Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.04
Sequence: scaffold337
Parameters: 2 7 7 80 10 50 500
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 500
Length: 1638316
ACGTcount: A:0.28, C:0.14, G:0.14, T:0.28
Warning! 264207 characters in sequence are not A, C, G, or T
File 5 of 5
Found at i:980847 original size:51 final size:51
Alignment explanation
Indices: 980785--981140 Score: 262
Period size: 51 Copynumber: 6.5 Consensus size: 51
980775 ACGACAACTA
* * * *
980785 CAACAACACCGGCAACAACGACACTGAAAACAACTACGACTAAACTGTCAC
1 CAACGACACCGGCAACAAAGACACCGAAAACAACTACGACTACACTGTCAC
* ** *
980836 CAACGATACCGGCAACAAAGACACCGGCAACAACTAAGACTACACTGTCACCAACGACAAC
1 CAACGACACCGGCAACAAAGACACCGAAAACAACTACGACTACACTGT---------C-AC
* **
980897 TACAACGACACCGGCAACAATGACATTGAAAACAACTACGACTACACTGTCAC
1 --CAACGACACCGGCAACAAAGACACCGAAAACAACTACGACTACACTGTCAC
* * ** *
980950 CAACGACACTGGCAACAAGGACACCGGCAACAACTACGACTACTCTGTCACCATCGACAAC
1 CAACGACACCGGCAACAAAGACACCGAAAACAACTACGACTA------CA-C-T-GTC-AC
**
981011 TACAACGACACCGGCAACAAAGACATTGAAAACAACTACGACTACACTGTCAC
1 --CAACGACACCGGCAACAAAGACACCGAAAACAACTACGACTACACTGTCAC
* * ** *
981064 CAACGACACTGGCAACAAGGACACCGGCAACAACTACGACTACACTGACAC
1 CAACGACACCGGCAACAAAGACACCGAAAACAACTACGACTACACTGTCAC
* * *
981115 CAACTACACTGGCAACAACGACACCG
1 CAACGACACCGGCAACAAAGACACCG
981141 GCAACAACGA
Statistics
Matches: 243, Mismatches: 38, Indels: 48
0.74 0.12 0.15
Matches are distributed among these distances:
51 144 0.59
53 4 0.02
54 3 0.01
55 1 0.00
56 1 0.00
57 4 0.02
58 1 0.00
59 1 0.00
60 3 0.01
61 4 0.02
63 77 0.32
ACGTcount: A:0.41, C:0.34, G:0.15, T:0.11
Consensus pattern (51 bp):
CAACGACACCGGCAACAAAGACACCGAAAACAACTACGACTACACTGTCAC
Found at i:980852 original size:63 final size:65
Alignment explanation
Indices: 980729--980869 Score: 155
Period size: 63 Copynumber: 2.2 Consensus size: 65
980719 CACCAACGAT
* * *
980729 ACCGGCAACAACACCATCGACAACAACTACAACTACACTGACACCAACGACAACTACAAC-A-AC
1 ACCGGCAACAACACCATCGAAAACAACTACAACTAAACTGACACCAACGACAACGACAACAAGAC
* * * * *
980792 ACCGGCAACAACGA-CA-CTGAAAACAACTACGACTAAACTGTCACCAACGATACCGGCAACAAA
1 ACCGGCAACAAC-ACCATC-GAAAACAACTACAACTAAACTGACACCAACGACAACGACAAC-AA
980855 GAC
63 GAC
980858 ACCGGCAACAAC
1 ACCGGCAACAAC
980870 TAAGACTACA
Statistics
Matches: 65, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
62 1 0.02
63 48 0.74
64 1 0.02
65 1 0.02
66 14 0.22
ACGTcount: A:0.45, C:0.35, G:0.12, T:0.08
Consensus pattern (65 bp):
ACCGGCAACAACACCATCGAAAACAACTACAACTAAACTGACACCAACGACAACGACAACAAGAC
Found at i:980903 original size:63 final size:63
Alignment explanation
Indices: 980836--980957 Score: 181
Period size: 63 Copynumber: 1.9 Consensus size: 63
980826 AAACTGTCAC
* **
980836 CAACGATACCGGCAACAAAGACACCGGCAACAACTAAGACTACACTGTCACCAACGACAACTA
1 CAACGACACCGGCAACAAAGACACCGAAAACAACTAAGACTACACTGTCACCAACGACAACTA
* ** *
980899 CAACGACACCGGCAACAATGACATTGAAAACAACTACGACTACACTGTCACCAACGACA
1 CAACGACACCGGCAACAAAGACACCGAAAACAACTAAGACTACACTGTCACCAACGACA
980958 CTGGCAACAA
Statistics
Matches: 52, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
63 52 1.00
ACGTcount: A:0.43, C:0.33, G:0.14, T:0.11
Consensus pattern (63 bp):
CAACGACACCGGCAACAAAGACACCGAAAACAACTAAGACTACACTGTCACCAACGACAACTA
Found at i:980972 original size:15 final size:15
Alignment explanation
Indices: 980940--980983 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
980930 AACTACGACT
* *
980940 ACACTGTCACCAACG
1 ACACTGGCAACAACG
*
980955 ACACTGGCAACAAGG
1 ACACTGGCAACAACG
*
980970 ACACCGGCAACAAC
1 ACACTGGCAACAAC
980984 TACGACTACT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.39, C:0.36, G:0.18, T:0.07
Consensus pattern (15 bp):
ACACTGGCAACAACG
Found at i:981017 original size:63 final size:63
Alignment explanation
Indices: 980950--981071 Score: 172
Period size: 63 Copynumber: 1.9 Consensus size: 63
980940 ACACTGTCAC
* * ** * *
980950 CAACGACACTGGCAACAAGGACACCGGCAACAACTACGACTACTCTGTCACCATCGACAACTA
1 CAACGACACCGGCAACAAAGACACCGAAAACAACTACGACTACACTGTCACCAACGACAACTA
**
981013 CAACGACACCGGCAACAAAGACATTGAAAACAACTACGACTACACTGTCACCAACGACA
1 CAACGACACCGGCAACAAAGACACCGAAAACAACTACGACTACACTGTCACCAACGACA
981072 CTGGCAACAA
Statistics
Matches: 51, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
63 51 1.00
ACGTcount: A:0.40, C:0.34, G:0.15, T:0.11
Consensus pattern (63 bp):
CAACGACACCGGCAACAAAGACACCGAAAACAACTACGACTACACTGTCACCAACGACAACTA
Found at i:981086 original size:15 final size:15
Alignment explanation
Indices: 981054--981493 Score: 86
Period size: 15 Copynumber: 26.9 Consensus size: 15
981044 AACTACGACT
* *
981054 ACACTGTCACCAACG
1 ACACTGGCAACAACG
*
981069 ACACTGGCAACAAGG
1 ACACTGGCAACAACG
*
981084 ACACCGGCAACAACTACG
1 ACACTGGCAAC-A--ACG
* * *
981102 ACTACACTGACACCAACT
1 ---ACACTGGCAACAACG
981120 ACACTGGCAACAACG
1 ACACTGGCAACAACG
*
981135 ACACCGGCAACAACG
1 ACACTGGCAACAACG
*
981150 ACACCGGCAACAACTACG
1 ACACTGGCAAC-A--ACG
* *
981168 ACTACACTGTCACCAACG
1 ---ACACTGGCAACAACG
981186 ACAACT----ACAACG
1 AC-ACTGGCAACAACG
*
981198 ACACCGGCAACAACG
1 ACACTGGCAACAACG
* * *
981213 ACATTGAAAACAACTACGACT
1 ACACTG---GCAAC-A--ACG
* *
981234 ACACTGTCACCAACG
1 ACACTGGCAACAACG
*
981249 ACACTGGCAACAAGG
1 ACACTGGCAACAACG
*
981264 ACACCGGCAACAACTACG
1 ACACTGGCAAC-A--ACG
* *
981282 ACTACTCTGTCACCAACG
1 AC-A--CTGGCAACAACG
981300 ACAACT----ACAACG
1 AC-ACTGGCAACAACG
*
981312 ACACCGGCAACAACG
1 ACACTGGCAACAACG
* * *
981327 ACATTGAAAACAACTACGACT
1 ACACTG---GCAAC-A--ACG
* *
981348 ACACTGTCACCAACG
1 ACACTGGCAACAACG
*
981363 ACACTGGCAACAAGG
1 ACACTGGCAACAACG
*
981378 ACACCGGCAACAACTACG
1 ACACTGGCAAC-A--ACG
* *
981396 ACTACACTGTCACCAACG
1 ---ACACTGGCAACAACG
*
981414 ACACTGGCAACAAGG
1 ACACTGGCAACAACG
*
981429 ACACCGGCAACAACTACG
1 ACACTGGCAAC-A--ACG
* *
981447 ACTACACTGTCACCAACG
1 ---ACACTGGCAACAACG
* *
981465 ACACTAGCAACAAGG
1 ACACTGGCAACAACG
*
981480 ACACCGGCAACAAC
1 ACACTGGCAACAAC
981494 TAAGACTACA
Statistics
Matches: 306, Mismatches: 68, Indels: 102
0.64 0.14 0.21
Matches are distributed among these distances:
11 4 0.01
12 14 0.05
15 173 0.57
16 10 0.03
17 2 0.01
18 44 0.14
19 3 0.01
20 5 0.02
21 51 0.17
ACGTcount: A:0.39, C:0.35, G:0.16, T:0.10
Consensus pattern (15 bp):
ACACTGGCAACAACG
Found at i:981121 original size:66 final size:66
Alignment explanation
Indices: 981054--981277 Score: 312
Period size: 66 Copynumber: 3.4 Consensus size: 66
981044 AACTACGACT
* * * * *
981054 ACACTGTCACCAACGACACTGGCAACAAGGACACCGGCAACAACTACGACTACACTGACACCAAC
1 ACACTGGCAACAACGACACCGGCAACAACGACACCGGCAACAACTACGACTACACTGTCACCAAC
*
981119 T
66 G
981120 ACACTGGCAACAACGACACCGGCAACAACGACACCGGCAACAACTACGACTACACTGTCACCAAC
1 ACACTGGCAACAACGACACCGGCAACAACGACACCGGCAACAACTACGACTACACTGTCACCAAC
981185 G
66 G
** **
981186 ACAACT----ACAACGACACCGGCAACAACGACATTGAAAACAACTACGACTACACTGTCACCAA
1 AC-ACTGGCAACAACGACACCGGCAACAACGACACCGGCAACAACTACGACTACACTGTCACCAA
981247 CG
65 CG
*
981249 ACACTGGCAACAAGGACACCGGCAACAAC
1 ACACTGGCAACAACGACACCGGCAACAAC
981278 TACGACTACT
Statistics
Matches: 142, Mismatches: 11, Indels: 10
0.87 0.07 0.06
Matches are distributed among these distances:
62 3 0.02
63 55 0.39
66 81 0.57
67 3 0.02
ACGTcount: A:0.40, C:0.36, G:0.16, T:0.09
Consensus pattern (66 bp):
ACACTGGCAACAACGACACCGGCAACAACGACACCGGCAACAACTACGACTACACTGTCACCAAC
G
Found at i:981163 original size:18 final size:15
Alignment explanation
Indices: 981064--981163 Score: 92
Period size: 15 Copynumber: 6.3 Consensus size: 15
981054 ACACTGTCAC
*
981064 CAACGACACTGGCAA
1 CAACGACACCGGCAA
*
981079 CAAGGACACCGGCAA
1 CAACGACACCGGCAA
* *
981094 CAACTACGACTACACTGACAC
1 C-A--ACGAC-AC-C-GGCAA
* *
981115 CAACTACACTGGCAA
1 CAACGACACCGGCAA
981130 CAACGACACCGGCAA
1 CAACGACACCGGCAA
981145 CAACGACACCGGCAA
1 CAACGACACCGGCAA
981160 CAAC
1 CAAC
981164 TACGACTACA
Statistics
Matches: 68, Mismatches: 11, Indels: 12
0.75 0.12 0.13
Matches are distributed among these distances:
15 49 0.72
16 1 0.01
17 2 0.03
18 8 0.12
19 2 0.03
20 2 0.03
21 4 0.06
ACGTcount: A:0.40, C:0.37, G:0.17, T:0.06
Consensus pattern (15 bp):
CAACGACACCGGCAA
Found at i:981181 original size:294 final size:294
Alignment explanation
Indices: 980722--981442 Score: 1134
Period size: 294 Copynumber: 2.5 Consensus size: 294
980712 AAATTGACAC
* * * * * * *
980722 CAACGATACCGGCAACAACA-CCATCGACAACAACTACAACTACACTGACACCAACGACAACT-A
1 CAACGACACCGGCAACAA-AGACATTGAAAACAACTACGACTACACTGTCACCAACGAC-ACTGG
* * * * * * * *
980785 CAAC-A--ACACCGGCAACAACGAC-ACTGAAAAC-AACTA-CGACTAAACTGTCACCAACGATA
64 CAACAAGGACACCGGCAACAACTACGACT--ACACTGAC-ACCAACTACACTGGCAACAACGACA
*
980844 CCGGCAACAAAGACACCGGCAACAACTAAGACTACACTGTCACCAACGACAACTACAACGACACC
126 CCGGCAACAACGACACCGGCAACAACTAAGACTACACTGTCACCAACGACAACTACAACGACACC
*
980909 GGCAACAATGACATTGAAAACAACTACGACTACACTGTCACCAACGACACTGGCAACAAGGACAC
191 GGCAACAACGACATTGAAAACAACTACGACTACACTGTCACCAACGACACTGGCAACAAGGACAC
*
980974 CGGCAACAACTACGACTACTCTGTCACCATCGACAACTA
256 CGGCAACAACTACGACTACTCTGTCACCAACGACAACTA
981013 CAACGACACCGGCAACAAAGACATTGAAAACAACTACGACTACACTGTCACCAACGACACTGGCA
1 CAACGACACCGGCAACAAAGACATTGAAAACAACTACGACTACACTGTCACCAACGACACTGGCA
981078 ACAAGGACACCGGCAACAACTACGACTACACTGACACCAACTACACTGGCAACAACGACACCGGC
66 ACAAGGACACCGGCAACAACTACGACTACACTGACACCAACTACACTGGCAACAACGACACCGGC
*
981143 AACAACGACACCGGCAACAACTACGACTACACTGTCACCAACGACAACTACAACGACACCGGCAA
131 AACAACGACACCGGCAACAACTAAGACTACACTGTCACCAACGACAACTACAACGACACCGGCAA
981208 CAACGACATTGAAAACAACTACGACTACACTGTCACCAACGACACTGGCAACAAGGACACCGGCA
196 CAACGACATTGAAAACAACTACGACTACACTGTCACCAACGACACTGGCAACAAGGACACCGGCA
981273 ACAACTACGACTACTCTGTCACCAACGACAACTA
261 ACAACTACGACTACTCTGTCACCAACGACAACTA
*
981307 CAACGACACCGGCAACAACGACATTGAAAACAACTACGACTACACTGTCACCAACGACACTGGCA
1 CAACGACACCGGCAACAAAGACATTGAAAACAACTACGACTACACTGTCACCAACGACACTGGCA
* * *
981372 ACAAGGACACCGGCAACAACTACGACTACACTGTCACCAACGACACTGGCAACAAGGACACCGGC
66 ACAAGGACACCGGCAACAACTACGACTACACTGACACCAACTACACTGGCAACAACGACACCGGC
981437 AACAAC
131 AACAAC
981443 TACGACTACA
Statistics
Matches: 399, Mismatches: 23, Indels: 13
0.92 0.05 0.03
Matches are distributed among these distances:
290 4 0.01
291 54 0.14
292 1 0.00
293 4 0.01
294 333 0.83
295 3 0.01
ACGTcount: A:0.41, C:0.34, G:0.15, T:0.10
Consensus pattern (294 bp):
CAACGACACCGGCAACAAAGACATTGAAAACAACTACGACTACACTGTCACCAACGACACTGGCA
ACAAGGACACCGGCAACAACTACGACTACACTGACACCAACTACACTGGCAACAACGACACCGGC
AACAACGACACCGGCAACAACTAAGACTACACTGTCACCAACGACAACTACAACGACACCGGCAA
CAACGACATTGAAAACAACTACGACTACACTGTCACCAACGACACTGGCAACAAGGACACCGGCA
ACAACTACGACTACTCTGTCACCAACGACAACTA
Found at i:981184 original size:21 final size:21
Alignment explanation
Indices: 981160--981247 Score: 52
Period size: 21 Copynumber: 4.2 Consensus size: 21
981150 ACACCGGCAA
* *
981160 CAACTACGACTACACTGTCAC
1 CAACTACAACTACACTGACAC
*
981181 CAACGACAACTACAAC-GACAC
1 CAACTACAACTAC-ACTGACAC
** * * * * *
981202 CGGCAACAACGACATTGAAAA
1 CAACTACAACTACACTGACAC
* *
981223 CAACTACGACTACACTGTCAC
1 CAACTACAACTACACTGACAC
981244 CAAC
1 CAAC
981248 GACACTGGCA
Statistics
Matches: 46, Mismatches: 19, Indels: 4
0.67 0.28 0.06
Matches are distributed among these distances:
20 1 0.02
21 43 0.93
22 2 0.04
ACGTcount: A:0.41, C:0.35, G:0.11, T:0.12
Consensus pattern (21 bp):
CAACTACAACTACACTGACAC
Found at i:981276 original size:51 final size:51
Alignment explanation
Indices: 981193--981325 Score: 166
Period size: 51 Copynumber: 2.7 Consensus size: 51
981183 ACGACAACTA
* ** **
981193 CAACGACACCGGCAACAACGACATTGAAAACAACTACGACTACACTGTCAC
1 CAACGACACTGGCAACAACGACACCGGCAACAACTACGACTACACTGTCAC
* *
981244 CAACGACACTGGCAACAAGGACACCGGCAACAACTACGACTACTCTGTCAC
1 CAACGACACTGGCAACAACGACACCGGCAACAACTACGACTACACTGTCAC
