Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold29
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 5511024
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 57772 characters in sequence are not A, C, G, or T
File 17 of 34
Found at i:2529970 original size:97 final size:100
Alignment explanation
Indices: 2529746--2530034 Score: 316
Period size: 101 Copynumber: 2.9 Consensus size: 100
2529736 ACATTGACAC
* * * * * **
2529746 AAGCCCAGTATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTCAGACCGATGTCGTTG
1 AAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCGTCATCTTTAAGACCAATGTCACTG
*
2529811 GCCTTGAATTAGCACATCGGCACCTCAACTATCTTT
66 GCCTTGAATCAGCACATCGGCACCT-AACTATCTTT
*
2529847 AAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCA-CGTCATCTTTAAGTCCAATGTCACTG
1 AAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCGTCATCTTTAAGACCAATGTCACTG
* * *
2529911 GCCTTGAATCAGTACATTGGCACCT-TC-ATCTTT
66 GCCTTGAATCAGCACATCGGCACCTAACTATCTTT
* * * *
2529944 AAGTCCAATATCGCTGGCCCTGAATCAGCATATTGGTGC-CTTCGTCATCTTTAAAACCCAATAT
1 AAGCCCAATATCGCTGGCCTTGAATCAGCATATT-G-GCAC--CGTCATCTTTAAGA-CCAATGT
** * *
2530008 CGTTGGCCTTGAATCAACACATTGGCA
61 CACTGGCCTTGAATCAGCACATCGGCA
2530035 TTCTTCTCAT
Statistics
Matches: 161, Mismatches: 21, Indels: 11
0.83 0.11 0.06
Matches are distributed among these distances:
97 38 0.24
98 2 0.01
99 2 0.01
100 41 0.25
101 49 0.30
102 29 0.18
ACGTcount: A:0.25, C:0.27, G:0.18, T:0.30
Consensus pattern (100 bp):
AAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCGTCATCTTTAAGACCAATGTCACTG
GCCTTGAATCAGCACATCGGCACCTAACTATCTTT
Found at i:2530904 original size:20 final size:20
Alignment explanation
Indices: 2530875--2530926 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
2530865 CCAAGGAAAT
*
2530875 GTATCAATACATTACTCAAC
1 GTATCGATACATTACTCAAC
*
2530895 GTATCGATACATTACTCAAT
1 GTATCGATACATTACTCAAC
2530915 GTATCGATACAT
1 GTATCGATACAT
2530927 GGATCTTTGT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.37, C:0.21, G:0.10, T:0.33
Consensus pattern (20 bp):
GTATCGATACATTACTCAAC
Found at i:2533152 original size:24 final size:25
Alignment explanation
Indices: 2533125--2533176 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 25
2533115 ATCAAAAATT
2533125 CATTCATC-GGGGACACTCCAACCC
1 CATTCATCGGGGGACACTCCAACCC
*
2533149 CATTCCTCGGAGGGGACACTCCAACCC
1 CATTCATC-G-GGGGACACTCCAACCC
2533176 C
1 C
2533177 GTTTTCAACC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
24 7 0.29
27 17 0.71
ACGTcount: A:0.23, C:0.42, G:0.19, T:0.15
Consensus pattern (25 bp):
CATTCATCGGGGGACACTCCAACCC
Found at i:2536015 original size:7 final size:7
Alignment explanation
Indices: 2536003--2536038 Score: 63
Period size: 7 Copynumber: 5.1 Consensus size: 7
2535993 CAACTTTCAC
2536003 ACACTTT
1 ACACTTT
2536010 ACACTTT
1 ACACTTT
2536017 ACACTTT
1 ACACTTT
2536024 ACACTTT
1 ACACTTT
*
2536031 ACATTTT
1 ACACTTT
2536038 A
1 A
2536039 GTTTTAACTA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.31, C:0.25, G:0.00, T:0.44
Consensus pattern (7 bp):
ACACTTT
Found at i:2543066 original size:23 final size:25
Alignment explanation
Indices: 2543034--2543082 Score: 75
Period size: 24 Copynumber: 2.0 Consensus size: 25
2543024 TTTCTCTCTA
2543034 CTTTCTTCTTTTTTTCT-TCCTTTT
1 CTTTCTTCTTTTTTTCTCTCCTTTT
*
2543058 CTTTC-TCTTTTTTTCTCTCTTTTT
1 CTTTCTTCTTTTTTTCTCTCCTTTT
2543082 C
1 C
2543083 AGCTGAAGCT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 11 0.48
24 12 0.52
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (25 bp):
CTTTCTTCTTTTTTTCTCTCCTTTT
Found at i:2545127 original size:84 final size:84
Alignment explanation
Indices: 2545035--2545345 Score: 337
Period size: 84 Copynumber: 3.7 Consensus size: 84
2545025 GGGGTTAAGC
* *
2545035 CGACAGGTAAACAAGGAGATGAAGGTTGACCGGAGACTGAGCTGACAGGTCACCATAGAGGTGAG
1 CGACAGGTAAACAAAGAGATAAAGGTTGACCGGAGACTGAGCTGACAGGTCACCATAGAGGTGAG
*
2545100 GGTTTACTAGGGATTGAGT
66 GGTTTACTAGGGACTGAGT
* * ** * *
2545119 CGACAGGTAAATAAAGAGATGAAGGTTGACTAGAGATTGAGCTGACAGGTCACCATA-AGGGTAA
1 CGACAGGTAAACAAAGAGATAAAGGTTGACCGGAGACTGAGCTGACAGGTCACCATAGA-GGTGA
2545183 TGGGTTTACT-GTGGACTGAG-
65 -GGGTTTACTAG-GGACTGAGT
* * * * * *
2545203 CTAATAGGTAAACAAAGAGAATAAAGGTTGATCGGAGACTAAGTTGACAGGTCACTA-AG-GGAT
1 C-GACAGGTAAACAAAGAG-ATAAAGGTTGACCGGAGACTGAGCTGACAGGTCACCATAGAGG-T
*
2545266 GAAGGGTTTA-TCAGAGACTGAGT
63 G-AGGGTTTACT-AGGGACTGAGT
* * *
2545289 TGACAGGTAAATAAAGAGATAAAGGTTGACCGGAGACTGAGCTGACAAGTCACCATA
1 CGACAGGTAAACAAAGAGATAAAGGTTGACCGGAGACTGAGCTGACAGGTCACCATA
2545346 AGGGGTAAAG
Statistics
Matches: 186, Mismatches: 29, Indels: 23
0.78 0.12 0.10
Matches are distributed among these distances:
83 1 0.01
84 93 0.50
85 61 0.33
86 31 0.17
ACGTcount: A:0.35, C:0.13, G:0.31, T:0.21
Consensus pattern (84 bp):
CGACAGGTAAACAAAGAGATAAAGGTTGACCGGAGACTGAGCTGACAGGTCACCATAGAGGTGAG
GGTTTACTAGGGACTGAGT
Found at i:2545232 original size:170 final size:169
Alignment explanation
Indices: 2545039--2545349 Score: 439
Period size: 170 Copynumber: 1.8 Consensus size: 169
2545029 TTAAGCCGAC
* * *
2545039 AGGTAAACAAGGAGATGAAGGTTGACCGGAGACTGAGCTGACAGGTCACCATAGAGG-TG-AGGG
1 AGGTAAACAAAGAGATAAAGGTTGACCGGAGACTAAGCTGACAGGTCACCA-AG-GGATGAAGGG
* * * * *
2545102 TTTA-CTAGGGATTGAGTCGACAGGTAAATAAAGAGATGAAGGTTGACTAGAGATTGAGCTGACA
64 TTTATC-AGAGACTGAGTCGACAGGTAAATAAAGAGATAAAGGTTGACCAGAGACTGAGCTGACA
*
2545166 GGTCACCATAAGGGTAATGGGTTTACTGTGGACTGAGCTAAT
128 AGTCACCATAAGGGTAATGGGTTTACTGTGGACTGAGCTAAT
* * *
2545208 AGGTAAACAAAGAGAATAAAGGTTGATCGGAGACTAAGTTGACAGGTCACTAAGGGATGAAGGGT
1 AGGTAAACAAAGAG-ATAAAGGTTGACCGGAGACTAAGCTGACAGGTCACCAAGGGATGAAGGGT
* *
2545273 TTATCAGAGACTGAGTTGACAGGTAAATAAAGAGATAAAGGTTGACCGGAGACTGAGCTGACAAG
65 TTATCAGAGACTGAGTCGACAGGTAAATAAAGAGATAAAGGTTGACCAGAGACTGAGCTGACAAG
2545338 TCACCATAAGGG
130 TCACCATAAGGG
2545350 GTAAAGGTTT
Statistics
Matches: 124, Mismatches: 14, Indels: 7
0.86 0.10 0.05
Matches are distributed among these distances:
168 2 0.02
169 17 0.14
170 104 0.84
171 1 0.01
ACGTcount: A:0.35, C:0.12, G:0.32, T:0.21
Consensus pattern (169 bp):
AGGTAAACAAAGAGATAAAGGTTGACCGGAGACTAAGCTGACAGGTCACCAAGGGATGAAGGGTT
TATCAGAGACTGAGTCGACAGGTAAATAAAGAGATAAAGGTTGACCAGAGACTGAGCTGACAAGT
CACCATAAGGGTAATGGGTTTACTGTGGACTGAGCTAAT
Found at i:2545325 original size:42 final size:42
Alignment explanation
Indices: 2545036--2545335 Score: 162
Period size: 42 Copynumber: 7.1 Consensus size: 42
2545026 GGGTTAAGCC
* * *
2545036 GACAGGTAAACAAGGAGATGAAGGTTGACCGGAGACTGAGCT
1 GACAGGTAAATAAAGAGATAAAGGTTGACCGGAGACTGAGCT
* ** * * * * * * *
2545078 GACAGGTCACCATAGAGGTGAGGGTTTACTAGG-GATTGAG-T
1 GACAGGTAAATAAAGAGATAAAGGTTGAC-CGGAGACTGAGCT
* ** *
2545119 CGACAGGTAAATAAAGAGATGAAGGTTGACTAGAGATTGAGCT
1 -GACAGGTAAATAAAGAGATAAAGGTTGACCGGAGACTGAGCT
* * * * *
2545162 GACAGGTCACCAT-AAG-GGTAATGGGTTTACTGTG-GACTGAGCT
1 GACAGGT-A-AATAAAGAGATAA-AGGTTGACCG-GAGACTGAGCT
* * * * * *
2545205 AATAGGTAAACAAAGAGAATAAAGGTTGATCGGAGACTAAGTT
1 GACAGGTAAATAAAGAG-ATAAAGGTTGACCGGAGACTGAGCT
* * * * * * * *
2545248 GACAGGTCACT-AAGGGATGAAGGGTTTATCAGAGACTGAGTT
1 GACAGGTAAATAAAGAGAT-AAAGGTTGACCGGAGACTGAGCT
2545290 GACAGGTAAATAAAGAGATAAAGGTTGACCGGAGACTGAGCT
1 GACAGGTAAATAAAGAGATAAAGGTTGACCGGAGACTGAGCT
2545332 GACA
1 GACA
2545336 AGTCACCATA
Statistics
Matches: 190, Mismatches: 54, Indels: 28
0.70 0.20 0.10
Matches are distributed among these distances:
41 5 0.03
42 126 0.66
43 53 0.28
44 6 0.03
ACGTcount: A:0.35, C:0.12, G:0.32, T:0.21
Consensus pattern (42 bp):
GACAGGTAAATAAAGAGATAAAGGTTGACCGGAGACTGAGCT
Found at i:2545880 original size:12 final size:12
Alignment explanation
Indices: 2545863--2545889 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
2545853 TTTAATTATC
2545863 ATTATTATTGTT
1 ATTATTATTGTT
2545875 ATTATTATTGTT
1 ATTATTATTGTT
2545887 ATT
1 ATT
2545890 GTAGACACCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.26, C:0.00, G:0.07, T:0.67
Consensus pattern (12 bp):
ATTATTATTGTT
Found at i:2546224 original size:19 final size:19
Alignment explanation
Indices: 2546200--2546292 Score: 102
Period size: 19 Copynumber: 5.5 Consensus size: 19
2546190 AAACAGTAAA
2546200 TGTATCGATACATAAGTGT
1 TGTATCGATACATAAGTGT
2546219 TGTATCGATAC--AA----
1 TGTATCGATACATAAGTGT
2546232 TGTATCGATACATAAGTGT
1 TGTATCGATACATAAGTGT
2546251 TGTATCGATAC--AA----
1 TGTATCGATACATAAGTGT
2546264 TGTATCGATACATAAGTGT
1 TGTATCGATACATAAGTGT
2546283 TGTATCGATA
1 TGTATCGATA
2546293 TAATGTATCG
Statistics
Matches: 62, Mismatches: 0, Indels: 24
0.72 0.00 0.28
Matches are distributed among these distances:
13 22 0.35
15 4 0.06
17 4 0.06
19 32 0.52
ACGTcount: A:0.33, C:0.12, G:0.19, T:0.35
Consensus pattern (19 bp):
TGTATCGATACATAAGTGT
Found at i:2546237 original size:13 final size:13
Alignment explanation
Indices: 2546219--2546275 Score: 60
Period size: 13 Copynumber: 3.9 Consensus size: 13
2546209 ACATAAGTGT
2546219 TGTATCGATACAA
1 TGTATCGATACAA
2546232 TGTATCGATACATAA
1 TGTATCGATAC--AA
2546247 GTGTTGTATCGATACAA
1 ----TGTATCGATACAA
2546264 TGTATCGATACA
1 TGTATCGATACA
2546276 TAAGTGTTGT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 23 0.61
15 2 0.05
17 2 0.05
19 11 0.29
ACGTcount: A:0.35, C:0.14, G:0.18, T:0.33
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:2546239 original size:32 final size:32
Alignment explanation
Indices: 2546198--2546307 Score: 202
Period size: 32 Copynumber: 3.4 Consensus size: 32
2546188 ACAAACAGTA
2546198 AATGTATCGATACATAAGTGTTGTATCGATAC
1 AATGTATCGATACATAAGTGTTGTATCGATAC
2546230 AATGTATCGATACATAAGTGTTGTATCGATAC
1 AATGTATCGATACATAAGTGTTGTATCGATAC
*
2546262 AATGTATCGATACATAAGTGTTGTATCGATAT
1 AATGTATCGATACATAAGTGTTGTATCGATAC
*
2546294 AATGTATCGCTACA
1 AATGTATCGATACA
2546308 AAGCTACTGC
Statistics
Matches: 76, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 76 1.00
ACGTcount: A:0.35, C:0.13, G:0.18, T:0.35
Consensus pattern (32 bp):
AATGTATCGATACATAAGTGTTGTATCGATAC
Found at i:2546349 original size:20 final size:20
Alignment explanation
Indices: 2546324--2546399 Score: 152
Period size: 20 Copynumber: 3.8 Consensus size: 20
2546314 CTGCCAAGGA
2546324 AATGTATCGATACATTATTC
1 AATGTATCGATACATTATTC
2546344 AATGTATCGATACATTATTC
1 AATGTATCGATACATTATTC
2546364 AATGTATCGATACATTATTC
1 AATGTATCGATACATTATTC
2546384 AATGTATCGATACATT
1 AATGTATCGATACATT
2546400 GTATCGATAC
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 56 1.00
ACGTcount: A:0.36, C:0.14, G:0.11, T:0.39
Consensus pattern (20 bp):
AATGTATCGATACATTATTC
Found at i:2546404 original size:13 final size:13
Alignment explanation
Indices: 2546386--2546428 Score: 68
Period size: 13 Copynumber: 3.2 Consensus size: 13
2546376 CATTATTCAA
2546386 TGTATCGATACAT
1 TGTATCGATACAT
2546399 TGTATCGATACAATT
1 TGTATCGATAC-A-T
2546414 TGTATCGATACAT
1 TGTATCGATACAT
2546427 TG
1 TG
2546429 ATCTTTGTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
13 14 0.50
14 2 0.07
15 12 0.43
ACGTcount: A:0.30, C:0.14, G:0.16, T:0.40
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2546418 original size:15 final size:14
Alignment explanation
Indices: 2546386--2546425 Score: 64
Period size: 15 Copynumber: 2.9 Consensus size: 14
2546376 CATTATTCAA
2546386 TGTATCGATAC-AT
1 TGTATCGATACAAT
2546399 TGTATCGATACAATT
1 TGTATCGATACAA-T
2546414 TGTATCGATACA
1 TGTATCGATACA
2546426 TTGATCTTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
13 11 0.44
14 1 0.04
15 13 0.52
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.38
Consensus pattern (14 bp):
TGTATCGATACAAT
Found at i:2549977 original size:55 final size:55
Alignment explanation
Indices: 2549773--2550516 Score: 829
Period size: 55 Copynumber: 13.0 Consensus size: 55
2549763 GCCTTTTTCT
* *
2549773 TTTTAAAGCCCACACGAGTTGGTGGCACCTTT-AGTCCTCAAAGAGCAGGACACATTTTCC
1 TTTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGG--AC----GCC
*
2549833 TTTTAAAGCCCACACAAGTTGGTGGCACCTTT-AGTCCTCAAAAAGCAGGACGCC
1 TTTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACGCC
*
2549887 TTTTTTTTTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGATGCC
1 ------TTTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACGCC
* *
2549948 TTTTAAAGCCCACACAAGTAGGTGGCACCTTTCAGTCCTCAAAGAGCAGGATGCC
1 TTTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACGCC
* *
2550003 TTTTAAAGCCCACACAAGTTGGTGGCACCTTTTAGTCCTCAAAGAGTAGGACGCC
1 TTTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACGCC
*
2550058 TTTTAAAGCCCACACAAGTTGGTGGCA-CTTCCCAGTCCTCAAAGAGCAGGACGCC
1 TTTTAAAGCCCACACAAGTTGGTGGCACCTT-TCAGTCCTCAAAGAGCAGGACGCC
* *
2550113 TGTTAAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCCTCAAAGAGCAGGACGCC
1 TTTTAAAGCCCACACAAGTTGGTGGCACCTTT-CAGTCCTCAAAGAGCAGGACGCC
* * * * *
2550168 TCTTAAAGCCCACACAAGTTGGTGACA-TTTTCCAGTCCTCAAAGAGCAAGACACC
1 TTTTAAAGCCCACACAAGTTGGTGGCACCTTT-CAGTCCTCAAAGAGCAGGACGCC
* *
2550223 TCTTAAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCCTCAAAGAGCAGGACGCC
1 TTTTAAAGCCCACACAAGTTGGTGGCACCTTT-CAGTCCTCAAAGAGCAGGACGCC
* * *
2550278 TCTTAAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCCTCAAAGAGCAGGATTCTTTCTC
1 TTTTAAAGCCCACACAAGTTGGTGGCACCTTT-CAGTCCTCAAAGAGCAGGA--C--GC-C
* * * *
2550338 TTTGCAAAGCCCACACAAGTTGGTGGCACCTTCCAGTCCTTAAAGAGCAGGACACCTTC
1 TTT-TAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGAC-GC--C
* * *
2550397 TCCTCTTCAAAGCCCATACAAGTTGGTGGCACCTTTTAGTCCTCAAAGAGCAGGACACCTTTTTC
1 T--T-TT-AAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGAC-GC-----C
*
2550462 TTTTTAAATCCCACACAAGTTGGTGGCA-CTTTCGAGTCCTCAAAGAGCAGGACGC
1 -TTTTAAAGCCCACACAAGTTGGTGGCACCTTTC-AGTCCTCAAAGAGCAGGACGC
2550517 TCTCTCCTTT
Statistics
Matches: 618, Mismatches: 40, Indels: 51
0.87 0.06 0.07
Matches are distributed among these distances:
54 5 0.01
55 358 0.58
57 1 0.00
58 3 0.00
59 5 0.01
60 82 0.13
61 67 0.11
62 90 0.15
63 2 0.00
