Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr13
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: 91551117
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2824764 characters in sequence are not A, C, G, or T
File 161 of 276
Found at i:52431552 original size:9 final size:9
Alignment explanation
Indices: 52431538--52431565 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
52431528 TATTGTTTGA
52431538 TATTCGAAT
1 TATTCGAAT
52431547 TATTCGAAT
1 TATTCGAAT
52431556 TATTCGAAT
1 TATTCGAAT
52431565 T
1 T
52431566 CGAAAACTCA
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:0.32, C:0.11, G:0.11, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:52440119 original size:46 final size:46
Alignment explanation
Indices: 52440069--52440334 Score: 280
Period size: 46 Copynumber: 5.7 Consensus size: 46
52440059 TTGAGCATCT
52440069 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCC
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCC
* * *
52440115 GAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGGCATCC
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G--TCC
52440162 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCC
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCC
* * *
52440208 GAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGGCATCC
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G--TCC
*
52440255 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG-CC
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCC
* * *
52440300 TGAGCTCGTTGAGTTGAGTCCTAGTTCGCTTATGG
1 -GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
52440335 GCGGGTTACA
Statistics
Matches: 185, Mismatches: 16, Indels: 38
0.77 0.07 0.16
Matches are distributed among these distances:
42 4 0.02
43 10 0.05
45 8 0.04
46 86 0.46
47 58 0.31
48 6 0.03
50 9 0.05
51 4 0.02
ACGTcount: A:0.21, C:0.20, G:0.29, T:0.30
Consensus pattern (46 bp):
GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCC
Found at i:52440181 original size:47 final size:47
Alignment explanation
Indices: 52440112--52440280 Score: 240
Period size: 47 Copynumber: 3.6 Consensus size: 47
52440102 GATGCGAATG
52440112 TCCGAACTCGTTGAGTTGAGTCCGAGTTCGTGAGATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCGTGAGATGTAACTAGGCA
* * *
52440159 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G--
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGGCA
52440205 TCCGAACTCGTTGAGTTGAGTCCGAGTTCGTGAGATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCGTGAGATGTAACTAGGCA
52440252 TCCGAACTCGTTGAGTTGAGTCCGAGTTC
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC
52440281 ACTTATGGAT
Statistics
Matches: 107, Mismatches: 6, Indels: 18
0.82 0.05 0.14
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 3 0.03
46 29 0.27
47 58 0.54
48 3 0.03
50 5 0.05
51 2 0.02
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.29
Consensus pattern (47 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCGTGAGATGTAACTAGGCA
Found at i:52440222 original size:93 final size:93
Alignment explanation
Indices: 52440063--52440327 Score: 478
Period size: 93 Copynumber: 2.8 Consensus size: 93
52440053 GGATGATTGA
*
52440063 GCATCTGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
52440128 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
52440156 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
52440221 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* *
52440249 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG-CCTGAGCTCGTTGAG
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCC-GAACTCGTTGAG
*
52440313 TTGAGTCCTAGTTCG
65 TTGAGTCCGAGTTCG
52440328 CTTATGGGCG
Statistics
Matches: 167, Mismatches: 4, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
92 2 0.01
93 165 0.99
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.29
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:52446126 original size:28 final size:28
Alignment explanation
Indices: 52446095--52446183 Score: 78
Period size: 28 Copynumber: 3.2 Consensus size: 28
52446085 GAAAATTGAT
*
52446095 AAATTAAGGGTAAAATTGGAATATTGCA
1 AAATTAAGGGTAAAATAGGAATATTGCA
* *
52446123 AAATTAA--CT-AAATAAGGAAAATTG-A
1 AAATTAAGGGTAAAAT-AGGAATATTGCA
* * *
52446148 TAAATTAAGGGCAAAATGGGAGTATTGCA
1 -AAATTAAGGGTAAAATAGGAATATTGCA
52446177 AAATTAA
1 AAATTAA
52446184 CTAAATAAAA
Statistics
Matches: 47, Mismatches: 8, Indels: 12
0.70 0.12 0.18
Matches are distributed among these distances:
25 5 0.11
26 16 0.34
28 21 0.45
29 5 0.11
ACGTcount: A:0.51, C:0.04, G:0.19, T:0.26
Consensus pattern (28 bp):
AAATTAAGGGTAAAATAGGAATATTGCA
Found at i:52446147 original size:54 final size:54
Alignment explanation
Indices: 52446083--52446191 Score: 191
Period size: 54 Copynumber: 2.0 Consensus size: 54
52446073 TGAAATCAGC
* *
52446083 AGGAAAATTGATAAATTAAGGGTAAAATTGGAATATTGCAAAATTAACTAAATA
1 AGGAAAATTGATAAATTAAGGGCAAAATGGGAATATTGCAAAATTAACTAAATA
*
52446137 AGGAAAATTGATAAATTAAGGGCAAAATGGGAGTATTGCAAAATTAACTAAATA
1 AGGAAAATTGATAAATTAAGGGCAAAATGGGAATATTGCAAAATTAACTAAATA
52446191 A
1 A
52446192 AACTAGGACT
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
54 52 1.00
ACGTcount: A:0.51, C:0.05, G:0.18, T:0.26
Consensus pattern (54 bp):
AGGAAAATTGATAAATTAAGGGCAAAATGGGAATATTGCAAAATTAACTAAATA
Found at i:52449422 original size:21 final size:22
Alignment explanation
Indices: 52449383--52449423 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
52449373 GTTGAAATGT
52449383 CACACGGGCGTGTTGCCCCTCC
1 CACACGGGCGTGTTGCCCCTCC
*
52449405 CACACGGGTGTG-TGCCCCT
1 CACACGGGCGTGTTGCCCCT
52449424 GTGTTAAGAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.10, C:0.41, G:0.29, T:0.20
Consensus pattern (22 bp):
CACACGGGCGTGTTGCCCCTCC
Found at i:52457644 original size:132 final size:132
Alignment explanation
Indices: 52457407--52457669 Score: 517
Period size: 132 Copynumber: 2.0 Consensus size: 132
52457397 GCTTTGGGGC
*
52457407 AAAAGTGTAAATATGCAAATGTTTAGGGGCAAAATTGTAATTTTTCCAAAATATGATTTTGGGTC
1 AAAAGTGTAAATATGCAAAAGTTTAGGGGCAAAATTGTAATTTTTCCAAAATATGATTTTGGGTC
52457472 AATTTGAATAATGTGAGTCCTAATTAGACTATATTTTAAATGATAGAGCAAGGAAAATTGAAATT
66 AATTTGAATAATGTGAGTCCTAATTAGACTATATTTTAAATGATAGAGCAAGGAAAATTGAAATT
52457537 CA
131 CA
52457539 AAAAGTGTAAATATGCAAAAGTTTAGGGGCAAAATTGTAATTTTTCCAAAATATGATTTTGGGTC
1 AAAAGTGTAAATATGCAAAAGTTTAGGGGCAAAATTGTAATTTTTCCAAAATATGATTTTGGGTC
52457604 AATTTGAATAATGTGAGTCCTAATTAGACTATATTTTAAATGATAGAGCAAGGAAAATTGAAATT
66 AATTTGAATAATGTGAGTCCTAATTAGACTATATTTTAAATGATAGAGCAAGGAAAATTGAAATT
52457669 C
131 C
52457670 GGGCTAAAAT
Statistics
Matches: 130, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
132 130 1.00
ACGTcount: A:0.40, C:0.08, G:0.18, T:0.34
Consensus pattern (132 bp):
AAAAGTGTAAATATGCAAAAGTTTAGGGGCAAAATTGTAATTTTTCCAAAATATGATTTTGGGTC
AATTTGAATAATGTGAGTCCTAATTAGACTATATTTTAAATGATAGAGCAAGGAAAATTGAAATT
CA
Found at i:52460009 original size:46 final size:45
Alignment explanation
Indices: 52459942--52460302 Score: 353
Period size: 46 Copynumber: 7.8 Consensus size: 45
52459932 TGTAACCCGC
*
52459942 CCATAAGCGAACTCAGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTT-GCAT
* *
52459988 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTTACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGG--G-C--GTTGCAT
* *
52460038 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGGCGCTTGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCG-TTGCAT
* *
52460081 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTTACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGG--G-C--GTTGCAT
* *
52460131 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGGCGCTTGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCG-TTGCAT
* *
52460174 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTTACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGG--G-C--GTTGCAT
* *
52460224 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGGCGCTTGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCG-TTGCAT
* *
52460267 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGG
1 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGG
52460303 ATGCCCAAAT
Statistics
Matches: 263, Mismatches: 25, Indels: 54
0.77 0.07 0.16
Matches are distributed among these distances:
42 3 0.01
43 15 0.06
44 6 0.02
45 9 0.03
46 116 0.44
47 81 0.31
48 9 0.03
49 6 0.02
50 13 0.05
51 5 0.02
ACGTcount: A:0.27, C:0.30, G:0.22, T:0.21
Consensus pattern (45 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTGCAT
Found at i:52460062 original size:93 final size:93
Alignment explanation
Indices: 52459949--52460307 Score: 675
Period size: 93 Copynumber: 3.9 Consensus size: 93
52459939 CGCCCATAAG
* *
52459949 CGAACTCAGACTCAACTCAACGAGCTCGGGCG-TTCGCATCCATAAGTGAACTCGGACTCAACTC
1 CGAACTCGGACTCAACTCAACGAGTTCGGGCGCTT-GCATCCATAAGTGAACTCGGACTCAACTC
52460013 AACGAGCTCGGATGCCTAGTTACATCTCA
65 AACGAGCTCGGATGCCTAGTTACATCTCA
52460042 CGAACTCGGACTCAACTCAACGAGTTCGGGCGCTTGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGTTCGGGCGCTTGCATCCATAAGTGAACTCGGACTCAACTCA