981295 CAACGACAACT----ACAACGACACCGGCAACAAC
1 CAACGAC-ACTGGCAACAACGACACCGGCAACAAC
981326 GACATTGAAA
Statistics
Matches: 73, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
48 19 0.26
51 51 0.70
52 3 0.04
ACGTcount: A:0.40, C:0.35, G:0.15, T:0.10
Consensus pattern (51 bp):
CAACGACACTGGCAACAACGACACCGGCAACAACTACGACTACACTGTCAC
Found at i:981311 original size:63 final size:63
Alignment explanation
Indices: 981244--981391 Score: 181
Period size: 63 Copynumber: 2.3 Consensus size: 63
981234 ACACTGTCAC
* * ** *
981244 CAACGACACTGGCAACAAGGACACCGGCAACAACTACGACTACTCTGTCACCAACGACAACTA
1 CAACGACACCGGCAACAACGACACCGAAAACAACTACGACTACACTGTCACCAACGACAACTA
**
981307 CAACGACACCGGCAACAACGACATTGAAAACAACTACGACTACACTGTCACCAACGAC-ACTGGC
1 CAACGACACCGGCAACAACGACACCGAAAACAACTACGACTACACTGTCACCAACGACAACT---
981371 AA
63 -A
*
981373 CAAGGACACCGGCAACAAC
1 CAACGACACCGGCAACAAC
981392 TACGACTACA
Statistics
Matches: 73, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
62 3 0.04
63 51 0.70
66 19 0.26
ACGTcount: A:0.40, C:0.34, G:0.16, T:0.09
Consensus pattern (63 bp):
CAACGACACCGGCAACAACGACACCGAAAACAACTACGACTACACTGTCACCAACGACAACTA
Found at i:981390 original size:51 final size:51
Alignment explanation
Indices: 981307--981518 Score: 343
Period size: 51 Copynumber: 4.2 Consensus size: 51
981297 ACGACAACTA
* * ** **
981307 CAACGACACCGGCAACAACGACATTGAAAACAACTACGACTACACTGTCAC
1 CAACGACACTGGCAACAAGGACACCGGCAACAACTACGACTACACTGTCAC
981358 CAACGACACTGGCAACAAGGACACCGGCAACAACTACGACTACACTGTCAC
1 CAACGACACTGGCAACAAGGACACCGGCAACAACTACGACTACACTGTCAC
981409 CAACGACACTGGCAACAAGGACACCGGCAACAACTACGACTACACTGTCAC
1 CAACGACACTGGCAACAAGGACACCGGCAACAACTACGACTACACTGTCAC
* * *
981460 CAACGACACTAGCAACAAGGACACCGGCAACAACTAAGACTACATTGTCAC
1 CAACGACACTGGCAACAAGGACACCGGCAACAACTACGACTACACTGTCAC
981511 CAACGACA
1 CAACGACA
981519 ACTACAACGA
Statistics
Matches: 152, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 152 1.00
ACGTcount: A:0.40, C:0.34, G:0.16, T:0.10
Consensus pattern (51 bp):
CAACGACACTGGCAACAAGGACACCGGCAACAACTACGACTACACTGTCAC
Found at i:981417 original size:165 final size:165
Alignment explanation
Indices: 981193--981713 Score: 711
Period size: 165 Copynumber: 3.2 Consensus size: 165
981183 ACGACAACTA
**
981193 CAACGACACCGGCAACAACGACATTGAAAACAACTACGACTACACTGTCACCAACGACACTGGCA
1 CAACGACACCGGCAACAACGACACCGAAAACAACTACGACTACACTGTCACCAACGACACTGGCA
981258 ACAAGGACACCGGCAACAACTACGACTACTCTGTCACCAACGACAACTACAACGACACCGGCAAC
66 ACAAGGACACCGGCAACAACTACGACTACTCTGTCACCAACGACAACTACAACGACACCGGCAAC
981323 AACGACATTGAAAACAACTACGACTACACTGTCAC
131 AACGACATTGAAAACAACTACGACTACACTGTCAC
* * **
981358 CAACGACACTGGCAACAAGGACACCGGCAACAACTACGACTACACTGTCACCAACGACACTGGCA
1 CAACGACACCGGCAACAACGACACCGAAAACAACTACGACTACACTGTCACCAACGACACTGGCA
*
981423 ACAAGGACACCGGCAACAACTACGACTACACTGTCACCAACGAC-ACTAGCAACAAGGACACCGG
66 ACAAGGACACCGGCAACAACTACGACTACTCTGTCACCAACGACAACTA-CAAC---GACACCGG
* * *
981487 CAACAACTAAGACTACATTG---TCACCAACGAC-A-AC--T-A-
127 CAACAAC---G---ACATTGAAAACAACTACGACTACACTGTCAC
* **
981523 CAACGACACCGGCAACAGCGACATTGAAAACAACTACGACTACACTGTCACCAACGACACTGGCA
1 CAACGACACCGGCAACAACGACACCGAAAACAACTACGACTACACTGTCACCAACGACACTGGCA
* *
981588 ACAAGGACACCGGCAACAACTACGACTACTCTGTCACCATCGACAACTACAACGACACCAGCAAC
66 ACAAGGACACCGGCAACAACTACGACTACTCTGTCACCAACGACAACTACAACGACACCGGCAAC
*
981653 AACGACATTGAAAACAACTACGACTACACTGACAC
131 AACGACATTGAAAACAACTACGACTACACTGTCAC
* **
981688 CAACTACACTTGCAACAACGACACCG
1 CAACGACACCGGCAACAACGACACCG
981714 GCAACAACGA
Statistics
Matches: 306, Mismatches: 30, Indels: 40
0.81 0.08 0.11
Matches are distributed among these distances:
156 6 0.02
159 9 0.03
160 1 0.00
161 2 0.01
162 14 0.05
164 5 0.02
165 230 0.75
166 5 0.02
167 1 0.00
168 15 0.05
169 2 0.01
170 1 0.00
171 9 0.03
174 6 0.02
ACGTcount: A:0.40, C:0.34, G:0.15, T:0.11
Consensus pattern (165 bp):
CAACGACACCGGCAACAACGACACCGAAAACAACTACGACTACACTGTCACCAACGACACTGGCA
ACAAGGACACCGGCAACAACTACGACTACTCTGTCACCAACGACAACTACAACGACACCGGCAAC
AACGACATTGAAAACAACTACGACTACACTGTCAC
Found at i:981511 original size:330 final size:330
Alignment explanation
Indices: 981117--981721 Score: 1084
Period size: 330 Copynumber: 1.8 Consensus size: 330
981107 ACTGACACCA
* *
981117 ACTACACTGGCAACAACGACACCGGCAACAACGACACCGGCAACAACTACGACTACACTGTCACC
1 ACTACACTGGCAACAACGACACCAGCAACAACGACACCGGCAACAACTAAGACTACACTGTCACC
981182 AACGACAACTACAACGACACCGGCAACAACGACATTGAAAACAACTACGACTACACTGTCACCAA
66 AACGACAACTACAACGACACCGGCAACAACGACATTGAAAACAACTACGACTACACTGTCACCAA
981247 CGACACTGGCAACAAGGACACCGGCAACAACTACGACTACTCTGTCACCAACGACAACTACAACG
131 CGACACTGGCAACAAGGACACCGGCAACAACTACGACTACTCTGTCACCAACGACAACTACAACG
* * *
981312 ACACCGGCAACAACGACATTGAAAACAACTACGACTACACTGTCACCAACGACACTGGCAACAAG
196 ACACCAGCAACAACGACATTGAAAACAACTACGACTACACTGACACCAACGACACTGGCAACAAC
981377 GACACCGGCAACAACTACGACTACACTGTCACCAACGACACTGGCAACAAGGACACCGGCAACAA
261 GACACCGGCAACAACTACGACTACACTGTCACCAACGACACTGGCAACAAGGACACCGGCAACAA
981442 CTACG
326 CTACG
* * * * *
981447 ACTACACTGTCACCAACGACACTAGCAACAAGGACACCGGCAACAACTAAGACTACATTGTCACC
1 ACTACACTGGCAACAACGACACCAGCAACAACGACACCGGCAACAACTAAGACTACACTGTCACC
*
981512 AACGACAACTACAACGACACCGGCAACAGCGACATTGAAAACAACTACGACTACACTGTCACCAA
66 AACGACAACTACAACGACACCGGCAACAACGACATTGAAAACAACTACGACTACACTGTCACCAA
*
981577 CGACACTGGCAACAAGGACACCGGCAACAACTACGACTACTCTGTCACCATCGACAACTACAACG
131 CGACACTGGCAACAAGGACACCGGCAACAACTACGACTACTCTGTCACCAACGACAACTACAACG
* *
981642 ACACCAGCAACAACGACATTGAAAACAACTACGACTACACTGACACCAACTACACTTGCAACAAC
196 ACACCAGCAACAACGACATTGAAAACAACTACGACTACACTGACACCAACGACACTGGCAACAAC
981707 GACACCGGCAACAAC
261 GACACCGGCAACAAC
981722 GACACCGGCA
Statistics
Matches: 261, Mismatches: 14, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
330 261 1.00
ACGTcount: A:0.40, C:0.35, G:0.15, T:0.11
Consensus pattern (330 bp):
ACTACACTGGCAACAACGACACCAGCAACAACGACACCGGCAACAACTAAGACTACACTGTCACC
AACGACAACTACAACGACACCGGCAACAACGACATTGAAAACAACTACGACTACACTGTCACCAA
CGACACTGGCAACAAGGACACCGGCAACAACTACGACTACTCTGTCACCAACGACAACTACAACG
ACACCAGCAACAACGACATTGAAAACAACTACGACTACACTGACACCAACGACACTGGCAACAAC
GACACCGGCAACAACTACGACTACACTGTCACCAACGACACTGGCAACAAGGACACCGGCAACAA
CTACG
Found at i:981538 original size:63 final size:63
Alignment explanation
Indices: 981460--981581 Score: 156
Period size: 63 Copynumber: 1.9 Consensus size: 63
981450 ACACTGTCAC
* ** *
981460 CAACGACACTAGCAACAAG-GACACCGGCAACAACTAAGACTACATTGTCACCAACGACAACTA
1 CAACGACACCAGCAAC-AGCGACACCGAAAACAACTAAGACTACACTGTCACCAACGACAACTA
* ** *
981523 CAACGACACCGGCAACAGCGACATTGAAAACAACTACGACTACACTGTCACCAACGACA
1 CAACGACACCAGCAACAGCGACACCGAAAACAACTAAGACTACACTGTCACCAACGACA
981582 CTGGCAACAA
Statistics
Matches: 50, Mismatches: 8, Indels: 2
0.83 0.13 0.03
Matches are distributed among these distances:
62 2 0.04
63 48 0.96
ACGTcount: A:0.42, C:0.33, G:0.15, T:0.11
Consensus pattern (63 bp):
CAACGACACCAGCAACAGCGACACCGAAAACAACTAAGACTACACTGTCACCAACGACAACTA
Found at i:981567 original size:216 final size:216
Alignment explanation
Indices: 981193--981721 Score: 781
Period size: 216 Copynumber: 2.4 Consensus size: 216
981183 ACGACAACTA
** *
981193 CAACGACACCGGCAACAACGACATTGAAAACAACTACGACTACACTGTCACCAACGACACTGGCA
1 CAACGACACCGGCAACAACGACACCGAAAACAACTACGACTACACTGTCACCAACGACACTAGCA
*
981258 ACAAGGACACCGGCAACAACTACGACTACTCTGTCACCAACGACAACTACAACGACACCGGCAAC
66 ACAAGGACACCGGCAACAACTAAGACTACTCTGTCACCAACGACAACTACAACGACACCGGCAAC
981323 AACGACATTGAAAACAACTACGACTACACTGTCACCAACGACACTGGCAACAAGGACACCGGCAA
131 AACGACATTGAAAACAACTACGACTACACTGTCACCAACGACACTGGCAACAAGGACACCGGCAA
981388 CAACTACGACTACACTGTCAC
196 CAACTACGACTACACTGTCAC
* * **
981409 CAACGACACTGGCAACAAGGACACCGGCAACAACTACGACTACACTGTCACCAACGACACTAGCA
1 CAACGACACCGGCAACAACGACACCGAAAACAACTACGACTACACTGTCACCAACGACACTAGCA
981474 ACAAGGACACCGGCAACAACTAAGACTACAT-TGTCACCAACGACAACTACAACGACACCGGCAA
66 ACAAGGACACCGGCAACAACTAAGACTAC-TCTGTCACCAACGACAACTACAACGACACCGGCAA
*
981538 CAGCGACATTGAAAACAACTACGACTACACTGTCACCAACGACACTGGCAACAAGGACACCGGCA
130 CAACGACATTGAAAACAACTACGACTACACTGTCACCAACGACACTGGCAACAAGGACACCGGCA
*
981603 ACAACTACGACTACTCTGTCACCATCGACAAC
195 ACAACTACGACTA------CA-C-T-GTC-AC
* ** * * *
981635 TACAACGACACCAGCAACAACGACATTGAAAACAACTACGACTACACTGACACCAACTACACTTG
1 --CAACGACACCGGCAACAACGACACCGAAAACAACTACGACTACACTGTCACCAACGACACTAG
*
981700 CAACAACGACACCGGCAACAAC
64 CAACAAGGACACCGGCAACAAC
981722 GACACCGGCA
Statistics
Matches: 279, Mismatches: 21, Indels: 14
0.89 0.07 0.04
Matches are distributed among these distances:
216 196 0.70
217 1 0.00
222 2 0.01
223 1 0.00
224 1 0.00
225 2 0.01
226 2 0.01
228 74 0.27
ACGTcount: A:0.40, C:0.34, G:0.15, T:0.11
Consensus pattern (216 bp):
CAACGACACCGGCAACAACGACACCGAAAACAACTACGACTACACTGTCACCAACGACACTAGCA
ACAAGGACACCGGCAACAACTAAGACTACTCTGTCACCAACGACAACTACAACGACACCGGCAAC
AACGACATTGAAAACAACTACGACTACACTGTCACCAACGACACTGGCAACAAGGACACCGGCAA
CAACTACGACTACACTGTCAC
Found at i:981596 original size:15 final size:15
Alignment explanation
Indices: 981564--981607 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
981554 AACTACGACT
* *
981564 ACACTGTCACCAACG
1 ACACTGGCAACAACG
*
981579 ACACTGGCAACAAGG
1 ACACTGGCAACAACG
*
981594 ACACCGGCAACAAC
1 ACACTGGCAACAAC
981608 TACGACTACT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.39, C:0.36, G:0.18, T:0.07
Consensus pattern (15 bp):
ACACTGGCAACAACG
Found at i:981641 original size:63 final size:64
Alignment explanation
Indices: 981574--981762 Score: 220
Period size: 66 Copynumber: 2.9 Consensus size: 64
981564 ACACTGTCAC
* * * *
981574 CAACGACACTGGCAACAAGGACACCGGCAACAACTACGACTACTCTGTCACCATCGACAAC-T-A
1 CAACGACACCGGCAACAACGACACCGGCAACAACTACGACTACACTGTCACCAACGAC-ACTTAA
* ** ** * *
981637 CAACGACACCAGCAACAACGACATTGAAAACAACTACGACTACACTGACACCAACTACACTTGCA
1 CAACGACACCGGCAACAACGACACCGGCAACAACTACGACTACACTGTCACCAACGACACTT--A
981702 A
64 A
* *
981703 CAACGACACCGGCAACAACGACACCGGCAACAACTACGACTACACTGTCACTAATGACAC
1 CAACGACACCGGCAACAACGACACCGGCAACAACTACGACTACACTGTCACCAACGACAC
981763 CAGCAACGGC
Statistics
Matches: 102, Mismatches: 20, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
62 2 0.02
63 48 0.47
66 52 0.51
ACGTcount: A:0.40, C:0.35, G:0.14, T:0.12
Consensus pattern (64 bp):
CAACGACACCGGCAACAACGACACCGGCAACAACTACGACTACACTGTCACCAACGACACTTAA
Found at i:981692 original size:21 final size:21
Alignment explanation
Indices: 981604--981695 Score: 60
Period size: 21 Copynumber: 4.4 Consensus size: 21
981594 ACACCGGCAA
* * *
981604 CAACTACGACTACTCTGTCAC
1 CAACTACAACTACACTGACAC
* *
981625 CATCGACAACTACAAC-GACAC
1 CAACTACAACTAC-ACTGACAC
* * * * * *
981646 CAGCAACAACGACATTGAAAA
1 CAACTACAACTACACTGACAC
*
981667 CAACTACGACTACACTGACAC
1 CAACTACAACTACACTGACAC
981688 CAACTACA
1 CAACTACA
981696 CTTGCAACAA
Statistics
Matches: 50, Mismatches: 19, Indels: 4
0.68 0.26 0.05
Matches are distributed among these distances:
20 1 0.02
21 48 0.96
22 1 0.02
ACGTcount: A:0.41, C:0.35, G:0.10, T:0.14
Consensus pattern (21 bp):
CAACTACAACTACACTGACAC
Found at i:981706 original size:15 final size:15
Alignment explanation
Indices: 981688--981739 Score: 68
Period size: 15 Copynumber: 3.5 Consensus size: 15
981678 ACACTGACAC
**
981688 CAACTACACTTGCAA
1 CAACTACACCGGCAA
*
981703 CAACGACACCGGCAA
1 CAACTACACCGGCAA
*
981718 CAACGACACCGGCAA
1 CAACTACACCGGCAA
981733 CAACTAC
1 CAACTAC
981740 GACTACACTG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 33 1.00
ACGTcount: A:0.40, C:0.38, G:0.13, T:0.08
Consensus pattern (15 bp):
CAACTACACCGGCAA
Found at i:981736 original size:18 final size:15
Alignment explanation
Indices: 981699--981736 Score: 76
Period size: 15 Copynumber: 2.5 Consensus size: 15
981689 AACTACACTT
981699 GCAACAACGACACCG