64 1 0.00
65 3 0.00
66 1 0.00
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.25
Consensus pattern (55 bp):
TTTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACGCC
Found at i:2550005 original size:26 final size:26
Alignment explanation
Indices: 2549920--2550005 Score: 68
Period size: 27 Copynumber: 3.2 Consensus size: 26
2549910 GTTGGTGGCA
2549920 CCTTTCAGTCCTCAAAGAGCAGGATG
1 CCTTTCAGTCCTCAAAGAGCAGGATG
* * * * *
2549946 CCTTTTAAAGCCCACACA-AGTAGG-TGG
1 CC-TTT-CAGTCCTCAAAGAGCAGGAT-G
2549973 CACCTTTCAGTCCTCAAAGAGCAGGATG
1 --CCTTTCAGTCCTCAAAGAGCAGGATG
2550001 CCTTT
1 CCTTT
2550006 TAAAGCCCAC
Statistics
Matches: 43, Mismatches: 10, Indels: 14
0.64 0.15 0.21
Matches are distributed among these distances:
26 8 0.19
27 16 0.37
28 16 0.37
29 3 0.07
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (26 bp):
CCTTTCAGTCCTCAAAGAGCAGGATG
Found at i:2550514 original size:62 final size:62
Alignment explanation
Indices: 2550282--2550514 Score: 308
Period size: 62 Copynumber: 3.8 Consensus size: 62
2550272 GACGCCTCTT
* ** * *
2550282 AAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGA-TTCTTTCTCTTTGC
1 AAAGCCCACACAAGTTGGTGGCACTTTCCAGTCCTCAAAGAGCAGGACACCTTTTTCTTTTC
* * * * *
2550343 AAAGCCCACACAAGTTGGTGGCACCTTCCAGTCCTTAAAGAGCAGGACACCTTCTCCTCTTC
1 AAAGCCCACACAAGTTGGTGGCACTTTCCAGTCCTCAAAGAGCAGGACACCTTTTTCTTTTC
* * *
2550405 AAAGCCCATACAAGTTGGTGGCACCTTT-TAGTCCTCAAAGAGCAGGACACCTTTTTCTTTTT
1 AAAGCCCACACAAGTTGGTGGCA-CTTTCCAGTCCTCAAAGAGCAGGACACCTTTTTCTTTTC
* *
2550467 AAATCCCACACAAGTTGGTGGCACTTTCGAGTCCTCAAAGAGCAGGAC
1 AAAGCCCACACAAGTTGGTGGCACTTTCCAGTCCTCAAAGAGCAGGAC
2550515 GCTCTCTCCT
Statistics
Matches: 148, Mismatches: 21, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
61 48 0.32
62 97 0.66
63 3 0.02
ACGTcount: A:0.27, C:0.28, G:0.19, T:0.26
Consensus pattern (62 bp):
AAAGCCCACACAAGTTGGTGGCACTTTCCAGTCCTCAAAGAGCAGGACACCTTTTTCTTTTC
Found at i:2550626 original size:100 final size:101
Alignment explanation
Indices: 2550431--2550616 Score: 284
Period size: 100 Copynumber: 1.9 Consensus size: 101
2550421 GGTGGCACCT
* * * * * *
2550431 TTTAGTCCTCAAAGAGCAGGACACCTTTTTCTTTTTAAATCCCACACAAGTTGGTGGCACTTTCG
1 TTTAGTCCTCAAAGAGCAAGACACCTTTTTCCTCTTAAAGCCCACACAAGTTCGTGGCACCTTCG
2550496 AGTCCTCAAAGAGCAGGACGCTCTCTCCTTTCGCCC
66 AGTCCTCAAAGAGCAGGACGCTCTCTCCTTTCGCCC
* *
2550532 TTTAGTCCTCAAAGAGCAAGACTCC-TTTTCCTCTTAAAGCCCACACAAGTTCGTGGCACCTTCT
1 TTTAGTCCTCAAAGAGCAAGACACCTTTTTCCTCTTAAAGCCCACACAAGTTCGTGGCACCTTCG
*
2550596 AGTCCTCAAAGAGTAGGACGC
66 AGTCCTCAAAGAGCAGGACGC
2550617 CTTTTCCTTT
Statistics
Matches: 76, Mismatches: 9, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
100 53 0.70
101 23 0.30
ACGTcount: A:0.25, C:0.30, G:0.18, T:0.28
Consensus pattern (101 bp):
TTTAGTCCTCAAAGAGCAAGACACCTTTTTCCTCTTAAAGCCCACACAAGTTCGTGGCACCTTCG
AGTCCTCAAAGAGCAGGACGCTCTCTCCTTTCGCCC
Found at i:2550630 original size:61 final size:61
Alignment explanation
Indices: 2550530--2550746 Score: 310
Period size: 61 Copynumber: 3.6 Consensus size: 61
2550520 CTCCTTTCGC
* * * *
2550530 CCTT-TAGTCCTCAAAGAGCAAGACTCCTTTTCCTCTTAAAGCCCACACAAGTTCGTGGCA
1 CCTTCTAGTCCTCAAAGAGCAGGACGCCTTCTCCTCTTAAAGCCCACACAAGTTGGTGGCA
* * * **
2550590 CCTTCTAGTCCTCAAAGAGTAGGACGCCTTTTCCTTTTAAAGCCCACATGAGTTGGTGGCA
1 CCTTCTAGTCCTCAAAGAGCAGGACGCCTTCTCCTCTTAAAGCCCACACAAGTTGGTGGCA
* *
2550651 CTTTCCAGTCCTCAAAGAGCAGGACGCCTTCTCCTCTTAAAGCCCACACAAGTTGGTGGCA
1 CCTTCTAGTCCTCAAAGAGCAGGACGCCTTCTCCTCTTAAAGCCCACACAAGTTGGTGGCA
* *
2550712 CCTTCTAGTCTTCAAAGAGCAGGATGCCTTCTCCT
1 CCTTCTAGTCCTCAAAGAGCAGGACGCCTTCTCCT
2550747 TTCCACTTTG
Statistics
Matches: 138, Mismatches: 18, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
60 4 0.03
61 134 0.97
ACGTcount: A:0.24, C:0.30, G:0.18, T:0.27
Consensus pattern (61 bp):
CCTTCTAGTCCTCAAAGAGCAGGACGCCTTCTCCTCTTAAAGCCCACACAAGTTGGTGGCA
Found at i:2550672 original size:161 final size:163
Alignment explanation
Indices: 2550372--2550685 Score: 472
Period size: 161 Copynumber: 1.9 Consensus size: 163
2550362 GGCACCTTCC
* * * * *
2550372 AGTCCTTAAAGAGCAGGACACCTTCTCCTCTTCAAAGCCCATACAAGTTGGTGGCACCTTTTAGT
1 AGTCCTCAAAGAGCAAGACACCTTCTCCTCTTCAAAGCCCACACAAGTTCGTGGCACCTTCTAGT
* * *
2550437 CCTCAAAGAGCAGGACACCTTTTTCTTTTTAAATCCCACACAAGTTGGTGGCACTTTCGAGTCCT
66 CCTCAAAGAGCAGGACACCTTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTCCAGTCCT
2550502 CAAAGAGCAGGACG-CTCTCTCCTTTCGCCCTTT
131 CAAAGAGCAGGACGCCT-TCTCCTTTCGCCCTTT
* *
2550535 AGTCCTCAAAGAGCAAGACTCCTTTTCCTCTT-AAAGCCCACACAAGTTCGTGGCACCTTCTAGT
1 AGTCCTCAAAGAGCAAGACACCTTCTCCTCTTCAAAGCCCACACAAGTTCGTGGCACCTTCTAGT
* * **
2550599 CCTCAAAGAGTAGGACGCC-TTTTCCTTTTAAAGCCCACATGAGTTGGTGGCACTTTCCAGTCCT
66 CCTCAAAGAGCAGGACACCTTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTCCAGTCCT
2550663 CAAAGAGCAGGACGCCTTCTCCT
131 CAAAGAGCAGGACGCCTTCTCCT
2550686 CTTAAAGCCC
Statistics
Matches: 136, Mismatches: 14, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
161 60 0.44
162 48 0.35
163 28 0.21
ACGTcount: A:0.24, C:0.30, G:0.18, T:0.28
Consensus pattern (163 bp):
AGTCCTCAAAGAGCAAGACACCTTCTCCTCTTCAAAGCCCACACAAGTTCGTGGCACCTTCTAGT
CCTCAAAGAGCAGGACACCTTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTCCAGTCCT
CAAAGAGCAGGACGCCTTCTCCTTTCGCCCTTT
Found at i:2551539 original size:19 final size:18
Alignment explanation
Indices: 2551515--2551609 Score: 84
Period size: 19 Copynumber: 5.7 Consensus size: 18
2551505 AGACAGAAAC
2551515 TGTATCGATACATAAGTGT
1 TGTATCGATACATAAGT-T
2551534 TGTATCGAT--ATAA---
1 TGTATCGATACATAAGTT
2551547 TGTATCGATACATAAGTTT
1 TGTATCGATACATAAG-TT
2551566 TGTATCGATAC--AA---
1 TGTATCGATACATAAGTT
*
2551579 TGTATCGATATATAAGTTT
1 TGTATCGATACATAAG-TT
2551598 TGTATCGATACA
1 TGTATCGATACA
2551610 ATGTATCGCT
Statistics
Matches: 62, Mismatches: 2, Indels: 24
0.70 0.02 0.27
Matches are distributed among these distances:
13 19 0.31
15 6 0.10
17 6 0.10
19 31 0.50
ACGTcount: A:0.34, C:0.11, G:0.17, T:0.39
Consensus pattern (18 bp):
TGTATCGATACATAAGTT
Found at i:2551552 original size:13 final size:13
Alignment explanation
Indices: 2551534--2551590 Score: 51
Period size: 13 Copynumber: 3.9 Consensus size: 13
2551524 ACATAAGTGT
2551534 TGTATCGATATAA
1 TGTATCGATATAA
2551547 TGTATCGATACATAA
1 TGTATCGAT--ATAA
*
2551562 GTTTTGTATCGATACAA
1 ----TGTATCGATATAA
2551579 TGTATCGATATA
1 TGTATCGATATA
2551591 TAAGTTTTGT
Statistics
Matches: 36, Mismatches: 2, Indels: 12
0.72 0.04 0.24
Matches are distributed among these distances:
13 20 0.56
15 4 0.11
17 3 0.08
19 9 0.25
ACGTcount: A:0.35, C:0.11, G:0.16, T:0.39
Consensus pattern (13 bp):
TGTATCGATATAA
Found at i:2551556 original size:32 final size:32
Alignment explanation
Indices: 2551515--2551622 Score: 180
Period size: 32 Copynumber: 3.4 Consensus size: 32
2551505 AGACAGAAAC
* *
2551515 TGTATCGATACATAAGTGTTGTATCGATATAA
1 TGTATCGATACATAAGTTTTGTATCGATACAA
2551547 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTTTTGTATCGATACAA
*
2551579 TGTATCGATATATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTTTTGTATCGATACAA
*
2551611 TGTATCGCTACA
1 TGTATCGATACA
2551623 AAGCTGCTGC
Statistics
Matches: 71, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 71 1.00
ACGTcount: A:0.33, C:0.12, G:0.17, T:0.38
Consensus pattern (32 bp):
TGTATCGATACATAAGTTTTGTATCGATACAA
Found at i:2554169 original size:51 final size:51
Alignment explanation
Indices: 2554066--2554339 Score: 163
Period size: 51 Copynumber: 5.3 Consensus size: 51
2554056 AAATTTTCTT
* * * **
2554066 AATCGGGGATCCTCCAACTCCGATTTTA-TTTCTAAAGCA-TCGATTTACCAC
1 AATCGGGGATACTCCAACTCCGATTTTATTTTC-AAAACACT-AATTTTTCAC
2554117 AATCGGGGATACTCCAACTCCGATTTTATTTTCAAAACACTAATTTTTCAC
1 AATCGGGGATACTCCAACTCCGATTTTATTTTCAAAACACTAATTTTTCAC
* ** * **
2554168 AATTGGGGATACTCCAAC-CCTGTTATTTCATCGGGGATACTCCAAAC-C-CGTTATTTC-C
1 AATCGGGGATACTCCAACTCC-G--ATTT--T-----ATTTTCAAAACACTAATT-TTTCAC
* *
2554226 GA--GGGGATACTCCAAC-CTCGATTTTA-TTTCTAAAATACTAATTTTTCAC
1 AATCGGGGATACTCCAACTC-CGATTTTATTTTC-AAAACACTAATTTTTCAC
* * * * * **
2554275 AATCGGGGATACTCTAACTCCGATTTCATTTCCAAAATACCAATTTCACAC
1 AATCGGGGATACTCCAACTCCGATTTTATTTTCAAAACACTAATTTTTCAC
2554326 AATCGGGGATACTC
1 AATCGGGGATACTC
2554340 AAACCCCGTA
Statistics
Matches: 176, Mismatches: 25, Indels: 44
0.72 0.10 0.18
Matches are distributed among these distances:
46 2 0.01
47 4 0.02
48 5 0.03
49 4 0.02
50 2 0.01
51 106 0.60
52 10 0.06
53 4 0.02
54 4 0.02
55 1 0.01
56 16 0.09
57 1 0.01
58 4 0.02
59 5 0.03
60 8 0.05
ACGTcount: A:0.29, C:0.25, G:0.14, T:0.32
Consensus pattern (51 bp):
AATCGGGGATACTCCAACTCCGATTTTATTTTCAAAACACTAATTTTTCAC
Found at i:2554205 original size:28 final size:27
Alignment explanation
Indices: 2554172--2554242 Score: 97
Period size: 28 Copynumber: 2.6 Consensus size: 27
2554162 TTTCACAATT
**
2554172 GGGGATACTCCAACCCTGTTATTTCATC
1 GGGGATACTCCAACCC-GTTATTTCAGA
*
2554200 GGGGATACTCCAAACCCGTTATTTCCGA
1 GGGGATACTCC-AACCCGTTATTTCAGA
2554228 GGGGATACTCCAACC
1 GGGGATACTCCAACC
2554243 TCGATTTTAT
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
27 4 0.10
28 30 0.77
29 5 0.13
ACGTcount: A:0.24, C:0.30, G:0.21, T:0.25
Consensus pattern (27 bp):
GGGGATACTCCAACCCGTTATTTCAGA
Found at i:2554362 original size:158 final size:156
Alignment explanation
Indices: 2554070--2554373 Score: 380
Period size: 158 Copynumber: 1.9 Consensus size: 156
2554060 TTTCTTAATC
* *
2554070 GGGGATCCTCCAACTCCGATTTTATTTCTAAAGCATCGATTTACCACAATCGGGGATACTCCAAC
1 GGGGATACTCCAACTCCGATTTTATTTCTAAA-CATCAATTTACCACAATCGGGGATACTCCAAC
* * * ** * * * *
2554135 TCCGATTTTATTTTCAAAACACTAATTTTTCACAATTGGGGATACTCCAACCCTGTTATTTCATC
65 TCCGATTTCATTTCCAAAACACCAATTTCACACAATCGGGGATACTCAAACCCCGTAATTTCATC
2554200 GGGGATACTCCAAACCCGTTATTTCCGA
130 GGGGATACT-CAAACCCGTTATTTCCGA
** *
2554228 GGGGATACTCCAAC-CTCGATTTTATTTCTAAA-ATACTAATTTTTCACAATCGGGGATACTCTA
1 GGGGATACTCCAACTC-CGATTTTATTTCTAAACAT-C-AATTTACCACAATCGGGGATACTCCA
* *
2554291 ACTCCGATTTCATTTCCAAAATACCAATTTCACACAATCGGGGATACTCAAACCCCGTAATTT-T
63 ACTCCGATTTCATTTCCAAAACACCAATTTCACACAATCGGGGATACTCAAACCCCGTAATTTCA
*
2554355 TGTGGGGATACTCAAACCC
128 T-CGGGGATACTCAAACCC
2554374 CGATTTTATT
Statistics
Matches: 125, Mismatches: 17, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
156 2 0.02
157 10 0.08
158 113 0.90
ACGTcount: A:0.29, C:0.25, G:0.14, T:0.32
Consensus pattern (156 bp):
GGGGATACTCCAACTCCGATTTTATTTCTAAACATCAATTTACCACAATCGGGGATACTCCAACT
CCGATTTCATTTCCAAAACACCAATTTCACACAATCGGGGATACTCAAACCCCGTAATTTCATCG
GGGATACTCAAACCCGTTATTTCCGA
Found at i:2556018 original size:51 final size:51
Alignment explanation
Indices: 2555855--2556034 Score: 170
Period size: 51 Copynumber: 3.5 Consensus size: 51
2555845 TAAATTCCTA
* * * * * *
2555855 AATTTTTCAC-CTCGGGGATACTCCAA-TCCCGGTTCTGTTTCCAAAACATC
1 AATTTTTCACAATCGGGAATACTCCAACT-CCGATTTTATTTCTAAAACATC
** * *
2555905 AATTTTTCTTAATCGGGGATACTCCAACTCCGATTTTATTTCTAAAGCATC
1 AATTTTTCACAATCGGGAATACTCCAACTCCGATTTTATTTCTAAAACATC
* ** *
2555956 GATTTACCACAATCGGGAATACTCCAACTCCGATTTTATTTTTAAAACA-C
1 AATTTTTCACAATCGGGAATACTCCAACTCCGATTTTATTTCTAAAACATC
*
2556006 TAATTTTTCACAAT-TGGAGATACTCCAAC
1 -AATTTTTCACAATCGGGA-ATACTCCAAC
2556035 CCCGTTATTT
Statistics
Matches: 106, Mismatches: 20, Indels: 7
0.80 0.15 0.05
Matches are distributed among these distances:
50 12 0.11
51 93 0.88
52 1 0.01
ACGTcount: A:0.29, C:0.24, G:0.12, T:0.34
Consensus pattern (51 bp):
AATTTTTCACAATCGGGAATACTCCAACTCCGATTTTATTTCTAAAACATC
Found at i:2556139 original size:28 final size:28
Alignment explanation
Indices: 2556106--2556174 Score: 79
Period size: 28 Copynumber: 2.5 Consensus size: 28
2556096 ATAATCGGGG
*
2556106 TACTCCAAGCCTGTTATTTCATCG-A-GGA
1 TACTCCAAGCCCGTTATTT--TCGAAGGGA
*
2556134 TACTCCAATCCCGTTATTTTCGAAGGGA
1 TACTCCAAGCCCGTTATTTTCGAAGGGA
*
2556162 TACTCCAACCCCG
1 TACTCCAAGCCCG
2556175 ATTTTATTTC
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
26 3 0.08
27 1 0.03
28 32 0.89
ACGTcount: A:0.25, C:0.30, G:0.16, T:0.29
Consensus pattern (28 bp):
TACTCCAAGCCCGTTATTTTCGAAGGGA
Found at i:2556216 original size:51 final size:51
Alignment explanation
Indices: 2556158--2556272 Score: 169
Period size: 51 Copynumber: 2.3 Consensus size: 51
2556148 TATTTTCGAA
* *
2556158 GGGATACTCCAACCCCGATTTTA-TTTCTAAAATACCAATTTTTCACAATCG
1 GGGATACTCCAACCCCGATTTTATTTTC-AAAACACCAATTTCTCACAATCG
* * *
2556209 GGGATACTTCAACTCCGATTTTATTTTCAAAACACCAATTTCTCAGAATCG
1 GGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTCTCACAATCG
2556260 GGGATACTCCAAC
1 GGGATACTCCAAC
2556273 ACCGCTATTT
Statistics
Matches: 57, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
51 53 0.93
52 4 0.07
ACGTcount: A:0.31, C:0.25, G:0.12, T:0.31
Consensus pattern (51 bp):
GGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTCTCACAATCG
Found at i:2560538 original size:13 final size:13
Alignment explanation
Indices: 2560520--2560544 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2560510 CATAAAATGT
2560520 TGTATCGATACAA
1 TGTATCGATACAA
2560533 TGTATCGATACA
1 TGTATCGATACA
2560545 TATTTTTTTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:2560627 original size:13 final size:13
Alignment explanation
Indices: 2560609--2560633 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2560599 ATTACTCACA
2560609 TGTATCGATACAT
1 TGTATCGATACAT
2560622 TGTATCGATACA
1 TGTATCGATACA
2560634 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2560698 original size:52 final size:52
Alignment explanation
Indices: 2560642--2560766 Score: 223
Period size: 52 Copynumber: 2.4 Consensus size: 52
2560632 CACTGATCTT
*
2560642 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
2560694 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
2560746 TGTATCGATACATGCAAGCAA
1 TGTATCGATACATGCAGGCAA
2560767 CTTTTCATAT
Statistics
Matches: 70, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 70 1.00
