Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold84
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: 2025335
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 30794 characters in sequence are not A, C, G, or T
File 13 of 13
Found at i:1956269 original size:34 final size:33
Alignment explanation
Indices: 1956163--1956723 Score: 600
Period size: 34 Copynumber: 16.9 Consensus size: 33
1956153 ATTTTGTCTC
* * * * *
1956163 AAAGTCCACGACTCAGTGGCA-TTTTTTC-TTC
1 AAAGCCCACAACTCCGTGGCACCTTTTTCTTTT
*
1956194 AAAGCCCACAACTCCGTGGCACC-TTTTCCTTT
1 AAAGCCCACAACTCCGTGGCACCTTTTTCTTTT
*
1956226 AAAGCCCACAACTCCGTGGCACCTTCTTCTTTT
1 AAAGCCCACAACTCCGTGGCACCTTTTTCTTTT
* *
1956259 CAAAGCCCACAACTCTGTGGCACCTTCTTCTTTTT
1 -AAAGCCCACAACTCCGTGGCACCTTTTTC-TTTT
*
1956294 AAAGCCCACAACTCCGTGGCA-C--TCT-TTTT
1 AAAGCCCACAACTCCGTGGCACCTTTTTCTTTT
*
1956323 AAAGCCCACAACTCCGTGGCACTCTTTTTCCTTCT
1 AAAGCCCACAACTCCGTGGCAC-CTTTTT-CTTTT
* *
1956358 -AAGCCCACAACTCTGTGGCACTCTTTTTCCTTCT
1 AAAGCCCACAACTCCGTGGCAC-CTTTTT-CTTTT
*
1956392 -AAGCCCACAACTCTGTGGCACC-----CTTTT
1 AAAGCCCACAACTCCGTGGCACCTTTTTCTTTT
*
1956419 -AAGCCCACAACTCCGTGGCACTTTTTTCATCTTT
1 AAAGCCCACAACTCCGTGGCACCTTTTTC-T-TTT
*
1956453 -AAGTCCACAACTCCGTGGCACCTTTTTCTGTTT
1 AAAGCCCACAACTCCGTGGCACCTTTTTCT-TTT
*
1956486 AAAGCCCACAACTCCGTGGCACTTTTTTCATCTTT
1 AAAGCCCACAACTCCGTGGCACCTTTTTC-T-TTT
*
1956521 -AAGTCCACAACTCCGTGGCACCTTTTTCTTTTT
1 AAAGCCCACAACTCCGTGGCACCTTTTTC-TTTT
1956554 AAAGCCCACAACTCCGTGGCACCTTTTTCTATTT
1 AAAGCCCACAACTCCGTGGCACCTTTTTCT-TTT
1956588 AAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTTT
1 AAAGCCCACAACTCCGTGGCAC-CTTTTT--CTTTT
*
1956624 CAAAGCCCACAACTCCGTGGCACATTTTTCTTTT
1 -AAAGCCCACAACTCCGTGGCACCTTTTTCTTTT
*
1956658 AAAGGCCACAACTCCGTGGCACTCTTTTTTCGTTTT
1 AAAGCCCACAACTCCGTGGCAC-C-TTTTTC-TTTT
* * *
1956694 -AAGTCCACAACTCTGTGGCAACCTTCTTCT
1 AAAGCCCACAACTCCGTGGC-ACCTTTTTCT
1956724 AAAGCCCACA
Statistics
Matches: 467, Mismatches: 33, Indels: 58
0.84 0.06 0.10
Matches are distributed among these distances:
27 24 0.05
29 25 0.05
31 25 0.05
32 26 0.06
33 42 0.09
34 246 0.53
35 41 0.09
36 14 0.03
37 24 0.05
ACGTcount: A:0.21, C:0.33, G:0.13, T:0.33
Consensus pattern (33 bp):
AAAGCCCACAACTCCGTGGCACCTTTTTCTTTT
Found at i:1956334 original size:129 final size:129
Alignment explanation
Indices: 1956194--1956733 Score: 577
Period size: 129 Copynumber: 4.1 Consensus size: 129
1956184 TTTTTTCTTC
*
1956194 AAAGCCCACAACTCCGTGGCAC-C-TTTTCCTTTAAAGCCCACAACTCCGTGGCACCTTCTTCTT
1 AAAGCCCACAACTCCGTGGCACTCTTTTTCCTTTAAAGCCCACAACTCCGTGGCACCTTTTTCTT
*
1956257 TTCAAAGCCCACAACTCTGTGGCACCTTCTTCTTTTTAAAGCCCACAACTCCGTGGCACTCTTTT
66 TT-AAAGCCCACAACTCCGTGGCACCTTCTTCTTTTT-AAGCCCACAACTCCGTGGCACTCTTTT
1956322 T
129 T
*
1956323 AAAGCCCACAACTCCGTGGCACTCTTTTTCCTTCT-AAGCCCACAACTCTGTGGCACTCTTTTTC
1 AAAGCCCACAACTCCGTGGCACTCTTTTTCCTT-TAAAGCCCACAACTCCGTGGCAC-CTTTTT-
* *
1956387 CTTCT-AAGCCCACAACTCTGTGGCA-C--C--C-TTTTAAGCCCACAACTCCGTGGCACT-TTT
63 CTTTTAAAGCCCACAACTCCGTGGCACCTTCTTCTTTTTAAGCCCACAACTCCGTGGCACTCTTT
1956444 TT
128 TT
* * *
1956446 CATCTTTAAGTCCACAACTCCGTGGCAC-CTTTTTCTGTTTAAAGCCCACAACTCCGTGGCACTT
1 -A-----AAGCCCACAACTCCGTGGCACTCTTTTTC-CTTTAAAGCCCACAACTCCGTGGCACCT
* *
1956510 TTTTCATCTTT-AAGTCCACAACTCCGTGGCACCTTTTTCTTTTTAAAGCCCACAACTCCGTGGC
59 TTTTC-T-TTTAAAGCCCACAACTCCGTGGCACCTTCTTCTTTTT-AAGCCCACAACTCCGTGGC
*
1956574 ACCTTTTTCTATTT
121 A-C----TCTTTTT
*
1956588 AAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTTTCAAAGCCCACAACTCCGTGGCACATTTTT
1 AAAGCCCACAACTCCGTGGCACTCTTTTT-CC-TTT-AAAGCCCACAACTCCGTGGCACCTTTTT
* * * * *
1956653 CTTTTAAAGGCCACAACTCCGTGGCACTCTTTTTTCGTTTTAAGTCCACAACTCTGTGGCAAC-C
63 CTTTTAAAGCCCACAACTCCGTGGCAC-C-TTCTTCTTTTTAAGCCCACAACTCCGTGGC-ACTC
1956717 TTCTTCT
125 TT-TT-T
1956724 AAAGCCCACA
1 AAAGCCCACA
1956734 CAAGTCGGTG
Statistics
Matches: 353, Mismatches: 20, Indels: 69
0.80 0.05 0.16
Matches are distributed among these distances:
123 5 0.01
124 23 0.07
125 4 0.01
126 1 0.00
127 1 0.00
128 15 0.04
129 84 0.24
130 3 0.01
131 48 0.14
132 6 0.02
133 4 0.01
134 3 0.01
135 6 0.02
136 51 0.14
137 10 0.03
138 25 0.07
139 47 0.13
140 11 0.03
141 2 0.01
142 4 0.01
ACGTcount: A:0.21, C:0.34, G:0.13, T:0.32
Consensus pattern (129 bp):
AAAGCCCACAACTCCGTGGCACTCTTTTTCCTTTAAAGCCCACAACTCCGTGGCACCTTTTTCTT
TTAAAGCCCACAACTCCGTGGCACCTTCTTCTTTTTAAGCCCACAACTCCGTGGCACTCTTTTT
Found at i:1956378 original size:163 final size:164
Alignment explanation
Indices: 1956163--1956733 Score: 620
Period size: 163 Copynumber: 3.5 Consensus size: 164
1956153 ATTTTGTCTC
* * * *
1956163 AAAGTCCACGACTCAGTGGCA-TTTTTT-CTTCAAAGCCCACAACTCCGTGGCACC-TTTTCCTT
1 AAAGCCCACAACTCCGTGGCACTTTTTTCCTTCTAAGCCCACAACTCCGTGGCACCTTTTTCCTT
*
1956225 -TAAAGCCCACAACTCCGTGGCACCTTCTTCTTTTCAAAGCCCACAACTCTGTGGCACCTTCTTC
66 CTAAAGCCCACAACTCCGTGGCACCTTCTTCTTTT-AAAGCCCACAACTCCGTGGCACCTTCTTC
1956289 TTTTTAAAGCCCACAACTCCGTGGCAC-TCTTTTT
130 TTTTTAAAGCCCACAACTCCGTGGCACTTCTTTTT
*
1956323 AAAGCCCACAACTCCGTGGCACTCTTTTTCCTTCTAAGCCCACAACTCTGTGGCACTCTTTTTCC
1 AAAGCCCACAACTCCGTGGCACT-TTTTTCCTTCTAAGCCCACAACTCCGTGGCAC-CTTTTTCC
* * *
1956388 TTCT-AAGCCCACAACTCTGTGGCA-C--C--CTTTT-AAGCCCACAACTCCGTGGCACTTTTTT
64 TTCTAAAGCCCACAACTCCGTGGCACCTTCTTCTTTTAAAGCCCACAACTCCGTGGCACCTTCTT
* * *
1956446 CATCTTT-AAGTCCACAACTCCGTGGCACCTTTTTCTGTTT
129 C-TTTTTAAAGCCCACAACTCCGTGGCA-C---TTCTTTTT
* *
1956486 AAAGCCCACAACTCCGTGGCACTTTTTTCATCTT-TAAGTCCACAACTCCGTGGCACCTTTTTCT
1 AAAGCCCACAACTCCGTGGCACTTTTTTC--CTTCTAAGCCCACAACTCCGTGGCACCTTTTTCC
* * *
1956550 TTTTAAAGCCCACAACTCCGTGGCACCTTTTTCTATTTAAAGCCCACAACTCCGTGGCACTCTTT
64 TTCTAAAGCCCACAACTCCGTGGCACCTTCTTCT-TTTAAAGCCCACAACTCCGTGGCAC-CTTC
* *
1956615 TTCCCTTTTCAAAGCCCACAACTCCGTGGCACATTTTTCTTTT
127 TT--CTTTTTAAAGCCCACAACTCCGTGGCAC--TTCT-TTTT
* * * * *
1956658 AAAGGCCACAACTCCGTGGCACTCTTTTTTCGTTTTAAGTCCACAACTCTGTGGCAACC---TT-
1 AAAGCCCACAACTCCGTGGCA--CTTTTTTCCTTCTAAGCCCACAACTCCGTGGC-ACCTTTTTC
1956719 CTTCTAAAGCCCACA
63 CTTCTAAAGCCCACA
1956734 CAAGTCGGTG
Statistics
Matches: 350, Mismatches: 30, Indels: 52
0.81 0.07 0.12
Matches are distributed among these distances:
158 44 0.13
159 5 0.01
160 23 0.07
161 1 0.00
162 22 0.06
163 92 0.26
164 6 0.02
165 27 0.08
166 1 0.00
168 2 0.01
169 3 0.01
170 34 0.10
171 11 0.03
172 29 0.08
173 39 0.11
174 11 0.03
ACGTcount: A:0.22, C:0.33, G:0.13, T:0.32
Consensus pattern (164 bp):
AAAGCCCACAACTCCGTGGCACTTTTTTCCTTCTAAGCCCACAACTCCGTGGCACCTTTTTCCTT