1 GCAACAACGACACCG
981714 GCAACAACGACACCG
1 GCAACAACGACACCG
981729 GCAACAAC
1 GCAACAAC
981737 TACGACTACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.42, C:0.39, G:0.18, T:0.00
Consensus pattern (15 bp):
GCAACAACGACACCG
Found at i:981784 original size:114 final size:113
Alignment explanation
Indices: 980551--981762 Score: 883
Period size: 114 Copynumber: 10.6 Consensus size: 113
980541 ACTACGACTT
* * * * * *
980551 CACTGACAACAACGACGCTGGCATCAACGACACCGACAACAACTACGACTACAGTGACACCAACA
1 CACTG-CAACAACGACACCGGCAACAACGACACCGACAACAACTACGACTACACTGTCACCAACG
* * *
980616 ACAACT-ACAACGACACCTGCAACAACTACGACTACACTGTCACCAACGA
65 AC-ACTGGCAACGACACCGGCAACAACTACGACTACACTGACACCAACGA
* ** * * * *
980665 CAACT---ACAACAACACCGGCAACAACGACATTGAAAACAACTACGACTAAATTGACACCAACG
1 C-ACTGCAACAACGACACCGGCAACAACGACACCGACAACAACTACGACTACACTGTCACCAACG
* * * * *
980727 ATACCGGCAACAACACCATCGACAACAACTACAACTACACTGACACCAACGA
65 ACACTGGCAACGACA-C--CGGCAACAACTACGACTACACTGACACCAACGA
* * * *
980779 CAACT---ACAACAACACCGGCAACAACGACACTGAAAACAACTACGACTAAACTGTCACCAACG
1 C-ACTGCAACAACGACACCGGCAACAACGACACCGACAACAACTACGACTACACTGTCACCAACG
* * * *
980841 ATACCGGCAACAAAGACACCGGCAACAACTAAGACTACACTGTCACCAACGA
65 ACACTGGCAAC---GACACCGGCAACAACTACGACTACACTGACACCAACGA
* ** *
980893 CAACT---ACAACGACACCGGCAACAATGACATTGAAAACAACTACGACTACACTGTCACCAACG
1 C-ACTGCAACAACGACACCGGCAACAACGACACCGACAACAACTACGACTACACTGTCACCAACG
* * *
980955 ACACTGGCAACAAGGACACCGGCAACAACTACGACTACTCTGTCACCATCGA
65 ACACTGGCAAC---GACACCGGCAACAACTACGACTACACTGACACCAACGA
* ** *
981007 CAACT---ACAACGACACCGGCAACAAAGACATTGAAAACAACTACGACTACACTGTCACCAACG
1 C-ACTGCAACAACGACACCGGCAACAACGACACCGACAACAACTACGACTACACTGTCACCAACG
*
981069 ACACTGGCAACAAGGACACCGGCAACAACTACGACTACACTGACACCAACTA
65 ACACTGGCAAC---GACACCGGCAACAACTACGACTACACTGACACCAACGA
*
981121 CACTGGCAACAACGACACCGGCAACAACGACACCGGCAACAACTACGACTACACTGTCACCAACG
1 CACT-GCAACAACGACACCGGCAACAACGACACCGACAACAACTACGACTACACTGTCACCAACG
* * * * * * *
981186 ACAACT-ACAACGACACCGGCAACAACGAC-ATTGAAAAC-AACTA-CGACTA
65 AC-ACTGGCAACGACACCGGCAACAACTACGACT--ACACTGAC-ACCAACGA
* * * * *
981235 CACTGTCACCAACGACACTGGCAACAAGGACACCGGCAACAACTACGACTACTCTGTCACCAACG
1 CACTG-CAACAACGACACCGGCAACAACGACACCGACAACAACTACGACTACACTGTCACCAACG
* * * * * * *
981300 ACAACT-ACAACGACACCGGCAACAACGAC-ATTGAAAAC-AACTA-CGACTA
65 AC-ACTGGCAACGACACCGGCAACAACTACGACT--ACACTGAC-ACCAACGA
* * * *
981349 CACTGTCACCAACGACACTGGCAACAAGGACACCGGCAACAACTACGACTACACTGTCACCAACG
1 CACTG-CAACAACGACACCGGCAACAACGACACCGACAACAACTACGACTACACTGTCACCAACG
*
981414 ACACTGGCAACAAGGACACCGGCAACAACTACGACTACACTGTCACCAACGA
65 ACACTGGCAAC---GACACCGGCAACAACTACGACTACACTGACACCAACGA
* * * * * * *
981466 CACTAGCAACAAGGACACCGGCAACAACTA-A--GACTAC-ATTGTC-ACCA-AC-GACAACTAC
1 CACT-GCAACAACGACACCGGCAACAACGACACCGACAACAACT-ACGACTACACTGTC-AC--C
* ** ** *
981524 AACGACACCGGCAACAGCGACATTGAAAACAACTACGACTACACTGTCACCAACGA
61 AACGACACTGGC-A-A-CGACACCGGCAACAACTACGACTACACTGACACCAACGA
* * * * * * *
981580 CACTGGCAACAAGGACACCGGCAACAACTACGACTACTCTGTCACCATCGACAACTACAAC-GAC
1 CACT-GCAACAACGACACCGGCAAC-A--ACGAC-AC-C-GACAACAACTACGACTAC-ACTGTC
* ** ** *
981644 ACC-A-G-CA---ACAACGACATTGAAAACAACTACGACTACACTGACACCAACTA
58 ACCAACGACACTGGCAACGACACCGGCAACAACTACGACTACACTGACACCAACGA
* * *
981694 CACTTGCAACAACGACACCGGCAACAACGACACCGGCAACAACTACGACTACACTGTCACTAATG
1 CAC-TGCAACAACGACACCGGCAACAACGACACCGACAACAACTACGACTACACTGTCACCAACG
981759 ACAC
65 ACAC
981763 CAGCAACGGC
Statistics
Matches: 945, Mismatches: 102, Indels: 104
0.82 0.09 0.09
Matches are distributed among these distances:
107 2 0.00
108 17 0.02
109 2 0.00
110 5 0.01
111 64 0.07
112 5 0.01
113 15 0.02
114 679 0.72
115 11 0.01
116 8 0.01
117 111 0.12
118 6 0.01
119 1 0.00
120 2 0.00
121 1 0.00
122 1 0.00
123 5 0.01
124 3 0.00
125 2 0.00
126 5 0.01
ACGTcount: A:0.41, C:0.34, G:0.14, T:0.11
Consensus pattern (113 bp):
CACTGCAACAACGACACCGGCAACAACGACACCGACAACAACTACGACTACACTGTCACCAACGA
CACTGGCAACGACACCGGCAACAACTACGACTACACTGACACCAACGA
Found at i:986235 original size:12 final size:12
Alignment explanation
Indices: 986218--986243 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
986208 TTGTTTTATG
986218 TTTATTAATCAT
1 TTTATTAATCAT
986230 TTTATTAATCAT
1 TTTATTAATCAT
986242 TT
1 TT
986244 AATTCATTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.31, C:0.08, G:0.00, T:0.62
Consensus pattern (12 bp):
TTTATTAATCAT
Found at i:988079 original size:11 final size:11
Alignment explanation
Indices: 988063--988102 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
988053 TAAGCAAGTC
988063 CTTAAAGGTGG
1 CTTAAAGGTGG
*
988074 CTTAAAGGTGA
1 CTTAAAGGTGG
*
988085 CTTAAAGG-AG
1 CTTAAAGGTGG
988095 CTTAAAGG
1 CTTAAAGG
988103 CTATACGACC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
10 8 0.31
11 18 0.69
ACGTcount: A:0.35, C:0.10, G:0.30, T:0.25
Consensus pattern (11 bp):
CTTAAAGGTGG
Found at i:988368 original size:51 final size:51
Alignment explanation
Indices: 988288--988392 Score: 192
Period size: 51 Copynumber: 2.1 Consensus size: 51
988278 ATAAACACAT
*
988288 ATATTAAATGCAAAAGCTCTTTTATAGAGATGGACGGGGGTCATCCGAGTG
1 ATATTAAATGCAAAAGCTCTTTTAAAGAGATGGACGGGGGTCATCCGAGTG
*
988339 ATATTAAATGCAAAAGCTCTTTTAAAGAGATGGACTGGGGTCATCCGAGTG
1 ATATTAAATGCAAAAGCTCTTTTAAAGAGATGGACGGGGGTCATCCGAGTG
988390 ATA
1 ATA
988393 ATATAATTTC
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 52 1.00
ACGTcount: A:0.33, C:0.13, G:0.26, T:0.28
Consensus pattern (51 bp):
ATATTAAATGCAAAAGCTCTTTTAAAGAGATGGACGGGGGTCATCCGAGTG
Found at i:988640 original size:2 final size:2
Alignment explanation
Indices: 988635--988699 Score: 114
Period size: 2 Copynumber: 33.0 Consensus size: 2
988625 AAAATCTCCA
988635 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
*
988677 T- TC TC TC TC TC TC TT TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC
988700 AGTTCATCCG
Statistics
Matches: 60, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
1 1 0.02
2 59 0.98
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:989111 original size:112 final size:112
Alignment explanation
Indices: 988914--989136 Score: 401
Period size: 112 Copynumber: 2.0 Consensus size: 112
988904 AGTTTTGTTC
*
988914 GTTTGTGTATATCTAATTAGAGTCTATTGTTTGTACAACTTAAGAAAACCCCTGGAACTAACACA
1 GTTTGTGTATATCTAATTAAAGTCTATTGTTTGTACAACTTAAGAAAACCCCTGGAACTAACACA
*
988979 GAATATACAAGATATACACAACAGTTGTGTCGTATGCCCAGGTGCAT
66 GAATATACAAGATATACACAACAGGTGTGTCGTATGCCCAGGTGCAT
*
989026 GTTTGTGTATATCTAATTAAAGTCTATTGTTTGTCCAACTTAAGAAAACCCCTGGAACTAACACA
1 GTTTGTGTATATCTAATTAAAGTCTATTGTTTGTACAACTTAAGAAAACCCCTGGAACTAACACA
* *
989091 GAATATACTAGATATACACAACAGGTGTGTCGTGTGCCCAGGTGCA
66 GAATATACAAGATATACACAACAGGTGTGTCGTATGCCCAGGTGCA
989137 CGTCAGGGTT
Statistics
Matches: 106, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
112 106 1.00
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.30
Consensus pattern (112 bp):
GTTTGTGTATATCTAATTAAAGTCTATTGTTTGTACAACTTAAGAAAACCCCTGGAACTAACACA
GAATATACAAGATATACACAACAGGTGTGTCGTATGCCCAGGTGCAT
Found at i:994834 original size:17 final size:19
Alignment explanation
Indices: 994798--994836 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
994788 ATGTTTCGTT
*
994798 TTTTCCCTATATTATGACA
1 TTTTCCCGATATTATGACA
994817 TTTTCCCGAT-TT-TGACA
1 TTTTCCCGATATTATGACA
994834 TTT
1 TTT
994837 ACTTCGATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 8 0.42
18 2 0.11
19 9 0.47
ACGTcount: A:0.21, C:0.21, G:0.08, T:0.51
Consensus pattern (19 bp):
TTTTCCCGATATTATGACA
Found at i:994850 original size:18 final size:17
Alignment explanation
Indices: 994808--994850 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
994798 TTTTCCCTAT
*
994808 ATTATGACATTTTCCCG
1 ATTATGACATTTACCCG
* *
994825 ATTTTGACATTTACTTCG
1 ATTATGACATTTAC-CCG
994843 ATTATGAC
1 ATTATGAC
994851 GTGCTCAGTA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 12 0.57
18 9 0.43
ACGTcount: A:0.26, C:0.19, G:0.12, T:0.44
Consensus pattern (17 bp):
ATTATGACATTTACCCG
Found at i:998957 original size:21 final size:21
Alignment explanation
Indices: 998933--998983 Score: 77
Period size: 21 Copynumber: 2.4 Consensus size: 21
998923 TTTTTTCTAA
998933 TACACAAACGATC-CCGCACGT
1 TACACAAACGATCACC-CACGT
*
998954 TACACGAACGATCACCCACGT
1 TACACAAACGATCACCCACGT
998975 TACACAAAC
1 TACACAAAC
998984 TATTTAACAC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
21 25 0.93
22 2 0.07
ACGTcount: A:0.37, C:0.37, G:0.12, T:0.14
Consensus pattern (21 bp):
TACACAAACGATCACCCACGT
Found at i:1002981 original size:2 final size:2
Alignment explanation
Indices: 1002974--1003042 Score: 138
Period size: 2 Copynumber: 34.5 Consensus size: 2
1002964 TAATTTCACA
1002974 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1003016 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1003043 GCATTTACCT
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 67 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:1006192 original size:21 final size:20
Alignment explanation
Indices: 1006130--1006192 Score: 51
Period size: 21 Copynumber: 3.1 Consensus size: 20
1006120 AGCAGCAACC
*
1006130 ACACCGACAAC-ACTTAAT-
1 ACACCGACAACAACTTACTG
* *
1006148 ACATCGACAACAATGTTAAC-G
1 ACACCGACAACAA-CTT-ACTG
1006169 ACACCGACAACAACTTCACTG
1 ACACCGACAACAACTT-ACTG
1006190 ACA
1 ACA
1006193 ACAACTACGA
Statistics
Matches: 34, Mismatches: 6, Indels: 7
0.72 0.13 0.15
Matches are distributed among these distances:
18 10 0.29
19 1 0.03
20 6 0.18
21 17 0.50
ACGTcount: A:0.43, C:0.32, G:0.10, T:0.16
Consensus pattern (20 bp):
ACACCGACAACAACTTACTG
Found at i:1006223 original size:51 final size:51
Alignment explanation
Indices: 1006165--1006273 Score: 148
Period size: 51 Copynumber: 2.1 Consensus size: 51
1006155 CAACAATGTT
** *
1006165 AACGACACCGACAACAACTTCA-CTGACAACAACTACGACTACACTGTCACC
1 AACGACACCGACAACAACAACACCTG-CAACAACTACGACTACACTGCCACC
* * *
1006216 AACGACACCGGCAACATCAACACCTGCAACAACTATGACTACACTGCCACC
1 AACGACACCGACAACAACAACACCTGCAACAACTACGACTACACTGCCACC
1006267 AACGACA
1 AACGACA
1006274 ACAACGTCAA
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
51 48 0.94
52 3 0.06
ACGTcount: A:0.39, C:0.38, G:0.11, T:0.12
Consensus pattern (51 bp):
AACGACACCGACAACAACAACACCTGCAACAACTACGACTACACTGCCACC
Found at i:1009752 original size:10 final size:9
Alignment explanation
Indices: 1009735--1009764 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
1009725 GTTTTTTGAA
1009735 AAAATTGTC
1 AAAATTGTC
1009744 AAAATTTGTC
1 AAAA-TTGTC
1009754 AAAATTGTC
1 AAAATTGTC
1009763 AA
1 AA
1009765 CCATATTCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 11 0.55
10 9 0.45
ACGTcount: A:0.47, C:0.10, G:0.10, T:0.33
Consensus pattern (9 bp):
AAAATTGTC
Found at i:1014939 original size:16 final size:16
Alignment explanation
Indices: 1014918--1014950 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
1014908 ATGTACATAC
1014918 TATTAAGACACATTAT
1 TATTAAGACACATTAT
1014934 TATTAAGACACATTAT
1 TATTAAGACACATTAT
1014950 T
1 T
1014951 GCATAACTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.42, C:0.12, G:0.06, T:0.39
Consensus pattern (16 bp):
TATTAAGACACATTAT
Found at i:1020392 original size:4 final size:4
Alignment explanation
Indices: 1020383--1020434 Score: 104
Period size: 4 Copynumber: 13.0 Consensus size: 4
1020373 GTATTTTAGA
1020383 ATCT ATCT ATCT ATCT ATCT ATCT ATCT ATCT ATCT ATCT ATCT ATCT
1 ATCT ATCT ATCT ATCT ATCT ATCT ATCT ATCT ATCT ATCT ATCT ATCT
1020431 ATCT
1 ATCT
1020435 CATTATAGTT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 48 1.00
ACGTcount: A:0.25, C:0.25, G:0.00, T:0.50
Consensus pattern (4 bp):
ATCT
Found at i:1022528 original size:387 final size:386
Alignment explanation