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.28
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:2567934 original size:16 final size:16
Alignment explanation
Indices: 2567913--2567982 Score: 65
Period size: 17 Copynumber: 4.5 Consensus size: 16
2567903 TGTTCTTTTC
2567913 CAAAAAAGAAACAAAA
1 CAAAAAAGAAACAAAA
*
2567929 CAAAAAAGAAAAAAAAA
1 CAAAAAAG-AAACAAAA
*
2567946 CCAAAAA-AAA-AAAA
1 CAAAAAAGAAACAAAA
* *
2567960 C-AACAACAAACAAAA
1 CAAAAAAGAAACAAAA
*
2567975 AAAAAAAG
1 CAAAAAAG
2567983 GGAAAAACCC
Statistics
Matches: 44, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
13 4 0.09
14 8 0.18
15 7 0.16
16 12 0.27
17 13 0.30
ACGTcount: A:0.83, C:0.13, G:0.04, T:0.00
Consensus pattern (16 bp):
CAAAAAAGAAACAAAA
Found at i:2567952 original size:24 final size:22
Alignment explanation
Indices: 2567914--2567982 Score: 77
Period size: 23 Copynumber: 3.0 Consensus size: 22
2567904 GTTCTTTTCC
*
2567914 AAAAAAGAAACAAAACAAAAAAG
1 AAAAAA-AAACAAAAAAAAAAAG
2567937 AAAAAAAAACCAAAAAAAAAAA-
1 AAAAAAAAA-CAAAAAAAAAAAG
*
2567959 ACAACAACAAACAAAAAAAAAAAG
1 A-AA-AAAAAACAAAAAAAAAAAG
2567983 GGAAAAACCC
Statistics
Matches: 40, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
22 4 0.10
23 31 0.77
24 5 0.12
ACGTcount: A:0.84, C:0.12, G:0.04, T:0.00
Consensus pattern (22 bp):
AAAAAAAAACAAAAAAAAAAAG
Found at i:2567965 original size:34 final size:34
Alignment explanation
Indices: 2567912--2567979 Score: 93
Period size: 34 Copynumber: 2.0 Consensus size: 34
2567902 TTGTTCTTTT
* *
2567912 CCAAAAAAGAAACAAAACAAAAAAGAAAAAAAAA
1 CCAAAAAAGAAAAAAAACAAAAAACAAAAAAAAA
*
2567946 CCAAAAAA-AAAAAACAACAACAAACAAAAAAAAA
1 CCAAAAAAGAAAAAA-AACAAAAAACAAAAAAAAA
2567980 AAGGGAAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
33 5 0.17
34 25 0.83
ACGTcount: A:0.82, C:0.15, G:0.03, T:0.00
Consensus pattern (34 bp):
CCAAAAAAGAAAAAAAACAAAAAACAAAAAAAAA
Found at i:2568984 original size:32 final size:31
Alignment explanation
Indices: 2568923--2569071 Score: 169
Period size: 32 Copynumber: 4.8 Consensus size: 31
2568913 AATTCTTCAA
* * * *
2568923 ATCTCTTC-TCAAAGCCCACCACTCCGTGGC
1 ATCTTTTCTTCAAAGTCCACGACTCAGTGGC
**
2568953 ATCTTTTCTTTTTAAGTCCACGACTCAGTGGC
1 ATCTTTTC-TTCAAAGTCCACGACTCAGTGGC
2568985 ATCCTTTTCTTCAAAGTCCACGACTCAGTGGC
1 AT-CTTTTCTTCAAAGTCCACGACTCAGTGGC
2569017 AT-TTTGTC-TCAAAGTCCACGACTCAGTGGC
1 ATCTTT-TCTTCAAAGTCCACGACTCAGTGGC
* * *
2569047 ATTTTTTCTTCAAAGCCCACAACTC
1 ATCTTTTCTTCAAAGTCCACGACTC
2569072 CATGGCACCC
Statistics
Matches: 103, Mismatches: 10, Indels: 11
0.83 0.08 0.09
Matches are distributed among these distances:
30 36 0.35
31 19 0.18
32 42 0.41
33 6 0.06
ACGTcount: A:0.22, C:0.32, G:0.14, T:0.32
Consensus pattern (31 bp):
ATCTTTTCTTCAAAGTCCACGACTCAGTGGC
Found at i:2569249 original size:35 final size:33
Alignment explanation
Indices: 2568934--2569629 Score: 413
Period size: 27 Copynumber: 21.9 Consensus size: 33
2568924 TCTCTTCTCA
* * *
2568934 AAGCCCACCACTCCGTGGCATC-TTTTCTTTTT
1 AAGCCCACAACTCCGTGGCACCTTTTTCTCTTT
* * * **
2568966 AAGTCCACGACTCAGTGGCATCC-TTTTCT-TCA
1 AAGCCCACAACTCCGTGGCA-CCTTTTTCTCTTT
* * * *
2568998 AAGTCCACGACTCAGTGGCA--TTTTGTCTC--A
1 AAGCCCACAACTCCGTGGCACCTTTT-TCTCTTT
* * * *
2569028 AAGTCCACGACTCAGTGGCA--TTTTT-TCTTCA
1 AAGCCCACAACTCCGTGGCACCTTTTTCTCTT-T
*
2569059 AAGCCCACAACTCCATGGCACC-----CT-TTT
1 AAGCCCACAACTCCGTGGCACCTTTTTCTCTTT
**
2569086 AAGCCCACAACTCCGTGGCACCTTTTTCT-TCA
1 AAGCCCACAACTCCGTGGCACCTTTTTCTCTTT
2569118 AAGCCCACAACTCCGTGGCACC-----CT-TTT
1 AAGCCCACAACTCCGTGGCACCTTTTTCTCTTT
* *
2569145 AAGCCCATAACTCCGTGGCACTTTTTTCATCTTT
1 AAGCCCACAACTCCGTGGCACCTTTTTC-TCTTT
* *
2569179 AAGTCCACAACTCCGTGGTACC-----CT-TTT
1 AAGCCCACAACTCCGTGGCACCTTTTTCTCTTT
*
2569206 AAGCCCACAACTCCGTGGCACTTTTTTTCATCTTT
1 AAGCCCACAACTCCGTGGCAC-CTTTTTC-TCTTT
* *
2569241 AAGTCCACAACTCCATGGCACC-----CT-TTT
1 AAGCCCACAACTCCGTGGCACCTTTTTCTCTTT
*
2569268 AAGCCCACAACTCCGTGGCACCTTTCTC-CTTCT
1 AAGCCCACAACTCCGTGGCACCTTTTTCTCTT-T
*
2569301 AAGCCCACAACTCCGTGGCACCTTTCTC-CTTCT
1 AAGCCCACAACTCCGTGGCACCTTTTTCTCTT-T
** *
2569334 AAGCCCACAACTCTATGGCACCTTTTTCTTTTTT
1 AAGCCCACAACTCCGTGGCACCTTTTTC-TCTTT
* *
2569368 AAGCCCACAACTCCGTGGCATCTTTTTCCTTTTT
1 AAGCCCACAACTCCGTGGCACCTTTTT-CTCTTT
2569402 AAAGCCCACAACTCCGTGGCACTCTTTTTC-CTTCT
1 -AAGCCCACAACTCCGTGGCAC-CTTTTTCTCTT-T
* * *
2569437 AAGTCCACAACTCTGTGGCA-C-----CACTTT
1 AAGCCCACAACTCCGTGGCACCTTTTTCTCTTT
* * * * *
2569464 AAGCCCACAAATCCATGGCATCTCTTTCCTTTTT
1 AAGCCCACAACTCCGTGGCACCT-TTTTCTCTTT
* *
2569498 AAAGCCCACAACTCTGTGGCACCTTTTTCTTTTCT
1 -AAGCCCACAACTCCGTGGCACCTTTTTCTCTT-T
* * * *
2569533 AAGTCTACGACTCTGTGGCACCCTTTTT-TCCTTT
1 AAGCCCACAACTCCGTGGCA-CCTTTTTCT-CTTT
** *
2569567 AAAGCCCACAACTATGTGGCACTCTTTTCCT-TTT
1 -AAGCCCACAACTCCGTGGCAC-CTTTTTCTCTTT
* * *
2569601 AAGTCCACGACTCCGTGGCACCTTCTTCT
1 AAGCCCACAACTCCGTGGCACCTTTTTCT
2569630 AAAGCCCACA
Statistics
Matches: 539, Mismatches: 67, Indels: 116
0.75 0.09 0.16
Matches are distributed among these distances:
27 107 0.20
28 10 0.02
29 4 0.01
30 28 0.05
31 20 0.04
32 74 0.14
33 85 0.16
34 107 0.20
35 97 0.18
36 7 0.01
ACGTcount: A:0.21, C:0.34, G:0.13, T:0.32
Consensus pattern (33 bp):
AAGCCCACAACTCCGTGGCACCTTTTTCTCTTT
Found at i:2569264 original size:62 final size:60
Alignment explanation
Indices: 2569059--2569525 Score: 483
Period size: 62 Copynumber: 7.5 Consensus size: 60
2569049 TTTTTCTTCA
* **
2569059 AAGCCCACAACTCCATGGCACCCTTTTAAGCCCACAACTCCGTGGCACCTTTTTCT-TCA
1 AAGCCCACAACTCCGTGGCACCCTTTTAAGCCCACAACTCCGTGGCACCTTTTTCTCTTT
* *
2569118 AAGCCCACAACTCCGTGGCACCCTTTTAAGCCCATAACTCCGTGGCACTTTTTTCATCTTT
1 AAGCCCACAACTCCGTGGCACCCTTTTAAGCCCACAACTCCGTGGCACCTTTTTC-TCTTT
* * *
2569179 AAGTCCACAACTCCGTGGTACCCTTTTAAGCCCACAACTCCGTGGCACTTTTTTTCATCTTT
1 AAGCCCACAACTCCGTGGCACCCTTTTAAGCCCACAACTCCGTGGCAC-CTTTTTC-TCTTT
* * *
2569241 AAGTCCACAACTCCATGGCACCCTTTTAAGCCCACAACTCCGTGGCACCTTTCTC-CTTCT
1 AAGCCCACAACTCCGTGGCACCCTTTTAAGCCCACAACTCCGTGGCACCTTTTTCTCTT-T
** *
2569301 AAGCCCACAACTCCGTGGCACCTTTCTCCTTCTAAGCCCACAACTCTATGGCACCTTTTTCTTTT
1 AAGCCCACAACTCCGTGGCACC---CT--TT-TAAGCCCACAACTCCGTGGCACCTTTTTC-TCT
2569366 TT
59 TT
2569368 AAGCCCACAACTCCGTGGCATCTTTTTCCTTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTC-
1 AAGCCCACAACTCCGTGGCA-C-----CC-TTTT-AAGCCCACAACTCCGTGGCAC-CTTTTTCT
2569432 CTTCT
57 CTT-T
* * * * * * *
2569437 AAGTCCACAACTCTGTGGCACCAC-TTTAAGCCCACAAATCCATGGCATCTCTTTCCTTTTT
1 AAGCCCACAACTCCGTGGCACC-CTTTTAAGCCCACAACTCCGTGGCACCT-TTTTCTCTTT
* *
2569498 AAAGCCCACAACTCTGTGGCACCTTTTT
1 -AAGCCCACAACTCCGTGGCACCCTTTT
2569526 CTTTTCTAAG
Statistics
Matches: 351, Mismatches: 30, Indels: 51
0.81 0.07 0.12
Matches are distributed among these distances:
59 55 0.16
60 24 0.07
61 74 0.21
62 88 0.25
63 3 0.01
64 1 0.00
65 2 0.01
66 26 0.07
67 21 0.06
68 7 0.02
69 40 0.11
70 8 0.02
71 1 0.00
73 1 0.00
ACGTcount: A:0.22, C:0.35, G:0.12, T:0.31
Consensus pattern (60 bp):
AAGCCCACAACTCCGTGGCACCCTTTTAAGCCCACAACTCCGTGGCACCTTTTTCTCTTT
Found at i:2569493 original size:96 final size:95
Alignment explanation
Indices: 2569032--2569629 Score: 413
Period size: 96 Copynumber: 6.3 Consensus size: 95
2569022 GTCTCAAAGT
* * * * *
2569032 CCACGACTCAGTGGCA--TTTTT-TCTTCAAAGCCCACAACTCCATGGCACCCTTTTAAGCCCAC
1 CCACAACTCCGTGGCACCTTTTTCTCTTCTAAGTCCACAACTCTATGGCACCCTTTTAAGCCCAC
* * **
2569094 AACTCCGTGGCACCT-TTTTC-TTCAAAGC
66 AACTCCGTGGCATCTCTTTCCTTTTTAAGC
* * ** *
2569122 CCACAACTCCGTGGCACC-----CT-TT-TAAGCCCATAACTCCGTGGCACTTTTTTCATCTTTA
1 CCACAACTCCGTGGCACCTTTTTCTCTTCTAAGTCCACAACTCTATGGCAC------CCT-TTTA
* *
2569180 AGTCCACAACTCCGTGG--T-AC---CC-TTTTAAGC
59 AGCCCACAACTCCGTGGCATCTCTTTCCTTTTTAAGC
* *
2569210 CCACAACTCCGTGGCACTTTTTTTCATCTT-TAAGTCCACAACTCCATGGCACCCTTTTAAGCCC
1 CCACAACTCCGTGGCAC-CTTTTTC-TCTTCTAAGTCCACAACTCTATGGCACCCTTTTAAGCCC
* *
2569274 ACAACTCCGTGGCA-C-CTTTCTCCTTCTAAGC
64 ACAACTCCGTGGCATCTCTTTC-CTTTTTAAGC
* *
2569305 CCACAACTCCGTGGCACCTTTCTC-CTTCTAAGCCCACAACTCTATGGCACCTTTTTCTTTTTTA
1 CCACAACTCCGTGGCACCTTTTTCTCTTCTAAGTCCACAACTCTATGGCACC-----C--TTTTA
*
2569369 AGCCCACAACTCCGTGGCATCTTTTTCCTTTTTAAAGC
59 AGCCCACAACTCCGTGGCATCTCTTTCCTTTTT-AAGC
*
2569407 CCACAACTCCGTGGCACTCTTTTTC-CTTCTAAGTCCACAACTCTGTGGCACCAC-TTTAAGCCC
1 CCACAACTCCGTGGCAC-CTTTTTCTCTTCTAAGTCCACAACTCTATGGCACC-CTTTTAAGCCC
* *
2569470 ACAAATCCATGGCATCTCTTTCCTTTTTAAAGC
64 ACAACTCCGTGGCATCTCTTTCCTTTTT-AAGC
* * * * *
2569503 CCACAACTCTGTGGCACCTTTTTCTTTTCTAAGTCTACGACTCTGTGGCACCCTTTTTTCCTTTA
1 CCACAACTCCGTGGCACCTTTTTCTCTTCTAAGTCCACAACTCTATGGCACCC-----T--TTT-
** *
2569568 AAGCCCACAACTATGTGGCA-CTCTTTTCC-TTTTAAGT
58 AAGCCCACAACTCCGTGGCATCTC-TTTCCTTTTTAAGC
* *
2569605 CCACGACTCCGTGGCACCTTCTTCT
1 CCACAACTCCGTGGCACCTTTTTCT
2569630 AAAGCCCACA
Statistics
Matches: 413, Mismatches: 45, Indels: 88
0.76 0.08 0.16
Matches are distributed among these distances:
86 19 0.05
87 2 0.00
88 25 0.06
89 20 0.05
90 17 0.04
92 5 0.01
93 42 0.10
94 7 0.02
95 33 0.08
96 100 0.24
98 1 0.00
99 1 0.00
100 24 0.06
101 5 0.01
102 50 0.12
103 41 0.10
104 21 0.05
ACGTcount: A:0.21, C:0.34, G:0.12, T:0.32
Consensus pattern (95 bp):
CCACAACTCCGTGGCACCTTTTTCTCTTCTAAGTCCACAACTCTATGGCACCCTTTTAAGCCCAC
AACTCCGTGGCATCTCTTTCCTTTTTAAGC
Found at i:2569665 original size:33 final size:32
Alignment explanation
Indices: 2569615--2569700 Score: 124
Period size: 33 Copynumber: 2.7 Consensus size: 32
2569605 CCACGACTCC
2569615 GTGGC-ACCTTCTTCTAAAGCCCACACAAGTCG
1 GTGGCAACCTTC-TCTAAAGCCCACACAAGTCG
2569647 GTGGCAACCATTCTCTAAAGCCCACACAAGTCG
1 GTGGCAACC-TTCTCTAAAGCCCACACAAGTCG
*
2569680 GTGGCAACCCT-TCT-AAGCCCA
1 GTGGCAACCTTCTCTAAAGCCCA
2569701 ATATAGCTGG
Statistics
Matches: 51, Mismatches: 1, Indels: 6
0.88 0.02 0.10
Matches are distributed among these distances:
30 7 0.14
31 3 0.06
32 6 0.12
33 32 0.63
34 3 0.06
ACGTcount: A:0.27, C:0.35, G:0.19, T:0.20
Consensus pattern (32 bp):
GTGGCAACCTTCTCTAAAGCCCACACAAGTCG
Found at i:2569668 original size:165 final size:163
Alignment explanation
Indices: 2569080--2569672 Score: 412
Period size: 165 Copynumber: 3.7 Consensus size: 163
2569070 TCCATGGCAC
* * *
2569080 CCTTTT-AAGCCCACAACTCCGTGGCAC-CTTTTT-CTTCAAAGCCCACAACTCCGTGGCACC-C
1 CCTTTTAAAGCCCACAACTACGTGGCACTCTTTTTCCTTCTAAGTCCACAACTCCGTGGCACCAC
* * * ** * * * * ** *
2569141 TTTTAAGCCCATAACTCCGTGGC-ACTTTTTTCATCTTTAAGTCCACAACTCCGTGGTACC----
66 -TTTAAGCCCACAAATCCATGGCAACTCATTCCTTC-TAAAGCCCACAACTCTATGGCACCTTTT
*
2569201 -C-TTT-TAAGCCCACAACTCCGTGGCACTTTTTTT
129 TCTTTTCTAAGCCCACAACTCCGTGGCAC-CTTTTT
* * * * * *
2569234 CATCTTT-AAGTCCACAACTCCATGGCA--C-----CCTTTTAAGCCCACAACTCCGTGGCACCT
1 CCT-TTTAAAGCCCACAACTACGTGGCACTCTTTTTCCTTCTAAGTCCACAACTCCGTGGCA-C-
* * * * *
2569291 TTCTCCTTCTAAGCCCACAACTCCGTGGCACCT-TTCTCCTTCT-AAGCCCACAACTCTATGGCA
63 --C-ACTT-TAAGCCCACAAATCCATGGCAACTCAT-TCCTTCTAAAGCCCACAACTCTATGGCA
* *
2569354 CCTTTTTCTTTTTTAAGCCCACAACTCCGTGGCATCTTTTT
123 CCTTTTTCTTTTCTAAGCCCACAACTCCGTGGCACCTTTTT
* *
2569395 CCTTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCTTCTAAGTCCACAACTCTGTGGCACCA
1 CC-TTTTAAAGCCCACAACTACGTGGCACTCTTTTTCCTTCTAAGTCCACAACTCCGTGGCACCA
* * * *
2569460 CTTTAAGCCCACAAATCCATGGCATCTCTTTCCTTTTTAAAGCCCACAACTCTGTGGCACCTTTT
65 CTTTAAGCCCACAAATCCATGGCAACTCATTCC-TTCTAAAGCCCACAACTCTATGGCACCTTTT
* * * *
2569525 TCTTTTCTAAGTCTACGACTCTGTGGCACCCTTTTTT
129 TCTTTTCTAAGCCCACAACTCCGTGGCA-CC-TTTTT
* * * *
2569562 CC-TTTAAAGCCCACAACTATGTGGCACTC-TTTTCCTTTTAAGTCCACGACTCCGTGGCACCTT
1 CCTTTTAAAGCCCACAACTACGTGGCACTCTTTTTCCTTCTAAGTCCACAACTCCGTGGCACC-A
**
2569625 CTTCTAAAGCCCACACAAGTCGGTGGCAAC-CATT-C-TCTAAAGCCCACA
65 CTT-T-AAGCCCACA-AA-TCCATGGCAACTCATTCCTTCTAAAGCCCACA
2569673 CAAGTCGGTG
Statistics
Matches: 358, Mismatches: 44, Indels: 63
0.77 0.09 0.14
Matches are distributed among these distances:
150 23 0.06
151 1 0.00
154 4 0.01
155 41 0.11
156 23 0.06
157 6 0.02
160 1 0.00
161 12 0.03
162 40 0.11
163 24 0.07
164 38 0.11
165 89 0.25
166 2 0.01
167 17 0.05
168 6 0.02
169 31 0.09
ACGTcount: A:0.21, C:0.34, G:0.12, T:0.32
Consensus pattern (163 bp):
CCTTTTAAAGCCCACAACTACGTGGCACTCTTTTTCCTTCTAAGTCCACAACTCCGTGGCACCAC
TTTAAGCCCACAAATCCATGGCAACTCATTCCTTCTAAAGCCCACAACTCTATGGCACCTTTTTC
TTTTCTAAGCCCACAACTCCGTGGCACCTTTTT
Found at i:2569751 original size:49 final size:49
Alignment explanation
Indices: 2569693--2570781 Score: 1356
Period size: 49 Copynumber: 22.8 Consensus size: 49
2569683 GCAACCCTTC
*
2569693 TAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
* *
2569742 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA----C--CTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
* *
2569785 TAAGTCCAATATCGCTGGCCTTGAATCAACATATTGGCACCTTCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
* *
2569834 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA----C--CTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
* *
2569877 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
* * * * *
2569926 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCACCAT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
* *
2569975 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
* * * * *
2570024 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCACCAT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
*
2570073 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
* * * * *
2570122 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCACCAT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
*
2570171 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
* *
2570220 TAAGTCCAATGTAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
* * *
2570269 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
* *
2570318 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA----C--CTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
* * * *
2570361 TAAGCCCGATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