52460107 ACGAGCTCGGATGCCTAGTTACATCTCA
66 ACGAGCTCGGATGCCTAGTTACATCTCA
52460135 CGAACTCGGACTCAACTCAACGAGTTCGGGCGCTTGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGTTCGGGCGCTTGCATCCATAAGTGAACTCGGACTCAACTCA
52460200 ACGAGCTCGGATGCCTAGTTACATCTCA
66 ACGAGCTCGGATGCCTAGTTACATCTCA
52460228 CGAACTCGGACTCAACTCAACGAGTTCGGGCGCTTGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGTTCGGGCGCTTGCATCCATAAGTGAACTCGGACTCAACTCA
*
52460293 ACGAGTTCGGATGCC
66 ACGAGCTCGGATGCC
52460308 CAAATATCCC
Statistics
Matches: 262, Mismatches: 3, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
93 260 0.99
94 2 0.01
ACGTcount: A:0.27, C:0.30, G:0.22, T:0.21
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGTTCGGGCGCTTGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGCTCGGATGCCTAGTTACATCTCA
Found at i:52460063 original size:47 final size:47
Alignment explanation
Indices: 52459996--52460256 Score: 299
Period size: 47 Copynumber: 5.6 Consensus size: 47
52459986 ATCCATAAGT
52459996 GAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTTACATCTCAC
1 GAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTTACATCTCAC
* * * *
52460043 GAACTCGGACTCAACTCAACGAGTTCGG--G-C--GCTTGCATCCATAAGT
1 GAACTCGGACTCAACTCAACGAGCTCGGATGCCTAG-TTACAT-C-TCA-C
52460089 GAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTTACATCTCAC
1 GAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTTACATCTCAC
* * * *
52460136 GAACTCGGACTCAACTCAACGAGTTCGG--G-C--GCTTGCATCCATAAGT
1 GAACTCGGACTCAACTCAACGAGCTCGGATGCCTAG-TTACAT-C-TCA-C
52460182 GAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTTACATCTCAC
1 GAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTTACATCTCAC
*
52460229 GAACTCGGACTCAACTCAACGAGTTCGG
1 GAACTCGGACTCAACTCAACGAGCTCGG
52460257 GCGCTTGCAT
Statistics
Matches: 179, Mismatches: 17, Indels: 36
0.77 0.07 0.16
Matches are distributed among these distances:
42 2 0.01
43 10 0.06
44 4 0.02
45 6 0.03
46 54 0.30
47 81 0.45
48 6 0.03
49 4 0.02
50 10 0.06
51 2 0.01
ACGTcount: A:0.27, C:0.30, G:0.21, T:0.21
Consensus pattern (47 bp):
GAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTTACATCTCAC
Found at i:52463304 original size:30 final size:29
Alignment explanation
Indices: 52463265--52463338 Score: 85
Period size: 30 Copynumber: 2.5 Consensus size: 29
52463255 GTATCATATA
* * *
52463265 TTGGGTTTCTTTATCCTGGATCTCTTTATT
1 TTGGATTTCTTTATCC-GGATCTCTCTATC
* *
52463295 TTGGATTTCTTTATTCCGGGTTTCTCTATC
1 TTGGATTTCTTTA-TCCGGATCTCTCTATC
52463325 TTGGATTTCTTTAT
1 TTGGATTTCTTTAT
52463339 TCGGTTTTCT
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
29 1 0.03
30 34 0.89
31 3 0.08
ACGTcount: A:0.11, C:0.16, G:0.16, T:0.57
Consensus pattern (29 bp):
TTGGATTTCTTTATCCGGATCTCTCTATC
Found at i:52463309 original size:15 final size:15
Alignment explanation
Indices: 52463265--52463339 Score: 69
Period size: 15 Copynumber: 5.0 Consensus size: 15
52463255 GTATCATATA
* *
52463265 TTGGGTTTCTTTATC
1 TTGGATTTCTTTATT
* *
52463280 CTGGATCTCTTTATT
1 TTGGATTTCTTTATT
52463295 TTGGATTTCTTTATT
1 TTGGATTTCTTTATT
** * * *
52463310 CCGGGTTTCTCTATC
1 TTGGATTTCTTTATT
52463325 TTGGATTTCTTTATT
1 TTGGATTTCTTTATT
52463340 CGGTTTTCTT
Statistics
Matches: 44, Mismatches: 16, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
15 44 1.00
ACGTcount: A:0.11, C:0.16, G:0.16, T:0.57
Consensus pattern (15 bp):
TTGGATTTCTTTATT
Found at i:52463349 original size:14 final size:14
Alignment explanation
Indices: 52463270--52463349 Score: 61
Period size: 15 Copynumber: 5.4 Consensus size: 14
52463260 ATATATTGGG
*
52463270 TTTCTTTATCCTGGA
1 TTTCTTTATTC-GGA
* *
52463285 TCTCTTTATTTTGGA
1 TTTCTTTA-TTCGGA
*
52463300 TTTCTTTATTCCGGG
1 TTTCTTTATT-CGGA
* *
52463315 TTTCTCTATCTTGGA
1 TTTCTTTAT-TCGGA
*
52463330 TTTCTTTATTCGGT
1 TTTCTTTATTCGGA
52463344 TTTCTT
1 TTTCTT
52463350 GTTATCTTTG
Statistics
Matches: 50, Mismatches: 12, Indels: 7
0.72 0.17 0.10
Matches are distributed among these distances:
14 11 0.22
15 37 0.74
16 2 0.04
ACGTcount: A:0.10, C:0.17, G:0.14, T:0.59
Consensus pattern (14 bp):
TTTCTTTATTCGGA
Found at i:52470103 original size:10 final size:10
Alignment explanation
Indices: 52470090--52470127 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
52470080 TTATTTTCAT
52470090 TTATCTTTAA
1 TTATCTTTAA
52470100 TTATCTTTAA
1 TTATCTTTAA
*
52470110 TTAT-TTATAC
1 TTATCTT-TAA
52470120 TTATCTTT
1 TTATCTTT
52470128 TGGGATTTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
9 2 0.08
10 21 0.84
11 2 0.08
ACGTcount: A:0.26, C:0.11, G:0.00, T:0.63
Consensus pattern (10 bp):
TTATCTTTAA
Found at i:52476394 original size:16 final size:16
Alignment explanation
Indices: 52476373--52476444 Score: 60
Period size: 16 Copynumber: 4.6 Consensus size: 16
52476363 AGGCAACTTA
*
52476373 ATTTTTATTTCTCTTT
1 ATTTTTATTTATCTTT
* *
52476389 ATTTTTCTTTATTTTT
1 ATTTTTATTTATCTTT
52476405 ATTTTTATTTTAT-TTT
1 ATTTTTA-TTTATCTTT
* *
52476421 A--ATTATTTATCTTA
1 ATTTTTATTTATCTTT
52476435 ATTATTTATT
1 ATT-TTTATT
52476445 GCTTAATTAT
Statistics
Matches: 44, Mismatches: 7, Indels: 9
0.73 0.12 0.15
Matches are distributed among these distances:
13 5 0.11
14 6 0.14
16 23 0.52
17 10 0.23
ACGTcount: A:0.21, C:0.06, G:0.00, T:0.74
Consensus pattern (16 bp):
ATTTTTATTTATCTTT
Found at i:52476410 original size:17 final size:18
Alignment explanation
Indices: 52476386--52476444 Score: 61
Period size: 17 Copynumber: 3.3 Consensus size: 18
52476376 TTTATTTCTC
52476386 TTTA-TTTT-TCTTTATT
1 TTTATTTTTATCTTTATT
52476402 TTTATTTTTAT-TTTATT
1 TTTATTTTTATCTTTATT
* *
52476419 TTAATTATTTATCTTAATT
1 TTTATT-TTTATCTTTATT
52476438 ATTTATT
1 -TTTATT
52476445 GCTTAATTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
16 4 0.11
17 15 0.43
18 6 0.17
19 5 0.14
20 5 0.14
ACGTcount: A:0.22, C:0.03, G:0.00, T:0.75
Consensus pattern (18 bp):
TTTATTTTTATCTTTATT
Found at i:52476451 original size:15 final size:14
Alignment explanation
Indices: 52476413--52476459 Score: 71
Period size: 13 Copynumber: 3.4 Consensus size: 14
52476403 TTATTTTTAT
52476413 TTTATT-TTAATTA
1 TTTATTCTTAATTA
52476426 TTTA-TCTTAATTA
1 TTTATTCTTAATTA
52476439 TTTATTGCTTAATTA
1 TTTATT-CTTAATTA
52476454 TTTATT
1 TTTATT
52476460 TTATTTTTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
12 1 0.03
13 15 0.48
14 1 0.03
15 14 0.45
ACGTcount: A:0.28, C:0.04, G:0.02, T:0.66
Consensus pattern (14 bp):
TTTATTCTTAATTA
Found at i:52476468 original size:26 final size:24
Alignment explanation
Indices: 52476369--52476468 Score: 78
Period size: 26 Copynumber: 3.9 Consensus size: 24
52476359 TGGGAGGCAA
* *
52476369 CTTAATTTTTATTTCTCTTTATTTTT
1 CTTAATTTTTATTT-TATTT-TTATT
*
52476395 CTTTATTTTTATTTT-TATTTTATT
1 CTTAATTTTTATTTTAT-TTTTATT
*
52476419 -TTAATTATTTATCTTAATTATTTATT
1 CTTAATT-TTTAT-TTTATT-TTTATT
52476445 GCTTAATTATTTATTTTATTTTTA
1 -CTTAATT-TTTATTTTATTTTTA
52476469 ATATTAATAA
Statistics
Matches: 62, Mismatches: 5, Indels: 14
0.77 0.06 0.17
Matches are distributed among these distances:
23 5 0.08
24 10 0.16
25 6 0.10
26 24 0.39
27 5 0.08
28 12 0.19
ACGTcount: A:0.22, C:0.06, G:0.01, T:0.71
Consensus pattern (24 bp):
CTTAATTTTTATTTTATTTTTATT
Found at i:52479295 original size:96 final size:97
Alignment explanation
Indices: 52479147--52479328 Score: 260
Period size: 96 Copynumber: 1.9 Consensus size: 97
52479137 TTTAAGAATA
* * *
52479147 TGTTGGGCTGAGTAACCGGGGTGAGGTGTTTGTCTGTCATCTCTCTTCGCGTCGAAAGGTTCGAT
1 TGTTGGGCTGAGTAACCGGGGTGAGGTGTTGGTCTGTCATCTCTCTTCGCGTCAAAAGGTTCAAT
* *
52479212 ATGTTCTTAAG-AAAATTAAAAATTAGGAGTG
66 ATATTCTTAAGCAAAACTAAAAATTAGGAGTG
* * * *
52479243 TGTTGGGCTGAGTAACTGTGGTGAGGTGGTTGGT-TGTTATCTCTCTTTGCGTCAAAAGGTTCAA
1 TGTTGGGCTGAGTAACCGGGGTGAGGT-GTTGGTCTGTCATCTCTCTTCGCGTCAAAAGGTTCAA
52479307 TATATTCTTAAGCAAAACTAAA
65 TATATTCTTAAGCAAAACTAAA
52479329 TAAATAAATA
Statistics
Matches: 75, Mismatches: 9, Indels: 3
0.86 0.10 0.03
Matches are distributed among these distances:
96 62 0.83
97 13 0.17
ACGTcount: A:0.25, C:0.13, G:0.27, T:0.35
Consensus pattern (97 bp):
TGTTGGGCTGAGTAACCGGGGTGAGGTGTTGGTCTGTCATCTCTCTTCGCGTCAAAAGGTTCAAT
ATATTCTTAAGCAAAACTAAAAATTAGGAGTG
Found at i:52479997 original size:10 final size:10
Alignment explanation
Indices: 52479982--52480027 Score: 51
Period size: 10 Copynumber: 4.6 Consensus size: 10
52479972 TAATTTTAAG
52479982 ATTTAT-TTT
1 ATTTATCTTT
52479991 CATTTATCTTT
1 -ATTTATCTTT
*
52480002 AATTATCTTT
1 ATTTATCTTT
52480012 ATTTAT-TTGT
1 ATTTATCTT-T
52480022 ATTTAT
1 ATTTAT
52480028 ATTTTAGAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
9 2 0.06
10 27 0.84
11 3 0.09
ACGTcount: A:0.24, C:0.07, G:0.02, T:0.67
Consensus pattern (10 bp):
ATTTATCTTT
Found at i:52484144 original size:3 final size:3
Alignment explanation
Indices: 52484136--52484415 Score: 560
Period size: 3 Copynumber: 93.3 Consensus size: 3
52484126 ATTTGTATTT
52484136 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
52484184 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