Indices: 1021814--1022586 Score: 1528
Period size: 387 Copynumber: 2.0 Consensus size: 386
1021804 CGCTTTTCAG
1021814 TACTATAAGTACTTTGATTTTATTACATTTTTCTGTGAATTCCTTGTAGCGAATGCGATAATAAT
1 TACTATAAGTACTTTGATTTTATTACATTTTTCTGTGAATTCCTTGTAGCGAATGCGATAATAAT
1021879 TATATATGGAAAAAATTTATTGAATAATATAGCACTATTTATAATATTTTGAGCAAGAATCCGCA
66 TATATATGGAAAAAATTTATTGAATAATATAGCACTATTTATAATATTTTGAGCAAGAATCCGCA
1021944 TGGATAGCCTGATTGACATGCTTGTTTGCTATTTTATATCCTGTCAAAATCGCTTTTTCGTGTCT
131 TGGATAGCCTGATTGACATGCTTGTTTGCTATTTTATATCCTGTCAAAATCGCTTTTTCGTGTCT
*
1022009 GTGAATTCTTTATAATGAGTGTAATAATAACTATATAGGAAACGTTGTAATTTTATTCATTGAAG
196 GTGAATTCTTTATAATGAGTGTAATAATAACTATATAGGAAACGTTGTAATTTTATTCATGGAAG
1022074 ATGATAGATTCACCAAAAATTCAGTTGAAAATCTACAGCAGAATTTGTAATATTTTGAACACTTG
261 ATGATAGATTCACCAAAAATTCAGTTGAAAATCTACAGCAGAATTTGTAATATTTTGAACACTTG
1022139 GTCATTTTGTTTACAGAACGGGCGACGCGGATCCATTATCCCGCACCCCCCCCCCCCCCCC
326 GTCATTTTGTTTACAGAACGGGCGACGCGGATCCATTATCCCGCACCCCCCCCCCCCCCCC
1022200 NTACTATAAGTACTTTGATTTTATTACATTTTTCTGTGAATTCCTTGTAGCGAATGCGATAATAA
1 -TACTATAAGTACTTTGATTTTATTACATTTTTCTGTGAATTCCTTGTAGCGAATGCGATAATAA
1022265 TTATATATGGAAAAAATTTATTGAATAATATAGCACTATTTATAATATTTTGAGCAAGAATCCGC
65 TTATATATGGAAAAAATTTATTGAATAATATAGCACTATTTATAATATTTTGAGCAAGAATCCGC
1022330 ATGGATAGCCTGATTGACATGCTTGTTTGCTATTTTATATCCTGTCAAAATCGCTTTTTCGTGTC
130 ATGGATAGCCTGATTGACATGCTTGTTTGCTATTTTATATCCTGTCAAAATCGCTTTTTCGTGTC
1022395 TGTGAATTCTTTATAATGAGTGTAATAATAACTATATAGGAAACGTTGTAATTTTATTCATGGAA
195 TGTGAATTCTTTATAATGAGTGTAATAATAACTATATAGGAAACGTTGTAATTTTATTCATGGAA
1022460 GATGATAGATTCACCAAAAATTCAGTTGAAAATCTACAGCAGAATTTGTAATATTTTGAACACTT
260 GATGATAGATTCACCAAAAATTCAGTTGAAAATCTACAGCAGAATTTGTAATATTTTGAACACTT
1022525 GGTCATTTTGTTTACAGAACGGGCGACGCGGATCCATTATCCCGCACCCCCCCCCCCCCCCC
325 GGTCATTTTGTTTACAGAACGGGCGACGCGGATCCATTATCCCGCACCCCCCCCCCCCCCCC
1022587 CCCGCGGTCC
Statistics
Matches: 385, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
387 385 1.00
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.36
Consensus pattern (386 bp):
TACTATAAGTACTTTGATTTTATTACATTTTTCTGTGAATTCCTTGTAGCGAATGCGATAATAAT
TATATATGGAAAAAATTTATTGAATAATATAGCACTATTTATAATATTTTGAGCAAGAATCCGCA
TGGATAGCCTGATTGACATGCTTGTTTGCTATTTTATATCCTGTCAAAATCGCTTTTTCGTGTCT
GTGAATTCTTTATAATGAGTGTAATAATAACTATATAGGAAACGTTGTAATTTTATTCATGGAAG
ATGATAGATTCACCAAAAATTCAGTTGAAAATCTACAGCAGAATTTGTAATATTTTGAACACTTG
GTCATTTTGTTTACAGAACGGGCGACGCGGATCCATTATCCCGCACCCCCCCCCCCCCCCC
Found at i:1025851 original size:2 final size:2
Alignment explanation
Indices: 1025844--1025894 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
1025834 AAATTATGAT
1025844 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1025886 TC TC TC TC T
1 TC TC TC TC T
1025895 GTGTTCATCC
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:1025911 original size:2 final size:2
Alignment explanation
Indices: 1025906--1025943 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
1025896 TGTTCATCCT
*
1025906 GA GA GA GA GA GA GA GA GA GT GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1025944 AATTTGCACC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.47, C:0.00, G:0.50, T:0.03
Consensus pattern (2 bp):
GA
Found at i:1028001 original size:2 final size:2
Alignment explanation
Indices: 1027994--1028026 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1027984 GGTGCAAAAA
1027994 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1028027 TTGTTTCACA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:1029995 original size:32 final size:32
Alignment explanation
Indices: 1029954--1030169 Score: 360
Period size: 32 Copynumber: 6.8 Consensus size: 32
1029944 GACCACATCT
*
1029954 TGAGTACACGTTATACATTGATATTGTTATTA
1 TGAGTACACGTTATACACTGATATTGTTATTA
*
1029986 TGAGTACACGTTATACGCTGATATTGTTATTA
1 TGAGTACACGTTATACACTGATATTGTTATTA
1030018 TGAGTACACGTTATACACTGATATTGTTATTA
1 TGAGTACACGTTATACACTGATATTGTTATTA
*
1030050 TGAATACACGTTATACACTGATATTGTTATTA
1 TGAGTACACGTTATACACTGATATTGTTATTA
* * *
1030082 TGAATACAAGGTATACACTGATATTGTTATTA
1 TGAGTACACGTTATACACTGATATTGTTATTA
1030114 TGAGTACACGTTATACACTGATATTGTTATTA
1 TGAGTACACGTTATACACTGATATTGTTATTA
* *
1030146 TTAGTACGCGTTATACACTGATAT
1 TGAGTACACGTTATACACTGATAT
1030170 NCTGTAGGAC
Statistics
Matches: 173, Mismatches: 11, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 173 1.00
ACGTcount: A:0.32, C:0.12, G:0.16, T:0.40
Consensus pattern (32 bp):
TGAGTACACGTTATACACTGATATTGTTATTA
Found at i:1030214 original size:29 final size:29
Alignment explanation
Indices: 1030172--1030874 Score: 931
Period size: 29 Copynumber: 24.2 Consensus size: 29
1030162 ACTGATATNC
*
1030172 TGTAGGACATCTCCTCTAAGTGTATCTAG
1 TGTAGCACATCTCCTCTAAGTGTATCTAG
* *
1030201 TGTAGCACATCTCCTCTAAGTGAATCTAC
1 TGTAGCACATCTCCTCTAAGTGTATCTAG
* ** * *
1030230 TGTAACACATCTCAACTAAGTGTATATAC
1 TGTAGCACATCTCCTCTAAGTGTATCTAG
** *
1030259 TGTAGCACATCTCAACTAAGTGTATCTAC
1 TGTAGCACATCTCCTCTAAGTGTATCTAG
1030288 TGTAGCACATCTCCTCTAAGTG--TCTAG
1 TGTAGCACATCTCCTCTAAGTGTATCTAG
* * *
1030315 TGCAGCACATCTCCCCTTAGTGTATCTAG
1 TGTAGCACATCTCCTCTAAGTGTATCTAG
1030344 TGTAGCACATCTCCTCTAAGTGTATCTAG
1 TGTAGCACATCTCCTCTAAGTGTATCTAG
* *
1030373 TGTAGCACATCTCCTCTAGGTGTATCTAC
1 TGTAGCACATCTCCTCTAAGTGTATCTAG
** *
1030402 TGTAGCACATCTCAACTAAGTGTATCTAC
1 TGTAGCACATCTCCTCTAAGTGTATCTAG
* *
1030431 TGTAGCACATCTCCTCTAAGTGTATCCAC
1 TGTAGCACATCTCCTCTAAGTGTATCTAG
*
1030460 TGTAGCACATCTCCTCTAAGTGTATCTAC
1 TGTAGCACATCTCCTCTAAGTGTATCTAG
* *
1030489 TGTAGCACATCTCCTCTAAGTGTATCCAC
1 TGTAGCACATCTCCTCTAAGTGTATCTAG
1030518 TGTAGCACATCTCCTCTAAGTGTATCTACTG
1 TGTAGCACATCTCCTCTAAGTGTATCTA--G
*
1030549 TACTGTAGCACATCTCCTCTTAGTGTATCTAG
1 ---TGTAGCACATCTCCTCTAAGTGTATCTAG
* * *
1030581 TGTCGCATATCTCCTCTAAGTGTATCTAC
1 TGTAGCACATCTCCTCTAAGTGTATCTAG
* *
1030610 TGTAGCACATCTCCTCTAAGTGTATCCAC
1 TGTAGCACATCTCCTCTAAGTGTATCTAG
1030639 TGTAGCACATCTCCTCTAAGTGTATCTACTG
1 TGTAGCACATCTCCTCTAAGTGTATCTA--G
* *
1030670 TACTATAGCACATCTCCTCTTAGTGTATCTAG
1 ---TGTAGCACATCTCCTCTAAGTGTATCTAG
*
1030702 TGCAGCACATCTCCTCTAAGTGTATCTAG
1 TGTAGCACATCTCCTCTAAGTGTATCTAG
*
1030731 TGTAGCACATCTCCTCTCAGTGTATC---
1 TGTAGCACATCTCCTCTAAGTGTATCTAG
1030757 --T-GCACATCTCCTCTAAGTGTATCTAG
1 TGTAGCACATCTCCTCTAAGTGTATCTAG
1030783 TGTAGCACATCTCCTCTAAGTGTATCTAG
1 TGTAGCACATCTCCTCTAAGTGTATCTAG
*
1030812 TGTAGCACATCTCCTCTAAGTGTATCGAG
1 TGTAGCACATCTCCTCTAAGTGTATCTAG
1030841 TGTAGCACATCTCCTCTAAGTG--TCTAG
1 TGTAGCACATCTCCTCTAAGTGTATCTAG
1030868 TGTAGCA
1 TGTAGCA
1030875 TACATCTTGT
Statistics
Matches: 605, Mismatches: 51, Indels: 38
0.87 0.07 0.05
Matches are distributed among these distances:
23 21 0.03
24 1 0.00
27 34 0.06
28 1 0.00
29 493 0.81
32 2 0.00
34 53 0.09
ACGTcount: A:0.24, C:0.26, G:0.16, T:0.33
Consensus pattern (29 bp):
TGTAGCACATCTCCTCTAAGTGTATCTAG
Found at i:1030618 original size:121 final size:120
Alignment explanation
Indices: 1030171--1030863 Score: 930
Period size: 121 Copynumber: 6.0 Consensus size: 120
1030161 CACTGATATN
* * * *
1030171 CTGTAGGACATCTCCTCTAAGTGTATCTA-G---TGTAGCACATCTCCTCTAAGTGAATCTACTG
1 CTGTAGCACATCTCCTCTAAGTGTATCTACGTACTGTAGCACATCTCCTCTTAGTGTATCTAGTG
* ** * * ** *
1030232 TAACACATCTCAACTAAGTGTATATACTGTAGCACATCTCAACTAAGTGTATCTA
66 TAGCACATCTCCTCTAAGTGTATCTAGTGTAGCACATCTCCTCTAAGTGTATCCA
* *
1030287 CTGTAGCACATCTCCTCTAAGTG--TCTA-G---TGCAGCACATCTCCCCTTAGTGTATCTAGTG
1 CTGTAGCACATCTCCTCTAAGTGTATCTACGTACTGTAGCACATCTCCTCTTAGTGTATCTAGTG
* *
1030346 TAGCACATCTCCTCTAAGTGTATCTAGTGTAGCACATCTCCTCTAGGTGTATCTA
66 TAGCACATCTCCTCTAAGTGTATCTAGTGTAGCACATCTCCTCTAAGTGTATCCA
** * * *
1030401 CTGTAGCACATCTCAACTAAGTGTA--T-C-TACTGTAGCACATCTCCTCTAAGTGTATCCACTG
1 CTGTAGCACATCTCCTCTAAGTGTATCTACGTACTGTAGCACATCTCCTCTTAGTGTATCTAGTG
*
1030462 TAGCACATCTCCTCTAAGTGTATCTACTGTAGCACATCTCCTCTAAGTGTATCCA
66 TAGCACATCTCCTCTAAGTGTATCTAGTGTAGCACATCTCCTCTAAGTGTATCCA
1030517 CTGTAGCACATCTCCTCTAAGTGTATCTACTGTACTGTAGCACATCTCCTCTTAGTGTATCTAGT
1 CTGTAGCACATCTCCTCTAAGTGTATCTAC-GTACTGTAGCACATCTCCTCTTAGTGTATCTAGT
* * *
1030582 GTCGCATATCTCCTCTAAGTGTATCTACTGTAGCACATCTCCTCTAAGTGTATCCA
65 GTAGCACATCTCCTCTAAGTGTATCTAGTGTAGCACATCTCCTCTAAGTGTATCCA
*
1030638 CTGTAGCACATCTCCTCTAAGTGTATCTACTGTACTATAGCACATCTCCTCTTAGTGTATCTAGT
1 CTGTAGCACATCTCCTCTAAGTGTATCTAC-GTACTGTAGCACATCTCCTCTTAGTGTATCTAGT
* *
1030703 GCAGCACATCTCCTCTAAGTGTATCTAGTGTAGCACATCTCCTCTCAGTGTAT---
65 GTAGCACATCTCCTCTAAGTGTATCTAGTGTAGCACATCTCCTCTAAGTGTATCCA
*
1030756 C--T-GCACATCTCCTCTAAGTGTATCTA-G---TGTAGCACATCTCCTCTAAGTGTATCTAGTG
1 CTGTAGCACATCTCCTCTAAGTGTATCTACGTACTGTAGCACATCTCCTCTTAGTGTATCTAGTG
*
1030814 TAGCACATCTCCTCTAAGTGTATCGAGTGTAGCACATCTCCTCTAAGTGT
66 TAGCACATCTCCTCTAAGTGTATCTAGTGTAGCACATCTCCTCTAAGTGT
1030864 CTAGTGTAGC
Statistics
Matches: 524, Mismatches: 42, Indels: 28
0.88 0.07 0.05
Matches are distributed among these distances:
110 76 0.15
113 1 0.00
114 100 0.19
115 24 0.05
116 124 0.24
118 2 0.00
119 1 0.00
121 196 0.37
ACGTcount: A:0.24, C:0.27, G:0.16, T:0.33
Consensus pattern (120 bp):
CTGTAGCACATCTCCTCTAAGTGTATCTACGTACTGTAGCACATCTCCTCTTAGTGTATCTAGTG
TAGCACATCTCCTCTAAGTGTATCTAGTGTAGCACATCTCCTCTAAGTGTATCCA
Found at i:1030754 original size:20 final size:21
Alignment explanation
Indices: 1030729--1030778 Score: 66
Period size: 23 Copynumber: 2.3 Consensus size: 21
1030719 AAGTGTATCT
*
1030729 AGTGTA-GCACATCTCCTCTC
1 AGTGTATGCACATCTCCTCTA
1030749 AGTGTATCTGCACATCTCCTCTA
1 AGTGTA--TGCACATCTCCTCTA
1030772 AGTGTAT
1 AGTGTAT
1030779 CTAGTGTAGC
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
20 6 0.23
21 1 0.04
23 19 0.73
ACGTcount: A:0.22, C:0.28, G:0.16, T:0.34
Consensus pattern (21 bp):
AGTGTATGCACATCTCCTCTA
Found at i:1030812 original size:81 final size:83
Alignment explanation
Indices: 1030675--1030874 Score: 309
Period size: 81 Copynumber: 2.4 Consensus size: 83
1030665 TACTGTACTA
* *
1030675 TAGCACATCTCCTCTTAGTGTATCTAGTGCAGCACATCTCCTCTAAGTGTATCTAGTGTAGCACA
1 TAGCACATCTCCTCTAAGTGTATCTAGTGTAGCACATCTCCTCTAAGTGTATCTAGTGTAGCACA
*
1030740 TCTCCTCTCAGTGTATC-
66 TCTCCTCTAAGTGTATCG
1030757 T-GCACATCTCCTCTAAGTGTATCTAGTGTAGCACATCTCCTCTAAGTGTATCTAGTGTAGCACA
1 TAGCACATCTCCTCTAAGTGTATCTAGTGTAGCACATCTCCTCTAAGTGTATCTAGTGTAGCACA
1030821 TCTCCTCTAAGTGTATCGAGTG
66 TCTCCTCTAAGTGTATC----G
1030843 TAGCACATCTCCTCTAAGTG--TCTAGTGTAGCA
1 TAGCACATCTCCTCTAAGTGTATCTAGTGTAGCA
1030875 TACATCTTGT
Statistics
Matches: 109, Mismatches: 3, Indels: 9
0.90 0.02 0.07
Matches are distributed among these distances:
81 77 0.71
82 1 0.01
85 12 0.11
86 1 0.01
87 18 0.17
ACGTcount: A:0.23, C:0.26, G:0.17, T:0.34
Consensus pattern (83 bp):
TAGCACATCTCCTCTAAGTGTATCTAGTGTAGCACATCTCCTCTAAGTGTATCTAGTGTAGCACA
TCTCCTCTAAGTGTATCG
Found at i:1039657 original size:34 final size:34
Alignment explanation
Indices: 1039627--1039778 Score: 108
Period size: 34 Copynumber: 4.5 Consensus size: 34
1039617 TTAAAGTGTT
*
1039627 TGATTGTGTGTAACAGTATATGCATAAAAGTACC
1 TGATTGTGTGTAACAGTATATGCATAAAAGTGCC
* * ** * **
1039661 TGATTGTGTGCAACAGTTTATGTGTTAAAGTGTG
1 TGATTGTGTGTAACAGTATATGCATAAAAGTGCC
* * ** * *
1039695 TGAATGCGTGTAATGGTATATGTAGT-AAAGTGCG
1 TGATTGTGTGTAACAGTATATGCA-TAAAAGTGCC
* * * * *
1039729 TGATTTTGTGTAACGGTATATACCTAAAAGTACC
1 TGATTGTGTGTAACAGTATATGCATAAAAGTGCC
*
1039763 TGATTGTGTGCAACAG
1 TGATTGTGTGTAACAG
1039779 CTTATCTGTT
Statistics
Matches: 88, Mismatches: 28, Indels: 4
0.73 0.23 0.03
Matches are distributed among these distances:
33 1 0.01
34 86 0.98
35 1 0.01
ACGTcount: A:0.30, C:0.10, G:0.26, T:0.35
Consensus pattern (34 bp):
TGATTGTGTGTAACAGTATATGCATAAAAGTGCC
Found at i:1039789 original size:102 final size:102
Alignment explanation
Indices: 1039608--1039795 Score: 288
Period size: 102 Copynumber: 1.8 Consensus size: 102