CTAAAGCCCACAACTCCGTGGCACCTTCTTCTTTTAAAGCCCACAACTCCGTGGCACCTTCTTCT
TTTTAAAGCCCACAACTCCGTGGCACTTCTTTTT
Found at i:1956421 original size:27 final size:27
Alignment explanation
Indices: 1956386--1956439 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
1956376 CACTCTTTTT
*
1956386 CCTTCTAAGCCCACAACTCTGTGGCAC
1 CCTTCTAAGCCCACAACTCCGTGGCAC
*
1956413 CCTTTTAAGCCCACAACTCCGTGGCAC
1 CCTTCTAAGCCCACAACTCCGTGGCAC
1956440 TTTTTTCATC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.22, C:0.41, G:0.15, T:0.22
Consensus pattern (27 bp):
CCTTCTAAGCCCACAACTCCGTGGCAC
Found at i:1956810 original size:49 final size:49
Alignment explanation
Indices: 1956756--1957252 Score: 696
Period size: 49 Copynumber: 10.4 Consensus size: 49
1956746 AACCCTTCTA
*
1956756 AGCATATTGGCACCTTCATCTTTAAGTCCAATGTAACTGGCCTTGAATC
1 AGCATATTGGCACCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATC
*
1956805 AGCATATTGGCACCTTCATCTTTAAGTCCAATGTAGCTGGCTTTGAATC
1 AGCATATTGGCACCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATC
* * *
1956854 AGCACATTGGCA----C--CTTTAAGTCCAATATCGCTGGCCTTGAATC
1 AGCATATTGGCACCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATC
*
1956897 AGCATATTGGCACCTTCATCTTTAAGTCCAATATAGCTGGCCTTGAATC
1 AGCATATTGGCACCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATC
* *
1956946 AGCATATTGGCACCTTTATCTTTAAGTCCAATGTAGCTGGCCTTGACTC
1 AGCATATTGGCACCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATC
* * * *
1956995 AGCACATTGGCACCTTCACCATTAAGTCCAATATAGCTGGCCTTGAATC
1 AGCATATTGGCACCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATC
* *
1957044 AGCATATTGGCACCTTTATCTTTAAGTCCAATGTAGCTGGCCTTGACTC
1 AGCATATTGGCACCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATC
* *
1957093 AGCACATTGGCACCTTCATCTTTAAGTCCAATGTAGCTAGCCTTGAATC
1 AGCATATTGGCACCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATC
* * *
1957142 AGCACATTGGCACC-TCACCTTTAATTCCAATGTAGCTGGCCTTGAATC
1 AGCATATTGGCACCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATC
* * *
1957190 AGCACATTGGCA----C--CTTTAAGTCCAATATAGCTGGCCTTGAATT
1 AGCATATTGGCACCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATC
*
1957233 AGCATATTGGCACATTCATC
1 AGCATATTGGCACCTTCATC
1957253 ATCTTTAAAA
Statistics
Matches: 402, Mismatches: 34, Indels: 24
0.87 0.07 0.05
Matches are distributed among these distances:
43 76 0.19
45 2 0.00
47 2 0.00
48 43 0.11
49 279 0.69
ACGTcount: A:0.26, C:0.26, G:0.17, T:0.31
Consensus pattern (49 bp):
AGCATATTGGCACCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATC
Found at i:1958072 original size:33 final size:33
Alignment explanation
Indices: 1958035--1958101 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1958025 TTCAACGATT
1958035 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
1958068 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
1958101 T
1 T
1958102 TTAAGCTACT
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:1958073 original size:13 final size:13
Alignment explanation
Indices: 1958055--1958079 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1958045 CATAAAATGT
1958055 TGTATCGATACAA
1 TGTATCGATACAA
1958068 TGTATCGATACA
1 TGTATCGATACA
1958080 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:1958161 original size:13 final size:13
Alignment explanation
Indices: 1958143--1958167 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1958133 ATTACTCACA
1958143 TGTATCGATACAT
1 TGTATCGATACAT
1958156 TGTATCGATACA
1 TGTATCGATACA
1958168 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:1963069 original size:20 final size:20
Alignment explanation
Indices: 1963041--1963094 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
1963031 AAATGCCTGG
*
1963041 ATGTTTCGATACATTGAGAA
1 ATGTATCGATACATTGAGAA
1963061 ATGTATCGATACATTGAGAA
1 ATGTATCGATACATTGAGAA
1963081 ATGTATCGATACAT
1 ATGTATCGATACAT
1963095 CTGGGTAAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.37, C:0.11, G:0.19, T:0.33
Consensus pattern (20 bp):
ATGTATCGATACATTGAGAA
Found at i:1966942 original size:13 final size:13
Alignment explanation
Indices: 1966924--1966948 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1966914 CAAAGATCAG
1966924 TGTATCGATACAA
1 TGTATCGATACAA
1966937 TGTATCGATACA
1 TGTATCGATACA
1966949 TTTGAGTAAT
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:1967966 original size:22 final size:22
Alignment explanation
Indices: 1967941--1968009 Score: 56
Period size: 22 Copynumber: 3.2 Consensus size: 22
1967931 ATGCTGATTC
1967941 AAGGCCAGCTATATTGGACTTA
1 AAGGCCAGCTATATTGGACTTA
* * *
1967963 AAGG--TGCCA-ATGTGCTGA-TTC
1 AAGGCCAGCTATAT-TG--GACTTA
1967984 AAGGCCAGCTATATTGGACTTA
1 AAGGCCAGCTATATTGGACTTA
1968006 AAGG
1 AAGG
1968010 TGAAGGTGCC
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:0.30, C:0.17, G:0.26, T:0.26
Consensus pattern (22 bp):
AAGGCCAGCTATATTGGACTTA
Found at i:1968035 original size:49 final size:49
Alignment explanation
Indices: 1967875--1968103 Score: 317
Period size: 49 Copynumber: 4.7 Consensus size: 49
1967865 AAAAGGATGT
* * *
1967875 CAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGAT-G--AAGGTGC
1967927 CAATATGCTGATTCAAGGCCAGCTATATTGGACTT----A--AAGGTGC
1 CAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGC
* *
1967970 CAATGTGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGTGAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGC
*
1968019 CAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATAAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGC
* *
1968068 CAATATGGTGATTCAAGGCCAGCTATATTGGGCTTA
1 CAATATGCTGATTCAAGGCCAGCTATATTGGACTTA
1968104 GAAGGGTTGC
Statistics
Matches: 161, Mismatches: 10, Indels: 15
0.87 0.05 0.08
Matches are distributed among these distances:
43 41 0.25
48 1 0.01
49 87 0.54
52 32 0.20
ACGTcount: A:0.31, C:0.17, G:0.25, T:0.27
Consensus pattern (49 bp):
CAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGC
Found at i:1968130 original size:30 final size:30
Alignment explanation
Indices: 1968096--1968184 Score: 96
Period size: 30 Copynumber: 3.0 Consensus size: 30
1968086 CCAGCTATAT
*
1968096 TGGGCTTAGAAGGGTTGCCACCGACTTGTG
1 TGGGCTTAGAAGGGTTGCCACTGACTTGTG
*
1968126 TGGGCTTTGGAAAAGGG-TGCCACTGA-TT-TG
1 TGGGC-TT--AGAAGGGTTGCCACTGACTTGTG
*
1968156 TGGGCTTTGAA-GGTTGCCACTGACTTGTG
1 TGGGCTTAGAAGGGTTGCCACTGACTTGTG
1968185 GGCTTTCGAA
Statistics