52484232 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
52484280 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
52484328 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
52484376 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
52484416 AGTAAACAAA
Statistics
Matches: 277, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 277 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:52484795 original size:6 final size:6
Alignment explanation
Indices: 52484784--52484808 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
52484774 AAAACTACAC
52484784 AGATGA AGATGA AGATGA AGATGA A
1 AGATGA AGATGA AGATGA AGATGA A
52484809 CAAAACCGGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.52, C:0.00, G:0.32, T:0.16
Consensus pattern (6 bp):
AGATGA
Found at i:52498833 original size:46 final size:47
Alignment explanation
Indices: 52498586--52498901 Score: 215
Period size: 46 Copynumber: 6.7 Consensus size: 47
52498576 GTATAATACA
* * * * *
52498586 GATGCCATGTCCCA-ACATGGTCTTACACTGGC-TCATCCATCAAGTC
1 GATGCCATGTCCCAGACATGGTCTTACACTGGCTTAAT-CTTGAGGCC
* *** *
52498632 GATGCCATGTCCCAAACATGGTCTTACACTAAATATCGAA-ATTGAGGCC
1 GATGCCATGTCCCAGACATGGTCTTACACTGGCT-T--AATCTTGAGGCC
* * * * * * *
52498681 GACGCCATATCTCAGACATGGTCTTACACTAGCTCTCACATATCCG-TGCC
1 GATGCCATGTCCCAGACATGGTCTTACACTGGCT-T-A-ATCT-TGAGGCC
* *
52498731 GATGCCATGTCCCAGACATGGTCTTACACT-G-ATAATCTCGTA-GCC
1 GATGCCATGTCCCAGACATGGTCTTACACTGGCTTAATCTTG-AGGCC
*
52498776 GATG-CATGTCCCAGACAT-GTTTTACACTGGCTTACATCTTGAGGCC
1 GATGCCATGTCCCAGACATGGTCTTACACTGGCTTA-ATCTTGAGGCC
* * * *
52498822 GATG-CATGTCCCAGGCAT-GTCTTACACTAGCTCTTATC-TGAGTGTC
1 GATGCCATGTCCCAGACATGGTCTTACACTGGCT-TAATCTTGAG-GCC
*
52498868 GATGCCATGTCCAAGACATGGTCTTACACTGGCT
1 GATGCCATGTCCCAGACATGGTCTTACACTGGCT
52498902 CACAAATAAC
Statistics
Matches: 217, Mismatches: 35, Indels: 34
0.76 0.12 0.12
Matches are distributed among these distances:
43 9 0.04
44 17 0.08
45 17 0.08
46 61 0.28
47 29 0.13
48 14 0.06
49 36 0.17
50 32 0.15
51 2 0.01
ACGTcount: A:0.24, C:0.28, G:0.20, T:0.28
Consensus pattern (47 bp):
GATGCCATGTCCCAGACATGGTCTTACACTGGCTTAATCTTGAGGCC
Found at i:52498961 original size:22 final size:22
Alignment explanation
Indices: 52498910--52498951 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
52498900 CTCACAAATA
52498910 ACCCGAATGTCATGGCATGAAT
1 ACCCGAATGTCATGGCATGAAT
52498932 ACCCGAATGTCATGGCATGA
1 ACCCGAATGTCATGGCATGA
52498952 TTATTCGAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.31, C:0.24, G:0.24, T:0.21
Consensus pattern (22 bp):
ACCCGAATGTCATGGCATGAAT
Found at i:52500578 original size:40 final size:40
Alignment explanation
Indices: 52500534--52500795 Score: 337
Period size: 39 Copynumber: 6.7 Consensus size: 40
52500524 GCTCCTCGTT
* *
52500534 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAAT-TCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGT-ATCTCGCA
* * *
52500574 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
52500614 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
52500653 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
52500692 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
* *
52500731 CAAATGCCTTC-GGATCTTAGTCCGGATATT-GTCA-CTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGA-ATTAGT-ATC-TCGCA
52500772 C-AA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
52500796 CATCATTCAA
Statistics
Matches: 205, Mismatches: 9, Indels: 17
0.89 0.04 0.07
Matches are distributed among these distances:
38 2 0.01
39 128 0.62
40 64 0.31
41 11 0.05
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
Found at i:52508802 original size:29 final size:29
Alignment explanation
Indices: 52508768--52508841 Score: 96
Period size: 29 Copynumber: 2.6 Consensus size: 29
52508758 TAATCAACCA
*
52508768 CGCACACTTAGTGCCATGTACTTT-AAACT
1 CGCACACTTAGTGCCATGCA-TTTCAAACT
**
52508797 CGCACACTTAGTGCCATGCATTTCAAGTT
1 CGCACACTTAGTGCCATGCATTTCAAACT
*
52508826 CGCACACCTAGTGCCA
1 CGCACACTTAGTGCCA
52508842 ATCTCACAAC
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
28 3 0.08
29 37 0.93
ACGTcount: A:0.26, C:0.31, G:0.16, T:0.27
Consensus pattern (29 bp):
CGCACACTTAGTGCCATGCATTTCAAACT
Found at i:52527333 original size:18 final size:18
Alignment explanation
Indices: 52527291--52527335 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 18
52527281 TGGACTCTTC
52527291 CTTTTCTTTCTTCAATCT
1 CTTTTCTTTCTTCAATCT
*
52527309 CTCTTTCTTT-TTCAACTTT
1 CT-TTTCTTTCTTCAA-TCT
52527328 CTTTTCTT
1 CTTTTCTT
52527336 GCTCACATGA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
18 13 0.54
19 11 0.46
ACGTcount: A:0.09, C:0.27, G:0.00, T:0.64
Consensus pattern (18 bp):
CTTTTCTTTCTTCAATCT
Found at i:52529931 original size:50 final size:50
Alignment explanation
Indices: 52529867--52529992 Score: 198
Period size: 50 Copynumber: 2.5 Consensus size: 50
52529857 TGCAACCTTA
* *
52529867 AACTAACATGGGAGTTACATAATGCAAGTCATTATTGATGATGCTTATTT
1 AACTAACATGGGAGTTACATAATGCAAGCCATTATTGATGATGCTTACTT
* *
52529917 AACTAACATGGGAGTTACATAATACAAGCCATTATTTATGATGCTTACTT
1 AACTAACATGGGAGTTACATAATGCAAGCCATTATTGATGATGCTTACTT
**
52529967 AACTAACATGAAAGTTACATAATGCA
1 AACTAACATGGGAGTTACATAATGCA
52529993 TTACTTTATA
Statistics
Matches: 69, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
50 69 1.00
ACGTcount: A:0.38, C:0.14, G:0.15, T:0.33
Consensus pattern (50 bp):
AACTAACATGGGAGTTACATAATGCAAGCCATTATTGATGATGCTTACTT
Found at i:52531840 original size:18 final size:19
Alignment explanation
Indices: 52531793--52531842 Score: 61
Period size: 18 Copynumber: 2.7 Consensus size: 19
52531783 TTTCTTGGAC
52531793 ACTTCCTTTTCTTTCTTCA
1 ACTTCCTTTTCTTTCTTCA
52531812 A--TCTCTCTTTCTTT-TTCA
1 ACTTC-CT-TTTCTTTCTTCA
52531830 ACTTCCTTTTCTT
1 ACTTCCTTTTCTT
52531843 GCTCACATGA
Statistics
Matches: 27, Mismatches: 0, Indels: 9
0.75 0.00 0.25
Matches are distributed among these distances:
17 2 0.07
18 13 0.48
19 10 0.37
20 2 0.07
ACGTcount: A:0.10, C:0.30, G:0.00, T:0.60
Consensus pattern (19 bp):
ACTTCCTTTTCTTTCTTCA
Found at i:52531942 original size:20 final size:20
Alignment explanation
Indices: 52531910--52531956 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 20
52531900 TTTTTATTTC
52531910 CTTTTCTTTTTCT-TCCATGT
1 CTTTT-TTTTTCTCTCCATGT
* *
52531930 CTTTTTTTCTTCTCTCGATTT
1 CTTTTTTT-TTCTCTCCATGT
52531951 CTTTTT
1 CTTTTT
52531957 CTCGTTTCTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
19 3 0.13
20 9 0.39
21 11 0.48
ACGTcount: A:0.04, C:0.23, G:0.04, T:0.68
Consensus pattern (20 bp):
CTTTTTTTTTCTCTCCATGT
Found at i:52535396 original size:20 final size:20
Alignment explanation
Indices: 52535366--52535413 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
52535356 GCATCAATGA
52535366 TGCATAACAGAGGCACCGAAG
1 TGCA-AACAGAGGCACCGAAG
52535387 TGCAAACAGAGGCACCGAAG
1 TGCAAACAGAGGCACCGAAG
52535407 TGCAAAC
1 TGCAAAC
52535414 CAGTACAAGC
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 23 0.85
21 4 0.15
ACGTcount: A:0.40, C:0.25, G:0.27, T:0.08
Consensus pattern (20 bp):
TGCAAACAGAGGCACCGAAG
Found at i:52536582 original size:40 final size:40
Alignment explanation
Indices: 52536527--52536606 Score: 135
Period size: 40 Copynumber: 2.0 Consensus size: 40
52536517 CGTCTTCCAA
*
52536527 TCTTTACGAGTCCTCGGGCTCTGTGAGAGACA-GGGAAAG
1 TCTTTACGAGTCCTCGAGCTCTGTGAGAGACAGGGGAAAG
52536566 NTCTTTACGAGTCCTCGAGCTCTGTGAGAGACAGGGGAAAG
1 -TCTTTACGAGTCCTCGAGCTCTGTGAGAGACAGGGGAAAG
52536607 AGAGGGGTAA
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
40 31 0.82
41 7 0.18
ACGTcount: A:0.24, C:0.20, G:0.33, T:0.23
Consensus pattern (40 bp):
TCTTTACGAGTCCTCGAGCTCTGTGAGAGACAGGGGAAAG
Found at i:52545281 original size:49 final size:49
Alignment explanation
Indices: 52545228--52545351 Score: 194
Period size: 49 Copynumber: 2.5 Consensus size: 49
52545218 CTGGTACGCA
* * * * *
52545228 TAGTAGCCAGAACTTAGTACTACACTTGCGACCAATTATCCGGTACACG
1 TAGTAGCCTGCACTTAGTACTACACATGCCACCAATTATCCGATACACG
*
52545277 TAGTAGCCTGCACTTAGTACTACACATGCCACCAATTATCTGATACACG
1 TAGTAGCCTGCACTTAGTACTACACATGCCACCAATTATCCGATACACG
52545326 TAGTAGCCTGCACTTAGTACTACACA
1 TAGTAGCCTGCACTTAGTACTACACA
52545352 CGTGACCTCA
Statistics
Matches: 69, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
49 69 1.00
ACGTcount: A:0.31, C:0.27, G:0.16, T:0.26
Consensus pattern (49 bp):
TAGTAGCCTGCACTTAGTACTACACATGCCACCAATTATCCGATACACG
Found at i:52545553 original size:27 final size:27
Alignment explanation
Indices: 52545523--52545576 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
52545513 TCATACAACC
* *
52545523 CATGTAATAGTAATTTAACATTCAATT
1 CATGTAACAATAATTTAACATTCAATT
**
52545550 CATGTAACAATAATTTGCCATTCAATT
1 CATGTAACAATAATTTAACATTCAATT
52545577 TCACATGACA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.39, C:0.15, G:0.07, T:0.39
Consensus pattern (27 bp):
CATGTAACAATAATTTAACATTCAATT
Found at i:52553928 original size:39 final size:39
Alignment explanation
Indices: 52553880--52553965 Score: 136