1039598 AAACAGAATT
** *
1039608 GTATATGTGTTAAAGTGTTTGATTGTGTGTAACAGTATATGCATAAAAGTACCTGATTGTGTGCA
1 GTATATGTGTTAAAGTGCGTGATTGTGTGTAACAGTATATACATAAAAGTACCTGATTGTGTGCA
* *
1039673 ACAGTTTATGTGTTAAAGTGTGTGAATGCGTGTAATG
66 ACAGCTTATCTGTTAAAGTGTGTGAATGCGTGTAATG
* * *
1039710 GTATATGTAG-TAAAGTGCGTGATTTTGTGTAACGGTATATACCTAAAAGTACCTGATTGTGTGC
1 GTATATGT-GTTAAAGTGCGTGATTGTGTGTAACAGTATATACATAAAAGTACCTGATTGTGTGC
1039774 AACAGCTTATCTGTTAAAGTGT
65 AACAGCTTATCTGTTAAAGTGT
1039796 AATGTTATAT
Statistics
Matches: 77, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
102 76 0.99
103 1 0.01
ACGTcount: A:0.29, C:0.09, G:0.25, T:0.37
Consensus pattern (102 bp):
GTATATGTGTTAAAGTGCGTGATTGTGTGTAACAGTATATACATAAAAGTACCTGATTGTGTGCA
ACAGCTTATCTGTTAAAGTGTGTGAATGCGTGTAATG
Found at i:1039857 original size:34 final size:34
Alignment explanation
Indices: 1039792--1039865 Score: 103
Period size: 34 Copynumber: 2.2 Consensus size: 34
1039782 ATCTGTTAAA
* *
1039792 GTGTAATGTTATATGTAGTAAAGTACCTGATTTC
1 GTGTAATGGTATATGTAGTAAAGTACCTGATTGC
***
1039826 GTGTAATGGTATATGTAGTAAAGTGTTTGATTGC
1 GTGTAATGGTATATGTAGTAAAGTACCTGATTGC
1039860 GTGTAA
1 GTGTAA
1039866 CAGTATGTGA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.28, C:0.05, G:0.26, T:0.41
Consensus pattern (34 bp):
GTGTAATGGTATATGTAGTAAAGTACCTGATTGC
Found at i:1048245 original size:2 final size:2
Alignment explanation
Indices: 1048238--1048266 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1048228 GCTAAGGATA
1048238 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1048267 CAAAATATGT
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:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:1048528 original size:2 final size:2
Alignment explanation
Indices: 1048521--1048561 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
1048511 TTCTTTTAAG
1048521 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1048562 AACATTTACT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:1048692 original size:2 final size:2
Alignment explanation
Indices: 1048687--1048711 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1048677 AAACACACAA
1048687 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
1048712 TAAAGATTTA
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:1048822 original size:2 final size:2
Alignment explanation
Indices: 1048815--1048846 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
1048805 GTTTTTAGTT
*
1048815 TC TC TC TC TC TC TC TC TT TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1048847 CGACTTTTTC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (2 bp):
TC
Found at i:1049122 original size:2 final size:2
Alignment explanation
Indices: 1049115--1049167 Score: 79
Period size: 2 Copynumber: 26.5 Consensus size: 2
1049105 CTAATATGAA
* * *
1049115 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT GT TT TT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1049157 CT CT CT CT CT C
1 CT CT CT CT CT C
1049168 CTAAACTCTT
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.00, C:0.45, G:0.02, T:0.53
Consensus pattern (2 bp):
CT
Found at i:1049918 original size:17 final size:17
Alignment explanation
Indices: 1049896--1049929 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
1049886 TTACGGTGAA
1049896 GTCTCCGATTCCCGGTC
1 GTCTCCGATTCCCGGTC
1049913 GTCTCCGATTCCCGGTC
1 GTCTCCGATTCCCGGTC
1049930 ACTCTTATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.06, C:0.41, G:0.24, T:0.29
Consensus pattern (17 bp):
GTCTCCGATTCCCGGTC
Found at i:1054100 original size:42 final size:42
Alignment explanation
Indices: 1054041--1054210 Score: 304
Period size: 42 Copynumber: 4.0 Consensus size: 42
1054031 CAGCGCTTTA
*
1054041 ACCACTGAGCTATTGAGACCCGAAATATTGACTGACGGTCAC
1 ACCACTGAGCTATTGAGACCCGATATATTGACTGACGGTCAC
*
1054083 ACCACTGAGCTATTGAGACCAGATATATTGACTGACGGTCAC
1 ACCACTGAGCTATTGAGACCCGATATATTGACTGACGGTCAC
* *
1054125 ACCACTGATCTATTGAGACCCGATATATTGACTGACAGTCAC
1 ACCACTGAGCTATTGAGACCCGATATATTGACTGACGGTCAC
1054167 ACCACTGAGCTATTGAGACCCGATATATTGACTGACGGTCAC
1 ACCACTGAGCTATTGAGACCCGATATATTGACTGACGGTCAC
1054209 AC
1 AC
1054211 ACTTGTTTAC
Statistics
Matches: 121, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 121 1.00
ACGTcount: A:0.31, C:0.26, G:0.20, T:0.24
Consensus pattern (42 bp):
ACCACTGAGCTATTGAGACCCGATATATTGACTGACGGTCAC
Found at i:1057039 original size:33 final size:31
Alignment explanation
Indices: 1056985--1057071 Score: 86
Period size: 34 Copynumber: 2.7 Consensus size: 31
1056975 CGCCCCTCTC
*
1056985 AAAAAAGCAAGCAAACAAAC-AAACAAACAAACA
1 AAAAAAACAA-CAAA-AAACAAAAC-AACAAACA
* * *
1057018 GAAAAAAATGAACAAATAACAAAACAACAACCA
1 -AAAAAAA-CAACAAAAAACAAAACAACAAACA
1057051 AAAAAAACAACAAAAAACAAA
1 AAAAAAACAACAAAAAACAAA
1057072 TAGCATGAGG
Statistics
Matches: 45, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
31 12 0.27
32 7 0.16
33 10 0.22
34 14 0.31
35 2 0.04
ACGTcount: A:0.75, C:0.18, G:0.05, T:0.02
Consensus pattern (31 bp):
AAAAAAACAACAAAAAACAAAACAACAAACA
Found at i:1057063 original size:31 final size:34
Alignment explanation
Indices: 1056985--1057071 Score: 92
Period size: 31 Copynumber: 2.6 Consensus size: 34
1056975 CGCCCCTCTC
*
1056985 AAAAAAGCAAGCAAACAAAC-AAACAAACAAACAGA
1 AAAAAATCAA-CAAA-AAACAAAACAAACAAACAGA
* * *
1057020 AAAAAATGAACAAATAACAAAAC-AACAACCA-A
1 AAAAAATCAACAAAAAACAAAACAAACAAACAGA
1057052 AAAAAA-CAACAAAAAACAAA
1 AAAAAATCAACAAAAAACAAA
1057072 TAGCATGAGG
Statistics
Matches: 45, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
31 12 0.27
32 7 0.16
33 10 0.22
34 8 0.18
35 8 0.18
ACGTcount: A:0.75, C:0.18, G:0.05, T:0.02
Consensus pattern (34 bp):
AAAAAATCAACAAAAAACAAAACAAACAAACAGA
Found at i:1060103 original size:4 final size:4
Alignment explanation
Indices: 1060094--1060166 Score: 146
Period size: 4 Copynumber: 18.2 Consensus size: 4
1060084 TGTTATCTTT
1060094 TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC
1 TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC
1060142 TATC TATC TATC TATC TATC TATC T
1 TATC TATC TATC TATC TATC TATC T
1060167 CAATTACAGA
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 69 1.00
ACGTcount: A:0.25, C:0.25, G:0.00, T:0.51
Consensus pattern (4 bp):
TATC
Found at i:1062177 original size:106 final size:105
Alignment explanation
Indices: 1061988--1062319 Score: 355
Period size: 106 Copynumber: 3.0 Consensus size: 105
1061978 GTTTTATACG
* * *
1061988 ATATAAAATGGTTTGAAACAGTTTCTACTTTTTTATAAACCGCTTCGCGGTTTATAAAGCGTTAA
1 ATATAAAATGGTTTGAAACAGTTT-T-CTTTTTTATAAACGGCTTTGCGGTTTATAAAGCGTAAA
*
1062053 CTGCCCCAAACCATTTTATATCG-TAAAACAAATAATATTGA
64 CTGTCCCAAACCATTTTATATCGATAAAACAAATAATATTGA
1062094 AT-TCAAAATGGTTTGAAACAGTTTATGCTTTTTTATAAACGGCTTTGCGGTTTATAAAGCGTAA
1 ATAT-AAAATGGTTTGAAACAGTTT-T-CTTTTTTATAAACGGCTTTGCGGTTTATAAAGCGTAA
* * * *
1062158 ACTGTCCCGAACCATTTTATATCGTATAAAACAATCTCTATTAGTTTTATA
63 ACTGTCCCAAACCATTTTATATCG-ATAAAACAA-----A-TAATATT-GA
**
1062209 CGATATAAAATGGTTTGAAACACGCTTTT-TTTTAAATAAACGGCTTTGCGGTTTATAAAGCGTA
1 --ATATAAAATGGTTTGAAACA-G-TTTTCTTTTTTATAAACGGCTTTGCGGTTTATAAAGCGTA
* * *
1062273 AACTGTCCCAAACCGTTGTATATCGTATAAAACAAATATTTATTGA
62 AACTGTCCCAAACCATTTTATATCG-ATAAAACAAATA-ATATTGA
1062319 A
1 A
1062320 CTCATTCCTT
Statistics
Matches: 192, Mismatches: 18, Indels: 30
0.80 0.08 0.12
Matches are distributed among these distances:
105 1 0.01
106 79 0.41
108 9 0.05
110 3 0.02
111 4 0.02
113 1 0.01
114 5 0.03
115 1 0.01
116 65 0.34
117 18 0.09
118 3 0.02
119 3 0.02
ACGTcount: A:0.35, C:0.15, G:0.14, T:0.36
Consensus pattern (105 bp):
ATATAAAATGGTTTGAAACAGTTTTCTTTTTTATAAACGGCTTTGCGGTTTATAAAGCGTAAACT
GTCCCAAACCATTTTATATCGATAAAACAAATAATATTGA
Found at i:1062303 original size:116 final size:116
Alignment explanation
Indices: 1062098--1062307 Score: 334
Period size: 116 Copynumber: 1.8 Consensus size: 116
1062088 TATTGAATTC
**
1062098 AAAATGGTTTGAAACAGTTTATGCTTTTTTATAAACGGCTTTGCGGTTTATAAAGCGTAAACTGT
1 AAAATGGTTTGAAACAGTTTAT-CTTTTAAATAAACGGCTTTGCGGTTTATAAAGCGTAAACTGT
* *
1062163 CCCGAACCATTTTATATCGTATAAAACAATCTCTATTAGTTTTATACGATAT
65 CCCAAACCATTGTATATCGTATAAAACAATCTCTATTAGTTTTATACGATAT
1062215 AAAATGGTTTGAAACACGCTTT-T-TTTTAAATAAACGGCTTTGCGGTTTATAAAGCGTAAACTG
1 AAAATGGTTTGAAACA-G-TTTATCTTTTAAATAAACGGCTTTGCGGTTTATAAAGCGTAAACTG
*
1062278 TCCCAAACCGTTGTATATCGTATAAAACAA
64 TCCCAAACCATTGTATATCGTATAAAACAA
1062308 ATATTTATTG
Statistics
Matches: 86, Mismatches: 5, Indels: 5
0.90 0.05 0.05
Matches are distributed among these distances:
116 65 0.76
117 16 0.19
118 2 0.02
119 3 0.03
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.36
Consensus pattern (116 bp):
AAAATGGTTTGAAACAGTTTATCTTTTAAATAAACGGCTTTGCGGTTTATAAAGCGTAAACTGTC
CCAAACCATTGTATATCGTATAAAACAATCTCTATTAGTTTTATACGATAT
Found at i:1065680 original size:20 final size:20
Alignment explanation
Indices: 1065652--1065713 Score: 88
Period size: 20 Copynumber: 3.1 Consensus size: 20
1065642 ATTATGTTAT
*
1065652 ATTACGATTTGTTCGGACGA
1 ATTAGGATTTGTTCGGACGA
*
1065672 ATTAGGATTTGTTCGGACGT
1 ATTAGGATTTGTTCGGACGA
* *
1065692 ATTAGAATTTATTCGGACGA
1 ATTAGGATTTGTTCGGACGA
1065712 AT
1 AT
1065714 ATTTAAAAGT
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.27, C:0.11, G:0.24, T:0.37
Consensus pattern (20 bp):
ATTAGGATTTGTTCGGACGA
Found at i:1068105 original size:2 final size:2
Alignment explanation
Indices: 1068100--1068145 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
1068090 TATAAATATC
1068100 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1068142 CT CT
1 CT CT
1068146 ACATTCATTA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:1075372 original size:8 final size:8
Alignment explanation
Indices: 1075359--1075427 Score: 129
Period size: 8 Copynumber: 8.6 Consensus size: 8
1075349 TGGTTTCACC
1075359 CTGTCCGT
1 CTGTCCGT
1075367 CTGTCCGT
1 CTGTCCGT
1075375 CTGTCCGT
1 CTGTCCGT
1075383 CTGTCCGT
1 CTGTCCGT
*
1075391 CTGTCTGT
1 CTGTCCGT
1075399 CTGTCCGT
1 CTGTCCGT
1075407 CTGTCCGT
1 CTGTCCGT
1075415 CTGTCCGT
1 CTGTCCGT
1075423 CTGTC
1 CTGTC
1075428 TGTAGACGCA
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
8 59 1.00
ACGTcount: A:0.00, C:0.36, G:0.25, T:0.39
Consensus pattern (8 bp):
CTGTCCGT
Found at i:1077685 original size:2 final size:2
Alignment explanation
Indices: 1077678--1077782 Score: 158
Period size: 2 Copynumber: 52.5 Consensus size: 2
1077668 GCAAGCTCAC
*
1077678 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AA AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
* * *
1077720 AG AG AG AG AG AG AG AG AG AG AG AG AG AA AT AG AT AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1077762 AG AG AG AG A- ACG AG AG AG AG A
1 AG AG AG AG AG A-G AG AG AG AG A
1077783 AAAGAGAAAG
Statistics
Matches: 94, Mismatches: 7, Indels: 4
0.90 0.07 0.04
Matches are distributed among these distances:
1 1 0.01
2 92 0.98
3 1 0.01
ACGTcount: A:0.52, C:0.01, G:0.45, T:0.02
Consensus pattern (2 bp):
AG
Found at i:1079557 original size:2 final size:2
Alignment explanation
Indices: 1079550--1079600 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
1079540 GAAAATAATT
1079550 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1079592 TC TC TC TC T
1 TC TC TC TC T
1079601 GTTAAACATG
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:1085844 original size:22 final size:22
Alignment explanation
Indices: 1085819--1085865 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 22
1085809 TTGCTGTGTG
*
1085819 ATTTGACATG-TTTGTTATTGTT
1 ATTTGA-ATGTTTTGTTATAGTT
1085841 ATTTGAATGTTTTGTTATAGTT
1 ATTTGAATGTTTTGTTATAGTT
1085863 ATT
1 ATT
1085866 GTGTGTATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 3 0.13
22 20 0.87