Matches: 49, Mismatches: 4, Indels: 13
0.74 0.06 0.20
Matches are distributed among these distances:
26 2 0.04
27 11 0.22
28 2 0.04
29 4 0.08
30 12 0.24
31 4 0.08
32 8 0.16
33 6 0.12
ACGTcount: A:0.17, C:0.17, G:0.36, T:0.30
Consensus pattern (30 bp):
TGGGCTTAGAAGGGTTGCCACTGACTTGTG
Found at i:1968306 original size:117 final size:117
Alignment explanation
Indices: 1968124--1968365 Score: 360
Period size: 117 Copynumber: 2.1 Consensus size: 117
1968114 CACCGACTTG
* * *
1968124 TGTGGGCTTTGGAAAAGGGTGCCACTGATTTGTGGGCTTTGAAGGTTGCCACTGACTTGTGGGCT
1 TGTGGGCTTTGGAAAAGGGTGCCACTAACTTGTGGGCTTTAAAGGTTGCCACTGACTTGTGGGCT
* *
1968189 TTCGAAAAAAATGCCACCGACTTGTGGGC-TTTGAAAAATATGCCACTGACT
66 TTCGAAAAAAATGCCACCGACTTGTGGGCTTTTGAAAAAGATGCCACTAACT
* *
1968240 TGTGGGCTTTTGAACAGGGTGCCACTAACTTGTGGGCTTTTAAAGGTTGCCACTGACTTGTGGGC
1 TGTGGGCTTTGGAAAAGGGTGCCACTAACTTGTGGGC-TTTAAAGGTTGCCACTGACTTGTGGGC
* * * * *
1968305 TTTTGAAAAATATGCCACTGACTTGTGGGCTTTTGAAAAGGGTGCCACTAACT
65 TTTCGAAAAAAATGCCACCGACTTGTGGGCTTTTGAAAAAGATGCCACTAACT
1968358 TGTGGGCT
1 TGTGGGCT
1968366 GAAAAGAGTG
Statistics
Matches: 112, Mismatches: 12, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
116 33 0.29
117 53 0.47
118 26 0.23
ACGTcount: A:0.22, C:0.18, G:0.29, T:0.31
Consensus pattern (117 bp):
TGTGGGCTTTGGAAAAGGGTGCCACTAACTTGTGGGCTTTAAAGGTTGCCACTGACTTGTGGGCT
TTCGAAAAAAATGCCACCGACTTGTGGGCTTTTGAAAAAGATGCCACTAACT
Found at i:1968331 original size:88 final size:88
Alignment explanation
Indices: 1968108--1968365 Score: 335
Period size: 88 Copynumber: 2.9 Consensus size: 88
1968098 GGCTTAGAAG
* *** * *
1968108 GGTTGCCACCGACTTGTGTGGGCTTTGGAAAAGGGTGCCACTGATTTGTGGGC-TTTG-AAGGTT
1 GGTTGCCACCGAC-T-TGTGGGCTTTTGAAAAATATGCCACTGACTTGTGGGCTTTTGAAAGGGT
*
1968171 GCCACTGACTTGTGGGCTTTCGAAAA
64 GCCACTAACTTGTGGGCTTTC-AAAA
***
1968197 AAATGCCACCGACTTGTGGGC-TTTGAAAAATATGCCACTGACTTGTGGGCTTTTGAACAGGGTG
1 GGTTGCCACCGACTTGTGGGCTTTTGAAAAATATGCCACTGACTTGTGGGCTTTTGAA-AGGGTG
*
1968261 CCACTAACTTGTGGGCTTT-TAAA
65 CCACTAACTTGTGGGCTTTCAAAA
*
1968284 GGTTGCCACTGACTTGTGGGCTTTTGAAAAATATGCCACTGACTTGTGGGCTTTTGAAAAGGGTG
1 GGTTGCCACCGACTTGTGGGCTTTTGAAAAATATGCCACTGACTTGTGGGCTTTTG-AAAGGGTG
1968349 CCACTAACTTGTGGGCT
65 CCACTAACTTGTGGGCT
1968366 GAAAAGAGTG
Statistics
Matches: 149, Mismatches: 15, Indels: 11
0.85 0.09 0.06
Matches are distributed among these distances:
86 24 0.16
87 31 0.21
88 59 0.40
89 35 0.23
ACGTcount: A:0.21, C:0.19, G:0.29, T:0.31
Consensus pattern (88 bp):
GGTTGCCACCGACTTGTGGGCTTTTGAAAAATATGCCACTGACTTGTGGGCTTTTGAAAGGGTGC
CACTAACTTGTGGGCTTTCAAAA
Found at i:1968514 original size:57 final size:57
Alignment explanation
Indices: 1968105--1968549 Score: 310
Period size: 57 Copynumber: 7.5 Consensus size: 57
1968095 TTGGGCTTAG
* * *
1968105 AAGGGTTGCCACCGACTTGTGTGGGCTTTGGAAAAGGGTGCCACTGATTTGTGGGCTTTG--
1 AAGGG-TGCCACTGAC-T-TGTGGGCTTT-G-AAAGGATGCCACTGACTTGTGGGCTTTGAA
* ** *
1968165 AAGGTTGCCACTGACTTGTGGGCTTTCGAAAAAAATGCCACCGACTTGTGGGCTTTGAA
1 AAGGGTGCCACTGACTTGTGGGCTTT-G-AAAGGATGCCACTGACTTGTGGGCTTTGAA
*** * * *
1968224 AAATATGCCACTGACTTGTGGGCTTTTGAACAGGGTGCCACTAACTTGTGGGCTTT-TA
1 AAGGGTGCCACTGACTTGTGGGC-TTTGAA-AGGATGCCACTGACTTGTGGGCTTTGAA
* **
1968282 AAGGTTGCCACTGACTTGTGGGCTTTTGAAAAATATGCCACTGACTTGTGGGCTTTTGAA
1 AAGGGTGCCACTGACTTGTGGGC-TTTG-AAAGGATGCCACTGACTTGTGGGC-TTTGAA
* * * * * * *
1968342 AAGGGTGCCACTAACTTGTGGGC--TGAAAAGAGTGCTA-TAGAGTTATGAGCTTACAAAAGAAA
1 AAGGGTGCCACTGACTTGTGGGCTTTGAAAGGA-TGCCACT-GACTTGTGGGCTT-----TG-AA
* * * * * * * *
1968404 AAGAGTGCCACGGAGTTGTGGACTTTGGAAAAGATGCCGCCGACTTGTGGGCTTCGGAA
1 AAGGGTGCCACTGACTTGTGGGCTTT-GAAAGGATGCCACTGACTTGTGGGCTT-TGAA
*
1968463 AAGGGTGCCACTGACTTGTGGGCTTTG-AAGGTTGCCACTGACTTGTGGGCTTTCGAA
1 AAGGGTGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTT-GAA
*** *
1968520 AAAAATGCCACCGACTTGTGGGCTTTGAAA
1 AAGGGTGCCACTGACTTGTGGGCTTTGAAA
1968550 AAAAAAATGC
Statistics
Matches: 305, Mismatches: 59, Indels: 44
0.75 0.14 0.11
Matches are distributed among these distances:
56 8 0.03
57 96 0.31
58 50 0.16
59 79 0.26
60 30 0.10
61 1 0.00
62 20 0.07
64 14 0.05
65 7 0.02
ACGTcount: A:0.24, C:0.18, G:0.30, T:0.28
Consensus pattern (57 bp):
AAGGGTGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAA
Found at i:1968554 original size:30 final size:29
Alignment explanation
Indices: 1968124--1968551 Score: 325
Period size: 30 Copynumber: 14.6 Consensus size: 29
1968114 CACCGACTTG
* * *
1968124 TGTGGGCTTTGGAAAAGGGTGCCACTGATT
1 TGTGGGCTTT-GAAAAAGATGCCACTGACT
* *
1968154 TGTGGGCTTTG--AAGGTTGCCACTGACT
1 TGTGGGCTTTGAAAAAGATGCCACTGACT
* *
1968181 TGTGGGCTTTCGAAAAAAATGCCACCGACT
1 TGTGGGCTTT-GAAAAAGATGCCACTGACT
*
1968211 TGTGGGCTTTGAAAAATATGCCACTGACT
1 TGTGGGCTTTGAAAAAGATGCCACTGACT
* * * *
1968240 TGTGGGCTTTTGAACAGGGTGCCACTAACT
1 TGTGGGC-TTTGAAAAAGATGCCACTGACT
* * *
1968270 TGTGGGCTTT-TAAAGGTTGCCACTGACT
1 TGTGGGCTTTGAAAAAGATGCCACTGACT
*
1968298 TGTGGGCTTTTGAAAAATATGCCACTGACT
1 TGTGGGC-TTTGAAAAAGATGCCACTGACT
* * *
1968328 TGTGGGCTTTTGAAAAGGGTGCCACTAACT
1 TGTGGGC-TTTGAAAAAGATGCCACTGACT
* *
1968358 TGTGGGC--TG-AAAAGAGTGCTA-TAGAGT
1 TGTGGGCTTTGAAAAAGA-TGCCACT-GACT
* * * * *
1968385 TATGAGCTTACAAAAGAAAAAGAGTGCCACGGAGT
1 TGTGGGCTT-----TGAAAAAGA-TGCCACTGACT
* * * *
1968420 TGTGGACTTTGGAAAAGATGCCGCCGACT
1 TGTGGGCTTTGAAAAAGATGCCACTGACT
* * *
1968449 TGTGGGCTTCGGAAAAGGGTGCCACTGACT
1 TGTGGGCTT-TGAAAAAGATGCCACTGACT
* *
1968479 TGTGGGCTTTG--AAGGTTGCCACTGACT
1 TGTGGGCTTTGAAAAAGATGCCACTGACT
* *
1968506 TGTGGGCTTTCGAAAAAAATGCCACCGACT
1 TGTGGGCTTT-GAAAAAGATGCCACTGACT
1968536 TGTGGGCTTTGAAAAA
1 TGTGGGCTTTGAAAAA
1968552 AAAAATGCCA
Statistics
Matches: 321, Mismatches: 56, Indels: 43
0.76 0.13 0.10
Matches are distributed among these distances:
26 5 0.02
27 62 0.19
28 23 0.07
29 54 0.17
30 155 0.48
34 1 0.00
35 21 0.07
ACGTcount: A:0.25, C:0.17, G:0.30, T:0.28
Consensus pattern (29 bp):
TGTGGGCTTTGAAAAAGATGCCACTGACT
Found at i:1970037 original size:11 final size:11
Alignment explanation
Indices: 1970021--1970058 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
1970011 CGGACCCCCT
1970021 TTTTTTGTTTG
1 TTTTTTGTTTG
1970032 TTTTTT-TATTG
1 TTTTTTGT-TTG
1970043 TTTTTTGTTT-
1 TTTTTTGTTTG
1970053 TTTTTT
1 TTTTTT
1970059 TTCCTTTTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
10 7 0.28
11 17 0.68
12 1 0.04
ACGTcount: A:0.03, C:0.00, G:0.11, T:0.87
Consensus pattern (11 bp):
TTTTTTGTTTG
Found at i:1970076 original size:19 final size:17
