Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A03
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: 108673976
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.31
Warning! 5040000 characters in sequence are not A, C, G, or T
File 44 of 333
Found at i:12543214 original size:11 final size:11
Alignment explanation
Indices: 12543194--12543245 Score: 56
Period size: 10 Copynumber: 4.8 Consensus size: 11
12543184 TTATATTTTC
12543194 ATAATTTTTAA
1 ATAATTTTTAA
*
12543205 AT-ATTTTTTA
1 ATAATTTTTAA
12543215 ATAATTTTT--
1 ATAATTTTTAA
12543224 ATAATTTTCTATA
1 ATAATTTT-TA-A
12543237 ATAATTTTT
1 ATAATTTTT
12543246 GAAAAATTAT
Statistics
Matches: 35, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
9 8 0.23
10 10 0.29
11 8 0.23
12 1 0.03
13 8 0.23
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.62
Consensus pattern (11 bp):
ATAATTTTTAA
Found at i:12543218 original size:21 final size:21
Alignment explanation
Indices: 12543189--12543245 Score: 71
Period size: 21 Copynumber: 2.7 Consensus size: 21
12543179 AATTGTTATA
*
12543189 TTTTCATAATTTTTA-AATATT
1 TTTTAATAATTTTTATAAT-TT
12543210 TTTTAATAATTTTTATAATTT
1 TTTTAATAATTTTTATAATTT
*
12543231 TCTATAATAATTTTT
1 T-TTTAATAATTTTT
12543246 GAAAAATTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
21 17 0.53
22 15 0.47
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (21 bp):
TTTTAATAATTTTTATAATTT
Found at i:12543238 original size:22 final size:21
Alignment explanation
Indices: 12543194--12543245 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 21
12543184 TTATATTTTC
*
12543194 ATAATTTTTAAATATTTTTTA
1 ATAATTTTTAAATATTTTATA
12543215 ATAATTTTTATAAT-TTTCTATA
1 ATAATTTTTA-AATATTT-TATA
12543237 ATAATTTTT
1 ATAATTTTT
12543246 GAAAAATTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
21 13 0.46
22 15 0.54
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.62
Consensus pattern (21 bp):
ATAATTTTTAAATATTTTATA
Found at i:12543287 original size:9 final size:9
Alignment explanation
Indices: 12543273--12543360 Score: 61
Period size: 9 Copynumber: 9.4 Consensus size: 9
12543263 TAGGTGTAAT
12543273 TTTTTAAAA
1 TTTTTAAAA
12543282 TTTTTAAAA
1 TTTTTAAAA
* *
12543291 ATTCTAAAA
1 TTTTTAAAA
12543300 -TTTTAATAA
1 TTTTTAA-AA
* *
12543309 TTTTCTATTAT
1 TTTT-TA-AAA
*
12543320 TTTTTAATA
1 TTTTTAAAA
12543329 TTTTTATAAA
1 TTTTTA-AAA
* *
12543339 TTTGTAAAT
1 TTTTTAAAA
*
12543348 TTTTTATAA
1 TTTTTAAAA
12543357 TTTT
1 TTTT
12543361 ATAACTTTCA
Statistics
Matches: 60, Mismatches: 14, Indels: 10
0.71 0.17 0.12
Matches are distributed among these distances:
8 5 0.08
9 36 0.60
10 12 0.20
11 7 0.12
ACGTcount: A:0.36, C:0.02, G:0.01, T:0.60
Consensus pattern (9 bp):
TTTTTAAAA
Found at i:12543450 original size:19 final size:19
Alignment explanation
Indices: 12543407--12543452 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
12543397 AAGTTCTAAT
*
12543407 TCTTTTATAATTTTAGAAT
1 TCTTTTATAATTTTAGAAA
*
12543426 TCTTTTATAATTTCTATAAA
1 TCTTTTATAATTT-TAGAAA
12543446 T-TTTTAT
1 TCTTTTAT
12543453 GCTTTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 19 0.79
20 5 0.21
ACGTcount: A:0.30, C:0.07, G:0.02, T:0.61
Consensus pattern (19 bp):
TCTTTTATAATTTTAGAAA
Found at i:12544333 original size:37 final size:37
Alignment explanation
Indices: 12544292--12544387 Score: 104
Period size: 37 Copynumber: 2.6 Consensus size: 37
12544282 AGAGGGTTGT
* *
12544292 ATCTTAAGGTTTAGGTA-AAAGCCATGAGGGAGTTACA
1 ATCTTAAGGTTTAGGTAGAAA-CCATAAAGGAGTTACA
* * *
12544329 ATCTTAAGGTTTGGGTAGAAACCTTAAAGGAGTTGCA
1 ATCTTAAGGTTTAGGTAGAAACCATAAAGGAGTTACA
**
12544366 ATCTTAAAACTTTAGGTAGAAA
1 ATCTT-AAGGTTTAGGTAGAAA
12544388 TCTTAAAGTA
Statistics
Matches: 49, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
37 33 0.67
38 16 0.33
ACGTcount: A:0.36, C:0.10, G:0.24, T:0.29
Consensus pattern (37 bp):
ATCTTAAGGTTTAGGTAGAAACCATAAAGGAGTTACA
Found at i:12544393 original size:38 final size:37
Alignment explanation
Indices: 12544320--12544395 Score: 98
Period size: 38 Copynumber: 2.0 Consensus size: 37
12544310 AAGCCATGAG
** *
12544320 GGAGTTACAATCTTAAGGTTTGGGTAGAAACCTTAAA
1 GGAGTTACAATCTTAAACTTTAGGTAGAAACCTTAAA
* *
12544357 GGAGTTGCAATCTTAAAACTTTAGGTAGAAATCTTAAA
1 GGAGTTACAATCTT-AAACTTTAGGTAGAAACCTTAAA
12544395 G
1 G
12544396 TAGATTGTAA
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
37 13 0.39
38 20 0.61
ACGTcount: A:0.37, C:0.11, G:0.22, T:0.30
Consensus pattern (37 bp):
GGAGTTACAATCTTAAACTTTAGGTAGAAACCTTAAA
Found at i:12545872 original size:17 final size:17
Alignment explanation
Indices: 12545852--12545886 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
12545842 ATTTCGAAAC
12545852 TAAAAGATGAAAATAAT
1 TAAAAGATGAAAATAAT
12545869 TAAAAGATGAAAATAAT
1 TAAAAGATGAAAATAAT
12545886 T
1 T
12545887 CACTCTCCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.63, C:0.00, G:0.11, T:0.26
Consensus pattern (17 bp):
TAAAAGATGAAAATAAT
Found at i:12546844 original size:19 final size:19
Alignment explanation
Indices: 12546797--12546855 Score: 57
Period size: 20 Copynumber: 2.9 Consensus size: 19
12546787 AAAATGATAA
12546797 AATCAAGTTAAA-ATAGTTTC
1 AATCAAGTTAAACAT--TTTC
**
12546817 AATTGAGTTAAACATTTTC
1 AATCAAGTTAAACATTTTC
12546836 AATCAAGTTGAAACTATTTT
1 AATCAAGTT-AAAC-ATTTT
12546856 AAAAAAAGTT
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
19 11 0.34
20 14 0.44
21 7 0.22
ACGTcount: A:0.41, C:0.10, G:0.10, T:0.39
Consensus pattern (19 bp):
AATCAAGTTAAACATTTTC
Found at i:12549118 original size:22 final size:22
Alignment explanation
Indices: 12549090--12549135 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
12549080 TTCTTTGATT
12549090 CAATGCTAGAATAGTTTATGCA
1 CAATGCTAGAATAGTTTATGCA
12549112 CAATGCTAGAATAGTTTATGCA
1 CAATGCTAGAATAGTTTATGCA
12549134 CA
1 CA
12549136 TACCTATACC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.37, C:0.15, G:0.17, T:0.30
Consensus pattern (22 bp):
CAATGCTAGAATAGTTTATGCA
Found at i:12560319 original size:94 final size:91
Alignment explanation
Indices: 12560158--12560420 Score: 235
Period size: 94 Copynumber: 2.8 Consensus size: 91
12560148 GTGATTGTGT
** * ** * ** *
12560158 GCTAGTGTAAGACATGTCTGGGACATGCATTGGCCTCGAGATATTTAAGCCAGTGTAGGACATGT
1 GCTAGTGTAAGACATGTCTGGGACATGCATCAGCCTCGCGATA-GAAAGCTAGTGTAAAACCTGT
12560223 CTAGAACAT-GCATCAACATTGAGTCG-GGA
65 CTAG-ACATGGCATCAAC-TT--GTCGTGGA
* *
12560252 GCTAGTGTAAGACATGTCTGGGACATGCATCAGCCTCGCGGTAGACAAGCTAATGTAAAACCTGT
1 GCTAGTGTAAGACATGTCTGGGACATGCATCAGCCTCGCGATAGA-AAGCTAGTGTAAAACCTGT
* * * *
12560317 CTAGGCATGGCGTCAGCTTGTCGTGTA
65 CTAGACATGGCATCAACTTGTCGTGGA
* * * *
12560344 TC-AGTGTAAGACCTGTCTGGGACATGGCATCAACCTCGCTATATGAAAGCTAGTGTAAAACCAT
1 GCTAGTGTAAGACATGTCTGGGACAT-GCATCAGCCTCGCGATA-GAAAGCTAGTGTAAAACC-T
*
12560408 GTCTGGGACATGG
63 GTCT-AGACATGG
12560421 TTTCGGCATC
Statistics
Matches: 139, Mismatches: 23, Indels: 14
0.79 0.13 0.08
Matches are distributed among these distances:
91 26 0.19
92 32 0.23
93 12 0.09
94 69 0.50
ACGTcount: A:0.27, C:0.20, G:0.27, T:0.25
Consensus pattern (91 bp):
GCTAGTGTAAGACATGTCTGGGACATGCATCAGCCTCGCGATAGAAAGCTAGTGTAAAACCTGTC
TAGACATGGCATCAACTTGTCGTGGA
Found at i:12567257 original size:15 final size:15
Alignment explanation
Indices: 12567239--12567282 Score: 70
Period size: 15 Copynumber: 2.9 Consensus size: 15
12567229 GAAGCCCAGA
12567239 ATAAAGAAATCCAAG
1 ATAAAGAAATCCAAG
*
12567254 ATAAAGAAATCCATG
1 ATAAAGAAATCCAAG
*
12567269 ATAAGGAAATCCAA
1 ATAAAGAAATCCAA
12567283 TTTACAGCAC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.57, C:0.14, G:0.14, T:0.16
Consensus pattern (15 bp):
ATAAAGAAATCCAAG
Found at i:12572782 original size:79 final size:79
Alignment explanation
Indices: 12572690--12572847 Score: 289
Period size: 79 Copynumber: 2.0 Consensus size: 79
12572680 GGATATTAAA
*
12572690 ATTCCATGATATCCAACATTCATAAAGACATGAAATCCTATGAATCTGGTGAGGAGACATTTGGG
1 ATTCCATGATATCCAACATTCATAAAGACACGAAATCCTATGAATCTGGTGAGGAGACATTTGGG
12572755 TATACTAGGAGAAT
66 TATACTAGGAGAAT
*
12572769 ATTCCATGATATCCAACATTCATAAAGACACGAAATCCTATGAATCTGGTGAGTAGACATTTGGG
1 ATTCCATGATATCCAACATTCATAAAGACACGAAATCCTATGAATCTGGTGAGGAGACATTTGGG
*
12572834 TATACTAGTAGAAT
66 TATACTAGGAGAAT
12572848 TTACACATCT
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
79 76 1.00
ACGTcount: A:0.37, C:0.16, G:0.19, T:0.28
Consensus pattern (79 bp):
ATTCCATGATATCCAACATTCATAAAGACACGAAATCCTATGAATCTGGTGAGGAGACATTTGGG
TATACTAGGAGAAT
Found at i:12587876 original size:13 final size:13
Alignment explanation
Indices: 12587858--12587887 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
12587848 GGGAGGAGAC
12587858 ACGGCCGTGCGGT
1 ACGGCCGTGCGGT
*
12587871 ACGGCCTTGCGGT
1 ACGGCCGTGCGGT
12587884 ACGG
1 ACGG
12587888 GCGTATGGAA
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:0.10, C:0.30, G:0.43, T:0.17
Consensus pattern (13 bp):
ACGGCCGTGCGGT
Found at i:12602513 original size:94 final size:94
Alignment explanation
Indices: 12602352--12602524 Score: 258
Period size: 94 Copynumber: 1.8 Consensus size: 94
12602342 ATTGTATGCT
* ** *
12602352 AGTGTAAGACATGTCTGGGACATGCATCGGCCACAAGATGAGAGCCAGTGTAAGACATTTCTGGG
1 AGTGTAAGACATGTCTGGGACATGCATCAGCCACAAGACAAGAGCCAGTGTAAGACATGTCTGGG
*
12602417 ACATGCATCGGCCTTGAGATATTTAAGCC
66 ACATGCATCAGCCTTGAGATATTTAAGCC
* * *
12602446 AGTGTAAGACATGTTTGGGACATGCATCAG-CATTAAGACAAGAGCTAGTGTAAGACATGTCTGG
1 AGTGTAAGACATGTCTGGGACATGCATCAGCCA-CAAGACAAGAGCCAGTGTAAGACATGTCTGG
12602510 GACATGCATCAGCCT
65 GACATGCATCAGCCT
12602525 CGCGATAGAC
Statistics
Matches: 70, Mismatches: 8, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
93 2 0.03
94 68 0.97
ACGTcount: A:0.30, C:0.19, G:0.27, T:0.24
Consensus pattern (94 bp):
AGTGTAAGACATGTCTGGGACATGCATCAGCCACAAGACAAGAGCCAGTGTAAGACATGTCTGGG
ACATGCATCAGCCTTGAGATATTTAAGCC
Found at i:12602520 original size:46 final size:46
Alignment explanation
Indices: 12602352--12602522 Score: 202
Period size: 46 Copynumber: 3.7 Consensus size: 46
12602342 ATTGTATGCT
* * *
12602352 AGTGTAAGACATGTCTGGGACATGCATCGGCCA-CAAGATGAGAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCAG-CATTAAGATAAGAGCC
* * * *
12602398 AGTGTAAGACATTTCTGGGACATGCATCGGCCTTGAGATATTTA-AGCC
1 AGTGTAAGACATGTCTGGGACATGCATCAGCATTAAGATA---AGAGCC
* * *
12602446 AGTGTAAGACATGTTTGGGACATGCATCAGCATTAAGACAAGAGCT
1 AGTGTAAGACATGTCTGGGACATGCATCAGCATTAAGATAAGAGCC
12602492 AGTGTAAGACATGTCTGGGACATGCATCAGC
1 AGTGTAAGACATGTCTGGGACATGCATCAGC
12602523 CTCGCGATAG
Statistics
Matches: 107, Mismatches: 13, Indels: 10
0.82 0.10 0.08
Matches are distributed among these distances:
45 2 0.02
46 66 0.62
48 38 0.36
49 1 0.01
ACGTcount: A:0.30, C:0.19, G:0.27, T:0.23
Consensus pattern (46 bp):
AGTGTAAGACATGTCTGGGACATGCATCAGCATTAAGATAAGAGCC
