGACTCCGTGGCACCTTC
392568 TTCTTT
116 TTCTTT
*
392574 TCAAAGCCCACAACTCCGTGGCAC-CTTTT
1 TCAAAGCCCACGACTCCGTGGCACTCTTTT
392603 TCTGTTTAAA
Statistics
Matches: 491, Mismatches: 21, Indels: 31
0.90 0.04 0.06
Matches are distributed among these distances:
121 290 0.59
122 4 0.01
123 1 0.00
124 2 0.00
125 2 0.00
126 45 0.09
127 7 0.01
128 22 0.04
129 23 0.05
130 12 0.02
131 20 0.04
132 2 0.00
133 2 0.00
134 1 0.00
135 4 0.01
136 54 0.11
ACGTcount: A:0.21, C:0.35, G:0.15, T:0.29
Consensus pattern (121 bp):
TCAAAGCCCACGACTCCGTGGCACTCTTTTCAAAGCCCACGACTCCGTGGCACTCTTTTTAAAGC
CCACGACTCCGTGGCACTCTTTTTAAAGCCCACGACTCCGTGGCACCTTCTTCTTT
Found at i:392683 original size:54 final size:51
Alignment explanation
Indices: 392583--392685 Score: 154
Period size: 54 Copynumber: 2.0 Consensus size: 51
392573 TTCAAAGCCC
*
392583 ACAACTCCGTGGCACCTTTTTCTGTTTAAAGCCCACAACTCTGTGGCACCT
1 ACAACTCCGTGGCACCTTTTTCTGTTTAAAGCCCACAACTCCGTGGCACCT
392634 ACAACTCCGTGGCACTCTTTTTCCCT-TTTCAAAGCCCACAACTCCGTGGCAC
1 ACAACTCCGTGGCAC-CTTTTT--CTGTTT-AAAGCCCACAACTCCGTGGCAC
392686 TTTTTTCTTT
Statistics
Matches: 47, Mismatches: 1, Indels: 5
0.89 0.02 0.09
Matches are distributed among these distances:
51 15 0.32
52 6 0.13
53 3 0.06
54 23 0.49
ACGTcount: A:0.21, C:0.36, G:0.15, T:0.28
Consensus pattern (51 bp):
ACAACTCCGTGGCACCTTTTTCTGTTTAAAGCCCACAACTCCGTGGCACCT
Found at i:392741 original size:122 final size:119
Alignment explanation
Indices: 392515--392752 Score: 334
Period size: 122 Copynumber: 2.0 Consensus size: 119
392505 TTCAAAGCCC
*
392515 ACAACTCCGTGGCACCTTCTTCTTTTCAAAGCCCACGACTCCGTGGCACCTTCTTCTTTTCAAAG
1 ACAACTCCGTGGCACCTTCTTCTTTTCAAAGCCCACAACTCCGTGGCACCTTCTTCTTTTCAAAG
** *
392580 CCCACAACTCCGTGGCACCTTTTTCTGTTTAAAGCCCACAACTCTGTGGCACCT
66 CCCACAACTCCGTGGCACCTTTTTCCCTTTAAAGCCCACAACTCCGTGGCACCT
* * *
392634 ACAACTCCGTGGCACTCTTTTTCCCTTTTCAAAGCCCACAACTCCGTGGCACTTTTTTCTTTT-A
1 ACAACTCCGTGGCAC-CTTCTT--CTTTTCAAAGCCCACAACTCCGTGGCACCTTCTTCTTTTCA
* * * *
392698 AAGCTCACAACTCCGTGGCACTTTTTTTCCCTTTTAAGTCCACAACTCCGTGGCA
63 AAGCCCACAACTCCGTGGCAC-CTTTTTCCCTTTAAAGCCCACAACTCCGTGGCA
392753 TCTTTCTCCA
Statistics
Matches: 104, Mismatches: 11, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
119 15 0.14
120 5 0.05
121 21 0.20
122 63 0.61
ACGTcount: A:0.20, C:0.34, G:0.13, T:0.32
Consensus pattern (119 bp):
ACAACTCCGTGGCACCTTCTTCTTTTCAAAGCCCACAACTCCGTGGCACCTTCTTCTTTTCAAAG
CCCACAACTCCGTGGCACCTTTTTCCCTTTAAAGCCCACAACTCCGTGGCACCT
Found at i:392742 original size:35 final size:35
Alignment explanation
Indices: 392634--392757 Score: 166
Period size: 33 Copynumber: 3.5 Consensus size: 35
392624 TGTGGCACCT
*
392634 ACAACTCCGTGGCACTCTTTTTCCCTTTTCAAAGCCC
1 ACAACTCCGTGGCACTTTTTTTCCCTTTT-AAAG-CC
392671 ACAACTCCGTGGCAC-TTTTTT--CTTTTAAAGCTC
1 ACAACTCCGTGGCACTTTTTTTCCCTTTTAAAGC-C
392704 ACAACTCCGTGGCACTTTTTTTCCCTTTT-AAGTCC
1 ACAACTCCGTGGCACTTTTTTTCCCTTTTAAAG-CC
392739 ACAACTCCGTGGCATCTTT
1 ACAACTCCGTGGCA-CTTT
392758 CTCCATTCCT
Statistics
Matches: 80, Mismatches: 1, Indels: 13