Alignment explanation
Indices: 1970020--1970079 Score: 75
Period size: 18 Copynumber: 3.4 Consensus size: 17
1970010 CCGGACCCCC
*
1970020 TTTTTTTGTTTGTTTTT
1 TTTTTTTTTTTGTTTTT
*
1970037 TTATTGTTTTTTGTTTTT
1 TT-TTTTTTTTTGTTTTT
*
1970055 TTTTTTCCTTTTGTTTTT
1 TTTTTT-TTTTTGTTTTT
1970073 TTTTTTT
1 TTTTTTT
1970080 GGTTTGGAGG
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
17 5 0.14
18 31 0.86
ACGTcount: A:0.02, C:0.03, G:0.08, T:0.87
Consensus pattern (17 bp):
TTTTTTTTTTTGTTTTT
Found at i:1981784 original size:52 final size:51
Alignment explanation
Indices: 1981706--1981821 Score: 205
Period size: 52 Copynumber: 2.3 Consensus size: 51
1981696 AGTTGCTTGT
*
1981706 ATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGCCTGC
1 ATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAA-TTGCCTGC
*
1981758 ATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTGCCTGC
1 ATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTGCCTGC
1981809 ATGTATCGATACA
1 ATGTATCGATACA
1981822 AAGATCAGTG
Statistics
Matches: 62, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
51 21 0.34
52 41 0.66
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.34
Consensus pattern (51 bp):
ATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTGCCTGC
Found at i:1981834 original size:51 final size:52
Alignment explanation
Indices: 1981706--1981841 Score: 188
Period size: 52 Copynumber: 2.6 Consensus size: 52
1981696 AGTTGCTTGT
*
1981706 ATGTATCGATACATTTA-ATAGTGTATCGATACATCTGGGCAAATTTGCCTGC
1 ATGTATCGATACA-TAAGATAGTGTATCGATACATCTGGGCAAATTTGCCTGC
*** *
1981758 ATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAA-TTGCCTGC
1 ATGTATCGATACATAAGATAGTGTATCGATACATCTGGGCAAATTTGCCTGC
1981809 ATGTATCGATACA-AAGATCAGTGTATCGATACA
1 ATGTATCGATACATAAGAT-AGTGTATCGATACA
1981842 ATGTATCGAT
Statistics
Matches: 76, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
50 2 0.03
51 36 0.47
52 38 0.50
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Consensus pattern (52 bp):
ATGTATCGATACATAAGATAGTGTATCGATACATCTGGGCAAATTTGCCTGC
Found at i:1981848 original size:13 final size:13
Alignment explanation
Indices: 1981830--1981854 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1981820 CAAAGATCAG
1981830 TGTATCGATACAA
1 TGTATCGATACAA
1981843 TGTATCGATACA
1 TGTATCGATACA
1981855 TTTGAGTAAT
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:1981932 original size:33 final size:33
Alignment explanation
Indices: 1981895--1981961 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1981885 AGTAGCTTAA
1981895 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
1981928 ATTGTATCGATACAACATTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
1981961 A
1 A
1981962 CATCGTTGAA
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:0.40, C:0.13, G:0.12, T:0.34
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:1981935 original size:13 final size:13
Alignment explanation
Indices: 1981917--1981941 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1981907 CAAAAAAATA
1981917 TGTATCGATACAT
1 TGTATCGATACAT
1981930 TGTATCGATACA
1 TGTATCGATACA
1981942 ACATTTTATG
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:1990202 original size:40 final size:40
Alignment explanation
Indices: 1990047--1990543 Score: 331
Period size: 40 Copynumber: 12.5 Consensus size: 40
1990037 CAAATGTTAT
* * * ** * *
1990047 TCAACCCTTACTCTTTGTTAGCTAATCAGTTTCATCCTAA
1 TCAACCTTTATTCTTTGTTGGCTTGTCAGTTTTATCCTAG
** * *
1990087 TCTTCCTTTAATT-TTTGTT-GCTTGTCGGTTTTATCC-GG
1 TCAACCTTT-ATTCTTTGTTGGCTTGTCAGTTTTATCCTAG
* * * * *
1990125 TCAACCTTTATTCTATGTTTGCATGTCAGTTTCATCCTTG
1 TCAACCTTTATTCTTTGTTGGCTTGTCAGTTTTATCCTAG
* * *
1990165 TTAACCTTTATTCTTTGTTGGCTTATCAATTTTATCCTAAG
1 TCAACCTTTATTCTTTGTTGGCTTGTCAGTTTTATCCT-AG
* * * * * * *
1990206 -CAAGCTTTACTATTTGTTAGCATGTC-GATTTTGTCCCAG
1 TCAACCTTTATTCTTTGTTGGCTTGTCAG-TTTTATCCTAG
* * * *
1990245 TCAACCTTTGTTCTTTATTGGCTTGTCAGTTTTGT-CTCGG
1 TCAACCTTTATTCTTTGTTGGCTTGTCAGTTTTATCCT-AG
* * * *
1990285 CCAACCTTTACTT-TTTATTGGCTTGTTAGTTTTAT-CTCGG
1 TCAACCTTTA-TTCTTTGTTGGCTTGTCAGTTTTATCCT-AG
* * * * *
1990325 TCAACTTTTACTATTTGTTGGCATGTCAGTTTTGTCCTAG
1 TCAACCTTTATTCTTTGTTGGCTTGTCAGTTTTATCCTAG
* *
1990365 TCAA-CTTTACTCTTTGTTGGCTTGTC-GATTTTGTCCTAG
1 TCAACCTTTATTCTTTGTTGGCTTGTCAG-TTTTATCCTAG
* * * *
1990404 TCAA-CTTATATTTTTTGTTAGG-TTGTCGGTTTTATCTTGG
1 TCAACCTT-TATTCTTTGTT-GGCTTGTCAGTTTTATCCTAG
1990444 TCAACCTTTATTCTTTGTTGGCTTGTC-GATTTTATCCTAG
1 TCAACCTTTATTCTTTGTTGGCTTGTCAG-TTTTATCCTAG
* * * * *
1990484 TCAACTTTTATTTTTTGTTTGCTTGTCAGTTTTGT-CTCGG
1 TCAACCTTTATTCTTTGTTGGCTTGTCAGTTTTATCCT-AG
1990524 TCAACCTTT-TCTCTTTGTTG
1 TCAACCTTTAT-TCTTTGTTG
1990544 ATTTATCGAT
Statistics
Matches: 360, Mismatches: 75, Indels: 44
0.75 0.16 0.09
Matches are distributed among these distances:
37 3 0.01
38 13 0.04
39 74 0.21
40 255 0.71
41 15 0.04
ACGTcount: A:0.15, C:0.19, G:0.15, T:0.50
Consensus pattern (40 bp):
TCAACCTTTATTCTTTGTTGGCTTGTCAGTTTTATCCTAG
Found at i:1990467 original size:199 final size:199
Alignment explanation
Indices: 1990091--1990543 Score: 488
Period size: 199 Copynumber: 2.3 Consensus size: 199
1990081 TCCTAATCTT
* * * * *
1990091 CCTTTAATTTTTGTTGCTTGTCGGTTTTATC-CGGTCAACCTTTATTCTATGTTTGCATGTCAGT
1 CCTTTAATTTTTGTTGCTTGTCAGTTTTATCTCGGTCAACTTTTACTCTTTGTTGGCATGTCAGT
* * *
1990155 TTCATCCTTGTTAACCTTTATTCTTTGTTGGCTTATCAATTTTATCCTAAGCAAGCTTTACTATT
66 TTCATCCTAGTCAACCTTTACTCTTTGTTGGCTTATCAATTTTATCCTAAGCAAGCTTTACTATT
* * *
1990220 TGTTAGCATGTCGATTTTGTCCCAGTCAACCTTTGTTCTTTATTGGCTTGTC-AGTTTTGT-CTC
131 TGTTAGCATGTCGATTTTATCCCAGTCAACCTTTATTCTTTATTGGCTTGTCGA-TTTTATCCT-
*
1990283 GGCCAA
194 AGCCAA
* * * *
1990289 CCTTTACTTTTTATTGGCTTGTTAGTTTTATCTCGGTCAACTTTTACTATTTGTTGGCATGTCAG
1 CCTTTAATTTTTGTT-GCTTGTCAGTTTTATCTCGGTCAACTTTTACTCTTTGTTGGCATGTCAG
** * * * *
1990354 TTTTGTCCTAGTCAA-CTTTACTCTTTGTTGGCTTGTCGATTTTGTCCT-AGTCAA-CTTATATT
65 TTTCATCCTAGTCAACCTTTACTCTTTGTTGGCTTATCAATTTTATCCTAAG-CAAGCTT-TACT
* ** * *** *
1990416 TTTTGTTAGGTTGTCGGTTTTATCTTGGTCAACCTTTATTCTTTGTTGGCTTGTCGATTTTATCC
128 ATTTGTTAGCATGTCGATTTTATCCCAGTCAACCTTTATTCTTTATTGGCTTGTCGATTTTATCC
*
1990481 TAGTCAA
193 TAGCCAA
* * *
1990488 CTTTTATTTTTTGTTTGCTTGTCAGTTTTGTCTCGGTCAACCTTTT-CTCTTTGTTG
1 CCTTTAATTTTTG-TTGCTTGTCAGTTTTATCTCGGTCAA-CTTTTACTCTTTGTTG
1990544 ATTTATCGAT
Statistics
Matches: 210, Mismatches: 37, Indels: 15