Found at i:12602546 original size:94 final size:94
Alignment explanation
Indices: 12602349--12602555 Score: 254
Period size: 94 Copynumber: 2.2 Consensus size: 94
12602339 GTGATTGTAT
* ** *
12602349 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCACAAGATGAGAGCCAGTGTAAGACATTTCT
1 GCTAGTGTAAGACATGTCTGGGACATGCATCAGCCACAAGACAAGAGCCAGTGTAAGACATGTCT
* * ***
12602414 GGGACATGCATCGGCCTTGAGATATTTAA
66 GGGACATGCATCAGCCTCGAGATAGACAA
* * * *
12602443 GCCAGTGTAAGACATGTTTGGGACATGCATCAG-CATTAAGACAAGAGCTAGTGTAAGACATGTC
1 GCTAGTGTAAGACATGTCTGGGACATGCATCAGCCA-CAAGACAAGAGCCAGTGTAAGACATGTC
*
12602507 TGGGACATGCATCAGCCTCGCGATAGACAA
65 TGGGACATGCATCAGCCTCGAGATAGACAA
* *
12602537 GCTAATGTAAGACCTGTCT
1 GCTAGTGTAAGACATGTCT
12602556 AGACATGGCG
Statistics
Matches: 94, Mismatches: 18, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
93 2 0.02
94 92 0.98
ACGTcount: A:0.30, C:0.20, G:0.27, T:0.24
Consensus pattern (94 bp):
GCTAGTGTAAGACATGTCTGGGACATGCATCAGCCACAAGACAAGAGCCAGTGTAAGACATGTCT
GGGACATGCATCAGCCTCGAGATAGACAA
Found at i:12602555 original size:48 final size:48
Alignment explanation
Indices: 12602349--12602555 Score: 197
Period size: 46 Copynumber: 4.4 Consensus size: 48
12602339 GTGATTGTAT
* * * *
12602349 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCACAAGAT-GA-GA
1 GCTAGTGTAAGACATGTCTGGGACATGCATCAGCCTCGAGATAGACAA
* * * * ***
12602395 GCCAGTGTAAGACATTTCTGGGACATGCATCGGCCTTGAGATATTTAA
1 GCTAGTGTAAGACATGTCTGGGACATGCATCAGCCTCGAGATAGACAA
* * * ** * *
12602443 GCCAGTGTAAGACATGTTTGGGACATGCATCAGCATTAAGACA-A-GA
1 GCTAGTGTAAGACATGTCTGGGACATGCATCAGCCTCGAGATAGACAA
*
12602489 GCTAGTGTAAGACATGTCTGGGACATGCATCAGCCTCGCGATAGACAA
1 GCTAGTGTAAGACATGTCTGGGACATGCATCAGCCTCGAGATAGACAA
* *
12602537 GCTAATGTAAGACCTGTCT
1 GCTAGTGTAAGACATGTCT
12602556 AGACATGGCG
Statistics
Matches: 131, Mismatches: 26, Indels: 6
0.80 0.16 0.04
Matches are distributed among these distances:
46 74 0.56
47 1 0.01
48 56 0.43
ACGTcount: A:0.30, C:0.20, G:0.27, T:0.24
Consensus pattern (48 bp):
GCTAGTGTAAGACATGTCTGGGACATGCATCAGCCTCGAGATAGACAA
Found at i:12602706 original size:49 final size:49
Alignment explanation
Indices: 12602582--12602691 Score: 168
Period size: 49 Copynumber: 2.2 Consensus size: 49
12602572 TGTCGTGTGT
*
12602582 CAGTGTAAGACCTGTCTAGGACATGGCATCAACACCGATAGATGAGAGC
1 CAGTGTAAGACCTGTCTAGGACATGGCATCAACACCGATAGATGAAAGC
* * *
12602631 CAGTGTAAGACCTGTCTGGGACATGGCATCAAC-CTCGCTATATGAAAGC
1 CAGTGTAAGACCTGTCTAGGACATGGCATCAACAC-CGATAGATGAAAGC
12602680 CAGTGTAAGACC
1 CAGTGTAAGACC
12602692 ATATCTGGCC
Statistics
Matches: 56, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
48 1 0.02
49 55 0.98
ACGTcount: A:0.31, C:0.24, G:0.25, T:0.20
Consensus pattern (49 bp):
CAGTGTAAGACCTGTCTAGGACATGGCATCAACACCGATAGATGAAAGC
Found at i:12604883 original size:34 final size:34
Alignment explanation
Indices: 12604836--12604953 Score: 148
Period size: 34 Copynumber: 3.5 Consensus size: 34
12604826 ACATGGTTAA
* * *
12604836 CCATCTAGCACACCAGATGCTCTTATGAGCCAAT
1 CCATCCAGCACACCAAATGCTCTTATGAGCTAAT
* * * *
12604870 CCATCTAGGACACCAAATGCTCATATGAGCTAAA
1 CCATCCAGCACACCAAATGCTCTTATGAGCTAAT
*
12604904 CTATCCAGCACACCAAATGCT-TATATGAGCTAAT
1 CCATCCAGCACACCAAATGCTCT-TATGAGCTAAT
12604938 CCATCCAGCACACCAA
1 CCATCCAGCACACCAA
12604954 GTAACACTGT
Statistics
Matches: 72, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
34 72 1.00
ACGTcount: A:0.35, C:0.31, G:0.13, T:0.21
Consensus pattern (34 bp):
CCATCCAGCACACCAAATGCTCTTATGAGCTAAT
Found at i:12612295 original size:13 final size:13
Alignment explanation
Indices: 12612277--12612302 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
12612267 GGTTGTTTAT
12612277 TAAACTAATTAAC
1 TAAACTAATTAAC
12612290 TAAACTAATTAAC
1 TAAACTAATTAAC
12612303 CAATTAAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.15, G:0.00, T:0.31
Consensus pattern (13 bp):
TAAACTAATTAAC
Found at i:12619276 original size:65 final size:65
Alignment explanation
Indices: 12619172--12619328 Score: 305
Period size: 65 Copynumber: 2.4 Consensus size: 65
12619162 ATGTTTTTGT
12619172 TAGCTTAGTCCTCATGACTTGCCACTGATAGCTATTCAGTGACATTTCTTCAATGAATTCACTGA
1 TAGCTTAGTCCTCATGACTTGCCACTGATAGCTATTCAGTGACATTTCTTCAATGAATTCACTGA
*
12619237 TAGCTTAGTCCTCATGACTTGCCACTGATAGCTATTCAGTGACATTTCTTTAATGAATTCACTGA
1 TAGCTTAGTCCTCATGACTTGCCACTGATAGCTATTCAGTGACATTTCTTCAATGAATTCACTGA
12619302 TAGCTTAGTCCTCATGACTTGCCACTG
1 TAGCTTAGTCCTCATGACTTGCCACTG
12619329 CATCAACCAT
Statistics
Matches: 91, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
65 91 1.00
ACGTcount: A:0.25, C:0.24, G:0.16, T:0.36
Consensus pattern (65 bp):
TAGCTTAGTCCTCATGACTTGCCACTGATAGCTATTCAGTGACATTTCTTCAATGAATTCACTGA
Found at i:12620448 original size:13 final size:13
Alignment explanation
Indices: 12620430--12620458 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
12620420 GGTTGTTTCT
12620430 TAAACTAATTAAC
1 TAAACTAATTAAC
12620443 TAAACTAATTAAC
1 TAAACTAATTAAC
12620456 TAA
1 TAA
12620459 TTAAACTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (13 bp):
TAAACTAATTAAC
Found at i:12622212 original size:13 final size:13
Alignment explanation
Indices: 12622196--12622228 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
12622186 TTTAATTAAA
*
12622196 TTAGTTAATTAGT
1 TTAGATAATTAGT
12622209 TTAGATAATTAGT
1 TTAGATAATTAGT
12622222 TTA-ATAA
1 TTAGATAA
12622229 ACAAACCCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 4 0.21
13 15 0.79
ACGTcount: A:0.39, C:0.00, G:0.12, T:0.48
Consensus pattern (13 bp):
TTAGATAATTAGT
Found at i:12625796 original size:26 final size:26
Alignment explanation
Indices: 12625623--12625812 Score: 201
Period size: 26 Copynumber: 7.2 Consensus size: 26
12625613 GGGACGAAAT
* *
12625623 AATGACCGAAATACCTCCATAGGGTAA
1 AATGACTGAAATACC-CCATAAGGTAA
12625650 AATGA-TCGAAATACCCCAT-AGGATAA
1 AATGACT-GAAATACCCCATAAGG-TAA
*
12625676 AATGACCGAAATACCCCAT-AGGTTAA
1 AATGACTGAAATACCCCATAAGG-TAA
* *
12625702 AATGACTGAAAAACCCCATATGGTAA
1 AATGACTGAAATACCCCATAAGGTAA
*
12625728 AATGACTGAAATACCCCCATAGGGTAA
1 AATGACTGAAATA-CCCCATAAGGTAA
12625755 AATGACT-ATAATACCCCTATAAGGTAA
1 AATGACTGA-AATACCCC-ATAAGGTAA
* *
12625782 AATGACTGTAA-ACCCCTGTAAGGTAA
1 AATGACTGAAATACCCC-ATAAGGTAA
12625808 AATGA
1 AATGA
12625813 TTATTTTTCC
Statistics
Matches: 143, Mismatches: 12, Indels: 17
0.83 0.07 0.10
Matches are distributed among these distances:
25 2 0.01
26 86 0.60
27 55 0.38
ACGTcount: A:0.43, C:0.20, G:0.16, T:0.21
Consensus pattern (26 bp):
AATGACTGAAATACCCCATAAGGTAA
Found at i:12625865 original size:25 final size:25
Alignment explanation
Indices: 12625827--12625927 Score: 114
Period size: 25 Copynumber: 4.0 Consensus size: 25
12625817 TTTTCCCTTA
*
12625827 TGTGTTAAATTGACAGTTTTGCCCT
1 TGTGTTAAAATGACAGTTTTGCCCT
*
12625852 TGTGTTAAAATGAC-GATTTTTCCCTT
1 TGTGTTAAAATGACAG-TTTTGCCC-T
* *
12625878 ATATGATAAAATGACAGTTTTGCCCT
1 -TGTGTTAAAATGACAGTTTTGCCCT
**
12625904 TGTGTTAAAATGATTGTTTTGCCC
1 TGTGTTAAAATGACAGTTTTGCCC
12625928 CTATGTGACG
Statistics
Matches: 63, Mismatches: 9, Indels: 8
0.79 0.11 0.10
Matches are distributed among these distances:
24 1 0.02
25 40 0.63
26 2 0.03
27 19 0.30
28 1 0.02
ACGTcount: A:0.25, C:0.15, G:0.18, T:0.43
Consensus pattern (25 bp):
TGTGTTAAAATGACAGTTTTGCCCT
Found at i:12625893 original size:52 final size:52
Alignment explanation
Indices: 12625805--12625916 Score: 179
Period size: 52 Copynumber: 2.2 Consensus size: 52
12625795 CCCTGTAAGG
** * * *
12625805 TAAAATGATTATTTTTCCCTTATGTGTTAAATTGACAGTTTTGCCCTTGTGT
1 TAAAATGACGATTTTTCCCTTATATGATAAAATGACAGTTTTGCCCTTGTGT
12625857 TAAAATGACGATTTTTCCCTTATATGATAAAATGACAGTTTTGCCCTTGTGT
1 TAAAATGACGATTTTTCCCTTATATGATAAAATGACAGTTTTGCCCTTGTGT
12625909 TAAAATGA
1 TAAAATGA
12625917 TTGTTTTGCC
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
52 55 1.00
ACGTcount: A:0.29, C:0.13, G:0.15, T:0.43
Consensus pattern (52 bp):
TAAAATGACGATTTTTCCCTTATATGATAAAATGACAGTTTTGCCCTTGTGT
Found at i:12627438 original size:53 final size:53
Alignment explanation
Indices: 12627358--12627463 Score: 212
Period size: 53 Copynumber: 2.0 Consensus size: 53
12627348 TTTCCAATCT
12627358 CTTAAGGCACCACATACGCATTTGGGTAGTTTTTATACCTAGTATTGTTCTAA
1 CTTAAGGCACCACATACGCATTTGGGTAGTTTTTATACCTAGTATTGTTCTAA
12627411 CTTAAGGCACCACATACGCATTTGGGTAGTTTTTATACCTAGTATTGTTCTAA
1 CTTAAGGCACCACATACGCATTTGGGTAGTTTTTATACCTAGTATTGTTCTAA
12627464 TATTGTTCTA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 53 1.00
ACGTcount: A:0.26, C:0.19, G:0.17, T:0.38
Consensus pattern (53 bp):
CTTAAGGCACCACATACGCATTTGGGTAGTTTTTATACCTAGTATTGTTCTAA
Found at i:12628465 original size:26 final size:25
Alignment explanation
Indices: 12628429--12628512 Score: 105
Period size: 26 Copynumber: 3.2 Consensus size: 25
12628419 ATGAATTTTC
*
12628429 TCAAAACTTTATCGGGGCTAAAATCG
1 TCAAAATTTTATCGGGG-TAAAATCG
*
12628455 TCAAAATTTTATTGGGGGTAAAATCG
1 TCAAAATTTTA-TCGGGGTAAAATCG
* *
12628481 TCAAAATTTTACCGAGGGTAAAATTG
1 TCAAAATTTTATCG-GGGTAAAATCG
12628507 TCAAAA
1 TCAAAA
12628513 AATTTATTGG
Statistics
Matches: 51, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
25 1 0.02
26 45 0.88
27 5 0.10
ACGTcount: A:0.38, C:0.13, G:0.19, T:0.30
Consensus pattern (25 bp):
TCAAAATTTTATCGGGGTAAAATCG
Found at i:12628528 original size:26 final size:25
Alignment explanation
Indices: 12628429--12628528 Score: 101
Period size: 26 Copynumber: 3.8 Consensus size: 25
12628419 ATGAATTTTC
* *
12628429 TCAAAACTTTATCGGGGCTAAAATCG
1 TCAAAATTTTATTGGGG-TAAAATCG
12628455 TCAAAATTTTATTGGGGGTAAAATCG
1 TCAAAATTTTATT-GGGGTAAAATCG
** *
12628481 TCAAAATTTTACCGAGGGTAAAATTG
1 TCAAAATTTTATTG-GGGTAAAATCG
* *
12628507 TCAAAAAATTTATTGGGTTAAA
1 TC-AAAATTTTATTGGGGTAAA
12628529 TTTGGGATGA
Statistics
Matches: 62, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
25 1 0.02
26 48 0.77
27 13 0.21
ACGTcount: A:0.38, C:0.11, G:0.19, T:0.32
Consensus pattern (25 bp):
TCAAAATTTTATTGGGGTAAAATCG
Found at i:12639321 original size:28 final size:28
Alignment explanation
Indices: 12639289--12639344 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 28
12639279 ATTTAAGGAT
12639289 TAAAT-TGAGAAA-TGTGAAAATTGTATGG
1 TAAATATGAGAAATTGTG-AAA-TGTATGG
*
12639317 TAAATATGTGAAATTGTGAAATGTATGG
1 TAAATATGAGAAATTGTGAAATGTATGG
12639345 GCTTCTTTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
28 12 0.48
29 9 0.36
30 4 0.16
ACGTcount: A:0.41, C:0.00, G:0.25, T:0.34
Consensus pattern (28 bp):
TAAATATGAGAAATTGTGAAATGTATGG
Found at i:12645942 original size:13 final size:13
Alignment explanation
Indices: 12645920--12645952 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
12645910 AAGGGTTTGT
12645920 TTAT-TAAACTAA
1 TTATCTAAACTAA
12645932 TTATCTAAACTAA
1 TTATCTAAACTAA
*
12645945 TTAACTAA