*
2570410 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
* *
2570459 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
* * *
2570508 TAAGTCCAATGTAGCTGGCCTTGAATCAACACATTGGCA----C--CTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
* *
2570551 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
* *
2570600 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA----C--CTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
* * * * *
2570643 TAAGCCCGATATCGCCGGCCTTGAATCAGCATATTGGCATCTTCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
* * ** * **
2570692 TAAGTTCAATGTAGCTGGCCTTGAATCAGCACGTTGACATCCTTTTTCTCT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCA-CCTTCATCT-T
* * * * *
2570743 TAAGCCCAATATCGTTGGCCATGAATCAACATATTGGCA
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCA
2570782 TCTTTATCAC
Statistics
Matches: 897, Mismatches: 111, Indels: 62
0.84 0.10 0.06
Matches are distributed among these distances:
43 188 0.21
45 5 0.01
47 4 0.00
49 664 0.74
50 6 0.01
51 30 0.03
ACGTcount: A:0.25, C:0.26, G:0.18, T:0.31
Consensus pattern (49 bp):
TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
Found at i:2570025 original size:98 final size:94
Alignment explanation
Indices: 2569688--2570781 Score: 1553
Period size: 98 Copynumber: 11.5 Consensus size: 94
2569678 CGGTGGCAAC
* *
2569688 CCTTC-TAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAAT
1 CCTTCTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAAT
2569752 GTAGCTGGCCTTGAATCAGCACATTGGCA
66 GTAGCTGGCCTTGAATCAGCACATTGGCA
*
2569781 CC-T-TTAAGTCCAATATCGCTGGCCTTGAATCAACATATTGGCACCTTCATCTTTAAGTCCAAT
1 CCTTCTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAAT
2569844 GTAGCTGGCCTTGAATCAGCACATTGGCA
66 GTAGCTGGCCTTGAATCAGCACATTGGCA
*
2569873 CC-T-TTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAAT
1 CCTTCTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAAT
*
2569936 GTAGCTGGCCTTGACTCAGCACATTGGCA
66 GTAGCTGGCCTTGAATCAGCACATTGGCA
*
2569965 CCTTCACCATTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTC
1 CCTT---C-TTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTC
*
2570030 CAATGTAGCTGGCCTTGACTCAGCACATTGGCA
62 CAATGTAGCTGGCCTTGAATCAGCACATTGGCA
* *
2570063 CCTTCACCATTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTC
1 CCTT---C-TTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTC
*
2570128 CAATGTAGCTGGCCTTGACTCAGCACATTGGCA
62 CAATGTAGCTGGCCTTGAATCAGCACATTGGCA
* *
2570161 CCTTCACCATTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTC
1 CCTT---C-TTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTC
*
2570226 CAATGTAGCTGGCCTTGAATCAGCATATTGGCA
62 CAATGTAGCTGGCCTTGAATCAGCACATTGGCA
* * * *
2570259 CCTTTATCTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCATCTTTAAGTC
1 CC--T-TC-TTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTC
2570324 CAATGTAGCTGGCCTTGAATCAGCACATTGGCA
62 CAATGTAGCTGGCCTTGAATCAGCACATTGGCA
* * *
2570357 CC-T-TTAAGCCCGATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAAT
1 CCTTCTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAAT
* *
2570420 ATAGCTGGCCTTGAATCAGCATATTGGCA
66 GTAGCTGGCCTTGAATCAGCACATTGGCA
*
2570449 CCTTTATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTC
1 CC--T-TC-TTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTC
*
2570514 CAATGTAGCTGGCCTTGAATCAACACATTGGCA
62 CAATGTAGCTGGCCTTGAATCAGCACATTGGCA
*
2570547 CC-T-TTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAAT
1 CCTTCTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAAT
2570610 GTAGCTGGCCTTGAATCAGCACATTGGCA
66 GTAGCTGGCCTTGAATCAGCACATTGGCA
* * * * *
2570639 CC-T-TTAAGCCCGATATCGCCGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTTCAAT
1 CCTTCTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAAT
* *
2570702 GTAGCTGGCCTTGAATCAGCACGTTGACA
66 GTAGCTGGCCTTGAATCAGCACATTGGCA
* * * *
2570731 TCCTTTTTCTCTTAAGCCCAATATCGTTGGCCATGAATCAACATATTGGCA
1 -CC----T-TCTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCA
2570782 TCTTTATCAC
Statistics
Matches: 936, Mismatches: 41, Indels: 41
0.92 0.04 0.04
Matches are distributed among these distances:
92 433 0.46
93 5 0.01
94 2 0.00
96 1 0.00
98 457 0.49
99 1 0.00
100 36 0.04
101 1 0.00
ACGTcount: A:0.25, C:0.26, G:0.18, T:0.31
Consensus pattern (94 bp):
CCTTCTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAAT
GTAGCTGGCCTTGAATCAGCACATTGGCA
Found at i:2571671 original size:33 final size:33
Alignment explanation
Indices: 2571634--2571700 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
2571624 TTCAACGATT
2571634 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
2571667 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
2571700 T
1 T
2571701 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:2571672 original size:13 final size:13
Alignment explanation
Indices: 2571654--2571678 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2571644 CATAAAATGT
2571654 TGTATCGATACAA
1 TGTATCGATACAA
2571667 TGTATCGATACA
1 TGTATCGATACA
2571679 TATTTTTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:2571738 original size:13 final size:13
Alignment explanation
Indices: 2571720--2571744 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2571710 TGCCAAAAAA
2571720 TGTATCGATACAT
1 TGTATCGATACAT
2571733 TGTATCGATACA
1 TGTATCGATACA
2571745 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2571846 original size:52 final size:52
Alignment explanation
Indices: 2571753--2571876 Score: 214
Period size: 52 Copynumber: 2.4 Consensus size: 52
2571743 CACTGATCTT
*
2571753 TGTATCGATACATGCAGGC-AATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
2571804 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
2571856 TGTATCGATACATGCAAGCAA
1 TGTATCGATACATGCAGGCAA
2571877 CTTTTCATAT
Statistics
Matches: 69, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
51 19 0.28
52 50 0.72
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.28
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:2575032 original size:49 final size:49
Alignment explanation
Indices: 2574959--2575347 Score: 495
Period size: 49 Copynumber: 8.0 Consensus size: 49
2574949 CGTTGCGGCA
* * * *
2574959 ATCTTGAAGTCCAATATAGCTGGCCTTGAATTAGCATATTGGCACCTTT
1 ATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTT
* * *
2575008 ATCTTTAAGTCCAATGTAGTTGGCCTTGACTCAGCACATTGGCACCTTC
1 ATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTT
* * * * *
2575057 ACCATTAAGTCCAATATAGCTGGCCTTGAATTAGCATATTGGCACCTTT
1 ATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTT
* * *
2575106 ATCTTTAGGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTC
1 ATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTT
*
2575155 ATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACC-TC
1 ATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTT
*
2575203 ACCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA-C---
1 ATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTT
* * *
2575248 --CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACATTTT
1 ATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAC-CTTT
* *
2575296 CCATCTTTAAGTTCAATGTAGCTGGCCTTGAATCAGCACATTGACATCCTTT
1 --ATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA-CCTTT
2575348 TTCTCATCAT
Statistics
Matches: 296, Mismatches: 34, Indels: 17
0.85 0.10 0.05
Matches are distributed among these distances:
43 40 0.14
47 1 0.00
48 45 0.15
49 168 0.57
52 41 0.14
53 1 0.00
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.32
Consensus pattern (49 bp):
ATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTT
Found at i:2575266 original size:43 final size:43
Alignment explanation
Indices: 2575157--2575347 Score: 211
Period size: 43 Copynumber: 4.1 Consensus size: 43
2575147 GCACCTTCAT
2575157 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTCAC
1 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGG-----CAC
2575205 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAC
1 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAC
* *
2575248 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACATTTTCC
1 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGG--CA-----C
* *
2575298 ATCTTTAAGTTCAATGTAGCTGGCCTTGAATCAGCACATTGACATC
1 --CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA-C
2575344 CTTT
1 CTTT
2575348 TTCTCATCAT
Statistics
Matches: 127, Mismatches: 7, Indels: 22
0.81 0.04 0.14
Matches are distributed among these distances:
43 41 0.32
44 4 0.03
45 2 0.02
46 1 0.01
48 40 0.31
50 3 0.02
52 36 0.28
ACGTcount: A:0.26, C:0.25, G:0.18, T:0.31
Consensus pattern (43 bp):
CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAC
Found at i:2579774 original size:55 final size:54
Alignment explanation
Indices: 2579582--2580268 Score: 619
Period size: 55 Copynumber: 12.0 Consensus size: 54
2579572 GCTTTTTTCT
* * * *
2579582 TTTTAAAGCCCACACGAGTTGGTGGCACCTTTACTCCTCAAAGAGCAGGACACCTTTTCC
1 TTTTAAAGCCCACACAAGTTGGTGGCACTTTTAGTCCTCAAAGAGCAGG--A-C---GCC
* * * *
2579642 TTTTAAAGCCCACACAAGTTGGTGGCACCTTTAGTCCTCAAAAAGTAGGAGGTCTTTTC
1 TTTTAAAGCCCACACAAGTTGGTGGCACTTTTAGTCCTCAAAGAGCAGGACG-C----C
* * *
2579701 TTTTTAAAGCCCATACAAGTTGGTGGCAACTTTTAGTCCTCAAAGAACAGGACGCA
1 -TTTTAAAGCCCACACAAGTTGGTGGC-ACTTTTAGTCCTCAAAGAGCAGGACGCC
* * *
2579757 TTTTAAAGCCCACACAAGTTGATGGCACCTTTCAGTCCTCAAAGAGCAAGACGCC
1 TTTTAAAGCCCACACAAGTTGGTGGCA-CTTTTAGTCCTCAAAGAGCAGGACGCC
* * * *
2579812 TTTTAAAGCCCACACAAGTTGGTGCCACCTTTTAGTCCACAAAGAGCAAGACACC
1 TTTTAAAGCCCACACAAGTTGGTGGCA-CTTTTAGTCCTCAAAGAGCAGGACGCC
**
2579867 TTTTAAAGCCCACACAAGTTGGTGGCACTTCCCAGTCCTCAAAGAGCAGGACGCC
1 TTTTAAAGCCCACACAAGTTGGTGGCACTT-TTAGTCCTCAAAGAGCAGGACGCC
*
2579922 TCTTAAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCCTCAAAGAGCAGGACGCC
1 TTTTAAAGCCCACACAAGTTGGTGGCACTTTT--AGTCCTCAAAGAGCAGGACGCC
* *
2579977 TCTTAAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCCTCAAAGAGCAAGACGCC
1 TTTTAAAGCCCACACAAGTTGGTGGCACTTTT--AGTCCTCAAAGAGCAGGACGCC
* * *
2580032 TCTTAAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCCTCAAAGAGTAGGATGCTTTC
1 TTTTAAAGCCCACACAAGTTGGTGGCACTTTT--AGTCCTCAAAGAGCAGGACGC---C
** * *
2580090 TCTTTGCAAAG-CC-CACAAGTTGGTGGCACCTTCCAGACCTCAAAGAGCAGGACACCTTC
1 T-TTT--AAAGCCCACACAAGTTGGTGGCA-CTTTTAGTCCTCAAAGAGCAGGAC-GC--C
* *
2580149 TCCTCTTCAAAGCCCACACAAGTTGGTGGCACCTTTTAGTCCTCAAAGAGCAAGACACCTTTTTC
1 T--T-TT-AAAGCCCACACAAGTTGGTGGCA-CTTTTAGTCCTCAAAGAGCAGGAC-GC-----C
* **
2580214 TTTTTAAAGCCCAAACAAGTTGGTGGCACTTCCGAGTCCTCAAAGAGCAGGACGC
1 -TTTTAAAGCCCACACAAGTTGGTGGCACTT-TTAGTCCTCAAAGAGCAGGACGC
2580269 TCTCTCCTTT
Statistics
Matches: 545, Mismatches: 53, Indels: 57
0.83 0.08 0.09
Matches are distributed among these distances:
54 6 0.01
55 296 0.54
58 3 0.01
59 38 0.07
60 81 0.15
61 35 0.06
62 79 0.14
63 2 0.00
64 1 0.00
65 3 0.01
66 1 0.00
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.24
Consensus pattern (54 bp):
TTTTAAAGCCCACACAAGTTGGTGGCACTTTTAGTCCTCAAAGAGCAGGACGCC
Found at i:2579847 original size:110 final size:111
Alignment explanation
Indices: 2579521--2580271 Score: 720
Period size: 110 Copynumber: 6.5 Consensus size: 111
2579511 TTTTTTTTCT
*
2579521 TTTTAAAACCCACACAAGTTGGTGGCACC-TCCAGTCCTCAAAGAGCAAGACGCTTTTTTCTTTT
1 TTTTAAAGCCCACACAAGTTGGTGGCACCTTCCAGTCCTCAAAGAGCAAGACGC-----TC-TTT
* * *
2579585 TAAAGCCCACACGAGTTGGTGGCACC-TTTACTCCTCAAAGAGCAGGACACCTTTTCC
60 TAAAGCCCACACAAGTTGGTGGCACCTTTTAGTCCTCAAAGAGCAGG--A-C---GCC
* * * * *
2579642 TTTTAAAGCCCACACAAGTTGGTGGCACCTT-TAGTCCTCAAAAAGTAGGAGGTCTTTTCTTTTT
1 TTTTAAAGCCCACACAAGTTGGTGGCACCTTCCAGTCCTCAAAGAGCAAGACG-C---TC-TTTT
* * * *
2579706 AAAGCCCATACAAGTTGGTGGCAACTTTTAGTCCTCAAAGAACAGGACGCA
61 AAAGCCCACACAAGTTGGTGGCACCTTTTAGTCCTCAAAGAGCAGGACGCC
* *
2579757 TTTTAAAGCCCACACAAGTTGATGGCACCTTTCAGTCCTCAAAGAGCAAGACGC-CTTTTAAAGC
1 TTTTAAAGCCCACACAAGTTGGTGGCACCTTCCAGTCCTCAAAGAGCAAGACGCTCTTTTAAAGC
* * * *
2579821 CCACACAAGTTGGTGCCACCTTTTAGTCCACAAAGAGCAAGACACC
66 CCACACAAGTTGGTGGCACCTTTTAGTCCTCAAAGAGCAGGACGCC
* *
2579867 TTTTAAAGCCCACACAAGTTGGTGGCA-CTTCCCAGTCCTCAAAGAGCAGGACGC-CTCTTAAAG
1 TTTTAAAGCCCACACAAGTTGGTGGCACCTT-CCAGTCCTCAAAGAGCAAGACGCTCTTTTAAAG
2579930 CCCACACAAGTTGGTGGCA--TTTTCCAGTCCTCAAAGAGCAGGACGCC
65 CCCACACAAGTTGGTGGCACCTTTT--AGTCCTCAAAGAGCAGGACGCC
* ** *
2579977 TCTTAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAAGACGC-CTCTTAAAGC
1 TTTTAAAGCCCACACAAGTTGGTGGCACCTTCCAGTCCTCAAAGAGCAAGACGCTCTTTTAAAGC
* *
2580041 CCACACAAGTTGGTGGCA--TTTTCCAGTCCTCAAAGAGTAGGATGCTTTC
66 CCACACAAGTTGGTGGCACCTTTT--AGTCCTCAAAGAGCAGGACGC---C
* * *
2580090 TCTTTGCAAAG-CC-CACAAGTTGGTGGCACCTTCCAGACCTCAAAGAGCAGGACACCTTCTCCT
1 T-TTT--AAAGCCCACACAAGTTGGTGGCACCTTCCAGTCCTCAAAGAGCAAGAC-GC-TCT--T
* *
2580153 CTTCAAAGCCCACACAAGTTGGTGGCACCTTTTAGTCCTCAAAGAGCAAGACACCTTTTTC
59 -TT-AAAGCCCACACAAGTTGGTGGCACCTTTTAGTCCTCAAAGAGCAGGAC-GC-----C
* *
2580214 TTTTTAAAGCCCAAACAAGTTGGTGGCA-CTTCCGAGTCCTCAAAGAGCAGGACGCTCT
1 -TTTTAAAGCCCACACAAGTTGGTGGCACCTTCC-AGTCCTCAAAGAGCAAGACGCTCT
2580272 CTCCTTTCAC
Statistics
Matches: 546, Mismatches: 54, Indels: 59
0.83 0.08 0.09
Matches are distributed among these distances:
108 4 0.01
109 3 0.01
110 240 0.44
111 3 0.01
113 2 0.00
114 38 0.07
115 35 0.06
116 20 0.04
117 2 0.00
118 1 0.00
119 1 0.00
120 34 0.06
121 101 0.18
122 10 0.02
123 12 0.02
124 39 0.07
125 1 0.00
ACGTcount: A:0.28, C:0.28, G:0.19, T:0.25
Consensus pattern (111 bp):
TTTTAAAGCCCACACAAGTTGGTGGCACCTTCCAGTCCTCAAAGAGCAAGACGCTCTTTTAAAGC
CCACACAAGTTGGTGGCACCTTTTAGTCCTCAAAGAGCAGGACGCC
Found at i:2579919 original size:165 final size:164
Alignment explanation
Indices: 2579394--2580492 Score: 807
Period size: 165 Copynumber: 6.4 Consensus size: 164
2579384 GATGCCTTTT
*
2579394 CCTTTTCAAAGCCCACACGAGTTGGTGGCACCTTT-AGTCCTCAAAGAGCAGGACGCCTTTTTCT