0.80 0.14 0.06
Matches are distributed among these distances:
198 18 0.09
199 144 0.69
200 48 0.23
ACGTcount: A:0.15, C:0.19, G:0.16, T:0.50
Consensus pattern (199 bp):
CCTTTAATTTTTGTTGCTTGTCAGTTTTATCTCGGTCAACTTTTACTCTTTGTTGGCATGTCAGT
TTCATCCTAGTCAACCTTTACTCTTTGTTGGCTTATCAATTTTATCCTAAGCAAGCTTTACTATT
TGTTAGCATGTCGATTTTATCCCAGTCAACCTTTATTCTTTATTGGCTTGTCGATTTTATCCTAG
CCAA
Found at i:1990556 original size:80 final size:80
Alignment explanation
Indices: 1990093--1990543 Score: 389
Period size: 80 Copynumber: 5.7 Consensus size: 80
1990083 CTAATCTTCC
* * * * * * *
1990093 TTTAATTTTTGTT-GCTTGTCGGTTTTATC-CGGTCAACCTTTATTCTATGTTTGCATGTC-AGT
1 TTTATTTTTTGTTGGCTTGTCAGTTTTGTCTCGGTCAACCTTTACTCTTTGTTGGCTTGTCGA-T
* * * *
1990155 TTCATCCTTGTTAACC
65 TTTATCCTAGTCAACT
* * * * ** * * * *
1990171 TTTATTCTTTGTTGGCTTATCAATTTTATCCTAAG-CAAGCTTTACTATTTGTTAGCATGTCGAT
1 TTTATTTTTTGTTGGCTTGTCAGTTTTGT-CTCGGTCAACCTTTACTCTTTGTTGGCTTGTCGAT
* * *
1990235 TTTGTCCCAGTCAACC
65 TTTATCCTAGTCAACT
* * * * * * *
1990251 TTTGTTCTTTATTGGCTTGTCAGTTTTGTCTCGGCCAACCTTTACTTTTTATTGGCTTGT-TAGT
1 TTTATTTTTTGTTGGCTTGTCAGTTTTGTCTCGGTCAACCTTTACTCTTTGTTGGCTTGTCGA-T
*
1990315 TTTAT-CTCGGTCAACT
65 TTTATCCT-AGTCAACT
* * * *
1990331 TTTACTATTTGTTGGCATGTCAGTTTTGTC-CTAGTCAA-CTTTACTCTTTGTTGGCTTGTCGAT
1 TTTATTTTTTGTTGGCTTGTCAGTTTTGTCTC-GGTCAACCTTTACTCTTTGTTGGCTTGTCGAT
*
1990394 TTTGTCCTAGTCAACT
65 TTTATCCTAGTCAACT
* * * * *
1990410 TATATTTTTTGTTAGG-TTGTCGGTTTTATCTTGGTCAACCTTTATTCTTTGTTGGCTTGTCGAT
1 TTTATTTTTTGTT-GGCTTGTCAGTTTTGTCTCGGTCAACCTTTACTCTTTGTTGGCTTGTCGAT
1990474 TTTATCCTAGTCAACT
65 TTTATCCTAGTCAACT
* *
1990490 TTTATTTTTTGTTTGCTTGTCAGTTTTGTCTCGGTCAACCTTTTCTCTTTGTTG
1 TTTATTTTTTGTTGGCTTGTCAGTTTTGTCTCGGTCAACCTTTACTCTTTGTTG
1990544 ATTTATCGAT
Statistics
Matches: 296, Mismatches: 63, Indels: 26
0.77 0.16 0.07
Matches are distributed among these distances:
78 11 0.04
79 76 0.26
80 207 0.70
81 2 0.01
ACGTcount: A:0.15, C:0.18, G:0.16, T:0.51
Consensus pattern (80 bp):
TTTATTTTTTGTTGGCTTGTCAGTTTTGTCTCGGTCAACCTTTACTCTTTGTTGGCTTGTCGATT
TTATCCTAGTCAACT
Found at i:1990781 original size:104 final size:105
Alignment explanation
Indices: 1990641--1990832 Score: 257
Period size: 104 Copynumber: 1.8 Consensus size: 105
1990631 TTTTAGTCAC
* *
1990641 TTTTAGTTGACTTTATTAGTTTCTCCCTAGTCAACCCCTTTAACTTGTTGAC-TTACAGTTTCAC
1 TTTTAGTTGACTTTATTAGTTTCTCCCTAATCAACCCCTTAAACTTGTTGACTTTACAGTTTCAC
*
1990705 CCTGGTCAACCATTTTTCTAACTTAAGTTTTATCCTAATCAT
66 CCTGGTCAACC--CTTTCTAACTTAAGTTTTATCCTAATCAT
* * ** *
1990747 TTTTA-TTGAC-TTGTTAGTTTCGT-CCTAATCAACCCCTTAAATTTGTTGACTTTTTAGTTTCG
1 TTTTAGTTGACTTTATTAGTTTC-TCCCTAATCAACCCCTTAAACTTGTTGACTTTACAGTTTCA
1990809 CCCTGGTCAACCCTTTCTAACTTA
65 CCCTGGTCAACCCTTTCTAACTTA
1990833 GGATTATATC
Statistics
Matches: 76, Mismatches: 8, Indels: 7
0.84 0.09 0.08
Matches are distributed among these distances:
103 11 0.14
104 34 0.45
105 26 0.34
106 5 0.07
ACGTcount: A:0.21, C:0.23, G:0.10, T:0.45
Consensus pattern (105 bp):
TTTTAGTTGACTTTATTAGTTTCTCCCTAATCAACCCCTTAAACTTGTTGACTTTACAGTTTCAC
CCTGGTCAACCCTTTCTAACTTAAGTTTTATCCTAATCAT
Found at i:1991435 original size:21 final size:20
Alignment explanation
Indices: 1991411--1991453 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
1991401 TTTTACAATT
*
1991411 TGTATCAATACAATAAGTTAA
1 TGTATCAATAC-ATAAGTGAA
**
1991432 TGTATTGATACATAAGTGAA
1 TGTATCAATACATAAGTGAA
1991452 TG
1 TG
1991454 CATTGATATT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 10 0.53
21 9 0.47
ACGTcount: A:0.42, C:0.07, G:0.16, T:0.35
Consensus pattern (20 bp):
TGTATCAATACATAAGTGAA
Found at i:1991448 original size:20 final size:21
Alignment explanation
Indices: 1991418--1991461 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
1991408 ATTTGTATCA
* *
1991418 ATACAATAAGTTAATGTATTG
1 ATACAATAAGTGAATGCATTG
1991439 ATAC-ATAAGTGAATGCATTG
1 ATACAATAAGTGAATGCATTG
1991459 ATA
1 ATA
1991462 TTGTACCTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 17 0.81
21 4 0.19
ACGTcount: A:0.43, C:0.07, G:0.16, T:0.34
Consensus pattern (21 bp):
ATACAATAAGTGAATGCATTG
Found at i:1994102 original size:97 final size:97
Alignment explanation
Indices: 1993933--1994168 Score: 271
Period size: 97 Copynumber: 2.4 Consensus size: 97
1993923 TTATTCACAG
* * * * *
1993933 GGGATATTTCAACCCCATT-CTTCCGAGGGGATACTCGAACCCCAGTTTTAAACTTATCGAGATT
1 GGGATACTCCAACCCCATTCCTT-CGAAGGGATACTCCAACCCCAGTTTTAAACTTATCAAGATT
* * * * * *
1993997 TAATTCTTATTTTTGCTTATATTGTCATCTTTA
65 TAAATCTTATTTTTGCCTAAATTATCATCATCA
* * * * *
1994030 GGGATACTCTAACCCTATTCTTTTGAAGGGATACTCCAACCTCA-TTTTCAAACTTGA-CAAGAT
1 GGGATACTCCAACCCCATTCCTTCGAAGGGATACTCCAACCCCAGTTTT-AAACTT-ATCAAGAT
1994093 TTAAATCTTATTTTTGCCTAAATTATCATCATCA
64 TTAAATCTTATTTTTGCCTAAATTATCATCATCA
*
1994127 GGGATACTCCAACCCCATTCCTTCGAGGGGATACTCCAACCC
1 GGGATACTCCAACCCCATTCCTTCGAAGGGATACTCCAACCC
1994169 GTTTTTTAAC
Statistics
Matches: 114, Mismatches: 22, Indels: 6
0.80 0.15 0.04
Matches are distributed among these distances:
96 4 0.04
97 107 0.94
98 3 0.03
ACGTcount: A:0.27, C:0.24, G:0.14, T:0.35
Consensus pattern (97 bp):
GGGATACTCCAACCCCATTCCTTCGAAGGGATACTCCAACCCCAGTTTTAAACTTATCAAGATTT
AAATCTTATTTTTGCCTAAATTATCATCATCA
Found at i:1995576 original size:154 final size:152
Alignment explanation
Indices: 1995368--1995798 Score: 467
Period size: 154 Copynumber: 2.8 Consensus size: 152
1995358 TTTTAGGGTG
* ** *
1995368 ACCAAGATACTTTCATGTCAAAGGTATACCTACAGGCATTTTCATAATTTTTTTAGAACTGAA-T
1 ACCAAGATACTTTCATGTCGAAGGTATACCTAGGGGCATTTTGATAA-TTTTTTAGAACT-AAGT
* * * * *
1995432 TCTATG-TAGTCACTAAGTCACTTTTATGCCAAAGGTATACATTTAGAATAGGCTT-GTCTTTTT
64 CCTA-GATAGTCACCAGGTCGCTTTTATGCCAAAGGTATACATTTAGAATAGG-TTCATCTTTTT
*
1995495 ATGATCCTTTTGTGTCCTTTAAGG-TA
127 ATGATCCTTTTGTATCC-TTAAGGATA
* * *
1995521 ACTAAGATACTTTCATCGTCGAAGGTATACCTTAGGGGTATTTTGATAATTTTTTAAAACTAAGT
1 ACCAAGATACTTTCAT-GTCGAAGGTATACC-TAGGGGCATTTTGATAATTTTTTAGAACTAAGT
* * *
1995586 CCTAGATAGTCACCAGGTTGCTTTTATGCCAAAGGTATATATTTAGGATAGGTTCATCTTTTTAT
64 CCTAGATAGTCACCAGGTCGCTTTTATGCCAAAGGTATACATTTAGAATAGGTTCATCTTTTTAT
** *
1995651 GATTTTTTTGTATCCTTCAGGATA
129 GATCCTTTTGTATCCTTAAGGATA
* * * * * *
1995675 ACCGAGATACTTTTATATCGAAGGTATATCCTAGGGACATTTTGTTAATTTTTCTAGGA-TCAAG
1 ACCAAGATACTTTCATGTCGAAGGTATA-CCTAGGGGCATTTTGATAATTTTT-TAGAACT-AAG
* * * *
1995739 TCCTAGATAGTCACCAGGTCGCTTTTATGCCAAAGGTGTGCACTTAGGAATAGTTTCATC
63 TCCTAGATAGTCACCAGGTCGCTTTTATGCCAAAGGTATACATTTA-GAATAGGTTCATC