1 TTATCTAA
12645953 TTTAATTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 4 0.21
13 15 0.79
ACGTcount: A:0.48, C:0.12, G:0.00, T:0.39
Consensus pattern (13 bp):
TTATCTAAACTAA
Found at i:12648873 original size:6 final size:6
Alignment explanation
Indices: 12648862--12648945 Score: 86
Period size: 6 Copynumber: 14.7 Consensus size: 6
12648852 AAGAAAATTG
** * * *
12648862 AAAAAT AAAAAT AAAAAT CTAAAG AAAAAT AAGAAT AAGAAT -AAAAT
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT
*
12648909 -AAAAT AAAAAT AAGAAT --AAAT AAAAAT AAAAAT AAAA
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAA
12648946 TAGGAGGATT
Statistics
Matches: 65, Mismatches: 10, Indels: 6
0.80 0.12 0.07
Matches are distributed among these distances:
4 3 0.05
5 9 0.14
6 53 0.82
ACGTcount: A:0.77, C:0.01, G:0.05, T:0.17
Consensus pattern (6 bp):
AAAAAT
Found at i:12648874 original size:22 final size:23
Alignment explanation
Indices: 12648847--12648947 Score: 88
Period size: 22 Copynumber: 4.5 Consensus size: 23
12648837 TATGTCTTTC
12648847 AAAATAAGAA-AATTGAAAAATA
1 AAAATAAGAATAATTGAAAAATA
* *
12648869 AAAATAAAAATCTAA-AGAAAAATA
1 AAAATAAGAA--TAATTGAAAAATA
* *
12648893 AGAATAAGAATAA--AATAAAATA
1 AAAATAAGAATAATTGA-AAAATA
*
12648915 AAAATAAGAATAAAT-AAAAATA
1 AAAATAAGAATAATTGAAAAATA
12648937 AAAATAA-AATA
1 AAAATAAGAATA
12648948 GGAGGATTCG
Statistics
Matches: 67, Mismatches: 6, Indels: 13
0.78 0.07 0.15
Matches are distributed among these distances:
21 5 0.07
22 43 0.64
23 1 0.01
24 16 0.24
25 2 0.03
ACGTcount: A:0.75, C:0.01, G:0.06, T:0.18
Consensus pattern (23 bp):
AAAATAAGAATAATTGAAAAATA
Found at i:12648920 original size:16 final size:16
Alignment explanation
Indices: 12648887--12648947 Score: 79
Period size: 16 Copynumber: 3.7 Consensus size: 16
12648877 AATCTAAAGA
*
12648887 AAAATAAGAATAAGAAT
1 AAAATAA-AATAAAAAT
12648904 AAAATAAAATAAAAAT
1 AAAATAAAATAAAAAT
12648920 AAGAAT-AAATAAAAAT
1 AA-AATAAAATAAAAAT
12648936 AAAAATAAAATA
1 -AAAATAAAATA
12648948 GGAGGATTCG
Statistics
Matches: 40, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
16 23 0.57
17 17 0.43
ACGTcount: A:0.77, C:0.00, G:0.05, T:0.18
Consensus pattern (16 bp):
AAAATAAAATAAAAAT
Found at i:12648925 original size:28 final size:28
Alignment explanation
Indices: 12648870--12648945 Score: 93
Period size: 28 Copynumber: 2.7 Consensus size: 28
12648860 TGAAAAATAA
** *
12648870 AAATAAAAATCTAAAGAAAAATAAGAAT
1 AAATAAAAATAAAAATAAAAATAAGAAT
12648898 AAGA-ATAAAAT-AAAATAAAAATAAGAAT
1 AA-ATA-AAAATAAAAATAAAAATAAGAAT
12648926 AAATAAAAATAAAAATAAAA
1 AAATAAAAATAAAAATAAAA
12648946 TAGGAGGATT
Statistics
Matches: 42, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
27 6 0.14
28 30 0.71
29 6 0.14
ACGTcount: A:0.76, C:0.01, G:0.05, T:0.17
Consensus pattern (28 bp):
AAATAAAAATAAAAATAAAAATAAGAAT
Found at i:12653846 original size:9 final size:9
Alignment explanation
Indices: 12653832--12653859 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
12653822 AAATCAGAAT
12653832 ATAAAAATA
1 ATAAAAATA
12653841 ATAAAAATA
1 ATAAAAATA
12653850 ATAAAAATA
1 ATAAAAATA
12653859 A
1 A
12653860 CTAACTTAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (9 bp):
ATAAAAATA
Found at i:12654378 original size:27 final size:26
Alignment explanation
Indices: 12654331--12654381 Score: 66
Period size: 27 Copynumber: 1.9 Consensus size: 26
12654321 CGAGGCTGCT
*
12654331 AGATATTGTGACGAAGTCACCAGAAC
1 AGATATTGTGACGAAGCCACCAGAAC
* *
12654357 AGATATATGTGGCGACGCCACCAGA
1 AGATAT-TGTGACGAAGCCACCAGA
12654382 TTGCAGCGAG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 6 0.29
27 15 0.71
ACGTcount: A:0.35, C:0.22, G:0.25, T:0.18
Consensus pattern (26 bp):
AGATATTGTGACGAAGCCACCAGAAC
Found at i:12654737 original size:28 final size:28
Alignment explanation
Indices: 12654706--12654762 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
12654696 AAATGCACAC
12654706 TCTGCACTCTAATCATCCAAATACACCA
1 TCTGCACTCTAATCATCCAAATACACCA
*
12654734 TCTGCACTCTAATCATCCAAATGCACCA
1 TCTGCACTCTAATCATCCAAATACACCA
12654762 T
1 T
12654763 ATTCATTAAC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.33, C:0.35, G:0.05, T:0.26
Consensus pattern (28 bp):
TCTGCACTCTAATCATCCAAATACACCA
Found at i:12656457 original size:5 final size:5
Alignment explanation
Indices: 12656447--12656471 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
12656437 ATAAATAGTA
12656447 AAATT AAATT AAATT AAATT AAATT
1 AAATT AAATT AAATT AAATT AAATT
12656472 GCAAGAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
AAATT
Found at i:12656776 original size:13 final size:13
Alignment explanation
Indices: 12656754--12656786 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
12656744 AAGGGTTTGT
12656754 TTAT-TAAACTAA
1 TTATCTAAACTAA
12656766 TTATCTAAACTAA
1 TTATCTAAACTAA
*
12656779 TTAACTAA
1 TTATCTAA
12656787 TTTAATTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 4 0.21
13 15 0.79
ACGTcount: A:0.48, C:0.12, G:0.00, T:0.39
Consensus pattern (13 bp):
TTATCTAAACTAA
Found at i:12662448 original size:27 final size:26
Alignment explanation
Indices: 12662413--12662524 Score: 152
Period size: 27 Copynumber: 4.2 Consensus size: 26
12662403 AGCATGGTTG
* *
12662413 CCAGAACAGATAATGTGACAGAGTCA
1 CCAGAACAGATAATGTGGCAGAGCCA
12662439 CCAGATACAGATAATCGTGGCAGAGCCA
1 CCAGA-ACAGATAAT-GTGGCAGAGCCA
12662467 CCAGAACAGATATATGTGGCAGAGCCA
1 CCAGAACAGATA-ATGTGGCAGAGCCA
* *
12662494 CCAGATCAGATAATTGTGGCATAGCCA
1 CCAGAACAGATAA-TGTGGCAGAGCCA
12662521 CCAG
1 CCAG
12662525 GACTCTTCCT
Statistics
Matches: 78, Mismatches: 4, Indels: 7
0.88 0.04 0.08
Matches are distributed among these distances:
26 6 0.08
27 55 0.71
28 17 0.22
ACGTcount: A:0.37, C:0.23, G:0.24, T:0.16
Consensus pattern (26 bp):
CCAGAACAGATAATGTGGCAGAGCCA
Found at i:12662476 original size:54 final size:54
Alignment explanation
Indices: 12662413--12662524 Score: 172
Period size: 54 Copynumber: 2.1 Consensus size: 54
12662403 AGCATGGTTG
*
12662413 CCAGAACAGATA-ATGTGACAGAGTCACCAGATACAGATAATCGTGGCAGAGCCA
1 CCAGAACAGATATATGTGACAGAGCCACCAGAT-CAGATAATCGTGGCAGAGCCA
* * *
12662467 CCAGAACAGATATATGTGGCAGAGCCACCAGATCAGATAATTGTGGCATAGCCA
1 CCAGAACAGATATATGTGACAGAGCCACCAGATCAGATAATCGTGGCAGAGCCA
12662521 CCAG
1 CCAG
12662525 GACTCTTCCT
Statistics
Matches: 53, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
54 35 0.66
55 18 0.34
ACGTcount: A:0.37, C:0.23, G:0.24, T:0.16
Consensus pattern (54 bp):
CCAGAACAGATATATGTGACAGAGCCACCAGATCAGATAATCGTGGCAGAGCCA
Found at i:12667716 original size:56 final size:57
Alignment explanation
Indices: 12667588--12667741 Score: 229
Period size: 56 Copynumber: 2.7 Consensus size: 57
12667578 ATGTATATGA
* * * * * *
12667588 GGCATTGATATGTGATTCCGATATATGAGTGTGAGTAAGACCACATTTTTATATGTT
1 GGCATCGATATGTGACTCCGATATATGTGTGCGAGTAAGACAACAGTTTTATATGTT
12667645 GGCATCGATATGTGACTCCGATATATGTGTGCGAGTAAGACAAC-GTTTTATATGTT
1 GGCATCGATATGTGACTCCGATATATGTGTGCGAGTAAGACAACAGTTTTATATGTT
* *
12667701 GGCATCGATATGTGACTCTGATATATTTGTGCGAGTAAGAC
1 GGCATCGATATGTGACTCCGATATATGTGTGCGAGTAAGAC
12667742 CTTGTCTGGG
Statistics
Matches: 89, Mismatches: 8, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
56 50 0.56
57 39 0.44
ACGTcount: A:0.27, C:0.13, G:0.25, T:0.35
Consensus pattern (57 bp):
GGCATCGATATGTGACTCCGATATATGTGTGCGAGTAAGACAACAGTTTTATATGTT
Found at i:12671821 original size:26 final size:26
Alignment explanation
Indices: 12671791--12671872 Score: 155
Period size: 26 Copynumber: 3.2 Consensus size: 26
12671781 TGAAATTCCC
12671791 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
*
12671817 ATCATGAAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
12671843 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
12671869 ATCA
1 ATCA
12671873 ATTTGTATCA
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 54 1.00
ACGTcount: A:0.37, C:0.27, G:0.06, T:0.30
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:12676810 original size:41 final size:41
Alignment explanation
Indices: 12676550--12676810 Score: 278
Period size: 41 Copynumber: 6.4 Consensus size: 41
12676540 CGTTCTAAAA
* ** * *
12676550 AAAACGCCGGTAAAAA-CAGAGCAACAGCGGC-ATTTTAGTCA
1 AAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTT-G-CT
* * *
12676591 AAAATGCCGCT-AAAACCAGAGCATTAGCGGCGCTTTAGGT
1 AAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTTGCT
* * * *
12676631 AAAAGGACGCTAAAAACCAGAGCATTAGCGGTGC-TTTCCGT
1 AAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTTGC-T
* * * *
12676672 AAAACGCCGCAAAAAACCAGAGCATTAGCGACGCTTTAGGT
1 AAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTTGCT
* * *
12676713 AAAACGCCGCTAAAAACTAGAGCATTAGCGGCGGTTTTGGT
1 AAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTTGCT
* *
12676754 AAAACGCCGCTAAAAACCAGAGCATTAGCGGCACTTTTTCT
1 AAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTTGCT
12676795 AAAACGCCGCTAAAAA
1 AAAACGCCGCTAAAAA
12676811 TCCCCTAACC
Statistics
Matches: 183, Mismatches: 32, Indels: 10
0.81 0.14 0.04
Matches are distributed among these distances:
40 15 0.08
41 163 0.89
42 5 0.03
ACGTcount: A:0.37, C:0.23, G:0.22, T:0.18
Consensus pattern (41 bp):
AAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTTGCT
Found at i:12676976 original size:14 final size:14
Alignment explanation
Indices: 12676954--12676993 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
12676944 TTAATTATCA
* *
12676954 TTATAGTTTAAGGT
1 TTATGGTTTAAGAT
12676968 TTATGGTTTAAGAT
1 TTATGGTTTAAGAT
*
12676982 ATATGGTTTAAG
1 TTATGGTTTAAG
12676994 CAGGTTTAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.30, C:0.00, G:0.23, T:0.47
Consensus pattern (14 bp):
TTATGGTTTAAGAT
Found at i:12677889 original size:10 final size:11
Alignment explanation
Indices: 12677870--12677928 Score: 57
Period size: 13 Copynumber: 5.0 Consensus size: 11
12677860 AAGATAAATG
12677870 TATATAATATAAA
1 TATAT-ATA-AAA
12677883 TATATATAAAA
1 TATATATAAAA
*
12677894 TATTATTTTAAAA
1 TA-TA-TATAAAA
12677907 TATATAT-AAA
1 TATATATAAAA
12677917 TATATATGAAAA
1 TATATAT-AAAA
12677929 GTGGTTTAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
10 10 0.25
11 7 0.17
12 10 0.25
13 13 0.32
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.41
Consensus pattern (11 bp):
TATATATAAAA
Found at i:12679508 original size:18 final size:17
Alignment explanation
Indices: 12679487--12679529 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 17
12679477 ATCTTAATGA
12679487 TGATGATGATGTTGATAC
1 TGATGATGATGTTGAT-C
*
12679505 TGATGTTGATGTTGATC
1 TGATGATGATGTTGATC
12679522 TCGATGAT
1 T-GATGAT
12679530 TATACCCTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 2 0.09
18 20 0.91
ACGTcount: A:0.23, C:0.07, G:0.28, T:0.42
Consensus pattern (17 bp):