Period size: 39 Copynumber: 2.2 Consensus size: 39
52553870 CGGCAATTAA
52553880 CCTGCTAGGTATAAACCTAAACTTATCACCGGCACGAGG
1 CCTGCTAGGTATAAACCTAAACTTATCACCGGCACGAGG
* * * *
52553919 CCTGTTAGGTATAAACTTGAATTTATCACCGGCACGAGG
1 CCTGCTAGGTATAAACCTAAACTTATCACCGGCACGAGG
52553958 CCTGCTAG
1 CCTGCTAG
52553966 ACATTAAGTC
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 42 1.00
ACGTcount: A:0.28, C:0.26, G:0.22, T:0.24
Consensus pattern (39 bp):
CCTGCTAGGTATAAACCTAAACTTATCACCGGCACGAGG
Found at i:52557082 original size:28 final size:28
Alignment explanation
Indices: 52557042--52557097 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
52557032 GGTACGAAAC
*
52557042 ACTAAGGAAGATGATGCCTTATTTTTTT
1 ACTAAGGAAGATGATGCCTCATTTTTTT
52557070 ACTAAGGAAGATGATGCCTCATTTTTTT
1 ACTAAGGAAGATGATGCCTCATTTTTTT
52557098 TACTTTATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.29, C:0.12, G:0.18, T:0.41
Consensus pattern (28 bp):
ACTAAGGAAGATGATGCCTCATTTTTTT
Found at i:52563911 original size:29 final size:29
Alignment explanation
Indices: 52563869--52563967 Score: 146
Period size: 29 Copynumber: 3.4 Consensus size: 29
52563859 CATGAAATTG
52563869 GCACTAAGTGTGCGGGTTCAAATTGTATA
1 GCACTAAGTGTGCGGGTTCAAATTGTATA
*
52563898 GCACTAAGTGTGCGGGTTCAAGTTGTATA
1 GCACTAAGTGTGCGGGTTCAAATTGTATA
* * *
52563927 GCACTAAGTGTGCGAGTTC-GATTATATA
1 GCACTAAGTGTGCGGGTTCAAATTGTATA
*
52563955 ACACTAAGTGTGC
1 GCACTAAGTGTGC
52563968 AGACTTACTA
Statistics
Matches: 64, Mismatches: 6, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
28 18 0.28
29 46 0.72
ACGTcount: A:0.27, C:0.15, G:0.27, T:0.30
Consensus pattern (29 bp):
GCACTAAGTGTGCGGGTTCAAATTGTATA
Found at i:52565950 original size:52 final size:52
Alignment explanation
Indices: 52565876--52565980 Score: 192
Period size: 52 Copynumber: 2.0 Consensus size: 52
52565866 GCGTAAGGAA
52565876 TTCTTAGAACTCAAGCAAGGCCGTATGACAGTATCTGAATACGAACATGAAT
1 TTCTTAGAACTCAAGCAAGGCCGTATGACAGTATCTGAATACGAACATGAAT
* *
52565928 TTCTTGGAACTCAAGCAAGGCCGTATGACTGTATCTGAATACGAACATGAAT
1 TTCTTAGAACTCAAGCAAGGCCGTATGACAGTATCTGAATACGAACATGAAT
52565980 T
1 T
52565981 CGTAAGACTC
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 51 1.00
ACGTcount: A:0.34, C:0.19, G:0.20, T:0.27
Consensus pattern (52 bp):
TTCTTAGAACTCAAGCAAGGCCGTATGACAGTATCTGAATACGAACATGAAT
Found at i:52577894 original size:21 final size:21
Alignment explanation
Indices: 52577853--52577894 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
52577843 AAGAAAGGAA
* **
52577853 ATAATAAAAGAAATACTAAGG
1 ATAATAAAAGAAAAAAAAAGG
52577874 ATAATAAAAGAAAAAAAAAGG
1 ATAATAAAAGAAAAAAAAAGG
52577895 GGTTATTACC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.69, C:0.02, G:0.14, T:0.14
Consensus pattern (21 bp):
ATAATAAAAGAAAAAAAAAGG
Found at i:52578041 original size:66 final size:66
Alignment explanation
Indices: 52577940--52578064 Score: 250
Period size: 66 Copynumber: 1.9 Consensus size: 66
52577930 AAGAAAAAGA
52577940 GGGGGGGCAAAGGCATTCGGCCTTTTGAATGAAGAGAAGGTTAGTAAATTTTGTTAATCGGGGGG
1 GGGGGGGCAAAGGCATTCGGCCTTTTGAATGAAGAGAAGGTTAGTAAATTTTGTTAATCGGGGGG
52578005 G
66 G
52578006 GGGGGGGCAAAGGCATTCGGCCTTTTGAATGAAGAGAAGGTTAGTAAATTTTGTTAATC
1 GGGGGGGCAAAGGCATTCGGCCTTTTGAATGAAGAGAAGGTTAGTAAATTTTGTTAATC
52578065 TTTCTTTTGA
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
66 59 1.00
ACGTcount: A:0.27, C:0.10, G:0.36, T:0.27
Consensus pattern (66 bp):
GGGGGGGCAAAGGCATTCGGCCTTTTGAATGAAGAGAAGGTTAGTAAATTTTGTTAATCGGGGGG
G
Found at i:52581035 original size:27 final size:27
Alignment explanation
Indices: 52580116--52581022 Score: 1663
Period size: 27 Copynumber: 33.6 Consensus size: 27
52580106 ATATCGAGTC
* * *
52580116 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAAAT
52580143 CGCACACTTAGTGCTACATAATCAAAT
1 CGCACACTTAGTGCTACATAATCAAAT
52580170 CGCACACTTAGTGCTACATAATCAAAT
1 CGCACACTTAGTGCTACATAATCAAAT
52580197 CGCACACTTAGTGCTACATAATCAAAT
1 CGCACACTTAGTGCTACATAATCAAAT
52580224 CGCACACTTAGTGCTACATAATCAAAT
1 CGCACACTTAGTGCTACATAATCAAAT
52580251 CGCACACTTAGTGCTACATAATCAAAT
1 CGCACACTTAGTGCTACATAATCAAAT
52580278 CGCACACTTAGTGCTACATAATCAAAT
1 CGCACACTTAGTGCTACATAATCAAAT
52580305 CGCACACTTAGTGCTACATAATCAAAT
1 CGCACACTTAGTGCTACATAATCAAAT
52580332 CGCACACTTAGTGCTACATAATCAAAT
1 CGCACACTTAGTGCTACATAATCAAAT
52580359 CGCACACTTAGTGCTACATAATCAAAT
1 CGCACACTTAGTGCTACATAATCAAAT
52580386 CGCACACTTAGTGCTACATAATCAAAT
1 CGCACACTTAGTGCTACATAATCAAAT
52580413 CGCACACTTAGTGCTACATAATCAAAT
1 CGCACACTTAGTGCTACATAATCAAAT
52580440 CGCACACTTAGTGCTACATAATCAAAT
1 CGCACACTTAGTGCTACATAATCAAAT
52580467 CGCACACTTAGTGCTACATAATCAAAT
1 CGCACACTTAGTGCTACATAATCAAAT
52580494 CGCACACTTAGTGCTACATAATCAAAT
1 CGCACACTTAGTGCTACATAATCAAAT
52580521 CGCACACTTAGTGCTACATAATCAAAT
1 CGCACACTTAGTGCTACATAATCAAAT
52580548 CGCACACTTAGTGCTACATAATCAAAT
1 CGCACACTTAGTGCTACATAATCAAAT
52580575 CGCACACTTAGTGCTACATAATCAAAT
1 CGCACACTTAGTGCTACATAATCAAAT
52580602 CGCACACTTAGTGCTACATAATCAAAT
1 CGCACACTTAGTGCTACATAATCAAAT
52580629 CGCACACTTAGTGCTACATAATCAAAT
1 CGCACACTTAGTGCTACATAATCAAAT
52580656 CGCACACTTAGTGCTACATAATCAAAT
1 CGCACACTTAGTGCTACATAATCAAAT
52580683 CGCACACTTAGTGCTACATAATCAAAT
1 CGCACACTTAGTGCTACATAATCAAAT
52580710 CGCACACTTAGTGCTACATAATCAAAT
1 CGCACACTTAGTGCTACATAATCAAAT
52580737 CGCACACTTAGTGCTACATAATCAAAT
1 CGCACACTTAGTGCTACATAATCAAAT
52580764 CGCACACTTAGTGCTACATAATCAAAT
1 CGCACACTTAGTGCTACATAATCAAAT
52580791 CGCACACTTAGTGCTACATAATCAAAT
1 CGCACACTTAGTGCTACATAATCAAAT
52580818 CGCACACTTAGTGCTACATAATCAAAT
1 CGCACACTTAGTGCTACATAATCAAAT
52580845 CGCACACTTAGTGCTACATAATCAAAT
1 CGCACACTTAGTGCTACATAATCAAAT
52580872 CGCACACTTAGTGCTACATAATCAAAT
1 CGCACACTTAGTGCTACATAATCAAAT
*
52580899 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAATCAAA-T
** ** *
52580927 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAAAT
* **
52580954 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAATCAAAT
* *
52580981 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAATCAAAT
52581008 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
52581023 GTACAATTTA
Statistics
Matches: 861, Mismatches: 16, Indels: 6
0.98 0.02 0.01
Matches are distributed among these distances:
27 837 0.97
28 24 0.03
ACGTcount: A:0.36, C:0.26, G:0.12, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAAAT
Found at i:52593398 original size:48 final size:48
Alignment explanation
Indices: 52593334--52593457 Score: 160
Period size: 48 Copynumber: 2.6 Consensus size: 48
52593324 AAGTGTCTCG
* *
52593334 CGACAT-CAATCCCGATGTTGCAACATCAGTATCTTGCAGAGGTGTCA
1 CGACATGCAACCCCGATGTCGCAACATCAGTATCTTGCAGAGGTGTCA
** *
52593381 CGACATGCAACCCCGATGTCGTGACATCAGTATCTTGTAGAGGTGTCA
1 CGACATGCAACCCCGATGTCGCAACATCAGTATCTTGCAGAGGTGTCA
* * * *
52593429 CGACATGGAACCTCAATGTCGCAATATCA
1 CGACATGCAACCCCGATGTCGCAACATCA
52593458 CTACAAATTT
Statistics
Matches: 65, Mismatches: 11, Indels: 1
0.84 0.14 0.01
Matches are distributed among these distances:
47 6 0.09
48 59 0.91
ACGTcount: A:0.28, C:0.26, G:0.22, T:0.24
Consensus pattern (48 bp):
CGACATGCAACCCCGATGTCGCAACATCAGTATCTTGCAGAGGTGTCA
Found at i:52596857 original size:33 final size:33
Alignment explanation
Indices: 52596814--52596906 Score: 159
Period size: 33 Copynumber: 2.8 Consensus size: 33
52596804 ATAGTGCTTG
52596814 CAGTAATAGTCTGGGCCCGAGCCCTATTCAGTAT
1 CAGT-ATAGTCTGGGCCCGAGCCCTATTCAGTAT
52596848 CAGTATAGTCTGGGCCCGAGCCCTATTCAGTAT
1 CAGTATAGTCTGGGCCCGAGCCCTATTCAGTAT
**
52596881 CAGTATAGTCTGGGCCTTAGCCCTAT
1 CAGTATAGTCTGGGCCCGAGCCCTAT
52596907 ACAATAATAG
Statistics
Matches: 57, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
33 53 0.93
34 4 0.07
ACGTcount: A:0.22, C:0.27, G:0.24, T:0.28
Consensus pattern (33 bp):
CAGTATAGTCTGGGCCCGAGCCCTATTCAGTAT
Found at i:52597131 original size:27 final size:27
Alignment explanation
Indices: 52597101--52597154 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
52597091 AGCTGCCTGA
*
52597101 AACAGTAAATGTGGCAAAGCCACCAGT
1 AACAGTAAATGTGACAAAGCCACCAGT
* * *
52597128 AACAGTGAATGTGACATAGTCACCAGT
1 AACAGTAAATGTGACAAAGCCACCAGT
52597155 CCAGTACTGC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.39, C:0.20, G:0.22, T:0.19
Consensus pattern (27 bp):
AACAGTAAATGTGACAAAGCCACCAGT
Found at i:52597343 original size:27 final size:27
Alignment explanation
Indices: 52597313--52597399 Score: 79
Period size: 27 Copynumber: 3.2 Consensus size: 27
52597303 ACCATACAGG
*
52597313 TACCCTACAAGGGAATTACTGTCATTT
1 TACCCTACAGGGGAATTACTGTCATTT
* **
52597340 TACCCT-CTAGGGGCATTACAATCATTT
1 TACCCTAC-AGGGGAATTACTGTCATTT
* * *
52597367 TACCTTACAGGGGTAGTA-TGGTCATTT
1 TACCCTACAGGGGAATTACT-GTCATTT
52597394 TACCCT
1 TACCCT
52597400 TAAGGGGTAT
Statistics
Matches: 47, Mismatches: 10, Indels: 6
0.75 0.16 0.10
Matches are distributed among these distances:
26 1 0.02
27 45 0.96
28 1 0.02
ACGTcount: A:0.25, C:0.23, G:0.17, T:0.34
Consensus pattern (27 bp):
TACCCTACAGGGGAATTACTGTCATTT
Found at i:52597418 original size:27 final size:27
Alignment explanation
Indices: 52597334--52597424 Score: 91