1995799 ATTTAAGGCC
Statistics
Matches: 233, Mismatches: 35, Indels: 18
0.81 0.12 0.06
Matches are distributed among these distances:
153 56 0.24
154 153 0.66
155 24 0.10
ACGTcount: A:0.28, C:0.16, G:0.17, T:0.39
Consensus pattern (152 bp):
ACCAAGATACTTTCATGTCGAAGGTATACCTAGGGGCATTTTGATAATTTTTTAGAACTAAGTCC
TAGATAGTCACCAGGTCGCTTTTATGCCAAAGGTATACATTTAGAATAGGTTCATCTTTTTATGA
TCCTTTTGTATCCTTAAGGATA
Found at i:1997599 original size:15 final size:15
Alignment explanation
Indices: 1997579--1997615 Score: 74
Period size: 15 Copynumber: 2.5 Consensus size: 15
1997569 TACAACTCAA
1997579 GAAAATTTTACAAAC
1 GAAAATTTTACAAAC
1997594 GAAAATTTTACAAAC
1 GAAAATTTTACAAAC
1997609 GAAAATT
1 GAAAATT
1997616 GCCTCTAAGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.54, C:0.11, G:0.08, T:0.27
Consensus pattern (15 bp):
GAAAATTTTACAAAC
Found at i:1997969 original size:20 final size:20
Alignment explanation
Indices: 1997944--1997996 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
1997934 GTTGGGCACA
** *
1997944 ATGTATCGATACTTTTTACC
1 ATGTATCGATACAATGTACC
*
1997964 ATGTATCGATACAATGTCCC
1 ATGTATCGATACAATGTACC
1997984 ATGTATCGATACA
1 ATGTATCGATACA
1997997 TTTCACTTAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.30, C:0.21, G:0.13, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACAATGTACC
Found at i:1998068 original size:19 final size:19
Alignment explanation
Indices: 1998029--1998080 Score: 77
Period size: 19 Copynumber: 2.7 Consensus size: 19
1998019 CAGTTTAATC
* *
1998029 TATCGATACAAATGTGTATG
1 TATCGATAC-AATGAGCATG
1998049 TATCGATACAATGAGCATG
1 TATCGATACAATGAGCATG
1998068 TATCGATACAATG
1 TATCGATACAATG
1998081 TATCGATACA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 21 0.70
20 9 0.30
ACGTcount: A:0.37, C:0.13, G:0.19, T:0.31
Consensus pattern (19 bp):
TATCGATACAATGAGCATG
Found at i:1998083 original size:13 final size:13
Alignment explanation
Indices: 1998065--1998091 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1998055 TACAATGAGC
1998065 ATGTATCGATACA
1 ATGTATCGATACA
1998078 ATGTATCGATACA
1 ATGTATCGATACA
1998091 A
1 A
1998092 AGCATAATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1999173 original size:13 final size:13
Alignment explanation
Indices: 1999155--1999180 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1999145 TACACAAAGT
1999155 ATGTATCGATACA
1 ATGTATCGATACA
1999168 ATGTATCGATACA
1 ATGTATCGATACA
1999181 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1999178 original size:32 final size:33
Alignment explanation
Indices: 1999137--1999200 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
1999127 TAGCCAAACT
**
1999137 TGTATCGATACACAAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
1999169 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
1999201 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 17 0.59
33 12 0.41
ACGTcount: A:0.42, C:0.16, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:2003879 original size:22 final size:22
Alignment explanation
Indices: 2003851--2003892 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
2003841 ATTCGTTGGT
*
2003851 TTATTTAACATTTATAAAAAAA
1 TTATTTAAAATTTATAAAAAAA
2003873 TTATTTAAAATTTATAAAAA
1 TTATTTAAAATTTATAAAAA
2003893 TAAATAAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (22 bp):
TTATTTAAAATTTATAAAAAAA
Found at i:2003907 original size:18 final size:18
Alignment explanation
Indices: 2003886--2003928 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
2003876 TTTAAAATTT
2003886 ATAAAAATAAATAAATAA
1 ATAAAAATAAATAAATAA
* * * *
2003904 ATAAAAGTATATATATAT
1 ATAAAAATAAATAAATAA
2003922 ATAAAAA
1 ATAAAAA
2003929 AAAAAACTCG
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (18 bp):
ATAAAAATAAATAAATAA
Found at i:2003982 original size:13 final size:13
Alignment explanation
Indices: 2003964--2004030 Score: 71
Period size: 13 Copynumber: 4.8 Consensus size: 13
2003954 GAATAAATAT
2003964 TGCATGCATTTCA
1 TGCATGCATTTCA
2003977 TGCATGCATTTCA
1 TGCATGCATTTCA
* *
2003990 CGAAATTTGCATTTCA
1 TG-CA--TGCATTTCA
*
2004006 TGCATTACATTTCA
1 TGCA-TGCATTTCA
2004020 TGCATGCATTT
1 TGCATGCATTT
2004031 TACGTAATGT
Statistics
Matches: 45, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
13 20 0.44
14 14 0.31
15 1 0.02
16 10 0.22
ACGTcount: A:0.25, C:0.21, G:0.13, T:0.40
Consensus pattern (13 bp):
TGCATGCATTTCA
Found at i:2004024 original size:43 final size:43
Alignment explanation
Indices: 2003970--2004053 Score: 125
Period size: 43 Copynumber: 2.0 Consensus size: 43
2003960 ATATTGCATG
2003970 CATTTCATGCATGCATTTCACGAAAT-TTGCATTTCATGCATTA
1 CATTTCATGCATGCATTTCACGAAATGTT-CATTTCATGCATTA
* * *
2004013 CATTTCATGCATGCATTTTACGTAATGTTTATTTCATGCAT
1 CATTTCATGCATGCATTTCACGAAATGTTCATTTCATGCAT
2004054 GCAGGCATTA
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
43 35 0.95
44 2 0.05
ACGTcount: A:0.26, C:0.19, G:0.12, T:0.43
Consensus pattern (43 bp):
CATTTCATGCATGCATTTCACGAAATGTTCATTTCATGCATTA
Found at i:2004735 original size:61 final size:61
Alignment explanation
Indices: 2004656--2004799 Score: 218
Period size: 61 Copynumber: 2.4 Consensus size: 61
2004646 AAGGAGAGAA
* *
2004656 CAGAACTGAAACAAGCAGAAAAAAGACAAAACAGC-AAAAGAGAGAGAAAGCAAGAAAAAAC
1 CAGAACCGAAACAAGCAGAAAAAAGACAAAACAGCAAAAAAAGAGAGAAAGCAAG-AAAAAC
** *
2004717 CAGAACCGAAACAAGCAGAAAAAAGATGAAACAGCAAAAAAAGAGAGAAAGCAAGAAAAAT
1 CAGAACCGAAACAAGCAGAAAAAAGACAAAACAGCAAAAAAAGAGAGAAAGCAAGAAAAAC
*
2004778 CAGAACCGAAACAAGAAGAAAA
1 CAGAACCGAAACAAGCAGAAAA
2004800 CAAAGAAAAT
Statistics
Matches: 76, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
61 58 0.76
62 18 0.24
ACGTcount: A:0.64, C:0.15, G:0.19, T:0.02
Consensus pattern (61 bp):
CAGAACCGAAACAAGCAGAAAAAAGACAAAACAGCAAAAAAAGAGAGAAAGCAAGAAAAAC
Found at i:2004769 original size:17 final size:17
Alignment explanation
Indices: 2004729--2004776 Score: 53
Period size: 18 Copynumber: 2.6 Consensus size: 17
2004719 GAACCGAAAC
2004729 AAGCAGAAAAAAGATGAA
1 AAGCA-AAAAAAGATGAA
2004747 ACAGCAAAAAAAGA-GAGA
1 A-AGCAAAAAAAGATGA-A
2004765 AAGCAAGAAAAA
1 AAGCAA-AAAAA
2004777 TCAGAACCGA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
17 7 0.26
18 16 0.59
19 4 0.15
ACGTcount: A:0.69, C:0.08, G:0.21, T:0.02
Consensus pattern (17 bp):
AAGCAAAAAAAGATGAA
Found at i:2004775 original size:20 final size:19
Alignment explanation
Indices: 2004663--2004776 Score: 69