1 CCTTTT-AAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACG-C-----CT
* **
2579458 TTTCAAAGCCCACACGAGTTGGTGGCACC-TTTAGTCCTCAAAGAGCGGGACACTTTTTTTTCTT
59 TTT-AAAGCCCACACAAGTTGGTGGCACCTTTTAGTCCTCAAAGAGCAAGACAC--------C-T
* * *
2579522 TTTAAAACCCACACAAGTTGGTGGCACCTCCAGTCCTCAAAGAGCAAGACG
114 TTTAAAGCCCACACAAGTTGGTGGCACTTCCAGTCCTCAAAGAGCAGGACG
* *
2579573 CTTTTTTCTTTTTAAAGCCCACACGAGTTGGTGGCACCTTT-ACTCCTCAAAGAGCAGGACACCT
1 C------C-TTTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGG--A-C-
* * * * *
2579637 TTTCCTTTTAAAGCCCACACAAGTTGGTGGCACC-TTTAGTCCTCAAAAAGTAGGAGGTCTTTTC
55 --GCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTTAGTCCTC--AAAG-AGCAAGAC---AC
* * ** *
2579701 TTTTTAAAGCCCATACAAGTTGGTGGCAACTTTTAGTCCTCAAAGAACAGGACG
112 CTTTTAAAGCCCACACAAGTTGGTGGC-ACTTCCAGTCCTCAAAGAGCAGGACG
* * *
2579755 CATTTTAAAGCCCACACAAGTTGATGGCACCTTTCAGTCCTCAAAGAGCAAGACGCCTTTTAAAG
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACGCCTTTTAAAG
* *
2579820 CCCACACAAGTTGGTGCCACCTTTTAGTCCACAAAGAGCAAGACACCTTTTAAAGCCCACACAAG
66 CCCACACAAGTTGGTGGCACCTTTTAGTCCTCAAAGAGCAAGACACCTTTTAAAGCCCACACAAG
2579885 TTGGTGGCACTTCCCAGTCCTCAAAGAGCAGGACG
131 TTGGTGGCACTT-CCAGTCCTCAAAGAGCAGGACG
* * *
2579920 CCTCTTAAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCCTCAAAGAGCAGGACGCCTCTTAAA
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACCTTT-CAGTCCTCAAAGAGCAGGACGCCTTTTAAA
* *
2579984 GCCCACACAAGTTGGTGGCA--TTTTCCAGTCCTCAAAGAGCAAGACGCCTCTTAAAGCCCACAC
65 GCCCACACAAGTTGGTGGCACCTTTT--AGTCCTCAAAGAGCAAGACACCTTTTAAAGCCCACAC
* * *
2580047 AAGTTGGTGGCATTTTCCAGTCCTCAAAGAGTAGGATG
128 AAGTTGGTGGCA-CTTCCAGTCCTCAAAGAGCAGGACG
* * *
2580085 CTTTCTCTTTGCAAAG-CC-CACAAGTTGGTGGCACCTTCCAGACCTCAAAGAGCAGGACACCTT
1 C---CT-TTT--AAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGAC-GC--
2580148 CTCCTCTTCAAAGCCCACACAAGTTGGTGGCACCTTTTAGTCCTCAAAGAGCAAGACACCTTTTT
57 CT--T-TT-AAAGCCCACACAAGTTGGTGGCACCTTTTAGTCCTCAAAGAGCAAGACA-C-----
*
2580213 CTTTTTAAAGCCCAAACAAGTTGGTGGCACTTCCGAGTCCTCAAAGAGCAGGACG
112 C-TTTTAAAGCCCACACAAGTTGGTGGCACTTCC-AGTCCTCAAAGAGCAGGACG
* * * *
2580268 -C---T----CTCTC-C---TT--T--CACCCTTT-AGTCCTCAAAGAGCAAGACTCCTTTTCCT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCA-CCTTTCAGTCCTCAAAGAGCAGGACGCC---T--T
* * *
2580316 CTTAAAGCCCATACAAGTTGGTGGCA-CTTTCTTGTCCTCAAAGAGCAAGACGCCTTTTCCTTTT
60 -TTAAAGCCCACACAAGTTGGTGGCACCTTT-TAGTCCTCAAAGAGCAAGA---C---ACCTTTT
* * *
2580380 AAAGCCCACACGAGTTGGTGGCACTTTCCAGTCCTCAAAGAGTAGG-TG
117 AAAGCCCACACAAGTTGGTGGCAC-TTCCAGTCCTCAAAGAGCAGGACG
*
2580428 CCTTCTCCTGTTAAAGCCCACACAAGTTGGTGGCACC-TTCTAGTCCTCAAAGAGCAGGATGCCT
1 -C--CT--T-TTAAAGCCCACACAAGTTGGTGGCACCTTTC-AGTCCTCAAAGAGCAGGACGCCT
2580492 T
59 T
2580493 CTCCTTTCCA
Statistics
Matches: 757, Mismatches: 74, Indels: 180
0.75 0.07 0.18
Matches are distributed among these distances:
160 2 0.00
161 46 0.06
162 46 0.06
163 30 0.04
164 12 0.02
165 187 0.25
166 2 0.00
167 3 0.00
168 7 0.01
169 40 0.05
170 38 0.05
171 14 0.02
172 2 0.00
173 1 0.00
174 4 0.01
175 34 0.04
176 57 0.08
177 2 0.00
178 6 0.01
179 3 0.00
180 3 0.00
181 26 0.03
182 48 0.06
183 43 0.06
184 34 0.04
185 50 0.07
186 8 0.01
187 6 0.01
188 1 0.00
190 2 0.00
ACGTcount: A:0.26, C:0.28, G:0.19, T:0.26
Consensus pattern (164 bp):
CCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACGCCTTTTAAAG
CCCACACAAGTTGGTGGCACCTTTTAGTCCTCAAAGAGCAAGACACCTTTTAAAGCCCACACAAG
TTGGTGGCACTTCCAGTCCTCAAAGAGCAGGACG
Found at i:2580363 original size:61 final size:61
Alignment explanation
Indices: 2580286--2580483 Score: 274
Period size: 61 Copynumber: 3.3 Consensus size: 61
2580276 TTTCACCCTT
*
2580286 TAGTCCTCAAAGAGCAAGACTCCTTTTCCTCTTAAAGCCCATACAAGTTGGTGGCACTTTC
1 TAGTCCTCAAAGAGCAAGACTCCTTTTCCTCTTAAAGCCCACACAAGTTGGTGGCACTTTC
* * * *
2580347 TTGTCCTCAAAGAGCAAGACGCCTTTTCCTTTTAAAGCCCACACGAGTTGGTGGCACTTTC
1 TAGTCCTCAAAGAGCAAGACTCCTTTTCCTCTTAAAGCCCACACAAGTTGGTGGCACTTTC
* * * * * *
2580408 CAGTCCTCAAAGAG-TAG-GTGCCTTCTCCTGTTAAAGCCCACACAAGTTGGTGGCACCTTC
1 TAGTCCTCAAAGAGCAAGACT-CCTTTTCCTCTTAAAGCCCACACAAGTTGGTGGCACTTTC
2580468 TAGTCCTCAAAGAGCA
1 TAGTCCTCAAAGAGCA
2580484 GGATGCCTTC
Statistics
Matches: 119, Mismatches: 16, Indels: 4
0.86 0.12 0.03
Matches are distributed among these distances:
60 51 0.43
61 68 0.57
ACGTcount: A:0.25, C:0.28, G:0.19, T:0.27
Consensus pattern (61 bp):
TAGTCCTCAAAGAGCAAGACTCCTTTTCCTCTTAAAGCCCACACAAGTTGGTGGCACTTTC
Found at i:2580378 original size:100 final size:101
Alignment explanation
Indices: 2580178--2580368 Score: 294
Period size: 100 Copynumber: 1.9 Consensus size: 101
2580168 AAGTTGGTGG
* * *
2580178 CACCTTTTAGTCCTCAAAGAGCAAGACACCTTTTTCTTTTTAAAGCCCAAACAAGTTGGTGGCAC
1 CACCCTTTAGTCCTCAAAGAGCAAGACACCTTTTTCCTCTTAAAGCCCAAACAAGTTGGTGGCAC
*
2580243 TTCCGAGTCCTCAAAGAGCAGGACGCTCTCTCCTTT
66 TTCCGAGTCCTCAAAGAGCAAGACGCTCTCTCCTTT
* *
2580279 CACCCTTTAGTCCTCAAAGAGCAAGACTCC-TTTTCCTCTTAAAGCCCATACAAGTTGGTGGCAC
1 CACCCTTTAGTCCTCAAAGAGCAAGACACCTTTTTCCTCTTAAAGCCCAAACAAGTTGGTGGCAC
* **
2580343 TTTCTTGTCCTCAAAGAGCAAGACGC
66 TTCCGAGTCCTCAAAGAGCAAGACGC
2580369 CTTTTCCTTT
Statistics
Matches: 81, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
100 53 0.65
101 28 0.35
ACGTcount: A:0.26, C:0.29, G:0.17, T:0.28
Consensus pattern (101 bp):
CACCCTTTAGTCCTCAAAGAGCAAGACACCTTTTTCCTCTTAAAGCCCAAACAAGTTGGTGGCAC
TTCCGAGTCCTCAAAGAGCAAGACGCTCTCTCCTTT
Found at i:2580593 original size:40 final size:42
Alignment explanation
Indices: 2580503--2580596 Score: 113
Period size: 42 Copynumber: 2.3 Consensus size: 42
2580493 CTCCTTTCCA
* *
2580503 CTTTGTCCTCAAGAAGCAGGACACTTTTCTTTTCTTCTCTTC
1 CTTTGTCCTCAAGAAGCAAGACACTTTTCTATTCTTCTCTTC
* * *
2580545 CTTGGTCCTCAAGGAGCAAGAC-CTATTTC-ATTC-TCTTTTC
1 CTTTGTCCTCAAGAAGCAAGACACT-TTTCTATTCTTCTCTTC
2580585 CTTTGTCCTCAA
1 CTTTGTCCTCAA
2580597 AAAGTGGGCC
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
40 17 0.38
41 5 0.11
42 23 0.51
ACGTcount: A:0.18, C:0.29, G:0.13, T:0.40
Consensus pattern (42 bp):
CTTTGTCCTCAAGAAGCAAGACACTTTTCTATTCTTCTCTTC
Found at i:2583810 original size:28 final size:28
Alignment explanation
Indices: 2583778--2583848 Score: 108
Period size: 28 Copynumber: 2.5 Consensus size: 28
2583768 CACCATTGGA
* *
2583778 GATACTCCAACCCTGTTATTTC-ATCGGG
1 GATACTCCAACCCCGTTATTTCTA-AGGG
2583806 GATACTCCAACCCCGTTATTTCTAAGGG
1 GATACTCCAACCCCGTTATTTCTAAGGG
2583834 GATACTCCAACCCCG
1 GATACTCCAACCCCG
2583849 GCTTTATATC
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
28 39 0.98
29 1 0.03
ACGTcount: A:0.24, C:0.32, G:0.17, T:0.27
Consensus pattern (28 bp):
GATACTCCAACCCCGTTATTTCTAAGGG
Found at i:2583999 original size:79 final size:79
Alignment explanation
Indices: 2583908--2584082 Score: 192
Period size: 79 Copynumber: 2.2 Consensus size: 79
2583898 CTGTTATTTC
* ** * * *
2583908 ATCGGGGATACTCCAATC-TCGTTATTTTTGAAGGGATACTCCAACTCTGATTTTATTTCCAAAA
1 ATCGGGGATACTCCAA-CACCACTATTTTCGAAGGGATACTCCAACCCCGATTTTATTTCCAAAA
2583972 CACCAA-TTTCTCACA
65 CACCAATTTTCT-ACA
** * *
2583987 ATCGGGGATACTCCAACACCACTATTTTCGCGGGGATACTCCAACCCCGATTTTATTTTCAAAAT
1 ATCGGGGATACTCCAACACCACTATTTTCGAAGGGATACTCCAACCCCGATTTTATTTCCAAAAC
* *
2584052 ACCGATTTTCTATA
66 ACCAATTTTCTACA
**
2584066 ATCATGGATACTCCAAC
1 ATCGGGGATACTCCAAC
2584083 TCTATTTCTT
Statistics
Matches: 80, Mismatches: 14, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
78 1 0.01
79 74 0.93
80 5 0.06
ACGTcount: A:0.29, C:0.26, G:0.13, T:0.32
Consensus pattern (79 bp):
ATCGGGGATACTCCAACACCACTATTTTCGAAGGGATACTCCAACCCCGATTTTATTTCCAAAAC
ACCAATTTTCTACA
Found at i:2585090 original size:3 final size:3
Alignment explanation
Indices: 2585082--2585156 Score: 150
Period size: 3 Copynumber: 25.0 Consensus size: 3
2585072 CGTTGCGACA
2585082 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
2585130 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
2585157 TTAAAAAGGT
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 72 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:2602163 original size:18 final size:19
Alignment explanation
Indices: 2602136--2602172 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
2602126 TTTTATAAAA
*
2602136 TAATATTATTT-AATTTAT
1 TAATAATATTTAAATTTAT
2602154 TAATAATATTTAAATTTAT
1 TAATAATATTTAAATTTAT
2602173 ATACGATCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
TAATAATATTTAAATTTAT
Found at i:2607346 original size:21 final size:21
Alignment explanation
Indices: 2607306--2607353 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
2607296 TTATATATCC
*
2607306 ACATAAAACAACATAAATATA
1 ACATGAAACAACATAAATATA
*
2607327 ACATGAAACAACA-AAGATATG
1 ACATGAAACAACATAA-ATATA
2607348 ACATGA
1 ACATGA
2607354 TAAATATCAC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 2 0.08
21 22 0.92
ACGTcount: A:0.60, C:0.15, G:0.08, T:0.17
Consensus pattern (21 bp):
ACATGAAACAACATAAATATA
Found at i:2610513 original size:52 final size:52
Alignment explanation
Indices: 2610365--2610493 Score: 231
Period size: 52 Copynumber: 2.5 Consensus size: 52
2610355 CGAAATATGA
2610365 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
* *
2610417 AAATTTGCCTGTATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
*
2610469 AAATTTGCCTGCACGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
2610494 AAGATCAGTG
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 73 1.00
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.35
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
Found at i:2610602 original size:19 final size:19
Alignment explanation
Indices: 2610578--2610628 Score: 84
Period size: 19 Copynumber: 2.7 Consensus size: 19
2610568 AGCGATACAT
2610578 TGTATCGATACAACACTTA
1 TGTATCGATACAACACTTA
* *
2610597 TGTATCGATACAACATTTT
1 TGTATCGATACAACACTTA
2610616 TGTATCGATACAA
1 TGTATCGATACAA
2610629 ATCGTTGAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.35, C:0.18, G:0.12, T:0.35
Consensus pattern (19 bp):
TGTATCGATACAACACTTA
Found at i:2612259 original size:24 final size:24
Alignment explanation
Indices: 2612187--2612249 Score: 117
Period size: 24 Copynumber: 2.6 Consensus size: 24
2612177 AAGGAATTTT
2612187 TAATGAATATTTAATATGAGTTAAA
1 TAAT-AATATTTAATATGAGTTAAA
2612212 TAATAATATTTAATATGAGTTAAA
1 TAATAATATTTAATATGAGTTAAA
2612236 TAATAATATTTAAT
1 TAATAATATTTAAT
2612250 GAATATTAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
24 34 0.89
25 4 0.11
ACGTcount: A:0.49, C:0.00, G:0.08, T:0.43
Consensus pattern (24 bp):
TAATAATATTTAATATGAGTTAAA
Found at i:2613406 original size:24 final size:20
Alignment explanation
Indices: 2613364--2613520 Score: 82
Period size: 20 Copynumber: 7.8 Consensus size: 20
2613354 TTTTCACAAT
2613364 TTGTATCGATACATTGTTCA
1 TTGTATCGATACATTGTTCA
2613384 TTGTATCGATACATTCTGGGTTCACCCAGA
1 TTGTATCGATACA-T-T--GTT----C--A
2613414 TT-TATCGATACATT-TTGCA
1 TTGTATCGATACATTGTT-CA
*
2613433 TTGTATCGATACATTGCTCA
1 TTGTATCGATACATTGTTCA
*
2613453 TTGTATCG---C----TACA
1 TTGTATCGATACATTGTTCA
* *
2613466 TTGTATCGATACATTGCTCG
1 TTGTATCGATACATTGTTCA
*
2613486 TTCTATCGATACATT-TTACA
1 TTGTATCGATACATTGTT-CA
*
2613506 ATGTATCGATACATT
1 TTGTATCGATACATT
2613521 CAGGCATTTT
Statistics
Matches: 105, Mismatches: 12, Indels: 40
0.67 0.08 0.25
Matches are distributed among these distances:
13 10 0.10
16 1 0.01
17 1 0.01
19 4 0.04
20 64 0.61
21 3 0.03
22 1 0.01
24 5 0.05
27 1 0.01
28 2 0.02
29 10 0.10
30 3 0.03
ACGTcount: A:0.25, C:0.19, G:0.15, T:0.41
Consensus pattern (20 bp):
TTGTATCGATACATTGTTCA
Found at i:2613467 original size:13 final size:13
Alignment explanation
Indices: 2613451--2613481 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
2613441 ATACATTGCT
*
2613451 CATTGTATCGCTA
1 CATTGTATCGATA
2613464 CATTGTATCGATA
1 CATTGTATCGATA
2613477 CATTG
1 CATTG
2613482 CTCGTTCTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.26, C:0.19, G:0.16, T:0.39
Consensus pattern (13 bp):
CATTGTATCGATA
Found at i:2613473 original size:33 final size:33
Alignment explanation
Indices: 2613431--2613500 Score: 113
Period size: 33 Copynumber: 2.1 Consensus size: 33
2613421 ATACATTTTG
* *
2613431 CATTGTATCGATACATTGCTCATTGTATCGCTA
1 CATTGTATCGATACATTGCTCATTCTATCGATA
*
2613464 CATTGTATCGATACATTGCTCGTTCTATCGATA
1 CATTGTATCGATACATTGCTCATTCTATCGATA
2613497 CATT
1 CATT
2613501 TTACAATGTA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.24, C:0.21, G:0.14, T:0.40
Consensus pattern (33 bp):
CATTGTATCGATACATTGCTCATTCTATCGATA
Found at i:2615874 original size:51 final size:51
Alignment explanation
Indices: 2615819--2615934 Score: 187
Period size: 51 Copynumber: 2.3 Consensus size: 51
2615809 TTCTGAGGGA
*
2615819 ATACTCCAACCCCGATTTTATTTCTAAAACACCAATTCTCCATAATTGGGG
1 ATACTCCAACCCCGATTTTATTTCTAAAACACCAATTCTCCACAATTGGGG
* * * *
2615870 ATACTGCAACTCCGATTTTATTTCTAAAACACCAATTTTTCACAATTGGGG
1 ATACTCCAACCCCGATTTTATTTCTAAAACACCAATTCTCCACAATTGGGG
2615921 ATACTCCAACCCCG
1 ATACTCCAACCCCG
2615935 TTATTTCATC
Statistics
Matches: 58, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
51 58 1.00
ACGTcount: A:0.31, C:0.28, G:0.10, T:0.31
Consensus pattern (51 bp):
ATACTCCAACCCCGATTTTATTTCTAAAACACCAATTCTCCACAATTGGGG
Found at i:2615949 original size:28 final size:28
Alignment explanation
Indices: 2615917--2615988 Score: 92
Period size: 28 Copynumber: 2.6 Consensus size: 28
2615907 TTTCACAATT
* *
2615917 GGGGATACTCCAACCCCGTTATTTCAT-C
1 GGGGATACTCCAACCCCATTATTT-ATGA
* *
2615945 GGGGATACTCAAACCCCATTATTTTTGA
1 GGGGATACTCCAACCCCATTATTTATGA
2615973 GGGGATACTCCAACCC
1 GGGGATACTCCAACCC
2615989 TAATTTTTAT
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
27 1 0.03
28 37 0.97
ACGTcount: A:0.25, C:0.29, G:0.19, T:0.26
Consensus pattern (28 bp):
GGGGATACTCCAACCCCATTATTTATGA
Found at i:2628427 original size:1 final size:1
Alignment explanation
Indices: 2628423--2628483 Score: 50
Period size: 1 Copynumber: 61.0 Consensus size: 1