Period size: 27 Copynumber: 3.4 Consensus size: 27
52597324 GGAATTACTG
* *
52597334 TCATTTTACCCTCT-AGGGGCATTACAA
1 TCATTTTACCCT-TAAGGGGTATTGCAA
*
52597361 TCATTTTA-CCTTACAGGGGTAGTATG--G
1 TCATTTTACCCTTA-AGGGGTA-T-TGCAA
52597388 TCATTTTACCCTTAAGGGGTATTGCAA
1 TCATTTTACCCTTAAGGGGTATTGCAA
52597415 TCATTTTACC
1 TCATTTTACC
52597425 AATTTTGGGG
Statistics
Matches: 53, Mismatches: 4, Indels: 14
0.75 0.06 0.20
Matches are distributed among these distances:
25 3 0.06
26 4 0.08
27 39 0.74
28 6 0.11
29 1 0.02
ACGTcount: A:0.24, C:0.21, G:0.18, T:0.37
Consensus pattern (27 bp):
TCATTTTACCCTTAAGGGGTATTGCAA
Found at i:52602815 original size:29 final size:28
Alignment explanation
Indices: 52602760--52602874 Score: 113
Period size: 29 Copynumber: 4.0 Consensus size: 28
52602750 GTGAGCATGA
* * *
52602760 ATATGAATGTGACTGGGCCTAACGGGCC
1 ATATAAATGTGATTGGGCCTAATGGGCC
52602788 ATATAAATGTGATTTGGGCCTAATGGGCC
1 ATATAAATGTGA-TTGGGCCTAATGGGCC
* * * * *
52602817 ATATACAGGAGATTTGGGCCTAATAGGCG
1 ATATAAATGTGA-TTGGGCCTAATGGGCC
* * *
52602846 ATATGAATATGATTGGGCTTAATGGGCC
1 ATATAAATGTGATTGGGCCTAATGGGCC
52602874 A
1 A
52602875 GATACAGGTA
Statistics
Matches: 70, Mismatches: 16, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
28 25 0.36
29 45 0.64
ACGTcount: A:0.29, C:0.15, G:0.30, T:0.27
Consensus pattern (28 bp):
ATATAAATGTGATTGGGCCTAATGGGCC
Found at i:52602872 original size:57 final size:58
Alignment explanation
Indices: 52602773--52602882 Score: 150
Period size: 57 Copynumber: 1.9 Consensus size: 58
52602763 TGAATGTGAC
* * *
52602773 TGGGCCTAACGGGCCATATAAATGTGATTTGGGCCTAATGGGCCATATACAGGAGATT
1 TGGGCCTAACAGGCCATATAAATATGATTTGGGCCTAATGGGCCAGATACAGGAGATT
* * * *
52602831 TGGGCCTAATAGGCGATATGAATATGA-TTGGGCTTAATGGGCCAGATACAGG
1 TGGGCCTAACAGGCCATATAAATATGATTTGGGCCTAATGGGCCAGATACAGG
52602883 TATGTGAATT
Statistics
Matches: 45, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
57 23 0.51
58 22 0.49
ACGTcount: A:0.28, C:0.15, G:0.31, T:0.25
Consensus pattern (58 bp):
TGGGCCTAACAGGCCATATAAATATGATTTGGGCCTAATGGGCCAGATACAGGAGATT
Found at i:52607315 original size:28 final size:29
Alignment explanation
Indices: 52607205--52607319 Score: 153
Period size: 29 Copynumber: 4.0 Consensus size: 29
52607195 GTGAGCATGA
* *
52607205 ATATGAATGTGA-CTGGGCCTAATGCGCC
1 ATATGAATGTGATTTGGGCCTAATGGGCC
*
52607233 ATATAAATGTGATTTGGGCCTAATGGGCC
1 ATATGAATGTGATTTGGGCCTAATGGGCC
* *
52607262 ATATGCAGGTGATTTGGGCCTAATGGGCC
1 ATATGAATGTGATTTGGGCCTAATGGGCC
* *
52607291 ATATGAATATGA-TTGGGCTTAATGGGCC
1 ATATGAATGTGATTTGGGCCTAATGGGCC
52607319 A
1 A
52607320 GATACAGGTA
Statistics
Matches: 76, Mismatches: 10, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
28 27 0.36
29 49 0.64
ACGTcount: A:0.26, C:0.16, G:0.30, T:0.29
Consensus pattern (29 bp):
ATATGAATGTGATTTGGGCCTAATGGGCC
Found at i:52609149 original size:20 final size:20
Alignment explanation
Indices: 52609120--52609157 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
52609110 TGACACCCTC
*
52609120 AAACCCTAAAACCTAAACAT
1 AAACCATAAAACCTAAACAT
*
52609140 AAACCATAAACCCTAAAC
1 AAACCATAAAACCTAAAC
52609158 CCTACTCGGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.55, C:0.32, G:0.00, T:0.13
Consensus pattern (20 bp):
AAACCATAAAACCTAAACAT
Found at i:52609159 original size:7 final size:7
Alignment explanation
Indices: 52609114--52609161 Score: 53
Period size: 7 Copynumber: 6.9 Consensus size: 7
52609104 CTTAATTGAC
52609114 ACCCTCAA
1 ACCCT-AA
52609122 ACCCTAA
1 ACCCTAA
*
52609129 AACCTAA
1 ACCCTAA
*
52609136 A-CATAA
1 ACCCTAA
*
52609142 ACCATAA
1 ACCCTAA
52609149 ACCCTAA
1 ACCCTAA
52609156 ACCCTA
1 ACCCTA
52609162 CTCGGTCGAA
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
6 5 0.14
7 26 0.72
8 5 0.14
ACGTcount: A:0.48, C:0.38, G:0.00, T:0.15
Consensus pattern (7 bp):
ACCCTAA
Found at i:52609454 original size:20 final size:20
Alignment explanation
Indices: 52609414--52609454 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
52609404 GTTATTATTT
*
52609414 TGTTTTGTTCAATTGAATGG
1 TGTTTTGTTCAATGGAATGG
52609434 TGTTTTGTTCAA-GGAACTGG
1 TGTTTTGTTCAATGGAA-TGG
52609454 T
1 T
52609455 CGGTCTAGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 3 0.16
20 16 0.84
ACGTcount: A:0.20, C:0.07, G:0.27, T:0.46
Consensus pattern (20 bp):
TGTTTTGTTCAATGGAATGG
Found at i:52610905 original size:43 final size:42
Alignment explanation
Indices: 52610858--52611016 Score: 153
Period size: 42 Copynumber: 3.7 Consensus size: 42
52610848 AATGCCAACG
* *
52610858 TCCCAGACATGGCCTTACATGTAATTTAGTATCGATGCCTCTA
1 TCCCAGACATGGTCTTACACGTAATTTAG-ATCGATGCCTCTA
* * * * * *
52610901 TCCCAGACAGGGTCTTATACG-AAATCAGATACGATGCCTATG
1 TCCCAGACATGGTCTTACACGTAATTTAGAT-CGATGCCTCTA
*
52610943 TCCCAGACATGGTCTTACACGTAAATTTCAAATCGATG-C-CTA
1 TCCCAGACATGGTCTTACACGT-AATTT-AGATCGATGCCTCTA
* *
52610985 TCCCAGACACGGTCTTACACGATAATTCAGAT
1 TCCCAGACATGGTCTTACACG-TAATTTAGAT
52611017 TAATACCAAT
Statistics
Matches: 93, Mismatches: 18, Indels: 12
0.76 0.15 0.10
Matches are distributed among these distances:
41 5 0.05
42 58 0.62
43 19 0.20
44 8 0.09
45 3 0.03
ACGTcount: A:0.30, C:0.26, G:0.17, T:0.28
Consensus pattern (42 bp):
TCCCAGACATGGTCTTACACGTAATTTAGATCGATGCCTCTA
Found at i:52630710 original size:44 final size:43
Alignment explanation
Indices: 52630578--52630726 Score: 153
Period size: 42 Copynumber: 3.5 Consensus size: 43
52630568 TAATGCCAAC
* * *
52630578 GTCCCAGACGTGGTCTTACATGT-AATTCAGTATCGATGCCTCT
1 GTCCCAGACATGGTCTTACATGTAAATTCA-AATCGATGCCTGT
* * * * *
52630621 GTCCCAGACAGGGCCTTATACG-AAA-TCAGATACGATGCC-GAT
1 GTCCCAGACATGGTCTTACATGTAAATTCAAAT-CGATGCCTG-T
52630663 GTCCCAGACATGGTCTTACATGTAAATTTCAAATCGATGCCTGT
1 GTCCCAGACATGGTCTTACATGTAAA-TTCAAATCGATGCCTGT
*
52630707 GTCCCAGACACGGTCTTACA
1 GTCCCAGACATGGTCTTACA
52630727 CAATAATTCA
Statistics
Matches: 86, Mismatches: 13, Indels: 13
0.77 0.12 0.12
Matches are distributed among these distances:
41 2 0.02
42 29 0.34
43 22 0.26
44 27 0.31
45 6 0.07
ACGTcount: A:0.26, C:0.26, G:0.21, T:0.27
Consensus pattern (43 bp):
GTCCCAGACATGGTCTTACATGTAAATTCAAATCGATGCCTGT
Found at i:52636360 original size:93 final size:93
Alignment explanation
Indices: 52636201--52636372 Score: 263
Period size: 93 Copynumber: 1.8 Consensus size: 93
52636191 CGGCCATAAG
* * * * *
52636201 CGAACTCATACTCAACTCAATGAGCTCGGGCGTTCGCATCCATGAGTGAACTCGAACTCAACTCA
1 CGAACTCAGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGAACTCAACTCA
52636266 ACGAGTTCGGATGCCTAGTTACATCTCA
66 ACGAGTTCGGATGCCTAGTTACATCTCA
* * * *
52636294 CGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCAGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGAACTCAACTCA
52636359 ACGAGTTCGGATGC
66 ACGAGTTCGGATGC
52636373 TCAACCATCC
Statistics
Matches: 70, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
93 70 1.00
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.23
Consensus pattern (93 bp):
CGAACTCAGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGAACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATCTCA
Found at i:52636361 original size:46 final size:46
Alignment explanation
Indices: 52636194--52636369 Score: 169
Period size: 46 Copynumber: 3.8 Consensus size: 46
52636184 TGTAACCCGG
** * * * * *
52636194 CCATAAGCGAACTCATACTCAACTCAATGAGCTCGGGCGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCAT
* * * * *
52636240 CCATGAGTGAACTCGAACTCAACTCAACGAGTTCGGATGCCTAGTTACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA---C-ATTTGCAT
*
52636290 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCAT
*
52636333 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA
52636370 TGCTCAACCA
Statistics
Matches: 105, Mismatches: 18, Indels: 14
0.77 0.13 0.10
Matches are distributed among these distances:
43 6 0.06
44 2 0.02
45 2 0.02
46 59 0.56
47 28 0.27
48 2 0.02
49 2 0.02
50 4 0.04
ACGTcount: A:0.30, C:0.28, G:0.20, T:0.22
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCAT
Found at i:52636388 original size:46 final size:45
Alignment explanation
Indices: 52636245--52636388 Score: 127
Period size: 46 Copynumber: 3.1 Consensus size: 45
52636235 CGCATCCATG
*
52636245 AGTGAACTCGAACTCAACTCAACGAGTTCGGATGC-CTAGTTA-CATCT
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTC-A---ACCATCT
* * * *
52636292 CA-CGAACTCGGACTCAACTCAACGAGTTCGGACAT-TTGCATCCAT-A
1 -AGTGAACTCGGACTCAACTCAACGAGTTCGG--ATGCT-CAACCATCT
52636338 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATCCT
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCAT-CT
52636384 AGTGA
1 AGTGA
52636389 CATGTCACTT
Statistics
Matches: 78, Mismatches: 9, Indels: 20
0.73 0.08 0.19
Matches are distributed among these distances:
44 8 0.10
45 2 0.03
46 33 0.42
47 30 0.38
48 1 0.01
49 3 0.04
50 1 0.01
ACGTcount: A:0.30, C:0.28, G:0.19, T:0.23
Consensus pattern (45 bp):
AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATCT
Found at i:52636836 original size:30 final size:30
Alignment explanation
Indices: 52636802--52636876 Score: 123