Period size: 20 Copynumber: 5.7 Consensus size: 19
2004653 GAACAGAACT
2004663 GAAACAAGCAGAAAAAAGACA
1 GAAACAAGCA-AAAAAAGA-A
*
2004684 -AAAC-AGC-AAAAGAGAGA
1 GAAACAAGCAAAAAAAGA-A
2004701 GAAAGCAAG-AAAAAACCAGAA
1 GAAA-CAAGCAAAAAA--AGAA
*
2004722 CCGAAACAAGCAGAAAAAAGAT
1 --GAAACAAGCA-AAAAAAGAA
2004744 GAAAC-AGCAAAAAAAGAGA
1 GAAACAAGCAAAAAAAGA-A
2004763 GAAAGCAAG-AAAAA
1 GAAA-CAAGCAAAAA
2004777 TCAGAACCGA
Statistics
Matches: 75, Mismatches: 5, Indels: 27
0.70 0.05 0.25
Matches are distributed among these distances:
17 8 0.11
18 11 0.15
19 12 0.16
20 21 0.28
21 3 0.04
22 10 0.13
23 5 0.07
24 5 0.07
ACGTcount: A:0.66, C:0.13, G:0.20, T:0.01
Consensus pattern (19 bp):
GAAACAAGCAAAAAAAGAA
Found at i:2004776 original size:18 final size:18
Alignment explanation
Indices: 2004724--2004760 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 18
2004714 AACCAGAACC
2004724 GAAACAAGCAGAAAAAAGAT
1 GAAAC-AGCA-AAAAAAGAT
2004744 GAAACAGCAAAAAAAGA
1 GAAACAGCAAAAAAAGA
2004761 GAGAAAGCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 8 0.47
19 4 0.24
20 5 0.29
ACGTcount: A:0.68, C:0.11, G:0.19, T:0.03
Consensus pattern (18 bp):
GAAACAGCAAAAAAAGAT
Found at i:2006014 original size:181 final size:179
Alignment explanation
Indices: 2005714--2006152 Score: 635
Period size: 179 Copynumber: 2.4 Consensus size: 179
2005704 TTCCGTCAGG
** *
2005714 TACGAAACATAATTTTTGAAATTAGAAGTTAAATTTAAAAATTTAGAAAAATTCGATTTTCCTAA
1 TACGAAACATAATTTTCAAAATTAGAAGTTAAATTTAAAAATTTAGAAAGATTCGA-TTTCCTAA
* * *
2005779 ACTAATATTTAAAAAAAAAGAATATGAGGTCGTTTATGTTTTCATATTCCTATGGTTTTCCGTTA
65 ATTAATATTT-TAAAAAAAGAATATGAGGTCGTTTATGTTTTCATATCCCTATGGTTTTCCG-TA
* * *
2005844 AGGGTATGAAATTTTTTTTTAACACCTTTCGTATCCCCTAGTTTTCCATCGGA
128 AGGGTATGAAA-ATTTTTATAACACCTTTCATATCCCCTAGTTTTCCATCGGA
* *
2005897 TACGAAACATAATTTTCAAAATTAGAAGTTAAATTTAAGAATTTAGAAAGATTCGGTTTCCTAAA
1 TACGAAACATAATTTTCAAAATTAGAAGTTAAATTTAAAAATTTAGAAAGATTCGATTTCCTAAA
*
2005962 TTAATATTTTAAAAAAAGAATATGAGGTCGTTTATGTTTTCATATCCCTATGGTTTTCCGTAGGG
66 TTAATATTTTAAAAAAAGAATATGAGGTCGTTTATGTTTTCATATCCCTATGGTTTTCCGTAAGG
* * * *
2006027 GTATGAAAATTTTTATAACATCTTTCATATCCCCTGGTTTTCTATCGGG
131 GTATGAAAATTTTTATAACACCTTTCATATCCCCTAGTTTTCCATCGGA
** * * *
2006076 TACGAAATGTAATTTTCAAAATTAAAAATTAAATTTAAAAATTTAGAAAGATTCAATTTCTCTAA
1 TACGAAACATAATTTTCAAAATTAGAAGTTAAATTTAAAAATTTAGAAAGATTCGATTTC-CT-A
2006141 AATTAATATTTT
64 AATTAATATTTT
2006153 TTAAAAAATA
Statistics
Matches: 231, Mismatches: 23, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
179 87 0.38
180 14 0.06
181 62 0.27
182 17 0.07
183 51 0.22
ACGTcount: A:0.37, C:0.11, G:0.12, T:0.40
Consensus pattern (179 bp):
TACGAAACATAATTTTCAAAATTAGAAGTTAAATTTAAAAATTTAGAAAGATTCGATTTCCTAAA
TTAATATTTTAAAAAAAGAATATGAGGTCGTTTATGTTTTCATATCCCTATGGTTTTCCGTAAGG
GTATGAAAATTTTTATAACACCTTTCATATCCCCTAGTTTTCCATCGGA
Found at i:2006247 original size:13 final size:13
Alignment explanation
Indices: 2006229--2006254 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2006219 TATGAAATAT
2006229 AAAAAATTTTGTA
1 AAAAAATTTTGTA
2006242 AAAAAATTTTGTA
1 AAAAAATTTTGTA
2006255 TCCCTTAGTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.00, G:0.08, T:0.38
Consensus pattern (13 bp):
AAAAAATTTTGTA
Found at i:2007873 original size:13 final size:13
Alignment explanation
Indices: 2007855--2007880 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2007845 TACAGCAAGT
2007855 ATGTATCGATACA
1 ATGTATCGATACA
2007868 ATGTATCGATACA
1 ATGTATCGATACA
2007881 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2008402 original size:34 final size:35
Alignment explanation
Indices: 2008339--2008405 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
2008329 CTAAGTGATT
2008339 GAGAGGTTCTATCTTAGCCTTTGAAAAAGATAGAGA
1 GAGAGGTTCTATCTTAGCCTTTG-AAAAGATAGAGA
2008375 GAGAGGTTTCTATCTTAGCC-TTG-AAAGATAG
1 GAGAGG-TTCTATCTTAGCCTTTGAAAAGATAG
2008406 TGTTGTAAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 8 0.27
36 9 0.30
37 13 0.43
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.30
Consensus pattern (35 bp):
GAGAGGTTCTATCTTAGCCTTTGAAAAGATAGAGA
Found at i:2013327 original size:13 final size:13
Alignment explanation
Indices: 2013309--2013334 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2013299 TACAGCAAGT
2013309 ATGTATCGATACA
1 ATGTATCGATACA
2013322 ATGTATCGATACA
1 ATGTATCGATACA
2013335 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2013856 original size:34 final size:35
Alignment explanation
Indices: 2013793--2013859 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
2013783 CTAAGTGATT
2013793 GAGAGGTTCTATCTTAGCCTTTGAAAAAGATAGAGA
1 GAGAGGTTCTATCTTAGCCTTTG-AAAAGATAGAGA
2013829 GAGAGGTTTCTATCTTAGCC-TTG-AAAGATAG
1 GAGAGG-TTCTATCTTAGCCTTTGAAAAGATAG
2013860 TGTTGTAAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 8 0.27
36 9 0.30
37 13 0.43
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.30
Consensus pattern (35 bp):
GAGAGGTTCTATCTTAGCCTTTGAAAAGATAGAGA
Found at i:2018629 original size:19 final size:19
Alignment explanation
Indices: 2018591--2018646 Score: 85
Period size: 19 Copynumber: 2.9 Consensus size: 19
2018581 CTGCCAGTTT
2018591 CATGTATCGATACAAATGAG
1 CATGTATCGATAC-AATGAG
* *
2018611 TATGTATCGAAACAATGAG
1 CATGTATCGATACAATGAG
2018630 CATGTATCGATACAATG
1 CATGTATCGATACAATG
2018647 TATCAATACA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 21 0.66
20 11 0.34
ACGTcount: A:0.39, C:0.14, G:0.20, T:0.27
Consensus pattern (19 bp):
CATGTATCGATACAATGAG
Found at i:2019594 original size:14 final size:14
Alignment explanation
Indices: 2019571--2019600 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
2019561 ATTGTTCCAT
2019571 GACCTAATGCACAA
1 GACCTAATGCACAA
*
2019585 GACCTCATGCACAA
1 GACCTAATGCACAA
2019599 GA
1 GA
2019601 AGATAGAGGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.40, C:0.30, G:0.17, T:0.13
Consensus pattern (14 bp):
GACCTAATGCACAA
Found at i:2022632 original size:78 final size:78
Alignment explanation
Indices: 2022536--2022719 Score: 199
Period size: 79 Copynumber: 2.3 Consensus size: 78
2022526 TGTTCCCTTG
* * * * * *
2022536 AAATAACGGGGCTCGAGTATCCCCGGTTGTGAGAAATCGATGA-TTAGAAAAAAAATCGGGATTG
1 AAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAAT-ATTTAGAAAAAAAACCGGGATTG
2022600 GAGTATCCCCTCGA
65 GAGTATCCCCTCGA
* * * * * * *
2022614 AAATAACGGGGTTGGAGTATCCTCAATTATGAGAAATCAATATTTTGGGAATAAAGCCGGGGTTG