0.85 0.01 0.14
Matches are distributed among these distances:
32 1 0.01
33 20 0.25
34 11 0.14
35 18 0.22
36 15 0.19
37 15 0.19
ACGTcount: A:0.19, C:0.32, G:0.12, T:0.36
Consensus pattern (35 bp):
ACAACTCCGTGGCACTTTTTTTCCCTTTTAAAGCC
Found at i:392805 original size:33 final size:35
Alignment explanation
Indices: 392763--392831 Score: 124
Period size: 33 Copynumber: 2.0 Consensus size: 35
392753 TCTTTCTCCA
392763 TTCCTAAAGCCCACACAAGTCGGTGGCAA-CCTTC
1 TTCCTAAAGCCCACACAAGTCGGTGGCAACCCTTC
392797 TTCC-AAAGCCCACACAAGTCGGTGGCAACCCTTC
1 TTCCTAAAGCCCACACAAGTCGGTGGCAACCCTTC
392831 T
1 T
392832 ATGCCCACTA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
33 24 0.71
34 10 0.29
ACGTcount: A:0.26, C:0.36, G:0.17, T:0.20
Consensus pattern (35 bp):
TTCCTAAAGCCCACACAAGTCGGTGGCAACCCTTC
Found at i:393005 original size:49 final size:49
Alignment explanation
Indices: 392842--393297 Score: 507
Period size: 49 Copynumber: 9.5 Consensus size: 49
392832 ATGCCCACTA
*
392842 TAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCATCTTTAAGTCCAATG
1 TAGCTGGCCTTGAATCAGCACATTGGCACC-TTT--ATCTTTAAGTCCAATG
*
392894 TAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCATCTTTAAGTCCAATG
1 TAGCTGGCCTTGAATCAGCACATTGGCACC-TTT--ATCTTTAAGTCCAATG
* *
392946 TAGCTAGCCTTGACTCAGCACATTGGCACCTTTATCTTTAAGTCCAATG
1 TAGCTGGCCTTGAATCAGCACATTGGCACCTTTATCTTTAAGTCCAATG
*
392995 TAGCTGGCCTTGAATCAGCACATTGGCA-C----T-TTTAAGTCCAATA
1 TAGCTGGCCTTGAATCAGCACATTGGCACCTTTATCTTTAAGTCCAATG
* * * * * *
393038 TCGCTGGCCTTGAATTAGCATATTGGCATCTTCAACTTTAAGTCCAATG
1 TAGCTGGCCTTGAATCAGCACATTGGCACCTTTATCTTTAAGTCCAATG
* * *
393087 TAGCTGGCCTTGACTCAGCACATTCGCA-C-----CTTTAAGTCCAATA
1 TAGCTGGCCTTGAATCAGCACATTGGCACCTTTATCTTTAAGTCCAATG
* * * *
393130 TCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATG
1 TAGCTGGCCTTGAATCAGCACATTGGCACCTTTATCTTTAAGTCCAATG
*
393179 TAGCTGGCCTTGAATCAGCACATTGGCA-C-----CTTTAAGTCCAATA
1 TAGCTGGCCTTGAATCAGCACATTGGCACCTTTATCTTTAAGTCCAATG
* *
393222 TAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCATCTTTAAGTTCAATG
1 TAGCTGGCCTTGAATCAGCACATTGGCACC-TTT--ATCTTTAAGTCCAATG
*
393274 TAGCTGGCCTTGAATCAACACATT
1 TAGCTGGCCTTGAATCAGCACATT
393298 AACATCCTTT
Statistics
Matches: 353, Mismatches: 30, Indels: 42
0.83 0.07 0.10
Matches are distributed among these distances:
43 114 0.32
44 4 0.01
48 3 0.01
49 116 0.33
51 3 0.01
52 113 0.32
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.33
Consensus pattern (49 bp):
TAGCTGGCCTTGAATCAGCACATTGGCACCTTTATCTTTAAGTCCAATG
Found at i:393044 original size:43 final size:44
Alignment explanation
Indices: 392982--393255 Score: 311
Period size: 43 Copynumber: 6.1 Consensus size: 44
392972 CACCTTTATC
*
392982 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA-CT
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCATCT
* * *
393025 TTTAAGTCCAATATCGCTGGCCTTGAATTAGCATATTGGCATCTT
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCATC-T
* * * *