Period size: 30 Copynumber: 2.5 Consensus size: 30
52636792 TTTGGAAAAA
* * *
52636802 TTACAATTTTTCCCCTAAACTTTTGCATAT
1 TTACACTTTTGCCCCTAAACTTTTACATAT
52636832 TTACACTTTTGCCCCTAAACTTTTACATAT
1 TTACACTTTTGCCCCTAAACTTTTACATAT
52636862 TTACACTTTTGCCCC
1 TTACACTTTTGCCCC
52636877 AAAGCTCGTA
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 42 1.00
ACGTcount: A:0.24, C:0.28, G:0.04, T:0.44
Consensus pattern (30 bp):
TTACACTTTTGCCCCTAAACTTTTACATAT
Found at i:52642670 original size:48 final size:48
Alignment explanation
Indices: 52642618--52642838 Score: 289
Period size: 48 Copynumber: 4.6 Consensus size: 48
52642608 TATCGGTGCC
* * * * **
52642618 GATGCCATGTCCTAGACATAGTCTTACACTAGCACACATGTCATTACT
1 GATGCCATGTCCCAGACATGGTCTTACACTGGCACACATATCAACACT
* *
52642666 GATGCCATGTCCCAGACATGGTCTTACATTGGCACACATATCAACACC
1 GATGCCATGTCCCAGACATGGTCTTACACTGGCACACATATCAACACT
* * * * *
52642714 AATGCCATGTCCCAGACATGGTCTTATATTGGCATACATATCAACGCT
1 GATGCCATGTCCCAGACATGGTCTTACACTGGCACACATATCAACACT
* * * *
52642762 AATGCCATGTCCTAGACATGGTCTTACACTGGCACATATATCAACGCT
1 GATGCCATGTCCCAGACATGGTCTTACACTGGCACACATATCAACACT
52642810 GATGCCATGTCCCAGACATGGTCTTACAC
1 GATGCCATGTCCCAGACATGGTCTTACAC
52642839 ACGCTCTCAT
Statistics
Matches: 153, Mismatches: 20, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
48 153 1.00
ACGTcount: A:0.29, C:0.28, G:0.17, T:0.27
Consensus pattern (48 bp):
GATGCCATGTCCCAGACATGGTCTTACACTGGCACACATATCAACACT
Found at i:52642719 original size:96 final size:95
Alignment explanation
Indices: 52642619--52642887 Score: 290
Period size: 96 Copynumber: 2.8 Consensus size: 95
52642609 ATCGGTGCCG
* * *
52642619 ATGCCATGTCCTAGACATAGTCTTACACTAGCACACATGTCATTACTGATGCCATGTCCCAGACA
1 ATGCCATGTCCCAGACATGGTCTTACACTAGCACACATATCATT-CTGATGCCATGTCCCAGACA
*
52642684 TGGTCTTACATTGGCACACATATCAACACCA
65 TGGTCTTACACTGGCACACATATCAACACCA
* * * * ** * *
52642715 ATGCCATGTCCCAGACATGGTCTTATATTGGCATACATATCAACGCTAATGCCATGTCCTAGACA
1 ATGCCATGTCCCAGACATGGTCTTACACTAGCACACATATC-ATTCTGATGCCATGTCCCAGACA
* * **
52642780 TGGTCTTACACTGGCACATATATCAACGCTG
65 TGGTCTTACACTGGCACACATATCAACACCA
* * * *
52642811 ATGCCATGTCCCAGACATGGTCTTACAC-ACGCTCTCATCTTGGATGTC-GATGCCATGTCCCAG
1 ATGCCATGTCCCAGACATGGTCTTACACTA-GCACACAT-AT-CAT-TCTGATGCCATGTCCCAG
52642874 ACATGGTCTTACAC
62 ACATGGTCTTACAC
52642888 GGGATCTCAT
Statistics
Matches: 140, Mismatches: 28, Indels: 9
0.79 0.16 0.05
Matches are distributed among these distances:
96 109 0.78
97 30 0.21
98 1 0.01
ACGTcount: A:0.27, C:0.29, G:0.17, T:0.27
Consensus pattern (95 bp):
ATGCCATGTCCCAGACATGGTCTTACACTAGCACACATATCATTCTGATGCCATGTCCCAGACAT
GGTCTTACACTGGCACACATATCAACACCA
Found at i:52645533 original size:43 final size:43
Alignment explanation
Indices: 52645472--52645673 Score: 262
Period size: 43 Copynumber: 4.7 Consensus size: 43
52645462 CATGTGTGTG
* * *
52645472 CGTGTAAGACCATGTCTGGGACGTTGGCATCGATATGTCATTA
1 CGTGTAAGACCACGTCTGGGACGTTGGCATCGACATGTGATTA
* * *
52645515 CGTGTAAGACCACATCTGGGACGTTGGAATTGACATGTGATTA
1 CGTGTAAGACCACGTCTGGGACGTTGGCATCGACATGTGATTA
*
52645558 CGTGTAAGACCACGTCTGGGATGTTGGCATCGACATGTGATTA
1 CGTGTAAGACCACGTCTGGGACGTTGGCATCGACATGTGATTA
* * * * * *
52645601 CATGTCAGACCATGTCTAGGATAG-TGGCATCGATATGTGATTA
1 CGTGTAAGACCACGTCTGGGA-CGTTGGCATCGACATGTGATTA
*
52645644 CATGTAAGACCACGTCTGGGACGTTGGCAT
1 CGTGTAAGACCACGTCTGGGACGTTGGCAT
52645674 TGTATGATAT
Statistics
Matches: 137, Mismatches: 20, Indels: 4
0.85 0.12 0.02
Matches are distributed among these distances:
42 1 0.01
43 135 0.99
44 1 0.01
ACGTcount: A:0.25, C:0.18, G:0.28, T:0.28
Consensus pattern (43 bp):
CGTGTAAGACCACGTCTGGGACGTTGGCATCGACATGTGATTA
Found at i:52647058 original size:29 final size:29
Alignment explanation
Indices: 52646940--52647079 Score: 122
Period size: 29 Copynumber: 4.9 Consensus size: 29
52646930 ACATACACGC
*
52646940 ATATGGCCCACTT-GGCCC-AATCTCATTT
1 ATATGGCCCA-TTAGGCCCAAATCACATTT
* * **
52646968 ATATGGCCCATCAGGCCCAATTCACATCC
1 ATATGGCCCATTAGGCCCAAATCACATTT
* * * * * **
52646997 ATACGGCCTATCAGGCCCAATTCATATCC
1 ATATGGCCCATTAGGCCCAAATCACATTT
*
52647026 ATATGGCCCATTAGGCCCAAATCACCTTT
1 ATATGGCCCATTAGGCCCAAATCACATTT
* *
52647055 ATATGGACCGTTAGGCCCAAATCAC
1 ATATGGCCCATTAGGCCCAAATCAC
52647080 CTTATATTCA
Statistics
Matches: 92, Mismatches: 18, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
27 1 0.01
28 15 0.16
29 76 0.83
ACGTcount: A:0.27, C:0.33, G:0.15, T:0.25
Consensus pattern (29 bp):
ATATGGCCCATTAGGCCCAAATCACATTT
Found at i:52647080 original size:29 final size:28
Alignment explanation
Indices: 52647026--52647086 Score: 95
Period size: 29 Copynumber: 2.1 Consensus size: 28
52647016 ATTCATATCC
*
52647026 ATATGGCCCATTAGGCCCAAATCACCTTT
1 ATATGGACCATTAGGCCCAAATCACC-TT
*
52647055 ATATGGACCGTTAGGCCCAAATCACCTT
1 ATATGGACCATTAGGCCCAAATCACCTT
52647083 ATAT
1 ATAT
52647087 TCATGCTCAC
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
28 6 0.20
29 24 0.80
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.28
Consensus pattern (28 bp):
ATATGGACCATTAGGCCCAAATCACCTT
Found at i:52653042 original size:11 final size:11
Alignment explanation
Indices: 52653026--52653058 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
52653016 TAATTAAAGT
52653026 ATATTATATTA
1 ATATTATATTA
52653037 ATATTATATT-
1 ATATTATATTA
52653047 ATATTA-ATTA
1 ATATTATATTA
52653057 AT
1 AT
52653059 TAAATAAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 3 0.14
10 8 0.38
11 10 0.48
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (11 bp):
ATATTATATTA
Found at i:52653187 original size:14 final size:14
Alignment explanation
Indices: 52653163--52653197 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
52653153 TTTAATAATA
52653163 AAATA-AAGAAATG
1 AAATAGAAGAAATG
52653176 AAATAGAAGAAATG
1 AAATAGAAGAAATG
*
52653190 AAAAAGAA
1 AAATAGAA
52653198 AAAAAAGCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 5 0.25
14 15 0.75
ACGTcount: A:0.71, C:0.00, G:0.17, T:0.11
Consensus pattern (14 bp):
AAATAGAAGAAATG
Found at i:52653238 original size:4 final size:4
Alignment explanation
Indices: 52653229--52653259 Score: 53
Period size: 4 Copynumber: 7.5 Consensus size: 4
52653219 AAGAACAGGG
52653229 AGAA AGAA AGGAA AGAA AGAA AGAA AGAA AG
1 AGAA AGAA A-GAA AGAA AGAA AGAA AGAA AG
52653260 GGAGAAAAGG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 22 0.85
5 4 0.15
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (4 bp):
AGAA
Found at i:52654440 original size:17 final size:17
Alignment explanation
Indices: 52654420--52654455 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
52654410 TGAAATAAAA
52654420 TAAAT-TATGAATATGTG
1 TAAATATATGAAT-TGTG
52654437 TAAATATATGAATTGTG
1 TAAATATATGAATTGTG
52654454 TA
1 TA
52654456 TTGATTGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 11 0.61
18 7 0.39
ACGTcount: A:0.42, C:0.00, G:0.17, T:0.42
Consensus pattern (17 bp):
TAAATATATGAATTGTG
Found at i:52654584 original size:15 final size:15
Alignment explanation
Indices: 52654564--52654598 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
52654554 AAGTGAATTT
*
52654564 GAATTGAATTGAATG
1 GAATTGAATGGAATG
52654579 GAATTGAATGGAATG
1 GAATTGAATGGAATG
52654594 GAATT
1 GAATT
52654599 ATGATTAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.40, C:0.00, G:0.29, T:0.31
Consensus pattern (15 bp):
GAATTGAATGGAATG
Found at i:52655382 original size:15 final size:15
Alignment explanation
Indices: 52655362--52655396 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
52655352 AAGTGAATTT
*
52655362 GAATTGAATTGAATG
1 GAATTGAATGGAATG
52655377 GAATTGAATGGAATG
1 GAATTGAATGGAATG
52655392 GAATT
1 GAATT
52655397 ATGATTAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.40, C:0.00, G:0.29, T:0.31
Consensus pattern (15 bp):
GAATTGAATGGAATG
Found at i:52655834 original size:798 final size:798
Alignment explanation
Indices: 52654280--52655875 Score: 3003
Period size: 798 Copynumber: 2.0 Consensus size: 798
52654270 ATCTCGGCTA
**
52654280 AGAAAGGACAAGAAAAAGTCAACGAGAGTTAGCTCAAAAATTACGGCTTGTATTTCTATAACCGG
1 AGAAAGGACAAGAAAAAGTCAACGAGAGTTAGCTCAAAAATTACGGCTTGTATTTCTATAACCCA
52654345 AACTTAATATTTAATTATTTAATTTATTATTTATTATGGATGGTAGGTGCATTGATTAAATTATT
66 AACTTAATATTTAATTATTTAATTTATTATTTATTATGGATGGTAGGTGCATTGATTAAATTATT
52654410 TGAAATAAAATAAATTATGAATATGTGTAAATATATGAATTGTGTATTGATTGAAAAGTGGTTGG
131 TGAAATAAAATAAATTATGAATATGTGTAAATATATGAATTGTGTATTGATTGAAAAGTGGTTGG
* *
52654475 AATTGAACTGAAGTATGATTATATGTGAATTTTTAAAATATATATTGGTATTGAATTGTATACTG
196 AATTGAACCGAAGTATGATTATATGTGAATATTTAAAATATATATTGGTATTGAATTGTATACTG
52654540 ATCAGAAAGTGGAAAAGTGAATTTGAATTGAATTGAATGGAATTGAATGGAATGGAATTATGATT
261 ATCAGAAAGTGGAAAAGTGAATTTGAATTGAATTGAATGGAATTGAATGGAATGGAATTATGATT
52654605 AATTGAAATGTATATTGGTTGGATATTGAAATATGAGAAATTGTGATTGAATTGAAAGCGAATTT
326 AATTGAAATGTATATTGGTTGGATATTGAAATATGAGAAATTGTGATTGAATTGAAAGCGAATTT
*
52654670 GAAATAGAAAAATGATTTGAATACCCTATTAACTAATCGGACTGAATTGGATATAGTTGGCATGC
391 GAAATAGAAAAATGATTTGAATACCCTATTAACTAATCGGACTGAATCGGATATAGTTGGCATGC