2628413 TTTTTTCTTT
* * * * * * * *
2628423 AAAAAAAAAAAACAAAAAAAACAACAAAAAAATAAAAAAAGAAAAAAGAAAGAAAAGAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
2628484 GAACTTACTT
Statistics
Matches: 44, Mismatches: 16, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
1 44 1.00
ACGTcount: A:0.87, C:0.05, G:0.07, T:0.02
Consensus pattern (1 bp):
A
Found at i:2628474 original size:11 final size:10
Alignment explanation
Indices: 2628424--2628486 Score: 56
Period size: 10 Copynumber: 6.2 Consensus size: 10
2628414 TTTTTCTTTA
*
2628424 AAAAAAAAAA
1 AAAAAAAAAG
*
2628434 ACAAAAAAAAC
1 A-AAAAAAAAG
*
2628445 AACAAAAAA-
1 AAAAAAAAAG
*
2628454 ATAAAAAAAG
1 AAAAAAAAAG
2628464 AAAAAAGAAAG
1 AAAAAA-AAAG
*
2628475 AAAAGAAAAG
1 AAAAAAAAAG
2628485 AA
1 AA
2628487 CTTACTTAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
9 7 0.16
10 19 0.43
11 18 0.41
ACGTcount: A:0.86, C:0.05, G:0.08, T:0.02
Consensus pattern (10 bp):
AAAAAAAAAG
Found at i:2628478 original size:16 final size:15
Alignment explanation
Indices: 2628423--2628483 Score: 56
Period size: 14 Copynumber: 4.2 Consensus size: 15
2628413 TTTTTTCTTT
*
2628423 AAAAA-AAAAAAACA
1 AAAAAGAAAAAAAGA
* *
2628437 AAAAA-AACAACA-A
1 AAAAAGAAAAAAAGA
*
2628450 AAAAATAAAAAAAGA
1 AAAAAGAAAAAAAGA
2628465 AAAAAGAAAGAAAAGA
1 AAAAAGAAA-AAAAGA
2628481 AAA
1 AAA
2628484 GAACTTACTT
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
13 6 0.15
14 15 0.38
15 9 0.23
16 9 0.23
ACGTcount: A:0.87, C:0.05, G:0.07, T:0.02
Consensus pattern (15 bp):
AAAAAGAAAAAAAGA
Found at i:2629732 original size:55 final size:55
Alignment explanation
Indices: 2629557--2629912 Score: 406
Period size: 57 Copynumber: 6.3 Consensus size: 55
2629547 TTCACCCTTT
* * *
2629557 AGTCCTTAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCATTTTTC
1 AGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGTATTTTTC
* *
2629612 TAGTCCTCAAAGAGTAGGACGCCTTTTCCTTTCAAAGCCCACACAAGTTGGTGGTATTTTCC
1 -AGTCCTCAAAGAGCAGGACG------CCTTTCAAAGCCCACACAAGTTGGTGGTATTTTTC
* * * **
2629674 AGTCCTCAAAGAGCAGGATGCCTTTGAAAGCCCACACAAGTTAGTGGTACCTTTC
1 AGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGTATTTTTC
* * *
2629729 AGTCCTCAAAGAGCAGGACGCTTTTCAAAGCCCACATAAGTTGGTGGCATTTTTTTC
1 AGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGG--TATTTTTC
* *
2629786 AGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCATTTTTTTT
1 AGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGG--TATTTTTC
* * * * * **
2629843 AGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCAAACAAGTTGGTGGCACTTCCC
1 AGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGTATTTTTC
*
2629898 AGTCCTAAAAGAGCA
1 AGTCCTCAAAGAGCA
2629913 TGATGCCCTC
Statistics
Matches: 259, Mismatches: 33, Indels: 17
0.84 0.11 0.06
Matches are distributed among these distances:
55 88 0.34
56 18 0.07
57 103 0.40
61 18 0.07
62 32 0.12
ACGTcount: A:0.28, C:0.25, G:0.21, T:0.26
Consensus pattern (55 bp):
AGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGTATTTTTC
Found at i:2629911 original size:169 final size:167
Alignment explanation
Indices: 2629557--2629912 Score: 466
Period size: 169 Copynumber: 2.1 Consensus size: 167
2629547 TTCACCCTTT
*
2629557 AGTCCTTAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCATTTTTCTAGTCCTCAA
1 AGTCCTAAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCATTTTTCTAGTCCTCAA
*
2629622 AGAGTAGGACGCCTTTTCCTTTCAAAGCCCACACAAGTTGGTGGTATTTTCCAGTCCTCAAAGAG
66 AGAGCAGGACG-----TCCTTTCAAAGCCCACACAAGTTGGTGGTATTTTCCAGTCCTCAAAGAG
** * * *
2629687 CAGGATGCCTTTGAAAGCCCACACAAGTTAGTGGTACCTTTC
126 CAGGACACCTTTGAAAGCCCAAACAAGTTAGTGGCACCTTCC
* * *
2629729 AGTCCTCAAAGAGCAGGACG-CTTTTCAAAGCCCACATAAGTTGGTGGCATTTTTTTCAGTCCTC
1 AGTCCTAAAAGAGCAGGACGCCTTTT-AAAGCCCACACAAGTTGGTGGCATTTTTCT-AGTCCTC
* **
2629793 AAAGAGCAGGACG-CCTTTCAAAGCCCACACAAGTTGGTGGCATTTTTTTTAGTCCTCAAAGAGC
64 AAAGAGCAGGACGTCCTTTCAAAGCCCACACAAGTTGGTGG--TATTTTCCAGTCCTCAAAGAGC
* *
2629857 AGGACACCTTTTAAAGCCCAAACAAGTTGGTGGCA-CTTCCC
127 AGGACACCTTTGAAAGCCCAAACAAGTTAGTGGCACCTT-CC
2629898 AGTCCTAAAAGAGCA
1 AGTCCTAAAAGAGCA
2629913 TGATGCCCTC
Statistics
Matches: 164, Mismatches: 15, Indels: 13
0.85 0.08 0.07
Matches are distributed among these distances:
167 27 0.16
168 3 0.02
169 63 0.38
171 5 0.03
172 47 0.29
173 19 0.12
ACGTcount: A:0.28, C:0.25, G:0.21, T:0.26
Consensus pattern (167 bp):
AGTCCTAAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCATTTTTCTAGTCCTCAA
AGAGCAGGACGTCCTTTCAAAGCCCACACAAGTTGGTGGTATTTTCCAGTCCTCAAAGAGCAGGA
CACCTTTGAAAGCCCAAACAAGTTAGTGGCACCTTCC
Found at i:2630009 original size:100 final size:94
Alignment explanation
Indices: 2629840--2630018 Score: 241
Period size: 100 Copynumber: 1.8 Consensus size: 94
2629830 TGGCATTTTT
*
2629840 TTTAGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCAAACAAGTTGGTGGCACTTCCCAGTCCTA
1 TTTAGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCAAACAAGTTAGTGGCACTTCCCAGTCCTA
*
2629905 AAAGAGCATGATGCCCTCTCATTTCGCCC
66 AAAGAGCAAGATGCCCTCTCATTTCGCCC
* * * *
2629934 TTTAGTCCTCAAAGAGCAGGATGCATTTTCTTTTCAAAGCCCACACAAGTTAGTGGCATTTTCCA
1 TTTAGTCCTCAAAGAGCAGGA--CA---CCTTTT-AAAGCCCAAACAAGTTAGTGGCACTTCCCA
*
2629999 GTCCTCAAAGAGCAAGATGC
60 GTCCTAAAAGAGCAAGATGC
2630019 TTTCTCTTTG
Statistics
Matches: 72, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
94 21 0.29
96 2 0.03
99 5 0.07
100 44 0.61
ACGTcount: A:0.28, C:0.27, G:0.18, T:0.26
Consensus pattern (94 bp):
TTTAGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCAAACAAGTTAGTGGCACTTCCCAGTCCTA
AAAGAGCAAGATGCCCTCTCATTTCGCCC
Found at i:2630033 original size:61 final size:60
Alignment explanation
Indices: 2629937--2630134 Score: 272
Period size: 61 Copynumber: 3.2 Consensus size: 60
2629927 TTCGCCCTTT
*
2629937 AGTCCTCAAAGAGCAGGATGCATTTTCTTTTCAAAGCCCACACAAGTTAGTGGCATTTTCC
1 AGTCCTCAAAGAGCAGGATGC-TTTTCTTTTCAAAGCCCACACAAGTTGGTGGCATTTTCC
* * *
2629998 AGTCCTCAAAGAGCAAGATGCTTTCTCTTTGCAAAGCCCACACAAGTTGGTGGCACTTTCC
1 AGTCCTCAAAGAGCAGGATGCTTT-TCTTTTCAAAGCCCACACAAGTTGGTGGCATTTTCC
** * * *
2630059 AGTCCTCAAAGAGCAGGACACCTTTTTTTTTCAAAGCCCACACGAGTTGGTGGCACTTTT-T
1 AGTCCTCAAAGAGCAGGA-TGCTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCC
2630120 AGTCCTCAAAGAGCA
1 AGTCCTCAAAGAGCA
2630135 TGACGCACTT
Statistics
Matches: 122, Mismatches: 12, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
60 3 0.02
61 112 0.92
62 7 0.06
ACGTcount: A:0.27, C:0.26, G:0.19, T:0.28
Consensus pattern (60 bp):
AGTCCTCAAAGAGCAGGATGCTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCATTTTCC
Found at i:2630186 original size:42 final size:43
Alignment explanation
Indices: 2630121--2630311 Score: 230
Period size: 42 Copynumber: 4.4 Consensus size: 43
2630111 GCACTTTTTA
*
2630121 GTCCTCAAAGAGCATGACGCACTTTATTTTCC-TCTTTCCTTT
1 GTCCTCAAAGAGCAGGACGCACTTTATTTTCCTTCTTTCCTTT
* * *
2630163 GTCCTCAAAGAGCAGGACACACTTCA-TTCCCTTCTTTTCTCTTTT
1 GTCCTCAAAGAGCAGGACGCACTTTATTTTCCTTC-TTTC-C-TTT
*
2630208 GTCCTCAAAGAGCAGGACGCACTTTATTTTCC-TCTTTCTTTT
1 GTCCTCAAAGAGCAGGACGCACTTTATTTTCCTTCTTTCCTTT
* *
2630250 GTCCTCAAAGAGCAGGACGTA-TTTCATTTTCCTTTTTTCCTTT
1 GTCCTCAAAGAGCAGGACGCACTTT-ATTTTCCTTCTTTCCTTT
*
2630293 ATCCTCGAAA-AGCAGGACG
1 GTCCTC-AAAGAGCAGGACG
2630312 TACTCTTTTT
Statistics
Matches: 129, Mismatches: 12, Indels: 15
0.83 0.08 0.10
Matches are distributed among these distances:
41 7 0.05
42 55 0.43
43 26 0.20
44 8 0.06
45 29 0.22
46 4 0.03
ACGTcount: A:0.21, C:0.27, G:0.14, T:0.38
Consensus pattern (43 bp):
GTCCTCAAAGAGCAGGACGCACTTTATTTTCCTTCTTTCCTTT
Found at i:2630276 original size:87 final size:86
Alignment explanation
Indices: 2630116--2630311 Score: 272
Period size: 87 Copynumber: 2.3 Consensus size: 86
2630106 TGGTGGCACT
*
2630116 TTTTAGTCCTCAAAGAGCATGACGCACTTTATTTTCCTCTTTCCTTTGTCCTCAAAGAGCAGGAC
1 TTTT-GTCCTCAAAGAGCAGGACGCACTTTATTTTCCTCTTTCCTTTGTCCTCAAAGAGCAGGAC
2630181 ACACTTCA-TTCCCTTCTTTTCTC
65 ACACTTCATTTCCCTT-TTTTC-C
* *
2630204 TTTTGTCCTCAAAGAGCAGGACGCACTTTATTTTCCTCTTTCTTTTGTCCTCAAAGAGCAGGACG
1 TTTTGTCCTCAAAGAGCAGGACGCACTTTATTTTCCTCTTTCCTTTGTCCTCAAAGAGCAGGACA
* * *
2630269 TATTTCATTTTCCTTTTTTCC
66 CACTTCATTTCCCTTTTTTCC
*
2630290 -TTTATCCTCGAAA-AGCAGGACG
1 TTTTGTCCTC-AAAGAGCAGGACG
2630312 TACTCTTTTT
Statistics
Matches: 99, Mismatches: 7, Indels: 7
0.88 0.06 0.06
Matches are distributed among these distances:
85 17 0.17
86 4 0.04
87 68 0.69
88 10 0.10
ACGTcount: A:0.21, C:0.27, G:0.14, T:0.39
Consensus pattern (86 bp):
TTTTGTCCTCAAAGAGCAGGACGCACTTTATTTTCCTCTTTCCTTTGTCCTCAAAGAGCAGGACA
CACTTCATTTCCCTTTTTTCC
Found at i:2630396 original size:119 final size:116
Alignment explanation
Indices: 2630205--2630420 Score: 265
Period size: 119 Copynumber: 1.8 Consensus size: 116
2630195 TCTTTTCTCT
* * *
2630205 TTTGTCCTCAAAGAGCAGGACGCACTTTATTTTCCTCTTTCTTTTGTCCTCAAAGAGCAGGACGT
1 TTTGTCCTCAAAGAGCAGGAC-CACTTTATTTTCCTCTTTCCTTTGTCCTCAAAGAGCAAGACCT
* *
2630270 ATTTCATTTTCCTTTTTTCCTTTATCCTCGAAAAGCAGGACGTACTCTTTTTCAC
65 ATTTCA--TT-CTCTTTTCCTTTATCCTCAAAAAGCAGGACGTACTCTTTTTCAC
* * * * *
2630325 TTTGTCCTC-AAGAAGCAGGA-CACTTTCCTTTTCTTTTTTCCTTTGTCCTCAAGGAGTAAGACC
1 TTTGTCCTCAAAG-AGCAGGACCACTTT-ATTTTCCTCTTTCCTTTGTCCTCAAAGAGCAAGACC
*
2630388 TATTTCATTCTCTTTTCCTTTGTCCTCAAAAAG
64 TATTTCATTCTCTTTTCCTTTATCCTCAAAAAG
2630421 TGAGACACCC
Statistics
Matches: 83, Mismatches: 11, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
116 21 0.25
117 2 0.02
118 6 0.07
119 38 0.46
120 16 0.19
ACGTcount: A:0.21, C:0.25, G:0.13, T:0.41
Consensus pattern (116 bp):
TTTGTCCTCAAAGAGCAGGACCACTTTATTTTCCTCTTTCCTTTGTCCTCAAAGAGCAAGACCTA
TTTCATTCTCTTTTCCTTTATCCTCAAAAAGCAGGACGTACTCTTTTTCAC
Found at i:2630442 original size:40 final size:40
Alignment explanation
Indices: 2630318--2630442 Score: 99
Period size: 40 Copynumber: 3.1 Consensus size: 40
2630308 GACGTACTCT
* * * * * * *
2630318 TTTTCACTTTGTCCTCAAGAAGCAGGACACTTTCCTTTTCTT
1 TTTTC-CTTTGTCCTCAAAAAGTAAGACCCATTCC-ATTCTC
** * *
2630360 TTTTCCTTTGTCCTCAAGGAGTAAGACCTATTTCATTCTC
1 TTTTCCTTTGTCCTCAAAAAGTAAGACCCATTCCATTCTC
* *
2630400 TTTTCCTTTGTCCTCAAAAAGTGAGACACCCTTCCATT-TC
1 TTTTCCTTTGTCCTCAAAAAGTAAGAC-CCATTCCATTCTC
2630440 TTT
1 TTT
2630443 CCCCTCCTAA
Statistics
Matches: 67, Mismatches: 15, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
40 33 0.49
41 29 0.43
42 5 0.07
ACGTcount: A:0.20, C:0.26, G:0.11, T:0.42
Consensus pattern (40 bp):
TTTTCCTTTGTCCTCAAAAAGTAAGACCCATTCCATTCTC
Found at i:2631005 original size:13 final size:13
Alignment explanation
Indices: 2630987--2631016 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
2630977 ATATATTATT
*
2630987 CATTGTATCCATA
1 CATTGTATCAATA
2631000 CATTGTATCAATA
1 CATTGTATCAATA
2631013 CATT
1 CATT
2631017 CTGGGTTTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.33, C:0.20, G:0.07, T:0.40
Consensus pattern (13 bp):
CATTGTATCAATA
Found at i:2631057 original size:20 final size:20
Alignment explanation
Indices: 2631032--2631125 Score: 120
Period size: 20 Copynumber: 4.7 Consensus size: 20
2631022 TTTACCCAGA
*
2631032 TGTATCGATACATT-TTGCAT
1 TGTATCGATACATTGCT-CAT
*
2631052 TGTATCGACACATTGCTCAT
1 TGTATCGATACATTGCTCAT
2631072 TGTATCGATACATTGCTCAT
1 TGTATCGATACATTGCTCAT
* *
2631092 TGTATCGATACATT-TTACAA
1 TGTATCGATACATTGCT-CAT
2631112 TGTATCGATACATT
1 TGTATCGATACATT
2631126 CAGGCATTTT
Statistics
Matches: 67, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
19 1 0.01
20 65 0.97
21 1 0.01
ACGTcount: A:0.28, C:0.18, G:0.14, T:0.40
Consensus pattern (20 bp):
TGTATCGATACATTGCTCAT
Found at i:2633555 original size:28 final size:28
Alignment explanation
Indices: 2633519--2633601 Score: 103
Period size: 28 Copynumber: 3.0 Consensus size: 28
2633509 ATTTTTCACA
* *
2633519 ATCGAGGATACTCCAATCCCGTTATTTC
1 ATCGGGGATACTCCAACCCCGTTATTTC
*
2633547 ATCGGGGATACTCTAACCCCGTTATTTC
1 ATCGGGGATACTCCAACCCCGTTATTTC
*** *
2633575 CGAGGGGATACTCCAACCCCGATATTT
1 ATCGGGGATACTCCAACCCCGTTATTT
2633602 ATTTCTAGAA
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 47 1.00
ACGTcount: A:0.24, C:0.29, G:0.18, T:0.29
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCCCGTTATTTC
Found at i:2638496 original size:18 final size:18
Alignment explanation
Indices: 2638465--2638499 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2638455 TCCAAGATGG
*
2638465 CAAGCAACATAAAAATCA
1 CAAGCAACAGAAAAATCA
*
2638483 CAAGCAACGGAAAAATC
1 CAAGCAACAGAAAAATC
2638500 TTGCTTAAAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.57, C:0.23, G:0.11, T:0.09
Consensus pattern (18 bp):
CAAGCAACAGAAAAATCA
Found at i:2639998 original size:136 final size:136
Alignment explanation
Indices: 2639802--2640135 Score: 328
Period size: 136 Copynumber: 2.4 Consensus size: 136
2639792 AAATAACATC
* * * * * **
2639802 TCAACATTTTCAGCGTATAAACAAGTGACATCAAGTTAGTTATACTAATTAATGACCTCAAAGGT
1 TCAACA-TCTCAGCATATAAACAAATGACATCAAGTCACTTATACTAAGAAATGACCTCAAAGGT
* * * * *
2639867 TTAATCAACATCTTAGCATATAAATAAATGACACCAAGCAATTCATGCTAATAAACGACCTTA-A
65 TCAATCAACATCTCAACATATAAACAAATAACACCAAGCAATTCATGCTAATAAACGACC-TACA
*
2639931 AGGTCTGA
129 AAGTCTGA
* ** * *
2639939 TCAACATCTCAGCATATAAATAAATGACATCAAGTCACTTATGTTAAGAAATGATCTCAAGGGTT
1 TCAACATCTCAGCATATAAACAAATGACATCAAGTCACTTATACTAAGAAATGACCTCAAAGGTT
* * * * * * *
2640004 CGATCAATATCTCAACATATAAGCAAATAACACCGAGCCATTTATGCTAATAAATGACCTACAAA
66 CAATCAACATCTCAACATATAAACAAATAACACCAAGCAATTCATGCTAATAAACGACCTACAAA
*
2640069 GTTTGA
131 GTCTGA
* * * * * * * * *
2640075 TCAACATCTCAGAATATAAGCAAGTGACACCAAGTTACTTGTGCTAATAAACGACCTCAAA
1 TCAACATCTCAGCATATAAACAAATGACATCAAGTCACTTATACTAAGAAATGACCTCAAA
2640136 ATTTTGATTG
Statistics
Matches: 158, Mismatches: 38, Indels: 3
0.79 0.19 0.02
Matches are distributed among these distances:
135 2 0.01
136 150 0.95
137 6 0.04
ACGTcount: A:0.41, C:0.19, G:0.13, T:0.27
Consensus pattern (136 bp):
TCAACATCTCAGCATATAAACAAATGACATCAAGTCACTTATACTAAGAAATGACCTCAAAGGTT