TGATGATGATGTTGATC
Found at i:12680607 original size:23 final size:23
Alignment explanation
Indices: 12680581--12680624 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
12680571 CTTGGTCCTA
12680581 TTTCTCCTGTTAATGGTATACTG
1 TTTCTCCTGTTAATGGTATACTG
*
12680604 TTTCTCCTGTTAATGTTATAC
1 TTTCTCCTGTTAATGGTATAC
12680625 CAAATTGCTG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.18, C:0.18, G:0.14, T:0.50
Consensus pattern (23 bp):
TTTCTCCTGTTAATGGTATACTG
Found at i:12683020 original size:21 final size:21
Alignment explanation
Indices: 12682991--12683030 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
12682981 GTTTTTATAT
*
12682991 TTTGGTTCAACTTAAGTATTA
1 TTTGATTCAACTTAAGTATTA
12683012 TTTGATTCAACTTAAGTAT
1 TTTGATTCAACTTAAGTAT
12683031 GAATTAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.10, G:0.12, T:0.47
Consensus pattern (21 bp):
TTTGATTCAACTTAAGTATTA
Found at i:12683478 original size:467 final size:467
Alignment explanation
Indices: 12682605--12684350 Score: 3350
Period size: 467 Copynumber: 3.7 Consensus size: 467
12682595 TTCTCTCCAA
12682605 CCTTATTTTAAATATTTTAAAGATTCAAAGTATATAGGCTGGAAACCTGACGGGTTGCCTTATAT
1 CCTTATTTTAAATATTTTAAAGATTCAAAGTATATAGGCTGGAAACCTGACGGGTTGCCTTATAT
*
12682670 CGAGCTGCAAGATATAATGGATCCTCCCTAGGTGTAACAACGCCATGTATGATGAATCTTAAAAA
66 CGAGCTGCAAGATATAATGGATCCTCCCTAGGTGTAACAACGCCACGTATGATGAATCTTAAAAA
12682735 ATTCAAAAAGAATTGAAAAAAGTTCTATCGCTATTGAATATTTATATAACCTTAATTTATTTCCA
131 ATTCAAAAAGAATTGAAAAAAGTTCTATCGCTATTGAATATTTATATAACCTTAATTTATTTCCA
12682800 ATTTACTTATAAAAATTAAACTACGATTCTTTCTTGATATTATTATATTCAAATTACTATTTTGT
196 ATTTACTTATAAAAATTAAACTACGATTCTTTCTTGATATTATTATATTCAAATTACTATTTTGT
12682865 TATATTAAACATGTTTGATTTTAATATTTAATATTTTTAAATATCTTTAAAAGTTATAACTAATT
261 TATATTAAACATGTTTGATTTTAATATTTAATATTTTTAAATATCTTTAAAAGTTATAACTAATT
12682930 TTTATCAAAATAGTATTAATTATTATTTGAAGTATGAATAAGTATGAATAAGTTTTTATATTTTG
326 TTTATCAAAATAGTATTAATTATTATTTGAAGTATGAATAAGTATGAATAAGTTTTTATATTTTG
12682995 GTTCAACTTAAGTATTATTTGATTCAACTTAAGTATGAATTAATTTTATTACCATATATGTAGCT
391 GTTCAACTTAAGTATTATTTGATTCAACTTAAGTATGAATTAATTTTATTACCATATATGTAGCT
12683060 TGCTTGTCCATT
456 TGCTTGTCCATT
12683072 CCTTATTTTAAATATTTTAAAGATTCAAAGTATATAGGCTGGAAACCTGACGGGTTGCCTTATAT
1 CCTTATTTTAAATATTTTAAAGATTCAAAGTATATAGGCTGGAAACCTGACGGGTTGCCTTATAT
12683137 CGAGCTGCAAGATATAATGGATCCTCCCTAGGTGTAACAACGCCACGTATGATGAATCTTAAAAA
66 CGAGCTGCAAGATATAATGGATCCTCCCTAGGTGTAACAACGCCACGTATGATGAATCTTAAAAA
*
12683202 ATTCAAAAAGAATTGAAAAAAGTTCTATCGCTATTGAATATTCATATAACCTTAATTTATTTCCA
131 ATTCAAAAAGAATTGAAAAAAGTTCTATCGCTATTGAATATTTATATAACCTTAATTTATTTCCA
12683267 ATTTACTTATAAAAATTAAACTACGATTCTTTCTTGATATTATTATATTCAAATTACTATTTTGT
196 ATTTACTTATAAAAATTAAACTACGATTCTTTCTTGATATTATTATATTCAAATTACTATTTTGT
*
12683332 TATATTAAACATGTTTGATTTTAATATTTAATATTTTTATATATCTTTAAAAGTTATAACTAATT
261 TATATTAAACATGTTTGATTTTAATATTTAATATTTTTAAATATCTTTAAAAGTTATAACTAATT
12683397 TTTATCAAAATAGTATTAATTATTATTTGAAGTATGAATAAGTATGAATAAGTTTTTATATTTTG
326 TTTATCAAAATAGTATTAATTATTATTTGAAGTATGAATAAGTATGAATAAGTTTTTATATTTTG
*
12683462 GTTCAACTTAAGTATTATTTGACTCAACTTAAGTATGAATTAATTTTATTACCATATATGTAGCT
391 GTTCAACTTAAGTATTATTTGATTCAACTTAAGTATGAATTAATTTTATTACCATATATGTAGCT
12683527 TGCTTGTCCATT
456 TGCTTGTCCATT
12683539 CCTTATTTTAAATATTTTAAAGATTCAAAGTATATAGGCTGGAAACCTGACGGGTTGCCTTATAT
1 CCTTATTTTAAATATTTTAAAGATTCAAAGTATATAGGCTGGAAACCTGACGGGTTGCCTTATAT
*
12683604 CGAGCTGCAAGATATAATAGATCCTCCCTAGGTGTAACAACGCCACGTATGATGAATCTTAAAAA
66 CGAGCTGCAAGATATAATGGATCCTCCCTAGGTGTAACAACGCCACGTATGATGAATCTTAAAAA
*
12683669 ATTCAAAAAGAATTGAAAAAAGTTCTATCGCTATTAAATATTTATATAACCTTAATTTATTTCCA
131 ATTCAAAAAGAATTGAAAAAAGTTCTATCGCTATTGAATATTTATATAACCTTAATTTATTTCCA
12683734 ATTTACTTATAAAAATTAAACTACGATTCTTTCTTGATATTATTATATTCAAATTACTATTTTGT
196 ATTTACTTATAAAAATTAAACTACGATTCTTTCTTGATATTATTATATTCAAATTACTATTTTGT
* *
12683799 TATATTAAACATATTTGATTTTAATATTTAATATTTTTAAATGTCTTTAAAAGTTATAACTAATT
261 TATATTAAACATGTTTGATTTTAATATTTAATATTTTTAAATATCTTTAAAAGTTATAACTAATT
12683864 TTTATCAAAATAGTATTAATTATTATTTGAAGTATGAATAAGTATGAATAAGTTTTTATATTTTG
326 TTTATCAAAATAGTATTAATTATTATTTGAAGTATGAATAAGTATGAATAAGTTTTTATATTTTG
12683929 GTTCAACTTAAGTATTATTTGATTCAACTTAAGTATGAATTAATTTTATTACCATATATGTAGCT
391 GTTCAACTTAAGTATTATTTGATTCAACTTAAGTATGAATTAATTTTATTACCATATATGTAGCT
12683994 TGCTTGTCCATT
456 TGCTTGTCCATT
12684006 CCTTATTTTAAATATTTTAAAGATTCAAAGTATATAGGCTGGAAACCTGACGGGTTGCCTTATAT
1 CCTTATTTTAAATATTTTAAAGATTCAAAGTATATAGGCTGGAAACCTGACGGGTTGCCTTATAT
* * *
12684071 AGAGCTGCAAGATATAATGGATCCTCCCTGGGTGTAACAACGCCACGTATGGTGAATCTTAAAAA
66 CGAGCTGCAAGATATAATGGATCCTCCCTAGGTGTAACAACGCCACGTATGATGAATCTTAAAAA
*
12684136 ATTCAAAAAGAATTGAAAAAATTTCTAGT-GCTATTGAATATTTATATAACCTTAATTTATTTCC
131 ATTCAAAAAGAATTGAAAAAAGTTCTA-TCGCTATTGAATATTTATATAACCTTAATTTATTTCC
12684200 AATTTACTTATAAAAATTAAACTACGATTCTTTCTTGATATTATTATATTCAAATTACTATTTTG
195 AATTTACTTATAAAAATTAAACTACGATTCTTTCTTGATATTATTATATTCAAATTACTATTTTG
*
12684265 TTATATTAAACATGTTTGATTTTAATATTTAATATTTTTAAATGTCTTTAAAAGTTATAACTAAT
260 TTATATTAAACATGTTTGATTTTAATATTTAATATTTTTAAATATCTTTAAAAGTTATAACTAAT
*
12684330 TTTTATTAAAATAGTATTAAT
325 TTTTATCAAAATAGTATTAAT
12684351 ATTGATCATT
Statistics
Matches: 1259, Mismatches: 19, Indels: 2
0.98 0.01 0.00
Matches are distributed among these distances:
467 1258 1.00
468 1 0.00
ACGTcount: A:0.36, C:0.11, G:0.11, T:0.42
Consensus pattern (467 bp):
CCTTATTTTAAATATTTTAAAGATTCAAAGTATATAGGCTGGAAACCTGACGGGTTGCCTTATAT
CGAGCTGCAAGATATAATGGATCCTCCCTAGGTGTAACAACGCCACGTATGATGAATCTTAAAAA
ATTCAAAAAGAATTGAAAAAAGTTCTATCGCTATTGAATATTTATATAACCTTAATTTATTTCCA
ATTTACTTATAAAAATTAAACTACGATTCTTTCTTGATATTATTATATTCAAATTACTATTTTGT
TATATTAAACATGTTTGATTTTAATATTTAATATTTTTAAATATCTTTAAAAGTTATAACTAATT
TTTATCAAAATAGTATTAATTATTATTTGAAGTATGAATAAGTATGAATAAGTTTTTATATTTTG
GTTCAACTTAAGTATTATTTGATTCAACTTAAGTATGAATTAATTTTATTACCATATATGTAGCT
TGCTTGTCCATT
Found at i:12683954 original size:21 final size:21
Alignment explanation
Indices: 12683925--12683964 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
12683915 GTTTTTATAT
*
12683925 TTTGGTTCAACTTAAGTATTA
1 TTTGATTCAACTTAAGTATTA
12683946 TTTGATTCAACTTAAGTAT
1 TTTGATTCAACTTAAGTAT
12683965 GAATTAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.10, G:0.12, T:0.47
Consensus pattern (21 bp):
TTTGATTCAACTTAAGTATTA
Found at i:12684384 original size:9 final size:9
Alignment explanation
Indices: 12684361--12684413 Score: 52
Period size: 9 Copynumber: 5.6 Consensus size: 9
12684351 ATTGATCATT
*
12684361 ACTTAAATA
1 ACTTACATA
*
12684370 AATTACATA
1 ACTTACATA
12684379 ACTTACATA
1 ACTTACATA
*
12684388 ACGTACATAACA
1 ACTTACAT---A
12684400 ACTTACATA
1 ACTTACATA
12684409 ACTTA
1 ACTTA
12684414 ACTAATACAT
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
9 28 0.78
12 8 0.22
ACGTcount: A:0.49, C:0.19, G:0.02, T:0.30
Consensus pattern (9 bp):
ACTTACATA
Found at i:12689987 original size:21 final size:21
Alignment explanation
Indices: 12689961--12690008 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
12689951 TCAACTTAGA
*
12689961 GCGGAGGCAGCATCGAGGGAG
1 GCGGAGGCAGCAGCGAGGGAG
12689982 GCGGAGGCAGCAGCGAGGGAG
1 GCGGAGGCAGCAGCGAGGGAG
12690003 GCGGAG
1 GCGGAG
12690009 CAGAACAGGA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.23, C:0.19, G:0.56, T:0.02
Consensus pattern (21 bp):
GCGGAGGCAGCAGCGAGGGAG
Found at i:12690370 original size:43 final size:43
Alignment explanation
Indices: 12690307--12690509 Score: 241
Period size: 43 Copynumber: 4.7 Consensus size: 43
12690297 CTGGGCAAAT
12690307 TAGCGGCGTTTTTTATAAAAGCGCCGCTAAAAGTACAGGTCTA
1 TAGCGGCGTTTTTTATAAAAGCGCCGCTAAAAGTACAGGTCTA
* * *
12690350 TAGCGGCGTTTTTTAAAAAAGCGCCGCTAAAGGT-CTTGGTC-A
1 TAGCGGCGTTTTTTATAAAAGCGCCGCTAAAAGTAC-AGGTCTA
* * *
12690392 TTAGCGGCCTTTTTTTATAAAAGCGCCACTAAAAGTACAAGTCTA
1 -TAGCGG-CGTTTTTTATAAAAGCGCCGCTAAAAGTACAGGTCTA
* * * * * *
12690437 TAGCGGCGTTTTTTAAAAAAGCGCCGCTAAAGGTCCTGATCTT
1 TAGCGGCGTTTTTTATAAAAGCGCCGCTAAAAGTACAGGTCTA
*
12690480 TAGCGGCG-TTTTTATAAGAGCGCCGCTAAA
1 TAGCGGCGTTTTTTATAAAAGCGCCGCTAAA
12690510 GGTCAACGCC
Statistics
Matches: 135, Mismatches: 20, Indels: 11
0.81 0.12 0.07
Matches are distributed among these distances:
42 22 0.16
43 78 0.58
44 33 0.24
45 2 0.01
ACGTcount: A:0.29, C:0.20, G:0.23, T:0.29
Consensus pattern (43 bp):
TAGCGGCGTTTTTTATAAAAGCGCCGCTAAAAGTACAGGTCTA
Found at i:12690450 original size:87 final size:85
Alignment explanation
Indices: 12690305--12690509 Score: 320
Period size: 87 Copynumber: 2.4 Consensus size: 85
12690295 AACTGGGCAA
*
12690305 ATTAGCGGCGTTTTTTATAAAAGCGCCGCTAAAAGTACAGGTCTATAGCGGCGTTTTTTAAAAAA
1 ATTAGCGGC-TTTTTTATAAAAGCGCCGCTAAAAGTACAAGTCTATAGCGGCGTTTTTTAAAAAA
* *
12690370 GCGCCGCTAAAGGTCTTGGTC
65 GCGCCGCTAAAGGTCCTGATC
*
12690391 ATTAGCGGCCTTTTTTTATAAAAGCGCCACTAAAAGTACAAGTCTATAGCGGCGTTTTTTAAAAA
1 ATTAGCGG-C-TTTTTTATAAAAGCGCCGCTAAAAGTACAAGTCTATAGCGGCGTTTTTTAAAAA
12690456 AGCGCCGCTAAAGGTCCTGATC
64 AGCGCCGCTAAAGGTCCTGATC
* * *
12690478 TTTAGCGGCGTTTTTATAAGAGCGCCGCTAAA
1 ATTAGCGGCTTTTTTATAAAAGCGCCGCTAAA
12690510 GGTCAACGCC
Statistics
Matches: 109, Mismatches: 9, Indels: 3
0.90 0.07 0.02
Matches are distributed among these distances:
85 20 0.18
86 9 0.08
87 80 0.73
ACGTcount: A:0.29, C:0.20, G:0.22, T:0.29
Consensus pattern (85 bp):
ATTAGCGGCTTTTTTATAAAAGCGCCGCTAAAAGTACAAGTCTATAGCGGCGTTTTTTAAAAAAG
CGCCGCTAAAGGTCCTGATC
Found at i:12690599 original size:33 final size:33
Alignment explanation
Indices: 12690552--12690664 Score: 217
Period size: 33 Copynumber: 3.4 Consensus size: 33
12690542 ATAGCGACGT
*
12690552 TTTTTGCGGCGCTTGGGAAAGCGCCGCTAATAC
1 TTTTAGCGGCGCTTGGGAAAGCGCCGCTAATAC
12690585 TTTTAGCGGCGCTTGGGAAAGCGCCGCTAATAC
1 TTTTAGCGGCGCTTGGGAAAGCGCCGCTAATAC
12690618 TTTTAGCGGCGCTTGGGAAAGCGCCGCTAATAC
1 TTTTAGCGGCGCTTGGGAAAGCGCCGCTAATAC
12690651 TTTTAGCGGCGCTT
1 TTTTAGCGGCGCTT
12690665 AAAACGCCGC
Statistics
Matches: 79, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
33 79 1.00
ACGTcount: A:0.19, C:0.24, G:0.30, T:0.27
Consensus pattern (33 bp):
TTTTAGCGGCGCTTGGGAAAGCGCCGCTAATAC
Found at i:12690675 original size:30 final size:31
Alignment explanation
Indices: 12690552--12690677 Score: 173
Period size: 33 Copynumber: 3.9 Consensus size: 31
12690542 ATAGCGACGT
*
12690552 TTTTTGCGGCGCTTGGGAAAGCGCCGCTAATAC
1 TTTTAGCGGCGCTT--GAAAGCGCCGCTAATAC
12690585 TTTTAGCGGCGCTTGGGAAAGCGCCGCTAATAC
1 TTTTAGCGGCGCTT--GAAAGCGCCGCTAATAC
12690618 TTTTAGCGGCGCTTGGGAAAGCGCCGCTAATAC
1 TTTTAGCGGCGCTT--GAAAGCGCCGCTAATAC
*
12690651 TTTTAGCGGCGCTT-AAAACGCCGCTAA
1 TTTTAGCGGCGCTTGAAAGCGCCGCTAA
12690678 AGGCAAAAAA
Statistics
Matches: 91, Mismatches: 2, Indels: 3
0.95 0.02 0.03
Matches are distributed among these distances:
30 12 0.13
33 79 0.87