ACGTcount: A:0.21, C:0.02, G:0.17, T:0.60
Consensus pattern (22 bp):
ATTTGAATGTTTTGTTATAGTT
Found at i:1086918 original size:166 final size:166
Alignment explanation
Indices: 1086577--1087233 Score: 425
Period size: 166 Copynumber: 3.9 Consensus size: 166
1086567 TTTAAGGATT
* * * * * *
1086577 TTCTCTATATATTCCTATATAAGAATTC-A-ACCCGCCATCGTGGCCCCGCCCTACCCCCAGGGA
1 TTCTCTATATATTCCAATGTAA-AAATCAATACCC-CCATTGTGGCCCCGCCATACCCCCAGGAA
** * * * * * *
1086640 TTATGATTTTG--CAAACTTGAATTTACACTACCCGAGGATGCCTCTAC--ACAAGTTTAAGCTT
64 CCATGA-TTTGAACAAACTTGAATCTA-ACTACCTGAGGATGCTTCCACTTATAA-TTTGAGCTT
* * * * *
1086701 TTCTGGCCTAACAGTTTTTGAGAAAAAGAATTTTTGAGATT
126 TCCTGGCCAAATAGTTTTTGAGAAGAAGAATTTTTGAGATA
** * * *
1086742 TTCTCTATATA-TCCCTTGTTAAAAATCAATACCCCCATTGTGGCCCCGCCATGCCCCCGGGGAC
1 TTCTCTATATATTCCAATG-TAAAAATCAATACCCCCATTGTGGCCCCGCCATACCCCCAGGAAC
* * * *
1086806 CATGATTTGAACAACCTTGAATCTTTACTATCTGAGTATGCTTCCACTTAT-ATTTGAGCTTTCC
65 CATGATTTGAACAAACTTGAATC-TAACTACCTGAGGATGCTTCCACTTATAATTTGAGCTTTCC
* * *
1086870 TGGTCTAATTGTTTTTGAGAAGAAG-ATTTTT-ATTGATA
129 TGGCCAAATAGTTTTTGAGAAGAAGAATTTTTGA--GATA
* ** * * *
1086908 TTCTCTATATATTCCAATGTAAAAATCCATTTCCCCATTGTTGTCCCGCCATACCCCCAGGAACT
1 TTCTCTATATATTCCAATGTAAAAATCAATACCCCCATTGTGGCCCCGCCATACCCCCAGGAACC
* * * * * * **
1086973 ATGATTTGAAGAAATTTGAATCTAACTACCTTAGGATGCTTTCATTTTTAATTTGAGCTTTTTTG
66 ATGATTTGAACAAACTTGAATCTAACTACCTGAGGATGCTTCCACTTATAATTTGAGCTTTCCTG
* *
1087038 GCCAAATAGTTTTT--G-AGAAG-ATTTTTAAAAGATTT
131 GCCAAATAGTTTTTGAGAAGAAGAATTTTT--GAGA-TA
* * ** *
1087073 TCTCTACATACATATTGTATTCCTATGTAAAACTTGAT-CCCCCTATTGGGGCCCAC-CC-TACC
1 T-TCT-C-T--ATA---TATTCCAATGTAAAAATCAATACCCCC-ATTGTGGCCC-CGCCATACC
* * * * * * *
1087135 CCCGGGGACCATGATTTGAATAAACTTGAATTTACACAACCTGAGGATGCTGCCA-TT-TCAACT
56 CCCAGGAACCATGATTTGAACAAACTTGAATCTA-ACTACCTGAGGATGCTTCCACTTAT-AATT
*
1087198 TGAGCTTTTCTGGCCAAATAGTTTTTGAGAAGAAGA
119 TGAGCTTTCCTGGCCAAATAGTTTTTGAGAAGAAGA
1087234 TGTTTGAAAA
Statistics
Matches: 387, Mismatches: 73, Indels: 53
0.75 0.14 0.10
Matches are distributed among these distances:
163 11 0.03
164 16 0.04
165 72 0.19
166 159 0.41
167 8 0.02
168 2 0.01
170 3 0.01
171 1 0.00
172 66 0.17
173 42 0.11
174 2 0.01
175 5 0.01
ACGTcount: A:0.27, C:0.22, G:0.16, T:0.35
Consensus pattern (166 bp):
TTCTCTATATATTCCAATGTAAAAATCAATACCCCCATTGTGGCCCCGCCATACCCCCAGGAACC
ATGATTTGAACAAACTTGAATCTAACTACCTGAGGATGCTTCCACTTATAATTTGAGCTTTCCTG
GCCAAATAGTTTTTGAGAAGAAGAATTTTTGAGATA
Found at i:1088720 original size:16 final size:16
Alignment explanation
Indices: 1088701--1088731 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
1088691 AATCTAACGT
1088701 ATGTTAAACGTATGTA
1 ATGTTAAACGTATGTA
1088717 ATGTTAAACGTATGT
1 ATGTTAAACGTATGT
1088732 TATCCCACGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.35, C:0.06, G:0.19, T:0.39
Consensus pattern (16 bp):
ATGTTAAACGTATGTA
Found at i:1092558 original size:23 final size:23
Alignment explanation
Indices: 1092528--1092613 Score: 100
Period size: 23 Copynumber: 3.4 Consensus size: 23
1092518 AAACGAGACA
1092528 TCGCGCTAACACACAACACGCCG
1 TCGCGCTAACACACAACACGCCG
*
1092551 TCGCGCTAACGCAACTTTGCAAACACGCCG
1 TCGCGCTAA--C-AC---AC-AACACGCCG
1092581 TCGCGCTAACACACAACACGCCG
1 TCGCGCTAACACACAACACGCCG
1092604 TCGCGCTAAC
1 TCGCGCTAAC
1092614 GCAACTTTGC
Statistics
Matches: 54, Mismatches: 2, Indels: 14
0.77 0.03 0.20
Matches are distributed among these distances:
23 28 0.52
24 1 0.02
25 1 0.02
26 2 0.04
27 2 0.04
28 1 0.02
29 1 0.02
30 18 0.33
ACGTcount: A:0.28, C:0.41, G:0.19, T:0.13
Consensus pattern (23 bp):
TCGCGCTAACACACAACACGCCG
Found at i:1092630 original size:31 final size:31
Alignment explanation
Indices: 1092592--1092709 Score: 144
Period size: 31 Copynumber: 4.1 Consensus size: 31
1092582 CGCGCTAACA
1092592 CACAACACGCCGTCGCGCTAACGCAACTTTG
1 CACAACACGCCGTCGCGCTAACGCAACTTTG
*
1092623 CACAACACGCCGTCGCACTAA--C-A-----
1 CACAACACGCCGTCGCGCTAACGCAACTTTG
* *
1092646 CACAACACGCCGTCGCGCTAGCACAACTTTG
1 CACAACACGCCGTCGCGCTAACGCAACTTTG
*
1092677 CATAACACGCCGTCGCGCTAACGCAACTTTG
1 CACAACACGCCGTCGCGCTAACGCAACTTTG
1092708 CA
1 CA
1092710 AGTTTCACAG
Statistics
Matches: 73, Mismatches: 6, Indels: 16
0.77 0.06 0.17
Matches are distributed among these distances:
23 19 0.26
25 1 0.01
26 1 0.01
28 1 0.01
29 1 0.01
31 50 0.68
ACGTcount: A:0.28, C:0.39, G:0.18, T:0.15
Consensus pattern (31 bp):
CACAACACGCCGTCGCGCTAACGCAACTTTG
Found at i:1092649 original size:23 final size:23
Alignment explanation
Indices: 1092623--1092670 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
1092613 CGCAACTTTG
1092623 CACAACACGCCGTCGCACTAACA
1 CACAACACGCCGTCGCACTAACA
* *
1092646 CACAACACGCCGTCGCGCTAGCA
1 CACAACACGCCGTCGCACTAACA
1092669 CA
1 CA
1092671 ACTTTGCATA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.31, C:0.44, G:0.17, T:0.08
Consensus pattern (23 bp):
CACAACACGCCGTCGCACTAACA
Found at i:1092654 original size:54 final size:53
Alignment explanation
Indices: 1092528--1092698 Score: 297
Period size: 54 Copynumber: 3.2 Consensus size: 53
1092518 AAACGAGACA
1092528 TCGCGCTAACACACAACACGCCGTCGCGCTAACGCAACTTTGCAAACACGCCG
1 TCGCGCTAACACACAACACGCCGTCGCGCTAACGCAACTTTGCAAACACGCCG
1092581 TCGCGCTAACACACAACACGCCGTCGCGCTAACGCAACTTTGCACAACACGCCG
1 TCGCGCTAACACACAACACGCCGTCGCGCTAACGCAACTTTGCA-AACACGCCG
* * *
1092635 TCGCACTAACACACAACACGCCGTCGCGCTAGCACAACTTTGCATAACACGCCG
1 TCGCGCTAACACACAACACGCCGTCGCGCTAACGCAACTTTGCA-AACACGCCG
1092689 TCGCGCTAAC
1 TCGCGCTAAC
1092699 GCAACTTTGC
Statistics
Matches: 112, Mismatches: 5, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
53 44 0.39
54 68 0.61
ACGTcount: A:0.28, C:0.40, G:0.18, T:0.14
Consensus pattern (53 bp):
TCGCGCTAACACACAACACGCCGTCGCGCTAACGCAACTTTGCAAACACGCCG
Found at i:1093805 original size:31 final size:31
Alignment explanation
Indices: 1093767--1093879 Score: 154
Period size: 31 Copynumber: 3.9 Consensus size: 31
1093757 GAAACTTGCT
*
1093767 AAGTTGCGTTGGCGCGACGGCGTGTTGTGCA
1 AAGTTGCGTTAGCGCGACGGCGTGTTGTGCA
1093798 AAGTTGCGTTAGCGCGACGGCGTGTTGT---
1 AAGTTGCGTTAGCGCGACGGCGTGTTGTGCA
1093826 --G-T--GTTAGCGCGACGGCGTGTT-TGCA
1 AAGTTGCGTTAGCGCGACGGCGTGTTGTGCA
1093851 AAGTTGCGTTAGCGCGACGGCGTGTTGTG
1 AAGTTGCGTTAGCGCGACGGCGTGTTGTG
1093880 TGTTAGCGCG
Statistics
Matches: 72, Mismatches: 1, Indels: 18
0.79 0.01 0.20
Matches are distributed among these distances:
22 1 0.01
23 19 0.26
25 1 0.01
26 1 0.01
27 1 0.01
28 1 0.01
30 19 0.26
31 29 0.40
ACGTcount: A:0.13, C:0.19, G:0.41, T:0.27
Consensus pattern (31 bp):
AAGTTGCGTTAGCGCGACGGCGTGTTGTGCA
Found at i:1093831 original size:23 final size:23
Alignment explanation
Indices: 1093805--1093890 Score: 100
Period size: 23 Copynumber: 3.4 Consensus size: 23
1093795 GCAAAGTTGC
1093805 GTTAGCGCGACGGCGTGTTGTGT
1 GTTAGCGCGACGGCGTGTTGTGT
*
1093828 GTTAGCGCGACGGCGTGTTTGCAAAGTTGC
1 GTTAGCGCGACGGCGTG-TT-----G-TGT
1093858 GTTAGCGCGACGGCGTGTTGTGT
1 GTTAGCGCGACGGCGTGTTGTGT
1093881 GTTAGCGCGA
1 GTTAGCGCGA
1093891 TGTCTCGTTT
Statistics
Matches: 54, Mismatches: 2, Indels: 14
0.77 0.03 0.20
Matches are distributed among these distances:
23 29 0.54
24 3 0.06
29 3 0.06
30 19 0.35
ACGTcount: A:0.13, C:0.19, G:0.41, T:0.28
Consensus pattern (23 bp):
GTTAGCGCGACGGCGTGTTGTGT
Found at i:1093861 original size:53 final size:54
Alignment explanation
Indices: 1093778--1093890 Score: 219
Period size: 53 Copynumber: 2.1 Consensus size: 54
1093768 AGTTGCGTTG
1093778 GCGCGACGGCGTGTTGTGCAAAGTTGCGTTAGCGCGACGGCGTGTTGTGTGTTA
1 GCGCGACGGCGTGTTGTGCAAAGTTGCGTTAGCGCGACGGCGTGTTGTGTGTTA
1093832 GCGCGACGGCGTGTT-TGCAAAGTTGCGTTAGCGCGACGGCGTGTTGTGTGTTA
1 GCGCGACGGCGTGTTGTGCAAAGTTGCGTTAGCGCGACGGCGTGTTGTGTGTTA
1093885 GCGCGA
1 GCGCGA
1093891 TGTCTCGTTT
Statistics
Matches: 59, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
53 44 0.75
54 15 0.25
ACGTcount: A:0.13, C:0.19, G:0.41, T:0.27
Consensus pattern (54 bp):
GCGCGACGGCGTGTTGTGCAAAGTTGCGTTAGCGCGACGGCGTGTTGTGTGTTA
Found at i:1094589 original size:14 final size:14
Alignment explanation
Indices: 1094572--1094598 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1094562 GAAGATTGTA
1094572 TTTGAGTTTTAAAT
1 TTTGAGTTTTAAAT
1094586 TTTGAGTTTTAAA
1 TTTGAGTTTTAAA
1094599 ATTCAATATA
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:0.30, C:0.00, G:0.15, T:0.56
Consensus pattern (14 bp):
TTTGAGTTTTAAAT
Found at i:1098925 original size:11 final size:10
Alignment explanation
Indices: 1098890--1098925 Score: 54
Period size: 11 Copynumber: 3.4 Consensus size: 10
1098880 GTCAACTTAT
1098890 GACAAAAACG
1 GACAAAAACG
1098900 GACCAAAAACG
1 GA-CAAAAACG
1098911 GACAATAAACG
1 GACAA-AAACG
1098922 GACA
1 GACA
1098926 CACATTTGGA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 5 0.21
11 19 0.79
ACGTcount: A:0.56, C:0.22, G:0.19, T:0.03
Consensus pattern (10 bp):
GACAAAAACG
Found at i:1101566 original size:7 final size:7
Alignment explanation
Indices: 1101554--1101620 Score: 89
Period size: 7 Copynumber: 9.6 Consensus size: 7
1101544 GAGAAGGATC
1101554 ATTCGAG
1 ATTCGAG
1101561 ATTCGAG
1 ATTCGAG
*
1101568 ATTCGAA
1 ATTCGAG
*
1101575 ATACGAG
1 ATTCGAG
*
1101582 ATTCGAA
1 ATTCGAG
*
1101589 ATACGAG
1 ATTCGAG
1101596 ATTCGAG
1 ATTCGAG
*
1101603 ATTCGAA
1 ATTCGAG
1101610 ATTCGAG
1 ATTCGAG
1101617 ATTC
1 ATTC
1101621 AATATCTAAA
Statistics
Matches: 50, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
7 50 1.00
ACGTcount: A:0.36, C:0.15, G:0.22, T:0.27
Consensus pattern (7 bp):
ATTCGAG
Found at i:1102709 original size:7 final size:7
Alignment explanation
Indices: 1102694--1102760 Score: 89
Period size: 7 Copynumber: 9.6 Consensus size: 7
1102684 TTTAGATATT
1102694 GAATCTC
1 GAATCTC
*
1102701 GAATTTC
1 GAATCTC
1102708 GAATCTC
1 GAATCTC
1102715 GAATCTC
1 GAATCTC
* *
1102722 GTATTTC
1 GAATCTC
1102729 GAATCTC
1 GAATCTC
* *
1102736 GTATTTC
1 GAATCTC
1102743 GAATCTC
1 GAATCTC
1102750 GAATCTC
1 GAATCTC
1102757 GAAT
1 GAAT
1102761 GATCCTTCTC
Statistics
Matches: 50, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
7 50 1.00
ACGTcount: A:0.27, C:0.22, G:0.15, T:0.36
Consensus pattern (7 bp):
GAATCTC
Found at i:1102719 original size:21 final size:21
Alignment explanation
Indices: 1102694--1102760 Score: 98
Period size: 21 Copynumber: 3.2 Consensus size: 21
1102684 TTTAGATATT
1102694 GAATCTCGAATTTCGAATCTC
1 GAATCTCGAATTTCGAATCTC
*
1102715 GAATCTCGTATTTCGAATCTC
1 GAATCTCGAATTTCGAATCTC
* * *
1102736 GTATTTCGAATCTCGAATCTC
1 GAATCTCGAATTTCGAATCTC
1102757 GAAT
1 GAAT
1102761 GATCCTTCTC
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.27, C:0.22, G:0.15, T:0.36
Consensus pattern (21 bp):
GAATCTCGAATTTCGAATCTC
Found at i:1107430 original size:2 final size:2
Alignment explanation
Indices: 1107423--1107469 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
1107413 ATAAGTCAAT
*
1107423 AG AG AG AG AA AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1107465 AG AG A
1 AG AG A
1107470 ACATTTCCAA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1115433 original size:54 final size:54
Alignment explanation
Indices: 1115364--1115641 Score: 285
Period size: 54 Copynumber: 5.1 Consensus size: 54
1115354 TGGAAGTCTG
* * *
1115364 TATCCTTATGGAAACCAGCTTCAATATGGAAACCAAAATCCTTATGGTAGCCAA
1 TATCCATATGGAAACCAGCTTCCATATGGAAACCAATATCCTTATGGTAGCCAA
*
1115418 TATCCATATGGAAACCAGCTTCAATATGGAAACCAATATCCTTATGGTAGCCAA
1 TATCCATATGGAAACCAGCTTCCATATGGAAACCAATATCCTTATGGTAGCCAA
* * * ** * * * *
1115472 TATCAATATGGAAACCAGTTTCCCTATGGAAGTCAATACCCATATGGAAACCAA
1 TATCCATATGGAAACCAGCTTCCATATGGAAACCAATATCCTTATGGTAGCCAA
*** * *
1115526 TA-CCAGT-TAGGAAACCAAAATCCTTATGGAAACCAATATCCTTATGGTAGCCAG
1 TATCCA-TAT-GGAAACCAGCTTCCATATGGAAACCAATATCCTTATGGTAGCCAA