CAATCAACATCTCAACATATAAACAAATAACACCAAGCAATTCATGCTAATAAACGACCTACAAA
GTCTGA
Found at i:2640143 original size:68 final size:68
Alignment explanation
Indices: 2639817--2640135 Score: 293
Period size: 68 Copynumber: 4.7 Consensus size: 68
2639807 ATTTTCAGCG
* * * * * * * *
2639817 TATAAACAAGTGACATCAAGTTAGTTATACTAATTAATGACCTCAAAGGTTTAATCAACATCTTA
1 TATAAACAAATGACACCAAGTCACTTATGCTAATAAATGACCTCAAAGGTTTGATCAACATCTCA
*
2639882 GCA
66 GAA
* * * * *
2639885 TATAAATAAATGACACCAAG-CAATTCATGCTAATAAACGACCTTAAAGGTCTGATCAACATCTC
1 TATAAACAAATGACACCAAGTCACTT-ATGCTAATAAATGACCTCAAAGGTTTGATCAACATCTC
*
2639949 AGCA
65 AGAA
* * * * * * * *
2639953 TATAAATAAATGACATCAAGTCACTTATGTTAAGAAATGATCTCAAGGGTTCGATCAATATCTCA
1 TATAAACAAATGACACCAAGTCACTTATGCTAATAAATGACCTCAAAGGTTTGATCAACATCTCA
2640018 -ACA
66 GA-A
* * * * *
2640021 TATAAGCAAATAACACCGAGCCATTTATGCTAATAAATGACCTACAAA-GTTTGATCAACATCTC
1 TATAAACAAATGACACCAAGTCACTTATGCTAATAAATGACCT-CAAAGGTTTGATCAACATCTC
2640085 AGAA
65 AGAA
* * * * *
2640089 TATAAGCAAGTGACACCAAGTTACTTGTGCTAATAAACGACCTCAAA
1 TATAAACAAATGACACCAAGTCACTTATGCTAATAAATGACCTCAAA
2640136 ATTTTGATTG
Statistics
Matches: 201, Mismatches: 45, Indels: 11
0.78 0.18 0.04
Matches are distributed among these distances:
67 7 0.03
68 186 0.93
69 8 0.04
ACGTcount: A:0.42, C:0.19, G:0.13, T:0.27
Consensus pattern (68 bp):
TATAAACAAATGACACCAAGTCACTTATGCTAATAAATGACCTCAAAGGTTTGATCAACATCTCA
GAA
Found at i:2640314 original size:68 final size:67
Alignment explanation
Indices: 2640173--2640300 Score: 159
Period size: 68 Copynumber: 1.9 Consensus size: 67
2640163 AGTGGCGTCA
* * * *
2640173 AGTCACATATGTTAATAAATAACCTCAAAAGTCTATTCTACATTTCAGCATATAAATGAGAGACA
1 AGTCACATACGATAATAAATAACCTCAAAAGTCTATTCGACATTTCAGCATATAAACGAGAGACA
2640238 CC
66 CC
* * * *
2640240 ATGTCACATACGATAATAAATAACTTTAAAGGTCTATTCGACACTTT-GGCATATAAACGAG
1 A-GTCACATACGATAATAAATAACCTCAAAAGTCTATTCGACA-TTTCAGCATATAAACGAG
2640301 TTACATCGAG
Statistics
Matches: 51, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
67 1 0.02
68 47 0.92
69 3 0.06
ACGTcount: A:0.41, C:0.18, G:0.12, T:0.29
Consensus pattern (67 bp):
AGTCACATACGATAATAAATAACCTCAAAAGTCTATTCGACATTTCAGCATATAAACGAGAGACA
CC
Found at i:2645747 original size:155 final size:154
Alignment explanation
Indices: 2645460--2646123 Score: 755
Period size: 154 Copynumber: 4.3 Consensus size: 154
2645450 ATTTTGTAGG
* * ** * *
2645460 AAAATTACGAAAATGCTCAATAGGGGATACCTTCAACGTAAAAGTACCTGATACCCCTAAAGGAC
1 AAAATTATGAAAATGC-CCATAGGGGATACCTTTGACGTAAAAGTACCCGATACCCCTAAAAGAC
* * * * * *
2645525 TTAAAAAGGTTTGAA-A-A-GGGATGAACCTATCCTAATTGTCCACCTTTGGCATAAAAGCAGAC
65 TTAAAAAGG-AT-AATAGATGAGATGAACCTATCCTAAATATCTACCTTCGGCATAAAAGCAGAC
** *
2645587 CCGGTGGTAACCTAGGACTCGATTTTGA
128 CCGGTGACAACCTAAGACTCG-TTTTGA
* *
2645615 AAAATTATGAAAATGCCCACAGGGGATACCTTTGACGTAAAAGTACTCGATACCCCTAAAAGACT
1 AAAATTATGAAAATGCCCATAGGGGATACCTTTGACGTAAAAGTACCCGATACCCCTAAAAGACT
* *
2645680 TAAAAAGGATAATAGATGAGATGAACCTATCCTAAATAT-TAACCTTCGGTATAAAAGCAGACTC
66 TAAAAAGGATAATAGATGAGATGAACCTATCCTAAATATCT-ACCTTCGGCATAAAAGCAGACCC
*
2645744 GGTGACAACCTAAGACTCTGTTATGA
130 GGTGACAACCTAAGACTC-GTTTTGA
* * * * *
2645770 AAAATTACGAAAATG-CCTTA-GGGAGTACCTTTGATGTAAAAGTACCCGATAGCCCTAAAGGAC
1 AAAATTATGAAAATGCCCATAGGGGA-TACCTTTGACGTAAAAGTACCCGATACCCCTAAAAGAC
* * * * *
2645833 TTTAAAATGATAATAGATGAGATGAACCTATCCTAAATATCTACCTTTGTCATAAAAGTAGACCC
65 TTAAAAAGGATAATAGATGAGATGAACCTATCCTAAATATCTACCTTCGGCATAAAAGCAGACCC
* ** * *
2645898 GGTGACAACCTAGGTTTAGTTTTAA
130 GGTGACAACCTAAGACTCGTTTTGA
* * * * *
2645923 AAAATTCTGAAAATGCCCCTAGAGGATACCTTTGACGTAAAAGTACCCGATACCTCTAAAAGTCT
1 AAAATTATGAAAATGCCCATAGGGGATACCTTTGACGTAAAAGTACCCGATACCCCTAAAAGACT
* * * * *
2645988 TAGAAAGGATAATAGATAAGATGAACCTATCTTAAATATCTACCTTCAGCATAAAAGTAGACCCG
66 TAAAAAGGATAATAGATGAGATGAACCTATCCTAAATATCTACCTTCGGCATAAAAGCAGACCCG
* * *
2646053 ATGATAACCTAAGACTCAGTTTTGT
131 GTGACAACCTAAGACTC-GTTTTGA
* * *
2646078 AAAATTATGAAAATGCCCTTAGGAGATAGCTTTGACGTAAAAGTAC
1 AAAATTATGAAAATGCCCATAGGGGATACCTTTGACGTAAAAGTAC
2646124 TCGGAAACCT
Statistics
Matches: 429, Mismatches: 70, Indels: 20
0.83 0.13 0.04
Matches are distributed among these distances:
152 2 0.00
153 24 0.06
154 264 0.62
155 138 0.32
156 1 0.00
ACGTcount: A:0.38, C:0.18, G:0.18, T:0.26
Consensus pattern (154 bp):
AAAATTATGAAAATGCCCATAGGGGATACCTTTGACGTAAAAGTACCCGATACCCCTAAAAGACT
TAAAAAGGATAATAGATGAGATGAACCTATCCTAAATATCTACCTTCGGCATAAAAGCAGACCCG
GTGACAACCTAAGACTCGTTTTGA
Found at i:2645952 original size:308 final size:309
Alignment explanation
Indices: 2645460--2646123 Score: 840
Period size: 308 Copynumber: 2.1 Consensus size: 309
2645450 ATTTTGTAGG
* ** *
2645460 AAAATTACGAAAATGCTCAATAGGG-GATACCTTCAACGTAAAAGTACCTGATACCCCTAAAGGA
1 AAAATTACGAAAATGC-C-TTAGGGAGATACCTTTGACGTAAAAGTACCCGATACCCCTAAAGGA
* * * *
2645524 CTTAAAAAGGTTTGAAAAGGGATGAACCTATCCTAATTGTCCACCTTTGGCATAAAAGCAGACCC
64 CTTAAAAAGGTATGAAAAGAGATGAACCTATCCTAAATATCCACCTTTGGCATAAAAGCAGACCC
** * * *
2645589 GGTGGTAACCTAGGACTCGATTTTGAAAAATTATGAAAATGCCCACAGGGGATACCTTTGACGTA
129 GGTGACAACCTAGGACTAGATTTTAAAAAATTATGAAAATGCCCACAGAGGATACCTTTGACGTA
* *
2645654 AAAGTACTCGATACCCCTAAAAGACTTAAAAAGGATAATAGATGAGATGAACCTATCCTAAATAT
194 AAAGTACCCGATACCCCTAAAAGACTTAAAAAGGATAATAGATAAGATGAACCTATCCTAAATAT
* * * * *
2645719 -TAACCTTCGGTATAAAAGCAGACTCGGTGACAACCTAAGACTCTGTTATGA
259 CT-ACCTTCAGCATAAAAGCAGACCCGATGACAACCTAAGACTCAGTTATGA
* *
2645770 AAAATTACGAAAATGCCTTAGGGAG-TACCTTTGATGTAAAAGTACCCGATAGCCCTAAAGGACT
1 AAAATTACGAAAATGCCTTAGGGAGATACCTTTGACGTAAAAGTACCCGATACCCCTAAAGGACT
* * * * *
2645834 TTAAAATG-AT-AATAGATGAGATGAACCTATCCTAAATATCTACCTTTGTCATAAAAGTAGACC
66 TAAAAAGGTATGAA-A-A-GAGATGAACCTATCCTAAATATCCACCTTTGGCATAAAAGCAGACC
** *
2645897 CGGTGACAACCTAGGTTTAG-TTTTAAAAAATTCTGAAAATGCCC-CTAGAGGATACCTTTGACG
128 CGGTGACAACCTAGGACTAGATTTTAAAAAATTATGAAAATGCCCAC-AGAGGATACCTTTGACG
* * * *
2645960 TAAAAGTACCCGATACCTCTAAAAGTCTTAGAAAGGATAATAGATAAGATGAACCTATCTTAAAT
192 TAAAAGTACCCGATACCCCTAAAAGACTTAAAAAGGATAATAGATAAGATGAACCTATCCTAAAT
* * * *
2646025 ATCTACCTTCAGCATAAAAGTAGACCCGATGATAACCTAAGACTCAGTTTTGT
257 ATCTACCTTCAGCATAAAAGCAGACCCGATGACAACCTAAGACTCAGTTATGA
* *
2646078 AAAATTATGAAAATGCCCTTA-GGAGATAGCTTTGACGTAAAAGTAC
1 AAAATTACGAAAATG-CCTTAGGGAGATACCTTTGACGTAAAAGTAC
2646124 TCGGAAACCT
Statistics
Matches: 305, Mismatches: 41, Indels: 17
0.84 0.11 0.05
Matches are distributed among these distances:
306 2 0.01
307 3 0.01
308 203 0.67
309 81 0.27
310 16 0.05
ACGTcount: A:0.38, C:0.18, G:0.18, T:0.26
Consensus pattern (309 bp):
AAAATTACGAAAATGCCTTAGGGAGATACCTTTGACGTAAAAGTACCCGATACCCCTAAAGGACT
TAAAAAGGTATGAAAAGAGATGAACCTATCCTAAATATCCACCTTTGGCATAAAAGCAGACCCGG
TGACAACCTAGGACTAGATTTTAAAAAATTATGAAAATGCCCACAGAGGATACCTTTGACGTAAA
AGTACCCGATACCCCTAAAAGACTTAAAAAGGATAATAGATAAGATGAACCTATCCTAAATATCT
ACCTTCAGCATAAAAGCAGACCCGATGACAACCTAAGACTCAGTTATGA
Found at i:2647181 original size:20 final size:20
Alignment explanation
Indices: 2647156--2647223 Score: 78
Period size: 20 Copynumber: 3.8 Consensus size: 20
2647146 TTTTCACAAT
2647156 TTGTATCGATACATTGTTCA
1 TTGTATCGATACATTGTTCA
2647176 TTGTATCGAT--A----T-A
1 TTGTATCGATACATTGTTCA
*
2647189 TTGTATCAATACATTGTTCA
1 TTGTATCGATACATTGTTCA
2647209 TTGTATCGATACATT
1 TTGTATCGATACATT
2647224 CTGGGTTTAC
Statistics
Matches: 39, Mismatches: 2, Indels: 14
0.71 0.04 0.25
Matches are distributed among these distances:
13 10 0.26
14 1 0.03
15 1 0.03
18 1 0.03
19 1 0.03
20 25 0.64
ACGTcount: A:0.28, C:0.13, G:0.13, T:0.46
Consensus pattern (20 bp):
TTGTATCGATACATTGTTCA
Found at i:2647201 original size:33 final size:33
Alignment explanation
Indices: 2647156--2647219 Score: 119
Period size: 33 Copynumber: 1.9 Consensus size: 33
2647146 TTTTCACAAT
*
2647156 TTGTATCGATACATTGTTCATTGTATCGATATA
1 TTGTATCAATACATTGTTCATTGTATCGATATA
2647189 TTGTATCAATACATTGTTCATTGTATCGATA
1 TTGTATCAATACATTGTTCATTGTATCGATA
2647220 CATTCTGGGT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.28, C:0.12, G:0.14, T:0.45
Consensus pattern (33 bp):
TTGTATCAATACATTGTTCATTGTATCGATATA
Found at i:2649697 original size:79 final size:77
Alignment explanation
Indices: 2649566--2649942 Score: 288
Period size: 79 Copynumber: 4.8 Consensus size: 77
2649556 TTTCACCTCA
** * * * *
2649566 GGATACTCCAACCCCGGTTTTATTTCCAAAACATCAATATTTCATAATCGGGGATACTCCAATCC
1 GGATACTCCAACCCCGACTTTATTT-CTAAACATTAAT-TTTCACAATCGGGGATACTCCAACCC
* * *
2649631 TATTATTTCCTAAG
64 CATTATTTTCGAAG
* *
2649645 GGATACTCCAACCCCGACTTTATTTCTAAGATATTAATTTCTCACAATCGGGGGTACTCCAACCC
1 GGATACTCCAACCCCGACTTTATTTCTAA-ACATTAATTT-TCACAATCGGGGATACTCCAACCC
* * **
2649710 CGTTATTTTGGCGG
64 CATTATTTTCGAAG
* * * *
2649724 GGATACTCCAACCCC-AGCCTTATTTCTAAAGCACTGATTTTTCACAATCGGGGATACTCTAACC
1 GGATACTCCAACCCCGA-CTTTATTTCTAAA-CA-TTAATTTTCACAATCGGGGATACTCCAACC
2649788 CCATTATTTTCGAAG
63 CCATTATTTTCGAAG
* * * ** * * ** *
2649803 GGATACTCCAACCCCAATTTTATTTTCAAAACGCTAATTTTTTATAATTAGGGATACTCCAACTC
1 GGATACTCCAACCCCGACTTTA-TTTCTAAACATTAA-TTTTCACAATCGGGGATACTCCAACCC
** * * *
2649868 TGTCATTTCCGAGG
64 CATTATTTTCGAAG
* * * ** *
2649882 GGATACTCCAACCCCGATTTTATGTCCAGAACATCGATTTTCTATAATCGGGGATACTCCA
1 GGATACTCCAACCCCGACTTTATTTCTA-AACATTAATTTTC-ACAATCGGGGATACTCCA
2649943 GCCTCGTTTT
Statistics
Matches: 235, Mismatches: 53, Indels: 20
0.76 0.17 0.06
Matches are distributed among these distances:
78 16 0.07
79 206 0.88
80 13 0.06
ACGTcount: A:0.28, C:0.26, G:0.14, T:0.32
Consensus pattern (77 bp):
GGATACTCCAACCCCGACTTTATTTCTAAACATTAATTTTCACAATCGGGGATACTCCAACCCCA
TTATTTTCGAAG
Found at i:2649921 original size:158 final size:157
Alignment explanation
Indices: 2649566--2649942 Score: 384
Period size: 158 Copynumber: 2.4 Consensus size: 157
2649556 TTTCACCTCA
* * * *
2649566 GGATACTCCAACCCCGGTTTTATTTCCAAAACATCAATATTTCATAATCGGGGATACTCCAATCC
1 GGATACTCCAACCCCGATTTTATTTCC-AAACATCGATTTTTCATAATCGGGGATACTCCAACCC
* * * * * * *
2649631 TATTATTTCCTAAGGGATACTCCAACCCCGACTTTATTTCTAAGATATTAATTTCTCACAATCGG
65 CATTATTTCCGAAGGGATACTCCAACCCCAACTTTATTTCTAAAACACTAATTTCTCACAATCAG
* * ** *
2649696 GGGTACTCCAACCCCGTTATTTTGGCGG
130 GGATACTCCAACCCCGTCATTTCCGAGG
** * * *
2649724 GGATACTCCAACCCC-AGCCTTATTTCTAAAGCA-CTGATTTTTCACAATCGGGGATACTCTAAC
1 GGATACTCCAACCCCGA-TTTTATTTCCAAA-CATC-GATTTTTCATAATCGGGGATACTCCAAC
* * * * * *
2649787 CCCATTATTTTCGAAGGGATACTCCAACCCCAATTTTATTT-TCAAAACGCTAATTTTTTATAAT
63 CCCATTATTTCCGAAGGGATACTCCAACCCCAACTTTATTTCT-AAAACACTAATTTCTCACAAT
* * *
2649851 TAGGGATACTCCAACTCTGTCATTTCCGAGG
127 CAGGGATACTCCAACCCCGTCATTTCCGAGG
*
2649882 GGATACTCCAACCCCGATTTTATGTCCAGAACATCGA-TTTTCTATAATCGGGGATACTCCA
1 GGATACTCCAACCCCGATTTTATTTCCA-AACATCGATTTTTC-ATAATCGGGGATACTCCA
2649943 GCCTCGTTTT
Statistics
Matches: 175, Mismatches: 36, Indels: 16
0.77 0.16 0.07
Matches are distributed among these distances:
157 10 0.06
158 161 0.92
159 4 0.02
ACGTcount: A:0.28, C:0.26, G:0.14, T:0.32
Consensus pattern (157 bp):
GGATACTCCAACCCCGATTTTATTTCCAAACATCGATTTTTCATAATCGGGGATACTCCAACCCC
ATTATTTCCGAAGGGATACTCCAACCCCAACTTTATTTCTAAAACACTAATTTCTCACAATCAGG
GATACTCCAACCCCGTCATTTCCGAGG
Found at i:2652993 original size:52 final size:52
Alignment explanation
Indices: 2652840--2653072 Score: 229
Period size: 53 Copynumber: 4.5 Consensus size: 52
2652830 TAGATAACGA
** * * * * *
2652840 GGTTGGAGTATCCTTGATTGT-GAAAAATTGGTATTTTTTGGAAATAAAATCAG
1 GGTTGGAGTATCCCCGATTGTGGAAAAATTAG--TGTTTTAGAAATAAAACCGG
* ** *
2652893 AGTTGGAGTATCCCCGATTAAAGGAAAAATTGGTGTTTT-GAAAATAAAACCGG
1 GGTTGGAGTATCCCCGATT-GTGGAAAAATTAGTGTTTTAG-AAATAAAACCGG
* *
2652946 GGTTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTTAGCAATAAAACCGA
1 GGTTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTTAGAAATAAAACCGG
* * * * *
2652998 GGTTGGAGTATCCCTGATTAT-GAAAAATTAGTGTCTTAAAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTTAGAAATAAAACCGG
* *
2653049 AGTTGGAATATCCCCGATTGTGGA
1 GGTTGGAGTATCCCCGATTGTGGA
2653073 GAATAGAGAA
Statistics
Matches: 150, Mismatches: 25, Indels: 11
0.81 0.13 0.06
Matches are distributed among these distances:
51 42 0.28
52 48 0.32
53 50 0.33
55 10 0.07
ACGTcount: A:0.34, C:0.11, G:0.24, T:0.31
Consensus pattern (52 bp):
GGTTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTTAGAAATAAAACCGG
Found at i:2655449 original size:13 final size:13
Alignment explanation
Indices: 2655431--2655456 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2655421 ACAAAGATCC
2655431 ATGTATCGATACA
1 ATGTATCGATACA
2655444 ATGTATCGATACA
1 ATGTATCGATACA
2655457 CAGAAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2655468 original size:33 final size:33
Alignment explanation
Indices: 2655410--2655476 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
2655400 AAAATTTCCA
***
2655410 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
* *
2655443 AATGTATCGATACACAGAAAAATGTATTGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
2655476 A
1 A
2655477 TTTCCTTGGC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.43, C:0.15, G:0.15, T:0.27
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:2655520 original size:19 final size:18
Alignment explanation
Indices: 2655496--2655563 Score: 74
Period size: 19 Copynumber: 3.9 Consensus size: 18
2655486 CAGTAGCTAA
2655496 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
2655515 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
2655530 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
*
2655547 TTATTTATCGATACAAA
1 TTATGTATCGATACAAA
2655564 TTGTTGAATT
Statistics
Matches: 42, Mismatches: 1, Indels: 13
0.75 0.02 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.10
19 24 0.57
ACGTcount: A:0.38, C:0.15, G:0.10, T:0.37
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:2655536 original size:13 final size:13
Alignment explanation
Indices: 2655518--2655542 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2655508 ACAATACTTA