ACGTcount: A:0.21, C:0.25, G:0.29, T:0.25
Consensus pattern (31 bp):
TTTTAGCGGCGCTTGAAAGCGCCGCTAATAC
Found at i:12712440 original size:8 final size:8
Alignment explanation
Indices: 12712427--12712453 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
12712417 GTTAAAATAT
12712427 TTATTTTA
1 TTATTTTA
12712435 TTATTTTA
1 TTATTTTA
12712443 TTATTTTA
1 TTATTTTA
12712451 TTA
1 TTA
12712454 AAGTTTACAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (8 bp):
TTATTTTA
Found at i:12713701 original size:22 final size:23
Alignment explanation
Indices: 12713611--12713719 Score: 84
Period size: 23 Copynumber: 4.7 Consensus size: 23
12713601 CCAATATATT
* *
12713611 AGCTCG-TAAGAGCTTACTGTTATC
1 AGCTCGAT-AGAGCTTACCGAT-TC
*
12713635 AGCTC-ATTAGAGCTTACCGTTTC
1 AGCTCGA-TAGAGCTTACCGATTC
*
12713658 AGCTCG-TATGAGCTT-CCTATTC
1 AGCTCGATA-GAGCTTACCGATTC
*
12713680 AACTCGATAGAGCTTACC-ATTC
1 AGCTCGATAGAGCTTACCGATTC
*
12713702 TAGCTCAATAGAGCTTAC
1 -AGCTCGATAGAGCTTAC
12713720 TGTTCATCAG
Statistics
Matches: 72, Mismatches: 6, Indels: 15
0.77 0.06 0.16
Matches are distributed among these distances:
22 22 0.31
23 32 0.44
24 17 0.24
25 1 0.01
ACGTcount: A:0.26, C:0.25, G:0.17, T:0.32
Consensus pattern (23 bp):
AGCTCGATAGAGCTTACCGATTC
Found at i:12721041 original size:23 final size:25
Alignment explanation
Indices: 12721009--12721058 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 25
12720999 ATTCTTATTT
12721009 AATTAAG-AAATATA-TACTTTAAA
1 AATTAAGAAAATATATTACTTTAAA
* *
12721032 AATTATGAAAATATATTATTTTAAA
1 AATTAAGAAAATATATTACTTTAAA
12721057 AA
1 AA
12721059 ATAAATACTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 6 0.26
24 7 0.30
25 10 0.43
ACGTcount: A:0.56, C:0.02, G:0.04, T:0.38
Consensus pattern (25 bp):
AATTAAGAAAATATATTACTTTAAA
Found at i:12722078 original size:10 final size:10
Alignment explanation
Indices: 12722020--12722110 Score: 55
Period size: 10 Copynumber: 9.0 Consensus size: 10
12722010 ATATTTTTTG
12722020 TAATTTTTAA
1 TAATTTTTAA
12722030 -AATTTATTAA
1 TAATTT-TTAA
* *
12722040 TCATTATTT-G
1 TAATT-TTTAA
12722050 TAATTTTT-A
1 TAATTTTTAA
* *
12722059 TAACTCTTAA
1 TAATTTTTAA
12722069 TAATTTTTAAA
1 TAATTTTT-AA
12722080 TAATTTTCT-A
1 TAATTTT-TAA
*
12722090 TAATTATGTAA
1 TAATT-TTTAA
*
12722101 TAATTGTTAA
1 TAATTTTTAA
12722111 AGAAACTACT
Statistics
Matches: 62, Mismatches: 11, Indels: 16
0.70 0.12 0.18
Matches are distributed among these distances:
9 14 0.23
10 25 0.40
11 21 0.34
12 2 0.03
ACGTcount: A:0.38, C:0.04, G:0.03, T:0.54
Consensus pattern (10 bp):
TAATTTTTAA
Found at i:12722105 original size:32 final size:30
Alignment explanation
Indices: 12722050--12722111 Score: 79
Period size: 32 Copynumber: 2.0 Consensus size: 30
12722040 TCATTATTTG
* *
12722050 TAATTTTTATAACTCTTAATAATTTTTAAA
1 TAATTTTTATAACTATTAATAATTGTTAAA
*
12722080 TAATTTTCTATAATTATGTAATAATTGTTAAA
1 TAATTTT-TATAACTAT-TAATAATTGTTAAA
12722112 GAAACTACTC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
30 7 0.26
31 7 0.26
32 13 0.48
ACGTcount: A:0.40, C:0.05, G:0.03, T:0.52
Consensus pattern (30 bp):
TAATTTTTATAACTATTAATAATTGTTAAA
Found at i:12723579 original size:29 final size:28
Alignment explanation
Indices: 12723548--12723603 Score: 69
Period size: 30 Copynumber: 1.9 Consensus size: 28
12723538 TTAGTATTTT
*
12723548 AAAT-AATATATTTTTTATTATAACTTTATA
1 AAATAAATA-ATTATTT-TTATAA-TTTATA
12723578 AAATAAATAATTATTTTTATAATTTA
1 AAATAAATAATTATTTTTATAATTTA
12723604 ATTTTTTACG
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
28 4 0.17
29 6 0.25
30 10 0.42
31 4 0.17
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (28 bp):
AAATAAATAATTATTTTTATAATTTATA
Found at i:12727898 original size:14 final size:15
Alignment explanation
Indices: 12727805--12727914 Score: 89
Period size: 15 Copynumber: 7.4 Consensus size: 15
12727795 TTAATATTCA
12727805 AACCCTATATGTGCG
1 AACCCTATATGTGCG
**
12727820 AACCCTATATGTATG
1 AACCCTATATGTGCG
* *
12727835 AACCATGTATGTGCG
1 AACCCTATATGTGCG
* *
12727850 AACCCTATAAGTGTG
1 AACCCTATATGTGCG
* * * *
12727865 -ACCTTTACATATGAG
1 AACC-CTATATGTGCG
12727880 AACCC-ATATGTGCG
1 AACCCTATATGTGCG
* *
12727894 AACCCTGTATGTGTG
1 AACCCTATATGTGCG
12727909 AACCCT
1 AACCCT
12727915 TCGTGTGAAC
Statistics
Matches: 71, Mismatches: 21, Indels: 6
0.72 0.21 0.06
Matches are distributed among these distances:
14 14 0.20
15 54 0.76
16 3 0.04
ACGTcount: A:0.29, C:0.24, G:0.19, T:0.28
Consensus pattern (15 bp):
AACCCTATATGTGCG
Found at i:12732290 original size:21 final size:20
Alignment explanation
Indices: 12732253--12732292 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
12732243 GCCTAGAATG
*
12732253 TGAATTGAATTGAATTAAAC
1 TGAATTGAAATGAATTAAAC
*
12732273 TGAATATGAAATGGATTAAA
1 TGAAT-TGAAATGAATTAAA
12732293 TTGACGTTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.47, C:0.03, G:0.17, T:0.33
Consensus pattern (20 bp):
TGAATTGAAATGAATTAAAC
Found at i:12732629 original size:24 final size:25
Alignment explanation
Indices: 12732602--12732660 Score: 66
Period size: 24 Copynumber: 2.4 Consensus size: 25
12732592 TAACTTGAAA
*
12732602 GAGCATCCTGTTATAAGCCCTCT-C
1 GAGCATCCTATTATAAGCCCTCTGC
* * * *
12732626 GAGCTTCCTATTATATGGCTTCTGC
1 GAGCATCCTATTATAAGCCCTCTGC
12732651 GAGCATCCTA
1 GAGCATCCTA
12732661 ATCAGTAGTG
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
24 18 0.64
25 10 0.36
ACGTcount: A:0.20, C:0.29, G:0.19, T:0.32
Consensus pattern (25 bp):
GAGCATCCTATTATAAGCCCTCTGC
Found at i:12745114 original size:19 final size:19
Alignment explanation
Indices: 12745079--12745139 Score: 70
Period size: 19 Copynumber: 3.3 Consensus size: 19
12745069 GTGGATAGGC
*
12745079 CGTGTGG-TCACACACGCT
1 CGTGTGGCTCAAACACGCT
* *
12745097 CGTTTGGTTCAAACACGCT
1 CGTGTGGCTCAAACACGCT
* *
12745116 CGTGTGGCTCAGACATGCT
1 CGTGTGGCTCAAACACGCT
12745135 CGTGT
1 CGTGT
12745140 CCTCAGCTCG
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
18 6 0.17
19 30 0.83
ACGTcount: A:0.16, C:0.28, G:0.28, T:0.28
Consensus pattern (19 bp):
CGTGTGGCTCAAACACGCT
Found at i:12754497 original size:13 final size:13
Alignment explanation
Indices: 12754479--12754509 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
12754469 AACATTTGAC
12754479 TTGTTCTTAATTA
1 TTGTTCTTAATTA
*
12754492 TTGTTCTTAATTC
1 TTGTTCTTAATTA
12754505 TTGTT
1 TTGTT
12754510 TTGATATTCC
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:0.16, C:0.10, G:0.10, T:0.65
Consensus pattern (13 bp):
TTGTTCTTAATTA
Found at i:12755620 original size:48 final size:48
Alignment explanation
Indices: 12755566--12755942 Score: 461
Period size: 48 Copynumber: 7.9 Consensus size: 48
12755556 TACGAAGTCT
** * *
12755566 CATATCAGTGCCGATGCCATGTCCCAGACATGGTCTTACACTAGCGCA
1 CATATCAACGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCACA
* * * *
12755614 CTTATCATCACCGATGCCATGTCCCAAACATGGTCTTACACT-GCACA
1 CATATCAACGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCACA
* *
12755661 CATATCAACGCTGATGCCATGTCCCAAACATGGTCTTACACTGGCACA
1 CATATCAACGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCACA
* * * * *
12755709 CAAATCAATGCCGATGCAATGTCCCACACATGGTCTTACACT-ACACA
1 CATATCAACGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCACA
* * *
12755756 CATGTCAACACCGATTGCCATGTCCCAGACATGGTCTTACATTGGCACA
1 CATATCAACGCCGA-TGCCATGTCCCAGACATGGTCTTACACTGGCACA
* **
12755805 CATATCAACACCGATGCCATGTCTTAGACATGGTCTTACACTGGCACA
1 CATATCAACGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCACA
* ***
12755853 CATATCAACGCTGATGCCATGTCCCAGACATGGTCTTACACTGGCTTT
1 CATATCAACGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCACA
* * * *
12755901 CATCTCGGACGCCAATGTCATGTCCCAGACATGGTCTTACAC
1 CATATC-AACGCCGATGCCATGTCCCAGACATGGTCTTACAC
12755943 GGGATCTCAT
Statistics
Matches: 285, Mismatches: 40, Indels: 7
0.86 0.12 0.02
Matches are distributed among these distances:
47 56 0.20
48 181 0.64
49 48 0.17
ACGTcount: A:0.27, C:0.31, G:0.17, T:0.24
Consensus pattern (48 bp):
CATATCAACGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCACA
Found at i:12760844 original size:28 final size:28
Alignment explanation
Indices: 12760804--12760870 Score: 134
Period size: 28 Copynumber: 2.4 Consensus size: 28
12760794 TAATAATCAA
12760804 TTTATTAACGTGCTTTTGCCAAATTCTT
1 TTTATTAACGTGCTTTTGCCAAATTCTT
12760832 TTTATTAACGTGCTTTTGCCAAATTCTT
1 TTTATTAACGTGCTTTTGCCAAATTCTT
12760860 TTTATTAACGT
1 TTTATTAACGT
12760871 ATTCTCATGG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 39 1.00
ACGTcount: A:0.22, C:0.16, G:0.10, T:0.51
Consensus pattern (28 bp):
TTTATTAACGTGCTTTTGCCAAATTCTT
Found at i:12762013 original size:95 final size:95
Alignment explanation
Indices: 12761896--12762211 Score: 420
Period size: 95 Copynumber: 3.3 Consensus size: 95
12761886 ATATCAGTTT
* * *
12761896 CGATGCCATGTCCCAGACATGGTCTTACACTAGCACACATATCATCACCAATTCCATGTCCCAAA
1 CGATGCCATGTCCCAGACATGGTCTTACACTAGCACACATATCATCGCAAATGCCATGTCCCAAA
**
12761961 CATGGTCTTACACTGCACACATATCAATGC
66 CATGGTCTTACACTGCACACATATCAACAC
* * * * ** *
12761991 TGATGCCATGTCCCAGATATGGTCTTACACTAGTACACATATCAACGCAAATGCCATGTCTTAGA
1 CGATGCCATGTCCCAGACATGGTCTTACACTAGCACACATATCATCGCAAATGCCATGTCCCAAA
12762056 CATGGTCTTACACTGCACACATATCAACAC
66 CATGGTCTTACACTGCACACATATCAACAC
* * *
12762086 CGATG-CATGTCCTAGACATGGTCTTACACTGGCACACATATCAAT-GCTAATGCCATGTCCCAA
1 CGATGCCATGTCCCAGACATGGTCTTACACTAGCACACATATC-ATCGCAAATGCCATGTCCCAA
* *
12762149 ACATCGTCTTATACTGGCACACATATCAACAC
65 ACATGGTCTTACACT-GCACACATATCAACAC
* * *
12762181 CGACGCCATGTCCTAGACATGGTATTACACT
1 CGATGCCATGTCCCAGACATGGTCTTACACT
12762212 GGCTTTCATC
Statistics
Matches: 192, Mismatches: 26, Indels: 5
0.86 0.12 0.02
Matches are distributed among these distances:
94 60 0.31
95 108 0.56
96 24 0.12
ACGTcount: A:0.30, C:0.30, G:0.15, T:0.25
Consensus pattern (95 bp):
CGATGCCATGTCCCAGACATGGTCTTACACTAGCACACATATCATCGCAAATGCCATGTCCCAAA
CATGGTCTTACACTGCACACATATCAACAC
Found at i:12762158 original size:142 final size:142
Alignment explanation
Indices: 12761898--12762212 Score: 434
Period size: 142 Copynumber: 2.2 Consensus size: 142
12761888 ATCAGTTTCG
* *
12761898 ATGCCATGTCCCAGACATGGTCTTACACTAGCACACATATCATCACCAATTCCATGTCCCAAACA
1 ATGCCATGTCCTAGACATGGTCTTACACT-GCACACATATCAACACCAATTCCATGTCCCAAACA
* * * * *
12761963 TGGTCTTACACTGCACACATATCAATGCTGATGCCATGTCCCAGATATGGTCTTACACTAGTACA
65 TGGTCTTACACTGCACACATATCAATGCTAATGCCATGTCCCAAACATCGTCTTACACTAGCACA
*
12762028 CATATCAACGCAA
130 CATATCAACACAA
* * * * *
12762041 ATGCCATGTCTTAGACATGGTCTTACACTGCACACATATCAACACCGA-TGCATGTCCTAGACAT
1 ATGCCATGTCCTAGACATGGTCTTACACTGCACACATATCAACACCAATTCCATGTCCCAAACAT
* *
12762105 GGTCTTACACTGGCACACATATCAATGCTAATGCCATGTCCCAAACATCGTCTTATACTGGCACA
66 GGTCTTACACT-GCACACATATCAATGCTAATGCCATGTCCCAAACATCGTCTTACACTAGCACA