52654735 CATAGGATTTGGAAGTGTTCAGGCACTGAGTGCCATATTGGTGTGTTTGGTTGGAATCCGTATAT
456 CATAGGATTTGGAAGTGTTCAGGCACTGAGTGCCATATTGGTGTGTTTGGTTGGAATCCGTATAT
52654800 CCGCCAAAGTCCGAGTCTTGTTAATAGGGGTAAATATGAATATTAAGTAAAATTGGAATAAGAAT
521 CCGCCAAAGTCCGAGTCTTGTTAATAGGGGTAAATATGAATATTAAGTAAAATTGGAATAAGAAT
**
52654865 TAAATTTCCTATTAACTTGTCGGGCTAGTCGGATATAATTGGCATGCCATAGGGTTGGAAGAGTA
586 TAAATTTCCTATTAACTTGTCGGGCTAGTCGGATATAATTGGCATGCCATAGGGTCAGAAGAGTA
*
52654930 CGGGATTTATCGACTTTACCGATCGGGCACTTTATGTGCCGTATTTTAGGCACTTATGTGCTAGT
651 CGAGATTTATCGACTTTACCGATCGGGCACTTTATGTGCCGTATTTTAGGCACTTATGTGCTAGT
52654995 TACTGTTACCGCTACTGCTACAGTTACAGATTCGACACTTTGTGTGTCGAATATTGTTACTACTA
716 TACTGTTACCGCTACTGCTACAGTTACAGATTCGACACTTTGTGTGTCGAATATTGTTACTACTA
52655060 CTGTTACCGATTCGGCAC
781 CTGTTACCGATTCGGCAC
* * * *
52655078 AGAAAGGACAAGACAAAGTCAACGGGAGTTAGCTCGAAAATTACGGTTTGTATTTCTATAACCCA
1 AGAAAGGACAAGAAAAAGTCAACGAGAGTTAGCTCAAAAATTACGGCTTGTATTTCTATAACCCA
*
52655143 AACTTAATATTTAATTATTTAATTTATTATTTATTATGTATGGTAGGTGCATTGATTAAATTATT
66 AACTTAATATTTAATTATTTAATTTATTATTTATTATGGATGGTAGGTGCATTGATTAAATTATT
*
52655208 TGAAATAAAATAAATTATGAATATGTGTAAATATGTGAATTGTGTATTGATTGAAAAGTGGTTGG
131 TGAAATAAAATAAATTATGAATATGTGTAAATATATGAATTGTGTATTGATTGAAAAGTGGTTGG
*
52655273 AATTGAACCGAAGTATGATTATATGTGAATATTTGAAATATATATTGGTATTGAATTGTATACTG
196 AATTGAACCGAAGTATGATTATATGTGAATATTTAAAATATATATTGGTATTGAATTGTATACTG
52655338 ATCAGAAAGTGGAAAAGTGAATTTGAATTGAATTGAATGGAATTGAATGGAATGGAATTATGATT
261 ATCAGAAAGTGGAAAAGTGAATTTGAATTGAATTGAATGGAATTGAATGGAATGGAATTATGATT
*
52655403 AATTGAAATGTATATTGGTTGGATATTGAAATATGAGAAATTGTGATTGAATTGAAAGTGAATTT
326 AATTGAAATGTATATTGGTTGGATATTGAAATATGAGAAATTGTGATTGAATTGAAAGCGAATTT
*
52655468 GAAATAGAAAAATGATTTGAATACCCTATTAACTAATCGGACTGAGTCGGATATAGTTGGCATGC
391 GAAATAGAAAAATGATTTGAATACCCTATTAACTAATCGGACTGAATCGGATATAGTTGGCATGC
52655533 CATAGGATTTGGAAGTGTTCAGGCACTGAGTGCCATATTGGTGTGTTTGGTTGGAATCCGTATAT
456 CATAGGATTTGGAAGTGTTCAGGCACTGAGTGCCATATTGGTGTGTTTGGTTGGAATCCGTATAT
52655598 CCGCCAAAGTCCGAGTCTTGTTAATAGGGGTAAATATGAATATTAAGTAAAATTGGAATAAGAAT
521 CCGCCAAAGTCCGAGTCTTGTTAATAGGGGTAAATATGAATATTAAGTAAAATTGGAATAAGAAT
52655663 TAAATTTCCTATTAACTTGTCGGGCTAGTCGGATATAATTGGCATGCCATAGGGTCAGAAGAGTA
586 TAAATTTCCTATTAACTTGTCGGGCTAGTCGGATATAATTGGCATGCCATAGGGTCAGAAGAGTA
*
52655728 TGAGATTTATCGACTTTACCGATCGGGCACTTTATGTGCCGTATTTTAGGCACTTATGTGCTAGT
651 CGAGATTTATCGACTTTACCGATCGGGCACTTTATGTGCCGTATTTTAGGCACTTATGTGCTAGT
* * *
52655793 TACTGTTACCGCTACTGCTACTGTTACCGATTCGGCACTTTGTGTGTCGAATATTGTTACTACTA
716 TACTGTTACCGCTACTGCTACAGTTACAGATTCGACACTTTGTGTGTCGAATATTGTTACTACTA
52655858 CTGTTACCGATTCGGCAC
781 CTGTTACCGATTCGGCAC
52655876 TTTGTGTGTC
Statistics
Matches: 777, Mismatches: 21, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
798 777 1.00
ACGTcount: A:0.33, C:0.10, G:0.22, T:0.35
Consensus pattern (798 bp):
AGAAAGGACAAGAAAAAGTCAACGAGAGTTAGCTCAAAAATTACGGCTTGTATTTCTATAACCCA
AACTTAATATTTAATTATTTAATTTATTATTTATTATGGATGGTAGGTGCATTGATTAAATTATT
TGAAATAAAATAAATTATGAATATGTGTAAATATATGAATTGTGTATTGATTGAAAAGTGGTTGG
AATTGAACCGAAGTATGATTATATGTGAATATTTAAAATATATATTGGTATTGAATTGTATACTG
ATCAGAAAGTGGAAAAGTGAATTTGAATTGAATTGAATGGAATTGAATGGAATGGAATTATGATT
AATTGAAATGTATATTGGTTGGATATTGAAATATGAGAAATTGTGATTGAATTGAAAGCGAATTT
GAAATAGAAAAATGATTTGAATACCCTATTAACTAATCGGACTGAATCGGATATAGTTGGCATGC
CATAGGATTTGGAAGTGTTCAGGCACTGAGTGCCATATTGGTGTGTTTGGTTGGAATCCGTATAT
CCGCCAAAGTCCGAGTCTTGTTAATAGGGGTAAATATGAATATTAAGTAAAATTGGAATAAGAAT
TAAATTTCCTATTAACTTGTCGGGCTAGTCGGATATAATTGGCATGCCATAGGGTCAGAAGAGTA
CGAGATTTATCGACTTTACCGATCGGGCACTTTATGTGCCGTATTTTAGGCACTTATGTGCTAGT
TACTGTTACCGCTACTGCTACAGTTACAGATTCGACACTTTGTGTGTCGAATATTGTTACTACTA
CTGTTACCGATTCGGCAC
Found at i:52655871 original size:45 final size:45
Alignment explanation
Indices: 52655805--52656089 Score: 374
Period size: 45 Copynumber: 6.3 Consensus size: 45
52655795 CTGTTACCGC
* *
52655805 TACTGCTACTGTTACCGATTCGGCACTTTGTGTGTCGAATATTGT
1 TACTACTACTGTTACCAATTCGGCACTTTGTGTGTCGAATATTGT
*
52655850 TACTACTACTGTTACCGATTCGGCACTTTGTGTGTCGAATATTGT
1 TACTACTACTGTTACCAATTCGGCACTTTGTGTGTCGAATATTGT
** *
52655895 TACTGTTACCGTTACCAATTCGGCACTTTGTGTGTCGAATATTGT
1 TACTACTACTGTTACCAATTCGGCACTTTGTGTGTCGAATATTGT
** ** * * *
52655940 TACTGTTACCATTACCGATTCAGCACTGTGTGTGTCGAATATTGT
1 TACTACTACTGTTACCAATTCGGCACTTTGTGTGTCGAATATTGT
* *
52655985 TACTATTACCGTTACCAATTCGGCACTTTGTGTGTCGAATATTGT
1 TACTACTACTGTTACCAATTCGGCACTTTGTGTGTCGAATATTGT
* ** * *
52656030 TACTAATACTGTTACCAATTCAACACTTTGTGTGTTGAATACTGT
1 TACTACTACTGTTACCAATTCGGCACTTTGTGTGTCGAATATTGT
52656075 TACT-CTTACTGTTAC
1 TACTAC-TACTGTTAC
52656090 TGTTACTATT
Statistics
Matches: 218, Mismatches: 21, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
45 218 1.00
ACGTcount: A:0.22, C:0.20, G:0.18, T:0.40
Consensus pattern (45 bp):
TACTACTACTGTTACCAATTCGGCACTTTGTGTGTCGAATATTGT
Found at i:52655955 original size:90 final size:90
Alignment explanation
Indices: 52655805--52656089 Score: 417
Period size: 90 Copynumber: 3.2 Consensus size: 90
52655795 CTGTTACCGC
* * * *
52655805 TACTGCTACTGTTACCGATTCGGCACTTTGTGTGTCGAATATTGTTACTACTACTGTTACCGATT
1 TACTGTTACCGTTACCAATTCGGCACTTTGTGTGTCGAATATTGTTACTAATACTGTTACCGATT
*
52655870 CGGCACTTTGTGTGTCGAATATTGT
66 CAGCACTTTGTGTGTCGAATATTGT
** **
52655895 TACTGTTACCGTTACCAATTCGGCACTTTGTGTGTCGAATATTGTTACTGTTACCATTACCGATT
1 TACTGTTACCGTTACCAATTCGGCACTTTGTGTGTCGAATATTGTTACTAATACTGTTACCGATT
*
52655960 CAGCACTGTGTGTGTCGAATATTGT
66 CAGCACTTTGTGTGTCGAATATTGT
* *
52655985 TACTATTACCGTTACCAATTCGGCACTTTGTGTGTCGAATATTGTTACTAATACTGTTACCAATT
1 TACTGTTACCGTTACCAATTCGGCACTTTGTGTGTCGAATATTGTTACTAATACTGTTACCGATT
* * *
52656050 CAACACTTTGTGTGTTGAATACTGT
66 CAGCACTTTGTGTGTCGAATATTGT
* *
52656075 TACTCTTACTGTTAC
1 TACTGTTACCGTTAC
52656090 TGTTACTATT
Statistics
Matches: 174, Mismatches: 21, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
90 174 1.00
ACGTcount: A:0.22, C:0.20, G:0.18, T:0.40
Consensus pattern (90 bp):
TACTGTTACCGTTACCAATTCGGCACTTTGTGTGTCGAATATTGTTACTAATACTGTTACCGATT
CAGCACTTTGTGTGTCGAATATTGT
Found at i:52656047 original size:135 final size:135
Alignment explanation
Indices: 52655816--52656083 Score: 419
Period size: 135 Copynumber: 2.0 Consensus size: 135
52655806 ACTGCTACTG
* * * *
52655816 TTACCGATTCGGCACTTTGTGTGTCGAATATTGTTACTACTACTGTTACCGATTCGGCACTTTGT
1 TTACCGATTCAGCACTGTGTGTGTCGAATATTGTTACTACTACCGTTACCAATTCGGCACTTTGT
** ** * *
52655881 GTGTCGAATATTGTTACTGTTACCGTTACCAATTCGGCACTTTGTGTGTCGAATATTGTTACTGT
66 GTGTCGAATATTGTTACTAATACCGTTACCAATTCAACACTTTGTGTGTCGAATACTGTTACTCT
52655946 TACCA
131 TACCA
*
52655951 TTACCGATTCAGCACTGTGTGTGTCGAATATTGTTACTATTACCGTTACCAATTCGGCACTTTGT
1 TTACCGATTCAGCACTGTGTGTGTCGAATATTGTTACTACTACCGTTACCAATTCGGCACTTTGT
* *
52656016 GTGTCGAATATTGTTACTAATACTGTTACCAATTCAACACTTTGTGTGTTGAATACTGTTACTCT
66 GTGTCGAATATTGTTACTAATACCGTTACCAATTCAACACTTTGTGTGTCGAATACTGTTACTCT
52656081 TAC
131 TAC
52656084 TGTTACTGTT
Statistics
Matches: 120, Mismatches: 13, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
135 120 1.00
ACGTcount: A:0.22, C:0.20, G:0.18, T:0.40
Consensus pattern (135 bp):
TTACCGATTCAGCACTGTGTGTGTCGAATATTGTTACTACTACCGTTACCAATTCGGCACTTTGT
GTGTCGAATATTGTTACTAATACCGTTACCAATTCAACACTTTGTGTGTCGAATACTGTTACTCT
TACCA
Found at i:52656284 original size:18 final size:18
Alignment explanation
Indices: 52656263--52656515 Score: 124
Period size: 18 Copynumber: 13.6 Consensus size: 18
52656253 TAACTGATTA
*
52656263 TTACTGGATAATTGACTG
1 TTACTGAATAATTGACTG
*
52656281 TTACTGGAT-ATTAGACTG
1 TTACTGAATAATT-GACTG
* * *
52656299 TTACTGAATAACTGAATA
1 TTACTGAATAATTGACTG
*
52656317 TTACTGAATAATTGA-TCA
1 TTACTGAATAATTGACT-G
* *
52656335 TTACTGAATAACTGATTG
1 TTACTGAATAATTGACTG
*
52656353 TCACTGAATGAA-TGACTG
1 TTACTGAAT-AATTGACTG
* *
52656371 CTACTGAATAACTT-AATAG
1 TTACTGAATAA-TTGACT-G
*
52656390 TTACTGAAT-ATCTGA-TT
1 TTACTGAATAAT-TGACTG
* *
52656407 TTTCTGAATTATTGACTG
1 TTACTGAATAATTGACTG
52656425 TTACTGGATAACCGATCAATTGA-TCG
1 TTACT-G---A---AT-AATTGACT-G
* * ** *
52656451 ATACTGAATAACTGGTTA
1 TTACTGAATAATTGACTG
* *
52656469 TTATTGAATAATTGATTG
1 TTACTGAATAATTGACTG
*
52656487 TTACCGAATAATTGACTG
1 TTACTGAATAATTGACTG
52656505 TTACTGAATAA
1 TTACTGAATAA
52656516 ATAATTATCC
Statistics
Matches: 182, Mismatches: 31, Indels: 44
0.71 0.12 0.17
Matches are distributed among these distances:
17 18 0.10
18 128 0.70
19 20 0.11
22 2 0.01
25 4 0.02
26 10 0.05
ACGTcount: A:0.34, C:0.12, G:0.16, T:0.38
Consensus pattern (18 bp):
TTACTGAATAATTGACTG
Found at i:52656430 original size:54 final size:55
Alignment explanation
Indices: 52656317--52656436 Score: 138
Period size: 54 Copynumber: 2.2 Consensus size: 55
52656307 TAACTGAATA
*
52656317 TTACTGAATAA-TTGATCATTACTGAATAACTGATTGTCACTGAATGAATGACTG
1 TTACTGAATAACTTAATCATTACTGAATAACTGATTGTCACTGAATGAATGACTG
* * ** * *
52656371 CTACTGAATAACTTAAT-AGTTACTGAATATCTGATT-TTTCTGAATTATTGACTG
1 TTACTGAATAACTTAATCA-TTACTGAATAACTGATTGTCACTGAATGAATGACTG
*
52656425 TTACTGGATAAC
1 TTACTGAATAAC
52656437 CGATCAATTG
Statistics