1 AAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAATA-TTTAGAAAAAAAACCGGGATTG
*
2022679 GAGTATCCCTTCGA
65 GAGTATCCCCTCGA
* *
2022693 AAGTAACGGGGTTGAAGTATCCCCGAT
1 AAATAACGGGGTTGGAGTATCCCCGAT
2022720 GAAATAACGA
Statistics
Matches: 86, Mismatches: 18, Indels: 3
0.80 0.17 0.03
Matches are distributed among these distances:
77 1 0.01
78 34 0.40
79 51 0.59
ACGTcount: A:0.32, C:0.16, G:0.27, T:0.24
Consensus pattern (78 bp):
AAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAATATTTAGAAAAAAAACCGGGATTGG
AGTATCCCCTCGA
Found at i:2022727 original size:28 final size:29
Alignment explanation
Indices: 2022691--2022747 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 29
2022681 GTATCCCTTC
*
2022691 GAAAGTAACGGGGTTGAAGTATCCCCGAT
1 GAAAGTAACGAGGTTGAAGTATCCCCGAT
* * *
2022720 GAAA-TAACGAGTTTGGAGTATCCTCGAT
1 GAAAGTAACGAGGTTGAAGTATCCCCGAT
2022748 TGTGAAAAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
28 20 0.83
29 4 0.17
ACGTcount: A:0.32, C:0.16, G:0.28, T:0.25
Consensus pattern (29 bp):
GAAAGTAACGAGGTTGAAGTATCCCCGAT
Found at i:2022794 original size:52 final size:51
Alignment explanation
Indices: 2022732--2023067 Score: 243
Period size: 52 Copynumber: 6.4 Consensus size: 51
2022722 AATAACGAGT
* *
2022732 TTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGAG
1 TTGGAGTATCCCCGATTGTGAAAAATTGGT-GTTTTGGAAATAAAATCGGAG
** * * * * *
2022784 TTGGAGTATCCCCGATTAAAGGAAAATTGGCGTTTTGAAAATAAAACCGGGG
1 TTGGAGTATCCCCGATT-GTGAAAAATTGGTGTTTTGGAAATAAAATCGGAG
* * * * *
2022836 TTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTTAGCAATAAAACCGGGG
1 TTGGAGTATCCCCGATTGT-GAAAAATTGGTGTTTTGGAAATAAAATCGGAG
* *** * * *
2022888 TTGGAGTATCCCC--TTG-GAAATAACGGGGTTGGAGTATCCCCGATGAT-TAA-CGGGG
1 TTGGAGTATCCCCGATTGTGAAA-AA-----TTGGTGT-T-TTGGA-AATAAAATCGGAG
*
2022943 TTGGAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCAGAG
1 TTGGAGTATCCCCGATTGTGAA-AAATTGGTG--TTTTGGAAATAAAATCGGAG
* * *
2022997 TTGGAGTATCCCCGATTAT-AGAAAATTAGTGTTTTGAAAATAAAATCGGAG
1 TTGGAGTATCCCCGATTGTGA-AAAATTGGTGTTTTGGAAATAAAATCGGAG
* *
2023048 TTGGAATATCCTCGATTGTG
1 TTGGAGTATCCCCGATTGTG
2023068 GAGAATTGAG
Statistics
Matches: 223, Mismatches: 40, Indels: 42
0.73 0.13 0.14
Matches are distributed among these distances:
48 4 0.02
49 2 0.01
50 3 0.01
51 34 0.15
52 91 0.41
53 27 0.12
54 28 0.13
55 20 0.09
56 3 0.01
57 5 0.02
58 5 0.02
59 1 0.00
ACGTcount: A:0.31, C:0.12, G:0.26, T:0.30
Consensus pattern (51 bp):
TTGGAGTATCCCCGATTGTGAAAAATTGGTGTTTTGGAAATAAAATCGGAG
Found at i:2022914 original size:212 final size:212
Alignment explanation
Indices: 2022663--2023069 Score: 622
Period size: 212 Copynumber: 1.9 Consensus size: 212
2022653 ATATTTTGGG
*
2022663 AATAAAGCCGGGGTTGGAGTATCCCTTCGAAAGTAACGGGGTTGAAGTATCCCCGATGAAATAAC
1 AATAAAACCGGGGTTGGAGTATCCCTTCGAAAGTAACGGGGTTGAAGTATCCCCGATG-AATAAC
* * *
2022728 GAGTTTGGAGTATCCTCGATTGTGAA-AAATTGGT-ATTTTTGGAAATAAAATCGGAGTTGGAGT
65 GAGGTTGGAGTATCCCCGATTGTGAAGAAATTGGTGATTTTTGGAAATAAAATCAGAGTTGGAGT
* * *
2022791 ATCCCCGATTAAAGGAAAATTGGCGTTTTGAAAATAAAACCGGGGTTGGAGTATCCCCGATTGTG
130 ATCCCCGATTAAA-GAAAATTAGCGTTTTGAAAATAAAACCGGAGTTGGAATATCCCCGATTGTG
2022856 GAAAAATTAGTGTTTTAGC
194 GAAAAATTAGTGTTTTAGC
* * *
2022875 AATAAAACCGGGGTTGGAGTATCCCCTTGGAAA-TAACGGGGTTGGAGTATCCCCGATGATTAAC
1 AATAAAACCGGGGTTGGAGTAT-CCCTTCGAAAGTAACGGGGTTGAAGTATCCCCGATGAATAAC
* *
2022939 GGGGTTGGAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCAGAGTTGGAGT
65 GAGGTTGGAGTATCCCCGATTGTGAAGAAATTGGTGATTTTTGGAAATAAAATCAGAGTTGGAGT
* * * *
2023004 ATCCCCGATTATAGAAAATTAGTGTTTTGAAAATAAAATCGGAGTTGGAATATCCTCGATTGTGG
130 ATCCCCGATTAAAGAAAATTAGCGTTTTGAAAATAAAACCGGAGTTGGAATATCCCCGATTGTGG
2023069 A
195 A
2023070 GAATTGAGAA
Statistics
Matches: 176, Mismatches: 16, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
211 28 0.16
212 100 0.57
213 48 0.27
ACGTcount: A:0.31, C:0.13, G:0.27, T:0.29
Consensus pattern (212 bp):
AATAAAACCGGGGTTGGAGTATCCCTTCGAAAGTAACGGGGTTGAAGTATCCCCGATGAATAACG
AGGTTGGAGTATCCCCGATTGTGAAGAAATTGGTGATTTTTGGAAATAAAATCAGAGTTGGAGTA
TCCCCGATTAAAGAAAATTAGCGTTTTGAAAATAAAACCGGAGTTGGAATATCCCCGATTGTGGA
AAAATTAGTGTTTTAGC
Found at i:2022946 original size:27 final size:29
Alignment explanation
Indices: 2022883--2022958 Score: 113
Period size: 27 Copynumber: 2.7 Consensus size: 29
2022873 GCAATAAAAC
*
2022883 CGGGGTTGGAGTATCCCC-TTGGAAATAA
1 CGGGGTTGGAGTATCCCCGATGGAAATAA
*
2022911 CGGGGTTGGAGTATCCCCGAT-G-ATTAA
1 CGGGGTTGGAGTATCCCCGATGGAAATAA
2022938 CGGGGTTGGAGTATCCCCGAT
1 CGGGGTTGGAGTATCCCCGAT
2022959 TGTGAAGAAA
Statistics
Matches: 45, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
27 25 0.56
28 19 0.42
29 1 0.02
ACGTcount: A:0.21, C:0.20, G:0.34, T:0.25
Consensus pattern (29 bp):
CGGGGTTGGAGTATCCCCGATGGAAATAA
Found at i:2022959 original size:107 final size:105
Alignment explanation
Indices: 2022617--2023009 Score: 314
Period size: 107 Copynumber: 3.7 Consensus size: 105
2022607 CCCTCGAAAA
* * * * * * * * *
2022617 TAACGGGGTTGGAGTATCCTCAATTATGAGAAATCAATATTTTGGGAATAAAGCCGGGGTTGGAG
1 TAACGGGGTTGGAGTATCCCCGATTGTGAAAAATTAGTGTTTTGGAAATAAAACCGGGGTTGGAG
* *
2022682 TAT-CCCTTCGAAAGTAACGGGGTTGAAGTATCCCCGATGAAA
66 TATCCCCTT-GAAA-TAACGGGGTTGGAGTATCCCCGATG-AT
* * * * * * *
2022724 TAACGAGTTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGAGTTGGA
1 TAACGGGGTTGGAGTATCCCCGATTGTGAAAAATTAGT-GTTTTGGAAATAAAACCGGGGTTGGA
* * ** * ** **
2022789 GTATCCCC--G-ATTAAAGGAAAATTGGCGT-T--TTGAAAAT
65 GTATCCCCTTGAAATAACGG--GGTTGGAGTATCCCCGATGAT
* * *
2022826 AAAACCGGGGTTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTTAGCAATAAAACCGGGGTTG
1 -TAA-CGGGGTTGGAGTATCCCCGATTGT-GAAAAATTAGTGTTTTGGAAATAAAACCGGGGTTG
2022891 GAGTATCCCCTTGGAAATAACGGGGTTGGAGTATCCCCGATGAT
63 GAGTATCCCCTT-GAAATAACGGGGTTGGAGTATCCCCGATGAT
* * * *
2022935 TAACGGGGTTGGAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCAGAGTTG
1 TAACGGGGTTGGAGTATCCCCGATTGTGAA-AAATTAGTG--TTTTGGAAATAAAACCGGGGTTG
2023000 GAGTATCCCC
63 GAGTATCCCC
2023010 GATTATAGAA
Statistics
Matches: 219, Mismatches: 50, Indels: 32
0.73 0.17 0.11
Matches are distributed among these distances:
102 1 0.00
103 4 0.02
104 55 0.25
105 12 0.05
106 15 0.07
107 64 0.29
108 33 0.15
109 35 0.16
ACGTcount: A:0.30, C:0.14, G:0.27, T:0.28
Consensus pattern (105 bp):
TAACGGGGTTGGAGTATCCCCGATTGTGAAAAATTAGTGTTTTGGAAATAAAACCGGGGTTGGAG
TATCCCCTTGAAATAACGGGGTTGGAGTATCCCCGATGAT
Done.