**
12762170 CATATCAACACCG
130 CATATCAACACAA
* *
12762183 ACGCCATGTCCTAGACATGGTATTACACTG
1 ATGCCATGTCCTAGACATGGTCTTACACTG
12762213 GCTTTCATCT
Statistics
Matches: 151, Mismatches: 20, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
141 24 0.16
142 100 0.66
143 27 0.18
ACGTcount: A:0.30, C:0.30, G:0.15, T:0.25
Consensus pattern (142 bp):
ATGCCATGTCCTAGACATGGTCTTACACTGCACACATATCAACACCAATTCCATGTCCCAAACAT
GGTCTTACACTGCACACATATCAATGCTAATGCCATGTCCCAAACATCGTCTTACACTAGCACAC
ATATCAACACAA
Found at i:12762213 original size:48 final size:48
Alignment explanation
Indices: 12761898--12762258 Score: 377
Period size: 48 Copynumber: 7.6 Consensus size: 48
12761888 ATCAGTTTCG
* *
12761898 ATGCCATGTCCCAGACATGGTCTTACACTAGCACACATATCATCACCA
1 ATGCCATGTCCCAGACATGGTCTTACACTGGCACACATATCAACACCA
* * ** **
12761946 ATTCCATGTCCCAAACATGGTCTTACACT-GCACACATATCAATGCTG
1 ATGCCATGTCCCAGACATGGTCTTACACTGGCACACATATCAACACCA
* * * * *
12761993 ATGCCATGTCCCAGATATGGTCTTACACTAGTACACATATCAACGCAA
1 ATGCCATGTCCCAGACATGGTCTTACACTGGCACACATATCAACACCA
** *
12762041 ATGCCATGTCTTAGACATGGTCTTACACT-GCACACATATCAACACCG
1 ATGCCATGTCCCAGACATGGTCTTACACTGGCACACATATCAACACCA
* ** *
12762088 ATG-CATGTCCTAGACATGGTCTTACACTGGCACACATATCAATGCTA
1 ATGCCATGTCCCAGACATGGTCTTACACTGGCACACATATCAACACCA
* * * *
12762135 ATGCCATGTCCCAAACATCGTCTTATACTGGCACACATATCAACACCG
1 ATGCCATGTCCCAGACATGGTCTTACACTGGCACACATATCAACACCA
* * * *** * ** **
12762183 ACGCCATGTCCTAGACATGGTATTACACTGGCTTTCATCTTGGATGCCA
1 ATGCCATGTCCCAGACATGGTCTTACACTGGCACACAT-ATCAACACCA
12762232 ATGCCATGTCCCAGACATGGTCTTACA
1 ATGCCATGTCCCAGACATGGTCTTACA
12762259 GGGGATCTCA
Statistics
Matches: 257, Mismatches: 52, Indels: 7
0.81 0.16 0.02
Matches are distributed among these distances:
46 24 0.09
47 73 0.28
48 132 0.51
49 28 0.11
ACGTcount: A:0.29, C:0.29, G:0.15, T:0.26
Consensus pattern (48 bp):
ATGCCATGTCCCAGACATGGTCTTACACTGGCACACATATCAACACCA
Found at i:12773794 original size:11 final size:11
Alignment explanation
Indices: 12773778--12773802 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
12773768 CCACAATTAA
12773778 ACTCACATTTT
1 ACTCACATTTT
12773789 ACTCACATTTT
1 ACTCACATTTT
12773800 ACT
1 ACT
12773803 TACCGTTTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.28, C:0.28, G:0.00, T:0.44
Consensus pattern (11 bp):
ACTCACATTTT
Found at i:12775124 original size:23 final size:23
Alignment explanation
Indices: 12775094--12775147 Score: 99
Period size: 23 Copynumber: 2.3 Consensus size: 23
12775084 AGACAAAGAC
12775094 ATTTTCGATTTACCATGCTTCAA
1 ATTTTCGATTTACCATGCTTCAA
*
12775117 ATTTTCGATTTACCATGCTTTAA
1 ATTTTCGATTTACCATGCTTCAA
12775140 ATTTTCGA
1 ATTTTCGA
12775148 ACACATTTGA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.26, C:0.19, G:0.09, T:0.46
Consensus pattern (23 bp):
ATTTTCGATTTACCATGCTTCAA
Found at i:12785199 original size:23 final size:23
Alignment explanation
Indices: 12785173--12785218 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
12785163 TGTTAAATAA
12785173 ATAAAACAAAACAATTTTTTTAT
1 ATAAAACAAAACAATTTTTTTAT
12785196 ATAAAACAAAACAATTTTTTTAT
1 ATAAAACAAAACAATTTTTTTAT
12785219 CCCTTATCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.52, C:0.09, G:0.00, T:0.39
Consensus pattern (23 bp):
ATAAAACAAAACAATTTTTTTAT
Found at i:12792297 original size:21 final size:21
Alignment explanation
Indices: 12792252--12792307 Score: 69
Period size: 21 Copynumber: 2.6 Consensus size: 21
12792242 TTCTATATGC
*
12792252 ATATTTTAATTATTTTTTAAAAA
1 ATATTTT-ATT-TTTTGTAAAAA
*
12792275 ATATTTTATTTTTTGTAAGAA
1 ATATTTTATTTTTTGTAAAAA
12792296 ATATTTT-TTTTT
1 ATATTTTATTTTT
12792308 GGTGACATGT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
20 5 0.16
21 16 0.52
22 3 0.10
23 7 0.23
ACGTcount: A:0.34, C:0.00, G:0.04, T:0.62
Consensus pattern (21 bp):
ATATTTTATTTTTTGTAAAAA
Found at i:12793957 original size:15 final size:15
Alignment explanation
Indices: 12793927--12793955 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
12793917 ACTATTAGTA
12793927 ATTTTTTACATATTT
1 ATTTTTTACATATTT
12793942 ATTTTTTA-ATATTT
1 ATTTTTTACATATTT
12793956 TACCATACCC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (15 bp):
ATTTTTTACATATTT
Found at i:12796814 original size:21 final size:21
Alignment explanation
Indices: 12796773--12796814 Score: 50
Period size: 22 Copynumber: 2.0 Consensus size: 21
12796763 AAAAATACTC
*
12796773 TTTTAAAAATGTGATAATTAAT
1 TTTTAAAAAAGT-ATAATTAAT
12796795 TTTTAAAAAAGT-TAAGTTAA
1 TTTTAAAAAAGTATAA-TTAA
12796815 AACCAAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
20 3 0.17
21 4 0.22
22 11 0.61
ACGTcount: A:0.48, C:0.00, G:0.10, T:0.43
Consensus pattern (21 bp):
TTTTAAAAAAGTATAATTAAT
Found at i:12797043 original size:48 final size:48
Alignment explanation
Indices: 12796988--12797132 Score: 290
Period size: 48 Copynumber: 3.0 Consensus size: 48
12796978 ATCTAATTTA
12796988 ATTTAATAATGTTAAATATATTTTAATTTATCTAATTAACAATTTTTT
1 ATTTAATAATGTTAAATATATTTTAATTTATCTAATTAACAATTTTTT
12797036 ATTTAATAATGTTAAATATATTTTAATTTATCTAATTAACAATTTTTT
1 ATTTAATAATGTTAAATATATTTTAATTTATCTAATTAACAATTTTTT
12797084 ATTTAATAATGTTAAATATATTTTAATTTATCTAATTAACAATTTTTT
1 ATTTAATAATGTTAAATATATTTTAATTTATCTAATTAACAATTTTTT
12797132 A
1 A
12797133 AATATTGTTT
Statistics
Matches: 97, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 97 1.00
ACGTcount: A:0.40, C:0.04, G:0.02, T:0.54
Consensus pattern (48 bp):
ATTTAATAATGTTAAATATATTTTAATTTATCTAATTAACAATTTTTT
Found at i:12797131 original size:24 final size:24
Alignment explanation
Indices: 12797008--12797133 Score: 120
Period size: 24 Copynumber: 5.2 Consensus size: 24
12796998 GTTAAATATA
12797008 TTTTAATTTATCTAATTAACAATT
1 TTTTAATTTATCTAATTAACAATT
* *
12797032 TTTT-ATTTA-ATAATGTTAA-ATATA
1 TTTTAATTTATCTAA--TTAACA-ATT
12797056 TTTTAATTTATCTAATTAACAATT
1 TTTTAATTTATCTAATTAACAATT
* *
12797080 TTTT-ATTTA-ATAATGTTAA-ATATA
1 TTTTAATTTATCTAA--TTAACA-ATT
12797104 TTTTAATTTATCTAATTAACAATT
1 TTTTAATTTATCTAATTAACAATT
12797128 TTTTAA
1 TTTTAA
12797134 ATATTGTTTA
Statistics
Matches: 82, Mismatches: 8, Indels: 24
0.72 0.07 0.21
Matches are distributed among these distances:
22 6 0.07
23 12 0.15
24 46 0.56
25 12 0.15
26 6 0.07
ACGTcount: A:0.39, C:0.05, G:0.02, T:0.55
Consensus pattern (24 bp):
TTTTAATTTATCTAATTAACAATT
Found at i:12817696 original size:25 final size:24
Alignment explanation
Indices: 12817644--12817719 Score: 67
Period size: 20 Copynumber: 3.4 Consensus size: 24
12817634 CTTATTTTAT
* *
12817644 TAAATAAA-AAATTTAAAATATAA
1 TAAATAAATACATTTAAAACATAA
12817667 TAAATGAAATACATTTAAAAACATAA
1 TAAAT-AAATACATTT-AAAACATAA
12817693 -AAATAAAT--A-TTAAAACA-AA
1 TAAATAAATACATTTAAAACATAA
12817712 TAAA-AAAT
1 TAAATAAAT
12817720 GATATTAAAA
Statistics
Matches: 47, Mismatches: 2, Indels: 12
0.77 0.03 0.20
Matches are distributed among these distances:
19 6 0.13
20 9 0.19
21 2 0.04
22 1 0.02
23 5 0.11
24 7 0.15
25 9 0.19
26 8 0.17
ACGTcount: A:0.68, C:0.04, G:0.01, T:0.26
Consensus pattern (24 bp):
TAAATAAATACATTTAAAACATAA
Found at i:12817717 original size:22 final size:22
Alignment explanation
Indices: 12817673--12817732 Score: 63
Period size: 22 Copynumber: 2.8 Consensus size: 22
12817663 ATAATAAATG
* *
12817673 AAATACAT-TTAAAA-ACATAA
1 AAATAAATATTAAAACAAATAA
12817693 AAATAAATATTAAAACAAATAA
1 AAATAAATATTAAAACAAATAA
*
12817715 AAA-ATGATATTAAAACAA
1 AAATA-AATATTAAAACAA
12817733 TACACAAATT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
20 7 0.21
21 7 0.21
22 20 0.59
ACGTcount: A:0.68, C:0.07, G:0.02, T:0.23
Consensus pattern (22 bp):
AAATAAATATTAAAACAAATAA
Found at i:12820167 original size:56 final size:56
Alignment explanation
Indices: 12820106--12820247 Score: 196
Period size: 56 Copynumber: 2.5 Consensus size: 56
12820096 AACGTGGAAT
**
12820106 CGATATATCTATGGGAGTAAGACCACGTTTAATACGTTGGCATCGATATATGATTC
1 CGATATATCTATACGAGTAAGACCACGTTTAATACGTTGGCATCGATATATGATTC
* * *
12820162 CGATATATGTGTACGAGTAAGACCACGTTTAATACGTTGGCATCGATATGTGATTC
1 CGATATATCTATACGAGTAAGACCACGTTTAATACGTTGGCATCGATATATGATTC
*
12820218 CGATATATGTGATTAC-ATGTAAGACCACGT
1 CGATATATCT-A-TACGA-GTAAGACCACGT
12820248 CTGGGACGTT
Statistics
Matches: 77, Mismatches: 6, Indels: 4
0.89 0.07 0.05
Matches are distributed among these distances:
56 61 0.79
57 1 0.01
58 15 0.19
ACGTcount: A:0.30, C:0.16, G:0.22, T:0.32
Consensus pattern (56 bp):
CGATATATCTATACGAGTAAGACCACGTTTAATACGTTGGCATCGATATATGATTC
Found at i:12820447 original size:97 final size:97
Alignment explanation
Indices: 12820338--12820532 Score: 327
Period size: 97 Copynumber: 2.0 Consensus size: 97
12820328 GTTGTGATCG
* * * *
12820338 AATGTGTAATCGAGCTAAAGTGATCAGGTATGTGATAGTTAATTTCCTATTTGAAATTAAGGTAA
1 AATGTGTAATCGAGCTAAAGCGATCAAGTATGTGATAGTTAATTTCCTATTTAAAAGTAAGGTAA
12820403 GTTGGCTGTTTGGTATGTGATACAAAATGTAT
66 GTTGGCTGTTTGGTATGTGATACAAAATGTAT
*
12820435 AATGTGTAATCGAGCTAAAGCGATCAAGTATGTGATAGTTAATTTCCTATTTAAAAGTAAGGTAG
1 AATGTGTAATCGAGCTAAAGCGATCAAGTATGTGATAGTTAATTTCCTATTTAAAAGTAAGGTAA
* *
12820500 GTTGGTTGTTTGGTATGTGATACAAATTGTAT
66 GTTGGCTGTTTGGTATGTGATACAAAATGTAT
12820532 A
1 A
12820533 TGATAAAGTG
Statistics
Matches: 91, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
97 91 1.00
ACGTcount: A:0.32, C:0.07, G:0.24, T:0.37
Consensus pattern (97 bp):
AATGTGTAATCGAGCTAAAGCGATCAAGTATGTGATAGTTAATTTCCTATTTAAAAGTAAGGTAA
GTTGGCTGTTTGGTATGTGATACAAAATGTAT
Found at i:12823441 original size:216 final size:216
Alignment explanation
Indices: 12823067--12823501 Score: 852
Period size: 216 Copynumber: 2.0 Consensus size: 216
12823057 TAAATAATAT
12823067 ACTTTTCCACTTAGAGTTTGGGATTGGCCTGGGATGTTGATCCAACGATCTGATTTTAACTTATC
1 ACTTTTCCACTTAGAGTTTGGGATTGGCCTGGGATGTTGATCCAACGATCTGATTTTAACTTATC
*
12823132 TTGCGCACAGAAACAAACCGTACGCTGAGTATGAACTCAATGGTATTTCTATAATCCGAACACTT
66 TTGAGCACAGAAACAAACCGTACGCTGAGTATGAACTCAATGGTATTTCTATAATCCGAACACTT
12823197 AATAATATGAAAATATAACATTCATTTAAAAATCATATAACAATTACAATTATATAATTGTTCAA
131 AATAATATGAAAATATAACATTCATTTAAAAATCATATAACAATTACAATTATATAATTGTTCAA
12823262 TTCATAGATAAATCCTTTATA
196 TTCATAGATAAATCCTTTATA
12823283 ACTTTTCCACTTAGAGTTTGGGATTGGCCTGGGATGTTGATCCAACGATCTGATTTTAACTTATC
1 ACTTTTCCACTTAGAGTTTGGGATTGGCCTGGGATGTTGATCCAACGATCTGATTTTAACTTATC
12823348 TTGAGCACAGAAACAAACCGTACGCTGAGTATGAACTCAATGGTATTTCTATAATCCGAACACTT
66 TTGAGCACAGAAACAAACCGTACGCTGAGTATGAACTCAATGGTATTTCTATAATCCGAACACTT
*
12823413 AATAATATGAAAATATAACATTCATTTAAAAATCATTTAACAATTACAATTATATAATTGTTCAA
131 AATAATATGAAAATATAACATTCATTTAAAAATCATATAACAATTACAATTATATAATTGTTCAA
12823478 TTCATAGATAAATCCTTTATA
196 TTCATAGATAAATCCTTTATA
12823499 ACT
1 ACT
12823502 CAATTAATTC
Statistics
Matches: 217, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
216 217 1.00
ACGTcount: A:0.36, C:0.17, G:0.13, T:0.34