* * * * *
1115580 TATCCTTATGGAAACCAG-TTCCCCTATGGAAATCAATATCCATATGGAAGCCAA
1 TATCCATATGGAAACCAGCTT-CCATATGGAAACCAATATCCTTATGGTAGCCAA
1115634 -AGTCCATA
1 TA-TCCATA
1115642 CACTTTGGGA
Statistics
Matches: 185, Mismatches: 33, Indels: 12
0.80 0.14 0.05
Matches are distributed among these distances:
53 5 0.03
54 177 0.96
55 3 0.02
ACGTcount: A:0.37, C:0.23, G:0.15, T:0.25
Consensus pattern (54 bp):
TATCCATATGGAAACCAGCTTCCATATGGAAACCAATATCCTTATGGTAGCCAA
Found at i:1115526 original size:18 final size:18
Alignment explanation
Indices: 1115364--1115633 Score: 190
Period size: 18 Copynumber: 15.0 Consensus size: 18
1115354 TGGAAGTCTG
* *
1115364 TATCCTTATGGAAACCAGC
1 TATCCATATGGAAACCA-A
*
1115383 T-TCAATATGGAAACCAA
1 TATCCATATGGAAACCAA
* * * *
1115400 AATCCTTATGGTAGCCAA
1 TATCCATATGGAAACCAA
*
1115418 TATCCATATGGAAACCAGC
1 TATCCATATGGAAACCA-A
*
1115437 T-TCAATATGGAAACCAA
1 TATCCATATGGAAACCAA
* * *
1115454 TATCCTTATGGTAGCCAA
1 TATCCATATGGAAACCAA
* *
1115472 TATCAATATGGAAACCAG
1 TATCCATATGGAAACCAA
* * **
1115490 TTTCCCTATGGAAGTCAA
1 TATCCATATGGAAACCAA
*
1115508 TACCCATATGGAAACCAA
1 TATCCATATGGAAACCAA
1115526 TA-CCAGT-TAGGAAACCAA
1 TATCCA-TAT-GGAAACCAA
* *
1115544 AATCCTTATGGAAACCAA
1 TATCCATATGGAAACCAA
* * * *
1115562 TATCCTTATGGTAGCCAG
1 TATCCATATGGAAACCAA
* *
1115580 TATCCTTATGGAAACCAG
1 TATCCATATGGAAACCAA
* *
1115598 T-TCCCCTATGGAAATCAA
1 TAT-CCATATGGAAACCAA
*
1115616 TATCCATATGGAAGCCAA
1 TATCCATATGGAAACCAA
1115634 AGTCCATACA
Statistics
Matches: 193, Mismatches: 49, Indels: 19
0.74 0.19 0.07
Matches are distributed among these distances:
17 6 0.03
18 181 0.94
19 6 0.03
ACGTcount: A:0.37, C:0.23, G:0.15, T:0.25
Consensus pattern (18 bp):
TATCCATATGGAAACCAA
Found at i:1115703 original size:33 final size:33
Alignment explanation
Indices: 1115661--1115762 Score: 143
Period size: 33 Copynumber: 3.1 Consensus size: 33
1115651 AGGTGGTGTG
1115661 TTAGGAGGACCTTTCTCCGGAGTAGGATCTGGT
1 TTAGGAGGACCTTTCTCCGGAGTAGGATCTGGT
* * *
1115694 TTAGGAGGACC-TTCATCTGGAGTAGGATTTGGC
1 TTAGGAGGACCTTTC-TCCGGAGTAGGATCTGGT
* *
1115727 TTAGGAGAACCTTTGTCCGGAGTAGGATCTGGT
1 TTAGGAGGACCTTTCTCCGGAGTAGGATCTGGT
1115760 TTA
1 TTA
1115763 CAAGGATTGG
Statistics
Matches: 59, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
32 3 0.05
33 54 0.92
34 2 0.03
ACGTcount: A:0.21, C:0.16, G:0.32, T:0.31
Consensus pattern (33 bp):
TTAGGAGGACCTTTCTCCGGAGTAGGATCTGGT
Found at i:1121597 original size:4 final size:4
Alignment explanation
Indices: 1121590--1121644 Score: 110
Period size: 4 Copynumber: 13.8 Consensus size: 4
1121580 TGTATTTATT
1121590 TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC
1 TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC
1121638 TATC TAT
1 TATC TAT
1121645 ATGACTATTT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 51 1.00
ACGTcount: A:0.25, C:0.24, G:0.00, T:0.51
Consensus pattern (4 bp):
TATC
Found at i:1122832 original size:27 final size:26
Alignment explanation
Indices: 1122802--1123215 Score: 272
Period size: 27 Copynumber: 15.2 Consensus size: 26
1122792 ACGAGTAGCT
*
1122802 TCCATATCCGCTACCAATTGGGTTGTA
1 TCCATAACCGCTACCAA-TGGGTTGTA
* * *** *
1122829 TCCATATCCACTGTTTAATGGGTTATA
1 TCCATAACCGCT-ACCAATGGGTTGTA
* * *
1122856 TCCATATCCGCTACTCAATTGATTGTA
1 TCCATAACCGCTAC-CAATGGGTTGTA
*
1122883 TCCATAACCGCTACTCAATGGGTTGAA
1 TCCATAACCGCTAC-CAATGGGTTGTA
* * * *
1122910 TCTATAACCGTTAATCAATGGATTGTA
1 TCCATAACCGCT-ACCAATGGGTTGTA
* *
1122937 TCCATAACCACTACTCAATGGATTGTA
1 TCCATAACCGCTAC-CAATGGGTTGTA
* *
1122964 TCCATATCCGCTACTCAGTGGGTTGTA
1 TCCATAACCGCTAC-CAATGGGTTGTA
** * *
1122991 TCCATAACCGCTATTGAATTGATTGTA
1 TCCATAACCGCTA-CCAATGGGTTGTA
* * *
1123018 TCCATATCCGCTACTCAGTGGGTTGAA
1 TCCATAACCGCTAC-CAATGGGTTGTA
** * * *
1123045 TCCATAACCGCTATTGAATTGATTATA
1 TCCATAACCGCTA-CCAATGGGTTGTA
* * *
1123072 TCCATATCCGCTACTCAGTGGGTTATA
1 TCCATAACCGCTAC-CAATGGGTTGTA
* *
1123099 TCCATAACCACTACCTAATGGATTGTA
1 TCCATAACCGCTACC-AATGGGTTGTA
* *
1123126 TCCATAACCGCTACTCAGTGGGTTATTATA
1 TCCATAACCGCTAC-CAATGGG---TTGTA
1123156 TCCATAACCGCTACCTAA-GTGGTTGTA
1 TCCATAACCGCTACC-AATG-GGTTGTA
* ** *
1123183 TCCATAACCGGTATTGAATTGGTTGTA
1 TCCATAACCGCTA-CCAATGGGTTGTA
1123210 TCCATA
1 TCCATA
1123216 TCCAAGGTAA
Statistics
Matches: 299, Mismatches: 71, Indels: 34
0.74 0.18 0.08
Matches are distributed among these distances:
26 2 0.01
27 270 0.90
28 4 0.01
29 2 0.01
30 21 0.07
ACGTcount: A:0.27, C:0.23, G:0.16, T:0.34
Consensus pattern (26 bp):
TCCATAACCGCTACCAATGGGTTGTA
Found at i:1123150 original size:54 final size:54
Alignment explanation
Indices: 1122802--1123215 Score: 395
Period size: 54 Copynumber: 7.6 Consensus size: 54
1122792 ACGAGTAGCT
* * * ** * * *
1122802 TCCATATCCGCTAC-CAATTGGGTTGTATCCATATCCACTGTTTAATGGGTTATA
1 TCCATATCCGCTACTC-AGTGGGTTGTATCCATAACCGCTACTCAATGGATTGTA
* * * * *
1122856 TCCATATCCGCTACTCAATTGATTGTATCCATAACCGCTACTCAATGGGTTGAA
1 TCCATATCCGCTACTCAGTGGGTTGTATCCATAACCGCTACTCAATGGATTGTA
* * * * * * *
1122910 TCTATAACCGTTAATCAATGGATTGTATCCATAACCACTACTCAATGGATTGTA
1 TCCATATCCGCTACTCAGTGGGTTGTATCCATAACCGCTACTCAATGGATTGTA
* * *
1122964 TCCATATCCGCTACTCAGTGGGTTGTATCCATAACCGCTATTGAATTGATTGTA
1 TCCATATCCGCTACTCAGTGGGTTGTATCCATAACCGCTACTCAATGGATTGTA
* * * * *
1123018 TCCATATCCGCTACTCAGTGGGTTGAATCCATAACCGCTATTGAATTGATTATA
1 TCCATATCCGCTACTCAGTGGGTTGTATCCATAACCGCTACTCAATGGATTGTA
* *
1123072 TCCATATCCGCTACTCAGTGGGTTATATCCATAACCACTAC-CTAATGGATTGTA
1 TCCATATCCGCTACTCAGTGGGTTGTATCCATAACCGCTACTC-AATGGATTGTA
* *
1123126 TCCATAACCGCTACTCAGTGGGTTATTATATCCATAACCGCTAC-CTAAGTGG-TTGTA
1 TCCATATCCGCTACTCAGTGGG---TTGTATCCATAACCGCTACTC-AA-TGGATTGTA
* * * * * *
1123183 TCCATAACCGGTATTGAATTGGTTGTATCCATA
1 TCCATATCCGCTACTCAGTGGGTTGTATCCATA
1123216 TCCAAGGTAA
Statistics
Matches: 309, Mismatches: 45, Indels: 12
0.84 0.12 0.03
Matches are distributed among these distances:
54 261 0.84
55 1 0.00
57 44 0.14
58 3 0.01
ACGTcount: A:0.27, C:0.23, G:0.16, T:0.34
Consensus pattern (54 bp):
TCCATATCCGCTACTCAGTGGGTTGTATCCATAACCGCTACTCAATGGATTGTA
Found at i:1123972 original size:21 final size:23
Alignment explanation
Indices: 1123948--1123990 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
1123938 GTAGAATCTT
1123948 ATTTCG-TGATAAAAAA-AAATC
1 ATTTCGTTGATAAAAAATAAATC
*
1123969 ATTTCGTTTATAAAAAATAAAT
1 ATTTCGTTGATAAAAAATAAAT
1123991 GAATAAATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 6 0.32
22 9 0.47
23 4 0.21
ACGTcount: A:0.51, C:0.07, G:0.07, T:0.35
Consensus pattern (23 bp):
ATTTCGTTGATAAAAAATAAATC
Found at i:1131500 original size:18 final size:18
Alignment explanation
Indices: 1131477--1131514 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
1131467 CACTGTAGTA
1131477 GTTGTTCAATCCATATCC
1 GTTGTTCAATCCATATCC
1131495 GTTGTTCAATCCATATCC
1 GTTGTTCAATCCATATCC
1131513 GT
1 GT
1131515 ATGGGTTGTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.21, C:0.26, G:0.13, T:0.39
Consensus pattern (18 bp):
GTTGTTCAATCCATATCC
Found at i:1133645 original size:6 final size:6
Alignment explanation
Indices: 1133634--1133684 Score: 66
Period size: 6 Copynumber: 8.5 Consensus size: 6
1133624 GTTATTCAGA
* * * *
1133634 CCATAT CCATAT CCTTGT CCATAT CCATAT CCTTGT CCATAT CCATAT
1 CCATAT CCATAT CCATAT CCATAT CCATAT CCATAT CCATAT CCATAT
1133682 CCA
1 CCA
1133685 GTTCCTCCGT
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
6 37 1.00
ACGTcount: A:0.25, C:0.35, G:0.04, T:0.35
Consensus pattern (6 bp):
CCATAT
Found at i:1133655 original size:18 final size:18
Alignment explanation
Indices: 1133634--1133683 Score: 100
Period size: 18 Copynumber: 2.8 Consensus size: 18
1133624 GTTATTCAGA
1133634 CCATATCCATATCCTTGT
1 CCATATCCATATCCTTGT
1133652 CCATATCCATATCCTTGT
1 CCATATCCATATCCTTGT
1133670 CCATATCCATATCC
1 CCATATCCATATCC
1133684 AGTTCCTCCG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.24, C:0.36, G:0.04, T:0.36
Consensus pattern (18 bp):
CCATATCCATATCCTTGT
Found at i:1137891 original size:2 final size:2
Alignment explanation
Indices: 1137886--1137915 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1137876 AGTGTACTAT
1137886 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1137916 CTGTATTGAT
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:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1139909 original size:1 final size:1
Alignment explanation
Indices: 1139903--1139933 Score: 62
Period size: 1 Copynumber: 31.0 Consensus size: 1
1139893 GTTTTAATTT
1139903 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1139934 GATAATAAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:1141775 original size:4 final size:4
Alignment explanation
Indices: 1141756--1141815 Score: 70
Period size: 4 Copynumber: 15.5 Consensus size: 4
1141746 AAATAGATTG
* * * *
1141756 AATA AA-A AA-A AGTA AATA AATA AATA AAAA AATA AATA GATA AATT
1 AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA
1141802 AATA AATA AATA AA
1 AATA AATA AATA AA
1141816 AAAAAACAGT
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
3 5 0.11
4 42 0.89
ACGTcount: A:0.75, C:0.00, G:0.03, T:0.22
Consensus pattern (4 bp):
AATA
Found at i:1142113 original size:11 final size:11
Alignment explanation
Indices: 1142097--1142148 Score: 50
Period size: 11 Copynumber: 4.7 Consensus size: 11
1142087 GCACGCTGAT
1142097 AGAACGGTGAA
1 AGAACGGTGAA
* *
1142108 AGAACGGTTAG
1 AGAACGGTGAA
* * * *
1142119 CGCACGCTGAG
1 AGAACGGTGAA
1142130 AGAACGGTGAA
1 AGAACGGTGAA
1142141 AGAACGGT
1 AGAACGGT
1142149 TAGCACACGC
Statistics
Matches: 31, Mismatches: 10, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
11 31 1.00
ACGTcount: A:0.37, C:0.15, G:0.37, T:0.12
Consensus pattern (11 bp):
AGAACGGTGAA
Found at i:1142113 original size:33 final size:33
Alignment explanation
Indices: 1142076--1142194 Score: 184
Period size: 33 Copynumber: 3.6 Consensus size: 33
1142066 TTTCCGTATT
* *
1142076 GAACGGTGAGCGCACGCTGATAGAACGGTGAAA
1 GAACGGTTAGCGCACGCTGAGAGAACGGTGAAA
1142109 GAACGGTTAGCGCACGCTGAGAGAACGGTGAAA
1 GAACGGTTAGCGCACGCTGAGAGAACGGTGAAA
* * *
1142142 GAACGGTTAGCACACGCTGAGCGAACGGTGAGA
1 GAACGGTTAGCGCACGCTGAGAGAACGGTGAAA
*
1142175 TAACGGTTAGCGCACGCTGA
1 GAACGGTTAGCGCACGCTGA
1142195 ACGGAATTCG
Statistics
Matches: 79, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 79 1.00
ACGTcount: A:0.31, C:0.20, G:0.35, T:0.13
Consensus pattern (33 bp):
GAACGGTTAGCGCACGCTGAGAGAACGGTGAAA
Found at i:1142186 original size:22 final size:22
Alignment explanation
Indices: 1142098--1142186 Score: 63
Period size: 22 Copynumber: 4.0 Consensus size: 22
1142088 CACGCTGATA
* *
1142098 GAACGGTGAAAGAACGGTTAGC
1 GAACGGTGAGAGAACGGTGAGC
* * **
1142120 GCACGCTGAGAGAACGGTGAAA
1 GAACGGTGAGAGAACGGTGAGC
* * *
1142142 GAACGGTTAGCA-CACGCTGAGC
1 GAACGGTGAG-AGAACGGTGAGC
* *
1142164 GAACGGTGAGATAACGGTTAGC
1 GAACGGTGAGAGAACGGTGAGC
1142186 G
1 G
1142187 CACGCTGAAC
Statistics
Matches: 48, Mismatches: 17, Indels: 4
0.70 0.25 0.06
Matches are distributed among these distances:
21 1 0.02
22 46 0.96
23 1 0.02
ACGTcount: A:0.33, C:0.18, G:0.36, T:0.13
Consensus pattern (22 bp):
GAACGGTGAGAGAACGGTGAGC
Found at i:1154253 original size:9 final size:9
Alignment explanation
Indices: 1154222--1154264 Score: 59
Period size: 9 Copynumber: 4.8 Consensus size: 9
1154212 TCATAACGCC
1154222 TGTTGTAAT
1 TGTTGTAAT
**
1154231 CATTGTAAT
1 TGTTGTAAT
*
1154240 CGTTGTAAT
1 TGTTGTAAT
1154249 TGTTGTAAT
1 TGTTGTAAT
1154258 TGTTGTA
1 TGTTGTA
1154265 GCGGCTATTA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 30 1.00
ACGTcount: A:0.23, C:0.05, G:0.21, T:0.51
Consensus pattern (9 bp):
TGTTGTAAT
Found at i:1155072 original size:140 final size:146
Alignment explanation