2655518 TGTATCGATACAT
1 TGTATCGATACAT
2655531 TGTATCGATACA
1 TGTATCGATACA
2655543 AAACTTATTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2655537 original size:32 final size:32
Alignment explanation
Indices: 2655499--2655561 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
2655489 TAGCTAATTA
*
2655499 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
*
2655531 TGTATCGATACAAAACTTATTTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
2655562 AATTGTTGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.37, C:0.16, G:0.11, T:0.37
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:2655625 original size:21 final size:20
Alignment explanation
Indices: 2655599--2655677 Score: 95
Period size: 21 Copynumber: 3.8 Consensus size: 20
2655589 GTTGGGACCC
2655599 TGTATCGATACATTTGTAGAA
1 TGTATCGATACATTTGTA-AA
***
2655620 TGTATCGATACATTCCACAAA
1 TGTATCGATACATT-TGTAAA
*
2655641 TGTATCGATACATTCTATAAA
1 TGTATCGATACATT-TGTAAA
2655662 TGTATCGATACATTTG
1 TGTATCGATACATTTG
2655678 GATAAATTTT
Statistics
Matches: 51, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
20 1 0.02
21 49 0.96
22 1 0.02
ACGTcount: A:0.34, C:0.15, G:0.14, T:0.37
Consensus pattern (20 bp):
TGTATCGATACATTTGTAAA
Found at i:2656496 original size:19 final size:20
Alignment explanation
Indices: 2656454--2656505 Score: 79
Period size: 19 Copynumber: 2.6 Consensus size: 20
2656444 AAGCCAAGAA
* *
2656454 GTATCGATACATATTGCTTT
1 GTATCGATACATGTTGCATT
2656474 GTATCGATACATGTT-CATT
1 GTATCGATACATGTTGCATT
2656493 GTATCGATACATG
1 GTATCGATACATG
2656506 AAACTGGAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.53
20 14 0.47
ACGTcount: A:0.27, C:0.15, G:0.17, T:0.40
Consensus pattern (20 bp):
GTATCGATACATGTTGCATT
Found at i:2658198 original size:3 final size:3
Alignment explanation
Indices: 2658185--2658221 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
2658175 ATCAAAGATA
*
2658185 ATG AAG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG A
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG A
2658222 AGTTGACTCA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.38, C:0.00, G:0.32, T:0.30
Consensus pattern (3 bp):
ATG
Found at i:2660553 original size:19 final size:18
Alignment explanation
Indices: 2660507--2660592 Score: 74
Period size: 19 Copynumber: 4.8 Consensus size: 18
2660497 TTTCAACAAT
*
2660507 TTGTATCGATACAAATTG
1 TTGTATCGATACAAAGTG
2660525 TAACTGTATCGATACATAAGTG
1 T---TGTATCGATACA-AAGTG
2660547 TTGTATCGATAC-AA---
1 TTGTATCGATACAAAGTG
*
2660561 -TGTATCGATACATAAGTT
1 TTGTATCGATACA-AAGTG
2660579 TTGTATCGATACAA
1 TTGTATCGATACAA
2660593 TGTATCGCTA
Statistics
Matches: 57, Mismatches: 1, Indels: 20
0.73 0.01 0.26
Matches are distributed among these distances:
13 11 0.19
15 2 0.04
17 2 0.04
18 2 0.04
19 23 0.40
21 12 0.21
22 5 0.09
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.36
Consensus pattern (18 bp):
TTGTATCGATACAAAGTG
Found at i:2660566 original size:13 final size:13
Alignment explanation
Indices: 2660548--2660572 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2660538 ACATAAGTGT
2660548 TGTATCGATACAA
1 TGTATCGATACAA
2660561 TGTATCGATACA
1 TGTATCGATACA
2660573 TAAGTTTTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:2660570 original size:32 final size:32
Alignment explanation
Indices: 2660529--2660599 Score: 133
Period size: 32 Copynumber: 2.2 Consensus size: 32
2660519 AAATTGTAAC
2660529 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
*
2660561 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
2660593 TGTATCG
1 TGTATCG
2660600 CTACGAAGCT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 38 1.00
ACGTcount: A:0.32, C:0.13, G:0.18, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTGTATCGATACAA
Found at i:2668285 original size:22 final size:22
Alignment explanation
Indices: 2668249--2668293 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
2668239 TTTTTTAAAG
*
2668249 GAAAAGTTTATATTAAGGGGGA
1 GAAAAGTTTATATTAAAGGGGA
2668271 GAAAATGTTTA-ATTAAAGGGGA
1 GAAAA-GTTTATATTAAAGGGGA
2668293 G
1 G
2668294 TTATATTTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 16 0.76
23 5 0.24
ACGTcount: A:0.42, C:0.00, G:0.31, T:0.27
Consensus pattern (22 bp):
GAAAAGTTTATATTAAAGGGGA
Found at i:2685310 original size:14 final size:15
Alignment explanation
Indices: 2685291--2685320 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
2685281 AAATTTTATC
2685291 TTAATTTTTA-AATT
1 TTAATTTTTACAATT
2685305 TTAATTTTTACAATT
1 TTAATTTTTACAATT
2685320 T
1 T
2685321 AGTCCTTGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.67
15 5 0.33
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.63
Consensus pattern (15 bp):
TTAATTTTTACAATT
Found at i:2685612 original size:21 final size:22
Alignment explanation
Indices: 2685587--2685627 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
2685577 AATGGGCTTT
*
2685587 AGAAACTTTGAA-AAAAAAGTG
1 AGAAACTTGGAAGAAAAAAGTG
2685608 AGAAACTTGGAAGAAAAAAG
1 AGAAACTTGGAAGAAAAAAG
2685628 AAAGAAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.59, C:0.05, G:0.22, T:0.15
Consensus pattern (22 bp):
AGAAACTTGGAAGAAAAAAGTG
Found at i:2685633 original size:22 final size:21
Alignment explanation
Indices: 2685587--2685634 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 21
2685577 AATGGGCTTT
* **
2685587 AGAAACTTTGAAAAAAAAGTG
1 AGAAACTTGGAAAAAAAAGAA
2685608 AGAAACTTGGAAGAAAAAAGAA
1 AGAAACTTGGAA-AAAAAAGAA
2685630 AGAAA
1 AGAAA
2685635 AAAGAGAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 11 0.48
22 12 0.52
ACGTcount: A:0.62, C:0.04, G:0.21, T:0.12
Consensus pattern (21 bp):
AGAAACTTGGAAAAAAAAGAA
Found at i:2689927 original size:16 final size:15
Alignment explanation
Indices: 2689906--2689944 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
2689896 ATTTATCTCA
*
2689906 TCAAAATATTCAAAAT
1 TCAAAA-ATACAAAAT
*
2689922 TCAAAAATACATAAT
1 TCAAAAATACAAAAT
2689937 TCAAAAAT
1 TCAAAAAT
2689945 GATGTCAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 15 0.71
16 6 0.29
ACGTcount: A:0.59, C:0.13, G:0.00, T:0.28
Consensus pattern (15 bp):
TCAAAAATACAAAAT
Found at i:2691233 original size:20 final size:20
Alignment explanation
Indices: 2691221--2691261 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
2691211 GTATCAGTAT
*
2691221 AGTGTATCATGTATCGATAC
1 AGTGTACCATGTATCGATAC
2691241 AGTGTACCATGTATCGATAC
1 AGTGTACCATGTATCGATAC
2691261 A
1 A
2691262 TACAGTGGTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.32
Consensus pattern (20 bp):
AGTGTACCATGTATCGATAC
Found at i:2691316 original size:20 final size:20
Alignment explanation
Indices: 2691291--2691338 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
2691281 CTGCCAGTTT
2691291 CATGTATCGAAACAATTGTG
1 CATGTATCGAAACAATTGTG
* *
2691311 CATGTATTGATACAATTGTG
1 CATGTATCGAAACAATTGTG
2691331 CATGTATC
1 CATGTATC
2691339 TATACAACGT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.31, C:0.15, G:0.19, T:0.35
Consensus pattern (20 bp):
CATGTATCGAAACAATTGTG
Found at i:2691343 original size:20 final size:20
Alignment explanation
Indices: 2691291--2691345 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
2691281 CTGCCAGTTT
* *
2691291 CATGTATCGAAACAATTGTG
1 CATGTATCTATACAATTGTG
2691311 CATGTAT-TGATACAATTGTG
1 CATGTATCT-ATACAATTGTG
2691331 CATGTATCTATACAA
1 CATGTATCTATACAA
2691346 CGTATCGATA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 30 0.97
21 1 0.03
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.35
Consensus pattern (20 bp):
CATGTATCTATACAATTGTG
Found at i:2692064 original size:156 final size:156
Alignment explanation
Indices: 2691746--2692040 Score: 362
Period size: 156 Copynumber: 1.9 Consensus size: 156
2691736 ATTTCCACCA
* * * * * * *
2691746 TTTTTAAGTCTTTTAAGGGTATTAGGCACTTCTATGTCGAAGGTATCCCTTACGTGCATTTTCTT
1 TTTTTAAGTCCTTTAGGGGTATCAGGCACTTCTAAGTCGAAGGTATCCCATACGGGCATTTTCGT
* * *
2691811 AATTTTCCCAAAGCCAAGTCTTAGGTTGTGACTGGGTTTGCTTTTATGTCGAAGGTAGGTATTTA
66 AATTTTCCCAAAGCCAAGTCTTAGGTTGTCACCGGGTCTGCTTTTATGTCGAAGGTAGGTATTTA
2691876 GGATAGGTTCATCCCATCCATAATCC
131 GGATAGGTTCATCCCATCCATAATCC
* * *
2691902 TTTTTAAGTCCTTTAGGGGTATCGGGCACTTTTAAGTCGAAGGTATCCCATA-GGGATATTTTCG
1 TTTTTAAGTCCTTTAGGGGTATCAGGCACTTCTAAGTCGAAGGTATCCCATACGGG-CATTTTCG
*** * * *
2691966 TAATTTTTTTAGAA-CTAAGTCTTAGGTTGTCACCGGGTCTGCTTTTATGAT-GAATGTGGGTAT
65 TAATTTTCCCA-AAGCCAAGTCTTAGGTTGTCACCGGGTCTGCTTTTATG-TCGAAGGTAGGTAT
*
2692029 TTAGGATGGGTT
128 TTAGGATAGGTT
2692041 TATCTTGTCT
Statistics
Matches: 116, Mismatches: 20, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
155 2 0.02
156 111 0.96
157 3 0.03
ACGTcount: A:0.22, C:0.15, G:0.23, T:0.40
Consensus pattern (156 bp):
TTTTTAAGTCCTTTAGGGGTATCAGGCACTTCTAAGTCGAAGGTATCCCATACGGGCATTTTCGT
AATTTTCCCAAAGCCAAGTCTTAGGTTGTCACCGGGTCTGCTTTTATGTCGAAGGTAGGTATTTA
GGATAGGTTCATCCCATCCATAATCC
Found at i:2692087 original size:156 final size:156
Alignment explanation
Indices: 2691826--2692116 Score: 343
Period size: 156 Copynumber: 1.9 Consensus size: 156
2691816 TCCCAAAGCC
* * *
2691826 AAGTCTTAGGTTGTGACTGGGTTTGCTTTTATGTCGAAGGTAGGTATTTAGGATAGGTTCATCCC
1 AAGTCTTAGGTTGTCACCGGGTCTGCTTTTATGTCGAAGGTAGGTATTTAGGATAGGTTCATCCC
* * * * ** **
2691891 ATCCATAATCCTTTTTAAGTCCTTTAGGGGTATCGGGCACTTTTAAGTCGAAGGTATCCCATAGG
66 ATCCATAATCCTTTTTAAATCCTCTAGGGATACCAAGCACTTTTAAGTCGAAGGTAAACCATAGG
2691956 GATATTTTCGTAATTTTTTTAGAACT
131 GATATTTTCGTAATTTTTTTAGAACT
* * * * *
2691982 AAGTCTTAGGTTGTCACCGGGTCTGCTTTTATGAT-GAATGTGGGTATTTAGGATGGGTTTATCT
1 AAGTCTTAGGTTGTCACCGGGTCTGCTTTTATG-TCGAAGGTAGGTATTTAGGATAGGTTCATCC
** * * * * *
2692046 TGTCTATAATCTTTTTTAAATCCTCTA-GGATCACCAAGCACTTTTAGGTCGATGGTAAACCTTA
65 CATCCATAATCCTTTTTAAATCCTCTAGGGAT-ACCAAGCACTTTTAAGTCGAAGGTAAACCATA
2692110 GGGATAT
129 GGGATAT
2692117 CTTAGCTTTG
Statistics
Matches: 110, Mismatches: 23, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
155 3 0.03
156 106 0.96
157 1 0.01
ACGTcount: A:0.23, C:0.15, G:0.23, T:0.39
Consensus pattern (156 bp):
AAGTCTTAGGTTGTCACCGGGTCTGCTTTTATGTCGAAGGTAGGTATTTAGGATAGGTTCATCCC
ATCCATAATCCTTTTTAAATCCTCTAGGGATACCAAGCACTTTTAAGTCGAAGGTAAACCATAGG
GATATTTTCGTAATTTTTTTAGAACT
Found at i:2693803 original size:21 final size:21
Alignment explanation
Indices: 2693777--2693825 Score: 73
Period size: 21 Copynumber: 2.3 Consensus size: 21
2693767 TATGGATTAT
2693777 TTTAAAAAGGGTATT-TATTTG
1 TTTAAAAAGGGTATTCT-TTTG
*
2693798 TTTAAAGAGGGTATTCTTTTG
1 TTTAAAAAGGGTATTCTTTTG
2693819 TTTAAAA
1 TTTAAAA
2693826 TAATTGATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 24 0.96
22 1 0.04
ACGTcount: A:0.33, C:0.02, G:0.18, T:0.47
Consensus pattern (21 bp):
TTTAAAAAGGGTATTCTTTTG
Found at i:2693868 original size:97 final size:97
Alignment explanation
Indices: 2693692--2693871 Score: 243
Period size: 97 Copynumber: 1.9 Consensus size: 97
2693682 AAAAATTTTG
* * ***
2693692 ATTTACTTGTTTAAAGAAGGTATTCTTTTGTTCAAAATAATCGATGAGGTGTTTTTCATATACCA
1 ATTTACTTGTTTAAAGAAGGTATTCTTTTGTTCAAAATAATCGATAAGATAACTTTCATATACCA
2693757 AAAGAACACCTATGGATTATTTTAAAAAGGGT
66 AAAGAACACCTATGGATTATTTTAAAAAGGGT
* * * * * *
2693789 ATTTATTTGTTTAAAGAGGGTATTCTTTTGTTTAAAATAATTGATAAGATAACTTTCGTATACTA
1 ATTTACTTGTTTAAAGAAGGTATTCTTTTGTTCAAAATAATCGATAAGATAACTTTCATATACCA
* *
2693854 AAAGCACACTTATGGATT
66 AAAGAACACCTATGGATT
2693872 TAAAAAAGGT
Statistics
Matches: 70, Mismatches: 13, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
97 70 1.00
ACGTcount: A:0.35, C:0.09, G:0.16, T:0.40
Consensus pattern (97 bp):
ATTTACTTGTTTAAAGAAGGTATTCTTTTGTTCAAAATAATCGATAAGATAACTTTCATATACCA
AAAGAACACCTATGGATTATTTTAAAAAGGGT
Found at i:2694312 original size:58 final size:57
Alignment explanation
Indices: 2694250--2694431 Score: 161
Period size: 58 Copynumber: 3.2 Consensus size: 57
2694240 TTGCATGAAT
* * * *
2694250 GTCCCTAGATCATTGAAAATAACCTAAATTATATCAAGATTCAAAAAATTACATCCAA
1 GTCCCTAGATCA-TGAAAATAACCTAAATAATATCAACATTCATAAAATTACATCAAA
** * * * * * * *
2694308 GTCCCTAGGCCATGTAAATTGACCTAAATAATGTCAATATTCATAAAGTTGCATCTAA
1 GTCCCTAGATCATG-AAAATAACCTAAATAATATCAACATTCATAAAATTACATCAAA
* * * * *
2694366 GTCTCTAGATC-TAAAAATAACCTAAATGACATTAACATTCATAAAATTACATCAAA
1 GTCCCTAGATCATGAAAATAACCTAAATAATATCAACATTCATAAAATTACATCAAA
2694422 G-CCTCTAGAT
1 GTCC-CTAGAT
2694432 TGAAAAATGA
Statistics
Matches: 96, Mismatches: 26, Indels: 6
0.75 0.20 0.05
Matches are distributed among these distances:
55 1 0.01
56 40 0.42
57 3 0.03
58 52 0.54
ACGTcount: A:0.42, C:0.19, G:0.09, T:0.29
Consensus pattern (57 bp):
GTCCCTAGATCATGAAAATAACCTAAATAATATCAACATTCATAAAATTACATCAAA
Found at i:2694406 original size:56 final size:56
Alignment explanation
Indices: 2694346--2694460 Score: 151
Period size: 56 Copynumber: 2.1 Consensus size: 56
2694336 TAATGTCAAT
* * * *
2694346 ATTCATAAAGTTGCATCTAAGTCTCTAGATCT-AAAAATAACCTAAATGACATTAAC
1 ATTCATAAAATTACATCAAAGCCTCTAGAT-TGAAAAATAACCTAAATGACATTAAC
* * *
2694402 ATTCATAAAATTACATCAAAGCCTCTAGATTGAAAAATGACCTAACTGGCATTAAC
1 ATTCATAAAATTACATCAAAGCCTCTAGATTGAAAAATAACCTAAATGACATTAAC
2694458 ATT
1 ATT
2694461 TATGAAATGA
Statistics
Matches: 51, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
55 1 0.02
56 50 0.98
ACGTcount: A:0.43, C:0.18, G:0.10, T:0.30
Consensus pattern (56 bp):
ATTCATAAAATTACATCAAAGCCTCTAGATTGAAAAATAACCTAAATGACATTAAC
Found at i:2697757 original size:15 final size:15
Alignment explanation
Indices: 2697733--2697776 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
2697723 AATCCTACTA
*
2697733 TTTTTCCTTT-TTTT
1 TTTTTTCTTTCTTTT
2697747 CTTTTTTCTTTCTTTT
1 -TTTTTTCTTTCTTTT
*
2697763 TTTTTTCTCTCTTT
1 TTTTTTCTTTCTTT
2697777 ATTTCTCCAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
15 22 0.85
16 4 0.15
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (15 bp):
TTTTTTCTTTCTTTT
Done.