393070 CAACTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTCGCA-CC
1 ----TTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCATCT
* *
393117 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCAT
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCA---TC-T
* *
393165 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA-CC
1 -TTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCATCT
* *
393209 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCT
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCATCT
393253 TTT
1 TTT
393256 CCATCTTTAA
Statistics
Matches: 194, Mismatches: 24, Indels: 25
0.80 0.10 0.10
Matches are distributed among these distances:
43 112 0.58
44 5 0.03
45 2 0.01
47 1 0.01
48 1 0.01
49 73 0.38
ACGTcount: A:0.25, C:0.24, G:0.18, T:0.32
Consensus pattern (44 bp):
TTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCATCT
Found at i:393090 original size:92 final size:92
Alignment explanation
Indices: 392932--393297 Score: 561
Period size: 92 Copynumber: 3.9 Consensus size: 92
392922 CCTTTTCCAT
* * * * * *
392932 CTTTAAGTCCAATGTAGCTAGCCTTGACTCAGCACATTGGCACCTTTATCTTTAAGTCCAATGTA
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGTA
392997 GCTGGCCTTGAATCAGCACATTGGCAC
66 GCTGGCCTTGAATCAGCACATTGGCAC
* * * *
393024 TTTTAAGTCCAATATCGCTGGCCTTGAATTAGCATATTGGCATCTTCAACTTTAAGTCCAATGTA
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGTA
* *
393089 GCTGGCCTTGACTCAGCACATTCGCAC
66 GCTGGCCTTGAATCAGCACATTGGCAC
*
393116 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGTA
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGTA
393181 GCTGGCCTTGAATCAGCACATTGGCAC
66 GCTGGCCTTGAATCAGCACATTGGCAC
* *
393208 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCATCTTTAAGTTCAAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCA--TCTT-CATCTTTAAGTCCAAT
*
393273 GTAGCTGGCCTTGAATCAACACATT
63 GTAGCTGGCCTTGAATCAGCACATT
393298 AACATCCTTT
Statistics
Matches: 250, Mismatches: 21, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
92 208 0.83
94 3 0.01
95 39 0.16
ACGTcount: A:0.25, C:0.25, G:0.17, T:0.32
Consensus pattern (92 bp):
CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGTA
GCTGGCCTTGAATCAGCACATTGGCAC
Found at i:393338 original size:56 final size:52
Alignment explanation
Indices: 393208--393349 Score: 158
Period size: 52 Copynumber: 2.7 Consensus size: 52
393198 ACATTGGCAC
* * **
393208 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAACACATTAACACCTTTTCCAT
* *
393260 CTTTAAGTTCAATGTAGCTGGCCTTGAATCAACACATTAACATCCTTTTTCATCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAACACATTAACA-CC-TTTTC--CAT
* * * *
393316 CTTTAAGCCCAATATCGTTGGCCGTGAATCAACA
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAACA
393350 TATTGGCATC
Statistics
Matches: 74, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
52 36 0.49
53 2 0.03
54 5 0.07
56 31 0.42
ACGTcount: A:0.27, C:0.25, G:0.14, T:0.34
Consensus pattern (52 bp):
CTTTAAGTCCAATATAGCTGGCCTTGAATCAACACATTAACACCTTTTCCAT