Consensus pattern (216 bp):
ACTTTTCCACTTAGAGTTTGGGATTGGCCTGGGATGTTGATCCAACGATCTGATTTTAACTTATC
TTGAGCACAGAAACAAACCGTACGCTGAGTATGAACTCAATGGTATTTCTATAATCCGAACACTT
AATAATATGAAAATATAACATTCATTTAAAAATCATATAACAATTACAATTATATAATTGTTCAA
TTCATAGATAAATCCTTTATA
Found at i:12823772 original size:18 final size:18
Alignment explanation
Indices: 12823749--12823813 Score: 94
Period size: 18 Copynumber: 3.6 Consensus size: 18
12823739 TATCAGTATC
12823749 ATTCAGTAACAATCAATT
1 ATTCAGTAACAATCAATT
* * *
12823767 ATTCAGTAGCAACCAGTT
1 ATTCAGTAACAATCAATT
*
12823785 ATTCAGTAACAATCAATA
1 ATTCAGTAACAATCAATT
12823803 ATTCAGTAACA
1 ATTCAGTAACA
12823814 GTTAGTCATT
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 40 1.00
ACGTcount: A:0.43, C:0.18, G:0.09, T:0.29
Consensus pattern (18 bp):
ATTCAGTAACAATCAATT
Found at i:12823783 original size:28 final size:28
Alignment explanation
Indices: 12823730--12823783 Score: 65
Period size: 28 Copynumber: 1.9 Consensus size: 28
12823720 TTTTCAATAT
* **
12823730 CAATCAATTTATCAGTATCATTCAGTAA
1 CAATCAATTTATCAGTAGCAACCAGTAA
12823758 CAATCAA-TTATTCAGTAGCAACCAGT
1 CAATCAATTTA-TCAGTAGCAACCAGT
12823784 TATTCAGTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
27 3 0.14
28 19 0.86
ACGTcount: A:0.39, C:0.20, G:0.09, T:0.31
Consensus pattern (28 bp):
CAATCAATTTATCAGTAGCAACCAGTAA
Found at i:12823825 original size:36 final size:36
Alignment explanation
Indices: 12823747--12823828 Score: 110
Period size: 36 Copynumber: 2.3 Consensus size: 36
12823737 TTTATCAGTA
* *
12823747 TCATTCAGTAACAATCAATTATTCAGTAGCAACCAG
1 TCATTCAGTAACAATCAATAATTCAGTAACAACCAG
* ***
12823783 TTATTCAGTAACAATCAATAATTCAGTAACAGTTAG
1 TCATTCAGTAACAATCAATAATTCAGTAACAACCAG
12823819 TCATTCAGTA
1 TCATTCAGTA
12823829 CCTTTATCCA
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.39, C:0.18, G:0.11, T:0.32
Consensus pattern (36 bp):
TCATTCAGTAACAATCAATAATTCAGTAACAACCAG
Found at i:12825334 original size:19 final size:19
Alignment explanation
Indices: 12825310--12825359 Score: 64
Period size: 19 Copynumber: 2.6 Consensus size: 19
12825300 TAATAACAAT
* **
12825310 ATAATTTAATATTAATTTA
1 ATAATTTAATATAAAACTA
12825329 ATAATTTAATATAAAACTA
1 ATAATTTAATATAAAACTA
12825348 ATAATTATAATA
1 ATAATT-TAATA
12825360 AATATCTATT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 22 0.81
20 5 0.19
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (19 bp):
ATAATTTAATATAAAACTA
Found at i:12825684 original size:13 final size:13
Alignment explanation
Indices: 12825662--12825701 Score: 55
Period size: 13 Copynumber: 3.1 Consensus size: 13
12825652 GAAAACCATG
12825662 ATAATAATTAATA
1 ATAATAATTAATA
*
12825675 ATAATTATT-ATA
1 ATAATAATTAATA
12825687 ATAATAGATTAATA
1 ATAATA-ATTAATA
12825701 A
1 A
12825702 CAAAACCTCA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
12 8 0.35
13 11 0.48
14 4 0.17
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (13 bp):
ATAATAATTAATA
Found at i:12825879 original size:20 final size:19
Alignment explanation
Indices: 12825833--12825879 Score: 51
Period size: 19 Copynumber: 2.4 Consensus size: 19
12825823 AATCATTTTT
*
12825833 CCTAATTTCTCTTAATTAAG
1 CCTAA-TTCACTTAATTAAG
12825853 -CTAAATTCACTTAATTAAAG
1 CCT-AATTCACTTAATT-AAG
12825873 CCTAATT
1 CCTAATT
12825880 AGACACACAA
Statistics
Matches: 23, Mismatches: 1, Indels: 6
0.77 0.03 0.20
Matches are distributed among these distances:
19 12 0.52
20 9 0.39
21 2 0.09
ACGTcount: A:0.36, C:0.19, G:0.04, T:0.40
Consensus pattern (19 bp):
CCTAATTCACTTAATTAAG
Found at i:12826156 original size:5 final size:5
Alignment explanation
Indices: 12826146--12826177 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
12826136 ATTTATGTGA
12826146 AAAAT AAAAT AAAAT -AAAT AAAAT AAAAT AAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAA
12826178 GAACACACAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.15
5 22 0.85
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:12826166 original size:14 final size:14
Alignment explanation
Indices: 12826147--12826177 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
12826137 TTTATGTGAA
12826147 AAATAAAATAAAAT
1 AAATAAAATAAAAT
12826161 AAATAAAATAAAAT
1 AAATAAAATAAAAT
12826175 AAA
1 AAA
12826178 GAACACACAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (14 bp):
AAATAAAATAAAAT
Found at i:12830542 original size:5 final size:5
Alignment explanation
Indices: 12830532--12830559 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
12830522 CAATTTGTGA
12830532 AAAAT AAAAT AAAAT AAAAT AAAAT AAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAA
12830560 GAACACACAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (5 bp):
AAAAT
Found at i:12838125 original size:23 final size:23
Alignment explanation
Indices: 12838043--12838129 Score: 92
Period size: 21 Copynumber: 4.0 Consensus size: 23
12838033 CCTGGTCAGT
*
12838043 ATACGACACATAAAGTGCCT-AA
1 ATACGACACACAAAGTGCCTGAA
* *
12838065 A-ACGACACACGAGGTGCCTG--
1 ATACGACACACAAAGTGCCTGAA
* *
12838085 ATACGACACACGAGGTGCCTGAA
1 ATACGACACACAAAGTGCCTGAA
*
12838108 ATACGACACATAAAGTGCCTGA
1 ATACGACACACAAAGTGCCTGA
12838130 TCGATAAAGC
Statistics
Matches: 55, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
20 1 0.02
21 34 0.62
22 1 0.02
23 19 0.35
ACGTcount: A:0.38, C:0.25, G:0.22, T:0.15
Consensus pattern (23 bp):
ATACGACACACAAAGTGCCTGAA
Found at i:12838526 original size:15 final size:15
Alignment explanation
Indices: 12838501--12838558 Score: 89
Period size: 15 Copynumber: 3.8 Consensus size: 15
12838491 TCATATATAT
12838501 TATATAATTCAATCAA
1 TATA-AATTCAATCAA
12838517 TATAAATTCAATCAA
1 TATAAATTCAATCAA
* *
12838532 AATAATTTCAATCAA
1 TATAAATTCAATCAA
12838547 TATAAATTCAAT
1 TATAAATTCAAT
12838559 AAATTCATTG
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
15 34 0.89
16 4 0.11
ACGTcount: A:0.52, C:0.12, G:0.00, T:0.36
Consensus pattern (15 bp):
TATAAATTCAATCAA
Found at i:12839815 original size:5 final size:5
Alignment explanation
Indices: 12839807--12839841 Score: 70
Period size: 5 Copynumber: 7.0 Consensus size: 5
12839797 TCTTTAGTTT
12839807 ATATA ATATA ATATA ATATA ATATA ATATA ATATA
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA
12839842 TTTAAAACAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 30 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
ATATA
Found at i:12839879 original size:8 final size:8
Alignment explanation
Indices: 12839866--12839894 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
12839856 TATCTTTATT
12839866 ATATAATA
1 ATATAATA
12839874 ATATAATA
1 ATATAATA
12839882 ATATAATA
1 ATATAATA
12839890 ATATA
1 ATATA
12839895 CTAAACATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (8 bp):
ATATAATA
Found at i:12840830 original size:17 final size:17
Alignment explanation
Indices: 12840810--12840867 Score: 64
Period size: 17 Copynumber: 3.4 Consensus size: 17
12840800 AAAATTAATG
12840810 ATAATTATACATTTAAA
1 ATAATTATACATTTAAA
*
12840827 ATAATTATA-ATTTAAT
1 ATAATTATACATTTAAA
* * *
12840843 AGAAGTACACATTTAAA
1 ATAATTATACATTTAAA
12840860 ACTAATTA
1 A-TAATTA
12840868 AAATTATAAT
Statistics
Matches: 32, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
16 12 0.38
17 16 0.50
18 4 0.12
ACGTcount: A:0.52, C:0.07, G:0.03, T:0.38
Consensus pattern (17 bp):
ATAATTATACATTTAAA
Found at i:12841724 original size:25 final size:25
Alignment explanation
Indices: 12841682--12841730 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
12841672 AAAATTAAGG
*
12841682 TAAAAAATTTATGCTAATTTTATTT
1 TAAAAAAGTTATGCTAATTTTATTT
* *
12841707 TAAAAAAGTTGTGTTAATTTTATT
1 TAAAAAAGTTATGCTAATTTTATT
12841731 GATGTAAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.39, C:0.02, G:0.08, T:0.51
Consensus pattern (25 bp):
TAAAAAAGTTATGCTAATTTTATTT
Found at i:12847635 original size:17 final size:17
Alignment explanation
Indices: 12847613--12847645 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
12847603 AGGCGTTGCC
12847613 TCATCA-CATCACACAAA
1 TCATCATCATCA-ACAAA
12847630 TCATCATCATCAACAA
1 TCATCATCATCAACAA
12847646 GGGTAACAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.45, C:0.33, G:0.00, T:0.21
Consensus pattern (17 bp):
TCATCATCATCAACAAA
Found at i:12854038 original size:14 final size:14
Alignment explanation
Indices: 12854015--12854044 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
12854005 ATTGTCTCCT
12854015 AGAAACTTTTTTGG
1 AGAAACTTTTTTGG
*
12854029 AGAAAGTTTTTTGG
1 AGAAACTTTTTTGG
12854043 AG
1 AG
12854045 GTTTATCTCC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.30, C:0.03, G:0.27, T:0.40
Consensus pattern (14 bp):
AGAAACTTTTTTGG
Found at i:12875399 original size:20 final size:22
Alignment explanation
Indices: 12875360--12875401 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 22
12875350 TGTGATTGGA
12875360 TCACTTAATAAAACATTTTGTT
1 TCACTTAATAAAACATTTTGTT
*
12875382 TCACTTAA-AATA-ATTTTGTT
1 TCACTTAATAAAACATTTTGTT
12875402 CTACGTAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 8 0.42
21 3 0.16
22 8 0.42
ACGTcount: A:0.36, C:0.12, G:0.05, T:0.48
Consensus pattern (22 bp):
TCACTTAATAAAACATTTTGTT
Found at i:12883709 original size:20 final size:20
Alignment explanation
Indices: 12883686--12883724 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
12883676 GTTCTAAGTT
*
12883686 AATACCAAAATTTCTAATGC
1 AATAACAAAATTTCTAATGC
*
12883706 AATAACAATATTTCTAATG
1 AATAACAAAATTTCTAATG
12883725 GAAACCATTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.46, C:0.15, G:0.05, T:0.33
Consensus pattern (20 bp):
AATAACAAAATTTCTAATGC
Found at i:12884055 original size:19 final size:20
Alignment explanation
Indices: 12884015--12884061 Score: 69
Period size: 19 Copynumber: 2.4 Consensus size: 20
12884005 AGCATGTACT
* *
12884015 AATTTTTAATACGATACTAA
1 AATTTCTAATACGATACCAA
12884035 AATTTCTAATA-GATACCAA
1 AATTTCTAATACGATACCAA
12884054 AATTTCTA
1 AATTTCTA
12884062 GCCAAATACC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 15 0.60
20 10 0.40
ACGTcount: A:0.45, C:0.13, G:0.04, T:0.38
Consensus pattern (20 bp):
AATTTCTAATACGATACCAA
Found at i:12885969 original size:48 final size:48
Alignment explanation
Indices: 12885689--12885970 Score: 212
Period size: 48 Copynumber: 5.9 Consensus size: 48
12885679 ATAATTTACT
* * * *
12885689 GATGCCATGTCCTAGACATGGTCTTACACTGGCTTACATGTCGAGGCC
1 GATGCCATGTCCTAGACATGGTCTTACACTAGCTCACATATCGTGGCC
* * **
12885737 GATGCTATGTCCTAGACATGGTCTTACACTGGCTTTCATAAT-GTGGCC
1 GATGCCATGTCCTAGACATGGTCTTACACTAGCTCACAT-ATCGTGGCC
* * * * * * * *
12885785 GTTGCCATGTCCCAGGCATTGTCTTACACTAGCGCACCTAACAAT-GCC
1 GATGCCATGTCCTAGACATGGTCTTACACTAGCTCACATATC-GTGGCC
* * * ** * * *
12885833 GATGCCATGTCCCAGGCATGGTCTTACATTAGCTCTTATAACATTGCC