Indices: 1154811--1155237 Score: 473
Period size: 140 Copynumber: 3.0 Consensus size: 146
1154801 ATGTTTAGTC
* * * * * * * *
1154811 TAGTATGATTTAATTTAGTTATCAGTGTTACATCTAAAGTTTCTTGTGATCCCT-A-TTTTTTG-
1 TAGTATAATTTAATTTAGTTATTAGCGTTTCATCTAGAGTGTCTTGTGATCACTAACTTATTTGA
* * *
1154873 -TTAGAT-TAAAAAAAAGATTGAGGCAAAACTACGTATATTTCTGTTTTACATACACCCAAGTCC
66 ATTATATATAAAAAAAAG-TGGAGGCAAAACTACGTATATTTCTGTTTTAC-TACATCCAAGTCC
*
1154936 TAGCCGATCATTTAATTT
129 TAGCCGATCATTTAAGTT
* * * *
1154954 TAGTTTGATTTAATTTAGTTATTTGCGTTTCATCTAGAGTGTCTTTTGATCACT-AC-TATTTG-
1 TAGTATAATTTAATTTAGTTATTAGCGTTTCATCTAGAGTGTCTTGTGATCACTAACTTATTTGA
** * * *
1155016 A-TAT-TA-CCAAAACA-TGGAGGCAAAACTACCTATATTTCTGTTTTACTGACATCCAAGCCCT
66 ATTATATATAAAAAAAAGTGGAGGCAAAACTACGTATATTTCTGTTTTACT-ACATCCAAGTCCT
*
1155077 AGCTGATCATTTAAGTT
130 AGCCGATCATTTAAGTT
* *
1155094 TAGTATAATTTAATTTAGTTATTAGCGTTTCATCTAGCGTGTCTTGTGATCACTACACTTTTTTG
1 TAGTATAATTTAATTTAGTTATTAGCGTTTCATCTAGAGTGTCTTGTGATCACTA-ACTTATTTG
* *
1155159 ATATTATATATAAAAAAAAGTTTGTGGCAAAACTACGTATATTTCTGTTTTACTTACATCCAAGT
65 A-ATTATATATAAAAAAAAG-TGGAGGCAAAACTACGTATATTTCTGTTTTAC-TACATCCAAGT
1155224 CCTAGCCGATCATT
127 CCTAGCCGATCATT
1155238 GTAGTCGTCG
Statistics
Matches: 235, Mismatches: 34, Indels: 23
0.80 0.12 0.08
Matches are distributed among these distances:
139 1 0.00
140 105 0.45
142 8 0.03
143 58 0.25
145 1 0.00
146 3 0.01
147 2 0.01
148 5 0.02
150 51 0.22
151 1 0.00
ACGTcount: A:0.30, C:0.16, G:0.14, T:0.41
Consensus pattern (146 bp):
TAGTATAATTTAATTTAGTTATTAGCGTTTCATCTAGAGTGTCTTGTGATCACTAACTTATTTGA
ATTATATATAAAAAAAAGTGGAGGCAAAACTACGTATATTTCTGTTTTACTACATCCAAGTCCTA
GCCGATCATTTAAGTT
Found at i:1159275 original size:21 final size:21
Alignment explanation
Indices: 1159251--1159347 Score: 117
Period size: 21 Copynumber: 4.7 Consensus size: 21
1159241 CATAGCATAG
1159251 CATAGCATAGCATTGAAATCT
1 CATAGCATAGCATTGAAATCT
*
1159272 CATAGCATTGCATTGAAATCT
1 CATAGCATAGCATTGAAATCT
* *
1159293 CATAGCATACCATTGGAATCT
1 CATAGCATAGCATTGAAATCT
*
1159314 CATACCATAGCA-T-ACAATCT
1 CATAGCATAGCATTGA-AATCT
* *
1159334 CATAGAATCGCATT
1 CATAGCATAGCATT
1159348 CGTCATATCA
Statistics
Matches: 64, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
20 15 0.23
21 49 0.77
ACGTcount: A:0.36, C:0.23, G:0.12, T:0.29
Consensus pattern (21 bp):
CATAGCATAGCATTGAAATCT
Found at i:1159298 original size:42 final size:41
Alignment explanation
Indices: 1159251--1159384 Score: 126
Period size: 42 Copynumber: 3.2 Consensus size: 41
1159241 CATAGCATAG
* *
1159251 CATAGCATAGCATTGAAATCTCATAGCATTGCATTGA-AATCT
1 CATAGCATAGCATTGAAATCTCATACCATAGCA-T-ACAATCT
* *
1159293 CATAGCATACCATTGGAATCTCATACCATAGCATACAATCT
1 CATAGCATAGCATTGAAATCTCATACCATAGCATACAATCT
* * ** * * **
1159334 CATAGAATCGCATTCGTCATATCATACCATAGCATACCATAG
1 CATAGCATAGCATT-GAAATCTCATACCATAGCATACAATCT
1159376 CATAGCATA
1 CATAGCATA
1159385 CAACATTTTT
Statistics
Matches: 75, Mismatches: 15, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
40 1 0.01
41 17 0.23
42 57 0.76
ACGTcount: A:0.37, C:0.24, G:0.12, T:0.28
Consensus pattern (41 bp):
CATAGCATAGCATTGAAATCTCATACCATAGCATACAATCT
Found at i:1159369 original size:10 final size:10
Alignment explanation
Indices: 1159351--1159384 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
1159341 TCGCATTCGT
*
1159351 CATATCATAC
1 CATAGCATAC
1159361 CATAGCATAC
1 CATAGCATAC
*
1159371 CATAGCATAG
1 CATAGCATAC
1159381 CATA
1 CATA
1159385 CAACATTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.41, C:0.26, G:0.09, T:0.24
Consensus pattern (10 bp):
CATAGCATAC
Found at i:1159374 original size:15 final size:15
Alignment explanation
Indices: 1159351--1159385 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
1159341 TCGCATTCGT
*
1159351 CATATCATACCATAG
1 CATACCATACCATAG
*
1159366 CATACCATAGCATAG
1 CATACCATACCATAG
1159381 CATAC
1 CATAC
1159386 AACATTTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.40, C:0.29, G:0.09, T:0.23
Consensus pattern (15 bp):
CATACCATACCATAG
Found at i:1159610 original size:21 final size:21
Alignment explanation
Indices: 1159586--1159665 Score: 81
Period size: 21 Copynumber: 3.8 Consensus size: 21
1159576 CATTTCAATT
*
1159586 TCTCATATCATAGCATACAAA
1 TCTCATAGCATAGCATACAAA
* *
1159607 TCTCGTAGCAAAGCATACAAA
1 TCTCATAGCATAGCATACAAA
* *
1159628 TCTCATAGCCTATCATTA-AAA
1 TCTCATAGCATAGCA-TACAAA
* *
1159649 TCGCATACCATAGCATA
1 TCTCATAGCATAGCATA
1159666 GCATAAATTT
Statistics
Matches: 47, Mismatches: 11, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
20 2 0.04
21 43 0.91
22 2 0.04
ACGTcount: A:0.40, C:0.25, G:0.09, T:0.26
Consensus pattern (21 bp):
TCTCATAGCATAGCATACAAA
Found at i:1160166 original size:11 final size:11
Alignment explanation
Indices: 1160150--1160175 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
1160140 ATAGATAAGA
1160150 ATACGAAGACC
1 ATACGAAGACC
1160161 ATACGAAGACC
1 ATACGAAGACC
1160172 ATAC
1 ATAC
1160176 TTTCATGTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.46, C:0.27, G:0.15, T:0.12
Consensus pattern (11 bp):
ATACGAAGACC
Found at i:1164108 original size:12 final size:12
Alignment explanation
Indices: 1164091--1164115 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1164081 CGTTTCAGAT
1164091 GTAATTGTTATA
1 GTAATTGTTATA
1164103 GTAATTGTTATA
1 GTAATTGTTATA
1164115 G
1 G
1164116 CCTCCGCTAA
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:0.32, C:0.00, G:0.20, T:0.48
Consensus pattern (12 bp):
GTAATTGTTATA
Found at i:1168389 original size:11 final size:11
Alignment explanation
Indices: 1168363--1168407 Score: 56
Period size: 11 Copynumber: 3.9 Consensus size: 11
1168353 ACTAAACCCT
1168363 GGGTTTACTTTTG
1 GGGTTTAC--TTG
1168376 GGGTTTACTTG
1 GGGTTTACTTG
1168387 GGGTTTACTCT-
1 GGGTTTACT-TG
1168398 GGGTTTACTT
1 GGGTTTACTT
1168408 TTAGAAAATT
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
10 1 0.03
11 21 0.68
12 1 0.03
13 8 0.26
ACGTcount: A:0.09, C:0.11, G:0.31, T:0.49
Consensus pattern (11 bp):
GGGTTTACTTG
Found at i:1179976 original size:11 final size:11
Alignment explanation
Indices: 1179960--1179998 Score: 60
Period size: 11 Copynumber: 3.5 Consensus size: 11
1179950 CATTCAGTCA
1179960 ACTGAAAGGTG
1 ACTGAAAGGTG
*
1179971 ACTGAAAGGTA
1 ACTGAAAGGTG
*
1179982 ACTGAAATGTG
1 ACTGAAAGGTG
1179993 ACTGAA
1 ACTGAA
1179999 TGGTAGTTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 25 1.00
ACGTcount: A:0.41, C:0.10, G:0.28, T:0.21
Consensus pattern (11 bp):
ACTGAAAGGTG
Found at i:1179984 original size:22 final size:22
Alignment explanation
Indices: 1179959--1180003 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
1179949 CCATTCAGTC
1179959 AACTGAAAGGTGACTGAAAGGT
1 AACTGAAAGGTGACTGAAAGGT
* *
1179981 AACTGAAATGTGACTGAATGGT
1 AACTGAAAGGTGACTGAAAGGT
1180003 A
1 A
1180004 GTTATGTGCG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.40, C:0.09, G:0.29, T:0.22
Consensus pattern (22 bp):
AACTGAAAGGTGACTGAAAGGT
Found at i:1182857 original size:2 final size:2
Alignment explanation
Indices: 1182850--1182913 Score: 128
Period size: 2 Copynumber: 32.0 Consensus size: 2
1182840 TTCATTACCA
1182850 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1182892 AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG
1182914 NNNNNNNNNN
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 62 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1184513 original size:4 final size:4
Alignment explanation
Indices: 1184500--1184558 Score: 109
Period size: 4 Copynumber: 14.8 Consensus size: 4
1184490 GGATGGATCA
*
1184500 ATAG AAAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
1184548 ATAG ATAG ATA
1 ATAG ATAG ATA
1184559 TTCAAAATCA
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
4 53 1.00
ACGTcount: A:0.53, C:0.00, G:0.24, T:0.24
Consensus pattern (4 bp):
ATAG
Found at i:1185602 original size:2 final size:2
Alignment explanation
Indices: 1185595--1185640 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
1185585 NNNNNNNNNN
1185595 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1185637 CT CT
1 CT CT
1185641 TTTAAAAATG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:1187500 original size:1 final size:1
Alignment explanation
Indices: 1187496--1187535 Score: 62
Period size: 1 Copynumber: 40.0 Consensus size: 1
1187486 CCCCCCCCCC
* *
1187496 AAAAAAAAAAAAAAAAAAAAAAAAAAAAGAAAAAAGAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1187536 TGAGATCTAT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
1 35 1.00
ACGTcount: A:0.95, C:0.00, G:0.05, T:0.00
Consensus pattern (1 bp):
A
Found at i:1190088 original size:16 final size:16
Alignment explanation
Indices: 1190067--1190119 Score: 70
Period size: 16 Copynumber: 3.2 Consensus size: 16
1190057 TCATTTTTCG
1190067 AAAAAAAAAACCAAAA
1 AAAAAAAAAACCAAAA
1190083 AAAAAAAAAACCAAAA
1 AAAAAAAAAACCAAAA
* * *
1190099 CAATAAAACAATCAAAA
1 -AAAAAAAAAACCAAAA
1190116 AAAA
1 AAAA
1190120 GGCTATGTGA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
16 19 0.59
17 13 0.41
ACGTcount: A:0.83, C:0.13, G:0.00, T:0.04
Consensus pattern (16 bp):
AAAAAAAAAACCAAAA
Found at i:1200551 original size:2 final size:2
Alignment explanation
Indices: 1200544--1200602 Score: 118
Period size: 2 Copynumber: 29.5 Consensus size: 2
1200534 NNNNNNNNNN
1200544 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1200586 TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC T
1200603 GTAGACCGAG
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:1206451 original size:2 final size:2
Alignment explanation
Indices: 1206444--1206502 Score: 118
Period size: 2 Copynumber: 29.5 Consensus size: 2
1206434 GCATTGTATT
1206444 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1206486 TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC T
1206503 GTAGACCGAG
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:1208707 original size:65 final size:64
Alignment explanation
Indices: 1208599--1208724 Score: 207
Period size: 65 Copynumber: 2.0 Consensus size: 64
1208589 CACCAAATAT
* * *
1208599 ACATTGCTTTCTAAGTGTCCTTACATTTGCAGTTTATGATAAAAGATAAAGATAATGATAATTA
1 ACATTGCTTTCTAAGTATCCTTACATTTGCAGTTAATGATAAAAGAAAAAGATAATGATAATTA
*
1208663 ACATCTGCTTTCTAAGTATCCTTACATTTGCAGTTAATGCTAAAAGAAAAAGATAATGATAA
1 ACAT-TGCTTTCTAAGTATCCTTACATTTGCAGTTAATGATAAAAGAAAAAGATAATGATAA
1208725 AAAAAAAATC
Statistics
Matches: 57, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
64 4 0.07
65 53 0.93
ACGTcount: A:0.39, C:0.13, G:0.13, T:0.35
Consensus pattern (64 bp):
ACATTGCTTTCTAAGTATCCTTACATTTGCAGTTAATGATAAAAGAAAAAGATAATGATAATTA
Found at i:1208742 original size:65 final size:65
Alignment explanation
Indices: 1208603--1208742 Score: 165
Period size: 65 Copynumber: 2.2 Consensus size: 65
1208593 AAATATACAT
* * * * ** * **
1208603 TGCTTTCTAAGTGTCCTTACATTTGCAGTTTATGATAAAAGATAAAGATAATGATAATTAACATC
1 TGCTATCTAAGTATCCTTACATTTGCAGTTAATGATAAAAGAAAAAGATAATGATAAAAAAAAAA
* *
1208668 TGCTTTCTAAGTATCCTTACATTTGCAGTTAATGCTAAAAGAAAAAGATAATGATAAAAAAAAAA
1 TGCTATCTAAGTATCCTTACATTTGCAGTTAATGATAAAAGAAAAAGATAATGATAAAAAAAAAA
1208733 T-CATATCTAA
1 TGC-TATCTAA
1208743 TATTTTCATT
Statistics
Matches: 64, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
64 1 0.02
65 63 0.98
ACGTcount: A:0.42, C:0.12, G:0.12, T:0.34
Consensus pattern (65 bp):
TGCTATCTAAGTATCCTTACATTTGCAGTTAATGATAAAAGAAAAAGATAATGATAAAAAAAAAA
Found at i:1214027 original size:3 final size:3
Alignment explanation
Indices: 1214019--1214056 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
1214009 TTTGGATATA
1214019 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1214057 GTGTGTTTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Done.