Found at i:394168 original size:33 final size:33
Alignment explanation
Indices: 394131--394197 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
394121 TTCAACGATT
394131 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
394164 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
394197 T
1 T
394198 TTAAGCCACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:394169 original size:13 final size:13
Alignment explanation
Indices: 394151--394175 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
394141 CATAAAATGT
394151 TGTATCGATACAA
1 TGTATCGATACAA
394164 TGTATCGATACA
1 TGTATCGATACA
394176 TATTTTTTTG
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:394256 original size:13 final size:13
Alignment explanation
Indices: 394238--394262 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
394228 ATTACTCAAA
394238 TGTATCGATACAT
1 TGTATCGATACAT
394251 TGTATCGATACA
1 TGTATCGATACA
394263 CTGATCTTTG
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:394327 original size:52 final size:52
Alignment explanation
Indices: 394271--394395 Score: 223
Period size: 52 Copynumber: 2.4 Consensus size: 52
394261 CACTGATCTT
*
394271 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
394323 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
394375 TGTATCGATACATGCAAGCAA
1 TGTATCGATACATGCAGGCAA
394396 GTTTTCATAT
Statistics
Matches: 70, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 70 1.00
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.28
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:400604 original size:13 final size:13
Alignment explanation
Indices: 400586--400623 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
400576 GATTGTTCTT
400586 TGTATCGATACAA
1 TGTATCGATACAA
400599 TGTATCGATACAA
1 TGTATCGATACAA
*
400612 TGTATCAATACA
1 TGTATCGATACA
400624 TAGGTTACTA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.39, C:0.16, G:0.13, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:403258 original size:20 final size:20
Alignment explanation
Indices: 403229--403283 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
403219 ACCCTAAGTG
* *
403229 AATGTTTCGATACAT-AGGA
1 AATGTATCGATACATGAAGA
403248 CAATGTATCGATACATGAAGA
1 -AATGTATCGATACATGAAGA
*
403269 ATTGTATCGATACAT
1 AATGTATCGATACAT
403284 TATGCCCAAC
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
20 28 0.90
21 3 0.10
ACGTcount: A:0.38, C:0.13, G:0.18, T:0.31
Consensus pattern (20 bp):
AATGTATCGATACATGAAGA
Found at i:404612 original size:15 final size:16
Alignment explanation
Indices: 404588--404629 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 16
404578 CCTTTTCCAG
404588 TTCAACAATTTTC-TT
1 TTCAACAATTTTCTTT
*
404603 TTCAAGAA-TTTCTTT
1 TTCAACAATTTTCTTT
*
404618 TTCAATAATTTT
1 TTCAACAATTTT
404630 TGCTTTATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
14 4 0.17
15 16 0.70
16 3 0.13
ACGTcount: A:0.29, C:0.14, G:0.02, T:0.55
Consensus pattern (16 bp):
TTCAACAATTTTCTTT
Done.