1 GATGCCATGTCCTAGACATGGTCTTACACTAGCTCACATATCGTGGCC
* * * * * *
12885881 AATGTCATGTTCC-AAACATGGTTTTATACT-GACTCTCATATCGTGGCC
1 GATGCCATG-TCCTAGACATGGTCTTACACTAG-CTCACATATCGTGGCC
* *
12885929 GACGCCATGTCCTAGACATGGTCTTACACTAGCACACATATC
1 GATGCCATGTCCTAGACATGGTCTTACACTAGCTCACATATC
12885971 ACCCAAATGT
Statistics
Matches: 184, Mismatches: 42, Indels: 16
0.76 0.17 0.07
Matches are distributed among these distances:
47 7 0.04
48 171 0.93
49 6 0.03
ACGTcount: A:0.23, C:0.27, G:0.20, T:0.29
Consensus pattern (48 bp):
GATGCCATGTCCTAGACATGGTCTTACACTAGCTCACATATCGTGGCC
Found at i:12893335 original size:48 final size:46
Alignment explanation
Indices: 12893234--12893368 Score: 130
Period size: 48 Copynumber: 2.8 Consensus size: 46
12893224 AGGGTAAATT
* * * *
12893234 ACCGATGCCATGTCCCAGACATGGTTTTACACTGGCTCACATGTCGAG
1 ACCGATGCCATGTTCCAGACATGGTATTACACTGGCT--CTTGTCAAG
*
12893282 ACCGATGCCATGTTCCAGACATGGTATTACACTAGCTCTTGTCTTAATG
1 ACCGATGCCATGTTCCAGACATGGTATTACACTGGCTCTTGTC--AA-G
* * *
12893331 -CCGATGCCATG-TCCTGAACATGGTCTTAAACTGGCTCT
1 ACCGATGCCATGTTCCAG-ACATGGTATTACACTGGCTCT
12893369 CATAATGTGG
Statistics
Matches: 74, Mismatches: 9, Indels: 8
0.81 0.10 0.09
Matches are distributed among these distances:
46 5 0.07
47 4 0.05
48 64 0.86
49 1 0.01
ACGTcount: A:0.23, C:0.27, G:0.21, T:0.29
Consensus pattern (46 bp):
ACCGATGCCATGTTCCAGACATGGTATTACACTGGCTCTTGTCAAG
Found at i:12893399 original size:96 final size:96
Alignment explanation
Indices: 12893287--12893469 Score: 231
Period size: 96 Copynumber: 1.9 Consensus size: 96
12893277 TCGAGACCGA
* * *** ** * * *
12893287 TGCCATGTTCCAGACATGGTATTACACTAGCTCTTGTCTTAATGCCGATGCCATGTCCTGAACAT
1 TGCCATGTCCCAGACATGGTATTACACTAGCGCACCTAATAACGCCGATGCCATATCCCGAACAT
12893352 GGTCTTAAACTGGCTCTCATAATGTGGCCAT
66 GGTCTTAAACTGGCTCTCATAATGTGGCCAT
* * *
12893383 TGCCATGTCCCAGACATGTTCTTACACTAGCGCACCTAATAACGCCGATGCCGTATCCCGAACAT
1 TGCCATGTCCCAGACATGGTATTACACTAGCGCACCTAATAACGCCGATGCCATATCCCGAACAT
* *
12893448 TGTCTTACACTGGCTCTCATAA
66 GGTCTTAAACTGGCTCTCATAA
12893470 CATTGTTGAT
Statistics
Matches: 72, Mismatches: 15, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
96 72 1.00
ACGTcount: A:0.24, C:0.28, G:0.18, T:0.30
Consensus pattern (96 bp):
TGCCATGTCCCAGACATGGTATTACACTAGCGCACCTAATAACGCCGATGCCATATCCCGAACAT
GGTCTTAAACTGGCTCTCATAATGTGGCCAT
Found at i:12893483 original size:96 final size:93
Alignment explanation
Indices: 12893285--12893502 Score: 229
Period size: 96 Copynumber: 2.3 Consensus size: 93
12893275 TGTCGAGACC
* * *** ** * * *
12893285 GATGCCATGTTCCAGACATGGTATTACACTAGCTCTTGTCTTAATGCCGATGCCATGTCCTGAAC
1 GATGCCATGTTCCAGACATGGTCTTACACTAGCGCACCTAATAACGCCGATGCCATATCCCGAAC
12893350 ATGGTCTTAAACTGGCTCTCATAATGTG
66 ATGGTCTTAAACTGGCTCTCATAATGTG
* * *
12893378 GCCATTGCCATGTCCCAGACATGTTCTTACACTAGCGCACCTAATAACGCCGATGCCGTATCCCG
1 G--A-TGCCATGTTCCAGACATGGTCTTACACTAGCGCACCTAATAACGCCGATGCCATATCCCG
* * *
12893443 AACATTGTCTTACACTGGCTCTCATAACATTGTT
63 AACATGGTCTTAAACTGGCTCTCAT-A-A-TGTG
*
12893477 GATGCCATGTTCCAAACATGGTCTTA
1 GATGCCATGTTCCAGACATGGTCTTA
12893503 TACTGGCTCT
Statistics
Matches: 100, Mismatches: 19, Indels: 9
0.78 0.15 0.07
Matches are distributed among these distances:
93 1 0.01
95 1 0.01
96 91 0.91
97 2 0.02
98 1 0.01
99 4 0.04
ACGTcount: A:0.24, C:0.27, G:0.18, T:0.30
Consensus pattern (93 bp):
GATGCCATGTTCCAGACATGGTCTTACACTAGCGCACCTAATAACGCCGATGCCATATCCCGAAC
ATGGTCTTAAACTGGCTCTCATAATGTG
Found at i:12893532 original size:48 final size:48
Alignment explanation
Indices: 12893443--12893554 Score: 138
Period size: 48 Copynumber: 2.3 Consensus size: 48
12893433 CCGTATCCCG
* * *
12893443 AACATTGTCTTACACTGGCTCTCATAACATTGTTGATGCCATGTTCC-A
1 AACATGGTCTTATACTGGCTCTCATAACATTGTTGACGCCATG-TCCGA
* *
12893491 AACATGGTCTTATACTGGCTCTCATATC-GTGTTTGACGCCATGTCCGA
1 AACATGGTCTTATACTGGCTCTCATAACATTG-TTGACGCCATGTCCGA
*
12893539 GACATGGTCTTATACT
1 AACATGGTCTTATACT
12893555 AGTACACATA
Statistics
Matches: 56, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
47 5 0.09
48 51 0.91
ACGTcount: A:0.23, C:0.24, G:0.18, T:0.35
Consensus pattern (48 bp):
AACATGGTCTTATACTGGCTCTCATAACATTGTTGACGCCATGTCCGA
Found at i:12893565 original size:48 final size:48
Alignment explanation
Indices: 12893475--12893566 Score: 116
Period size: 48 Copynumber: 1.9 Consensus size: 48
12893465 CATAACATTG
* * *
12893475 TTGATGCCATGTTCCAAACATGGTCTTATACTGGCTCTCATATCGTGT
1 TTGACGCCATGTTCCAAACATGGTCTTATACTAGCTCACATATCGTGT
*
12893523 TTGACGCCATG-TCCGAGACATGGTCTTATACTAG-TACACATATC
1 TTGACGCCATGTTCC-AAACATGGTCTTATACTAGCT-CACATATC
12893567 ACCCAAATGT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
47 4 0.11
48 34 0.89
ACGTcount: A:0.24, C:0.24, G:0.18, T:0.34
Consensus pattern (48 bp):
TTGACGCCATGTTCCAAACATGGTCTTATACTAGCTCACATATCGTGT
Found at i:12899691 original size:11 final size:11
Alignment explanation
Indices: 12899672--12899705 Score: 59
Period size: 11 Copynumber: 3.1 Consensus size: 11
12899662 TGTATGTTAT
*
12899672 TGATGTGAATA
1 TGATTTGAATA
12899683 TGATTTGAATA
1 TGATTTGAATA
12899694 TGATTTGAATA
1 TGATTTGAATA
12899705 T
1 T
12899706 TCATTGTATG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.35, C:0.00, G:0.21, T:0.44
Consensus pattern (11 bp):
TGATTTGAATA
Found at i:12900135 original size:46 final size:45
Alignment explanation
Indices: 12900083--12900402 Score: 331
Period size: 46 Copynumber: 7.0 Consensus size: 45
12900073 GCTCTCTGAA
* * *
12900083 ATGAAATATGTAAGATCATGGTTGAAAGATACCATAGCAACATGAT
1 ATGAAATA-GTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
* * * *
12900129 ATGAAATGTGTAAGACCATAGTTTAAAGATACCATGGCAACATGAT
1 ATGAAAT-AGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
* * * *
12900175 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGACAACGTGAG
1 ATGAAAT-AGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
* *
12900221 ATGAAA-AGAATAAGACCATGGTTCAAAAATACCATGGCAACATGAC
1 ATGAAATAG--TAAGACCATGGTTGAAAGATACCATGGCAACATGAC
** * *
12900267 GGGAAATGAATAAGACCATGGTTGAAAGATACCATGGAAACATGAC
1 ATGAAAT-AGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
12900313 ATGAAA-AGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
1 ATGAAATAG--TAAGACCATGGTTGAAAGATACCATGGCAACATGAC
** * * *
12900359 A-GAAAATGAGTAAGACCATACTTGAAAGACACTATGGCATCATG
1 ATG-AAAT-AGTAAGACCATGGTTGAAAGATACCATGGCAACATG
12900403 TCAAAAATAA
Statistics
Matches: 233, Mismatches: 31, Indels: 20
0.82 0.11 0.07
Matches are distributed among these distances:
44 2 0.01
45 1 0.00
46 227 0.97
48 3 0.01
ACGTcount: A:0.43, C:0.14, G:0.22, T:0.21
Consensus pattern (45 bp):
ATGAAATAGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
Found at i:12900253 original size:92 final size:92
Alignment explanation
Indices: 12900083--12900387 Score: 384
Period size: 92 Copynumber: 3.3 Consensus size: 92
12900073 GCTCTCTGAA
* * * **
12900083 ATGAAAT-ATGTAAGATCATGGTTGAAAGATACCAT-AGCAACATGATATGAAATGTGTAAGACC
1 ATGAAATGA-GTAAGACCATGGTTGAAAGATACCATGA-CAACATGACATGAAAAGAATAAGACC
* * *
12900146 ATAGTTTAAAGATACCATGGCAACATGAT
64 ATGGTTCAAAGATACCATGGCAACATGAC
* * *
12900175 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGACAACGTGAGATGAAAAGAATAAGACCAT
1 ATGAAATGAGTAAGACCATGGTTGAAAGATACCATGACAACATGACATGAAAAGAATAAGACCAT
*
12900240 GGTTCAAAAATACCATGGCAACATGAC
66 GGTTCAAAGATACCATGGCAACATGAC
** *
12900267 GGGAAATGAATAAGACCATGGTTGAAAGATACCATGGA-AACATGACATGAAAAGAATAAGACCA
1 ATGAAATGAGTAAGACCATGGTTGAAAGATACCAT-GACAACATGACATGAAAAGAATAAGACCA
*
12900331 TGGTTGAAAGATACCATGGCAACATGAC
65 TGGTTCAAAGATACCATGGCAACATGAC
**
12900359 A-GAAAATGAGTAAGACCATACTTGAAAGA
1 ATG-AAATGAGTAAGACCATGGTTGAAAGA
12900388 CACTATGGCA
Statistics
Matches: 186, Mismatches: 23, Indels: 8
0.86 0.11 0.04
Matches are distributed among these distances:
91 1 0.01
92 182 0.98
93 3 0.02
ACGTcount: A:0.44, C:0.13, G:0.22, T:0.21
Consensus pattern (92 bp):
ATGAAATGAGTAAGACCATGGTTGAAAGATACCATGACAACATGACATGAAAAGAATAAGACCAT
GGTTCAAAGATACCATGGCAACATGAC
Found at i:12900281 original size:138 final size:138
Alignment explanation
Indices: 12900093--12900377 Score: 374
Period size: 138 Copynumber: 2.1 Consensus size: 138
12900083 ATGAAATATG
* * * * * ** *
12900093 TAAGATCATGGTTGAAAGATACCATAGCAACATGATATGAAATGTGTAAGACCATAGTTTAAAGA
1 TAAGACCATGGTTCAAAAATACCATAGCAACATGACAGGAAATGAATAAGACCATAGTTGAAAGA
* * * ** * *
12900158 TACCATGGCAACATGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGACAACGTGAGAT
66 TACCATGGAAACATGACATGAAAAGAATAAGACCATGGTTGAAAGATACCATGACAACATGACA-
12900223 GAAAA-GAA
130 GAAAATGAA
* * *
12900231 TAAGACCATGGTTCAAAAATACCATGGCAACATGACGGGAAATGAATAAGACCATGGTTGAAAGA
1 TAAGACCATGGTTCAAAAATACCATAGCAACATGACAGGAAATGAATAAGACCATAGTTGAAAGA
*
12900296 TACCATGGAAACATGACATGAAAAGAATAAGACCATGGTTGAAAGATACCATGGCAACATGACAG
66 TACCATGGAAACATGACATGAAAAGAATAAGACCATGGTTGAAAGATACCATGACAACATGACAG
*
12900361 AAAATGAG
131 AAAATGAA
12900369 TAAGACCAT
1 TAAGACCAT
12900378 ACTTGAAAGA
Statistics
Matches: 126, Mismatches: 20, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
137 5 0.04
138 121 0.96
ACGTcount: A:0.44, C:0.14, G:0.22, T:0.20
Consensus pattern (138 bp):
TAAGACCATGGTTCAAAAATACCATAGCAACATGACAGGAAATGAATAAGACCATAGTTGAAAGA
TACCATGGAAACATGACATGAAAAGAATAAGACCATGGTTGAAAGATACCATGACAACATGACAG
AAAATGAA
Found at i:12903628 original size:7 final size:7
Alignment explanation
Indices: 12903616--12903708 Score: 105
Period size: 7 Copynumber: 13.0 Consensus size: 7
12903606 GATTTTATTA
12903616 CCTAAAC
1 CCTAAAC
12903623 CCTAAAC
1 CCTAAAC
12903630 CCTAAAAC
1 CCT-AAAC
12903638 CCTAAAC
1 CCTAAAC
*
12903645 CATAAAC
1 CCTAAAC
* *
12903652 ACTAAAG
1 CCTAAAC
*
12903659 CTTAAAC
1 CCTAAAC
12903666 CCTAAAC
1 CCTAAAC
* *
12903673 CATAAAG
1 CCTAAAC
12903680 CCTAAAAC
1 CCT-AAAC
*
12903688 CCTAAAT
1 CCTAAAC
12903695 CCTAAAC
1 CCTAAAC
12903702 CCTAAAC
1 CCTAAAC
12903709 ATTTGAGCCC
Statistics
Matches: 70, Mismatches: 14, Indels: 4
0.80 0.16 0.05
Matches are distributed among these distances:
7 57 0.81
8 13 0.19
ACGTcount: A:0.47, C:0.34, G:0.02, T:0.16
Consensus pattern (7 bp):
CCTAAAC
Found at i:12903644 original size:22 final size:21
Alignment explanation
Indices: 12903616--12903708 Score: 105
Period size: 22 Copynumber: 4.3 Consensus size: 21
12903606 GATTTTATTA
12903616 CCTAAACCCTAAACCCTAAAAC
1 CCTAAACCCTAAACCCT-AAAC
* * *
12903638 CCTAAACCATAAACACTAAAG
1 CCTAAACCCTAAACCCTAAAC
* * *
12903659 CTTAAACCCTAAACCATAAAG
1 CCTAAACCCTAAACCCTAAAC
*
12903680 CCTAAAACCCTAAATCCTAAAC
1 CCT-AAACCCTAAACCCTAAAC
12903702 CCTAAAC
1 CCTAAAC
12903709 ATTTGAGCCC
Statistics
Matches: 59, Mismatches: 11, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
21 26 0.44
22 33 0.56
ACGTcount: A:0.47, C:0.34, G:0.02, T:0.16
Consensus pattern (21 bp):
CCTAAACCCTAAACCCTAAAC
Done.