Matches: 55, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
54 35 0.64
55 20 0.36
ACGTcount: A:0.33, C:0.13, G:0.15, T:0.38
Consensus pattern (55 bp):
TTACTGAATAACTTAATCATTACTGAATAACTGATTGTCACTGAATGAATGACTG
Found at i:52660852 original size:13 final size:13
Alignment explanation
Indices: 52660834--52660876 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
52660824 TTTAATAATA
52660834 AAATAAAGAAATG
1 AAATAAAGAAATG
52660847 AAATAAAGAAAT-
1 AAATAAAGAAATG
* *
52660859 AAATGAAATAAAAG
1 AAAT-AAAGAAATG
52660873 AAAT
1 AAAT
52660877 GAAAAAGAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
12 4 0.15
13 18 0.69
14 4 0.15
ACGTcount: A:0.72, C:0.00, G:0.12, T:0.16
Consensus pattern (13 bp):
AAATAAAGAAATG
Found at i:52660864 original size:17 final size:18
Alignment explanation
Indices: 52660830--52660876 Score: 69
Period size: 17 Copynumber: 2.7 Consensus size: 18
52660820 ATAGTTTAAT
* *
52660830 AATAAAATAAAGAAATGA
1 AATAAAAGAAATAAATGA
52660848 AAT-AAAGAAATAAATGA
1 AATAAAAGAAATAAATGA
52660865 AATAAAAGAAAT
1 AATAAAAGAAAT
52660877 GAAAAAGAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
17 15 0.58
18 11 0.42
ACGTcount: A:0.72, C:0.00, G:0.11, T:0.17
Consensus pattern (18 bp):
AATAAAAGAAATAAATGA
Found at i:52660868 original size:9 final size:9
Alignment explanation
Indices: 52660842--52660876 Score: 54
Period size: 9 Copynumber: 4.0 Consensus size: 9
52660832 TAAAATAAAG
52660842 AAATGAAAT
1 AAATGAAAT
52660851 AAA-GAAAT
1 AAATGAAAT
52660859 AAATGAAAT
1 AAATGAAAT
*
52660868 AAAAGAAAT
1 AAATGAAAT
52660877 GAAAAAGAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
8 8 0.33
9 16 0.67
ACGTcount: A:0.71, C:0.00, G:0.11, T:0.17
Consensus pattern (9 bp):
AAATGAAAT
Found at i:52662261 original size:5 final size:5
Alignment explanation
Indices: 52662246--52662281 Score: 63
Period size: 5 Copynumber: 7.0 Consensus size: 5
52662236 AGTGGAAAAG
52662246 TGAATT TGAAT TGAAT TGAAT TGAAT TGAAT TGAAT
1 TGAA-T TGAAT TGAAT TGAAT TGAAT TGAAT TGAAT
52662282 GAAATTATGA
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 26 0.87
6 4 0.13
ACGTcount: A:0.39, C:0.00, G:0.19, T:0.42
Consensus pattern (5 bp):
TGAAT
Found at i:52663771 original size:37 final size:37
Alignment explanation
Indices: 52663721--52663799 Score: 115
Period size: 37 Copynumber: 2.1 Consensus size: 37
52663711 TTATTACGAA
* *
52663721 GTCTTACCCGGACATAA-TCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATTC-CCACACGAAGTCATCGG
*
52663758 GTCTTACCCGGACAAAATTCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATTCCCACACGAAGTCATCGG
52663795 GTCTT
1 GTCTT
52663800 TAGAGCTCGG
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
37 36 0.95
38 2 0.05
ACGTcount: A:0.25, C:0.30, G:0.19, T:0.25
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATTCCCACACGAAGTCATCGG
Found at i:52663987 original size:47 final size:47
Alignment explanation
Indices: 52663918--52664030 Score: 208
Period size: 47 Copynumber: 2.4 Consensus size: 47
52663908 CCCTTCGGGA
*
52663918 CTTATCACATATATACACTTTCACATTCGTCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
52663965 CTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
52664012 CTTATCACATATATACACT
1 CTTATCACATATATACACT
52664031 GTCTTGGCTG
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
47 63 1.00
ACGTcount: A:0.30, C:0.30, G:0.08, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:52666520 original size:45 final size:45
Alignment explanation
Indices: 52666467--52666694 Score: 332
Period size: 45 Copynumber: 5.1 Consensus size: 45
52666457 ACTGCTACTA
* * **
52666467 TTACCGATTCGGCACTTTCTGTGTCGAATATTGTTACTGCTACTA
1 TTACCGATTCGGCACTTTGTGTGTCGAATATTGTTACTGTTACCG
*
52666512 TTACCGATTCTGCACTTTGTGTGTCGAATATTGTTACTGTTACCG
1 TTACCGATTCGGCACTTTGTGTGTCGAATATTGTTACTGTTACCG
* *
52666557 TTACCGATT-GGCACTGTGTTTGTCGAATATTGTTACTGTTACCG
1 TTACCGATTCGGCACTTTGTGTGTCGAATATTGTTACTGTTACCG
*
52666601 TTACCGATTCGGCACTTTGTGTGTCGAATATTGTTACTGATACCG
1 TTACCGATTCGGCACTTTGTGTGTCGAATATTGTTACTGTTACCG
** * * *
52666646 TTACCGATTCAACACTTTGTGTGTTGAATACTGTTACTGTTACTG
1 TTACCGATTCGGCACTTTGTGTGTCGAATATTGTTACTGTTACCG
52666691 TTAC
1 TTAC
52666695 TATTCTGGAT
Statistics
Matches: 165, Mismatches: 17, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
44 41 0.25
45 124 0.75
ACGTcount: A:0.20, C:0.20, G:0.20, T:0.41
Consensus pattern (45 bp):
TTACCGATTCGGCACTTTGTGTGTCGAATATTGTTACTGTTACCG
Found at i:52666585 original size:89 final size:90
Alignment explanation
Indices: 52666467--52666684 Score: 303
Period size: 89 Copynumber: 2.4 Consensus size: 90
52666457 ACTGCTACTA
* * *
52666467 TTACCGATTCGGCACTTTCTGTGTCGAATATTGTTACTGCTACTATTACCGATTCTGCACTTTGT
1 TTACCGATTCGGCACTGTCTGTGTCGAATATTGTTACTGCTACCATTACCGATTCGGCACTTTGT
*
52666532 GTGTCGAATATTGTTACTGTTACCG
66 GTGTCGAATATTGTTACTGATACCG
* * * *
52666557 TTACCGATT-GGCACTGTGTTTGTCGAATATTGTTACTGTTACCGTTACCGATTCGGCACTTTGT
1 TTACCGATTCGGCACTGTCTGTGTCGAATATTGTTACTGCTACCATTACCGATTCGGCACTTTGT
52666621 GTGTCGAATATTGTTACTGATACCG
66 GTGTCGAATATTGTTACTGATACCG
** * * * *
52666646 TTACCGATTCAACACTTTGTGTGTTGAATACTGTTACTG
1 TTACCGATTCGGCACTGTCTGTGTCGAATATTGTTACTG
52666685 TTACTGTTAC
Statistics
Matches: 113, Mismatches: 14, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
89 81 0.72
90 32 0.28
ACGTcount: A:0.20, C:0.20, G:0.20, T:0.40
Consensus pattern (90 bp):
TTACCGATTCGGCACTGTCTGTGTCGAATATTGTTACTGCTACCATTACCGATTCGGCACTTTGT
GTGTCGAATATTGTTACTGATACCG
Found at i:52666932 original size:18 final size:18
Alignment explanation
Indices: 52666881--52667064 Score: 92
Period size: 18 Copynumber: 10.2 Consensus size: 18
52666871 TTATTTCTGA
*
52666881 ATAATTGACTGTTACCGG
1 ATAATTGACTGTTACTGG
*
52666899 ATAATTGACTATTACTGG
1 ATAATTGACTGTTACTGG
*
52666917 AT-ATTAGACTGTTACTGA
1 ATAATT-GACTGTTACTGG
* * * * *
52666935 ATAACTGAATATTATTGA
1 ATAATTGACTGTTACTGG
* *
52666953 ATAATTGA-TCATTACTGA
1 ATAATTGACT-GTTACTGG
* * * *
52666971 ATAACTGATTGTCACTGA
1 ATAATTGACTGTTACTGG
* *
52666989 ATGAA-TGACTGCTACTGA
1 AT-AATTGACTGTTACTGG
* *
52667007 ATAACTT-AATAGTTACTGA
1 ATAA-TTGACT-GTTACTGG
* *
52667026 AT-ATCTGA-TTTTACTGA
1 ATAAT-TGACTGTTACTGG
52667043 ATAATTGACTGTTACTGG
1 ATAATTGACTGTTACTGG
52667061 ATAA
1 ATAA
52667065 CCGATCAATT
Statistics
Matches: 133, Mismatches: 21, Indels: 24
0.75 0.12 0.13
Matches are distributed among these distances:
17 19 0.14
18 98 0.74
19 16 0.12
ACGTcount: A:0.35, C:0.12, G:0.16, T:0.37
Consensus pattern (18 bp):
ATAATTGACTGTTACTGG
Found at i:52666948 original size:36 final size:36
Alignment explanation
Indices: 52666862--52667064 Score: 155
Period size: 36 Copynumber: 5.6 Consensus size: 36
52666852 AAAGGTATAA
* * *
52666862 AATAACTGATTATTTCTGAATAATTGACTGTTACCG
1 AATAACTGAATATTACTGAATAATTGACTGTTACTG
* * * *
52666898 GATAATTGACTATTACTGGAT-ATTAGACTGTTACTG
1 AATAACTGAATATTACTGAATAATT-GACTGTTACTG
* *
52666934 AATAACTGAATATTATTGAATAATTGA-TCATTACTG
1 AATAACTGAATATTACTGAATAATTGACT-GTTACTG
* * * *
52666970 AATAACTGATTGTCACTGAATGAA-TGACTGCTACTG
1 AATAACTGAATATTACTGAAT-AATTGACTGTTACTG
* *
52667006 AATAACTTAATAGTTACTGAAT-ATCTGA-TTTTACTG
1 AATAACTGAATA-TTACTGAATAAT-TGACTGTTACTG
* * * *
52667042 AATAATTGACTGTTACTGGATAA
1 AATAACTGAATATTACTGAATAA
52667065 CCGATCAATT
Statistics
Matches: 129, Mismatches: 29, Indels: 18
0.73 0.16 0.10
Matches are distributed among these distances:
35 13 0.10
36 99 0.77
37 17 0.13
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.37
Consensus pattern (36 bp):
AATAACTGAATATTACTGAATAATTGACTGTTACTG
Found at i:52670206 original size:59 final size:59
Alignment explanation
Indices: 52670114--52670229 Score: 223
Period size: 59 Copynumber: 2.0 Consensus size: 59
52670104 TTGAAAGTGT
*
52670114 AAATATTTTTAAGTATGGCATGTATAGGCTAGAATGTCTATGTATTTAAGCTTTGATGC
1 AAATATTTTTAAGAATGGCATGTATAGGCTAGAATGTCTATGTATTTAAGCTTTGATGC
52670173 AAATATTTTTAAGAATGGCATGTATAGGCTAGAATGTCTATGTATTTAAGCTTTGAT
1 AAATATTTTTAAGAATGGCATGTATAGGCTAGAATGTCTATGTATTTAAGCTTTGAT
52670230 ACGCATATAT
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
59 56 1.00
ACGTcount: A:0.32, C:0.08, G:0.20, T:0.41
Consensus pattern (59 bp):
AAATATTTTTAAGAATGGCATGTATAGGCTAGAATGTCTATGTATTTAAGCTTTGATGC
Found at i:52672042 original size:33 final size:33
Alignment explanation
Indices: 52672004--52672073 Score: 131
Period size: 33 Copynumber: 2.1 Consensus size: 33
52671994 AGGTACGAAA
52672004 AAGATATCAGGTAAATCACTTCAATCAAGATCC
1 AAGATATCAGGTAAATCACTTCAATCAAGATCC
*
52672037 AAGATATCAGGTAAATCACTTCAATCTAGATCC
1 AAGATATCAGGTAAATCACTTCAATCAAGATCC
52672070 AAGA
1 AAGA
52672074 AGTTTAGAGA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.43, C:0.20, G:0.13, T:0.24
Consensus pattern (33 bp):
AAGATATCAGGTAAATCACTTCAATCAAGATCC
Found at i:52686852 original size:15 final size:15
Alignment explanation
Indices: 52686832--52686870 Score: 69
Period size: 15 Copynumber: 2.5 Consensus size: 15
52686822 TTGGCATTAT
52686832 AGATCAAGAGAAACG
1 AGATCAAGAGAAACG
52686847 AGATCAAGAGAAACG
1 AGATCAAGAGAAACG
52686862 AGATTCAAG
1 AGA-TCAAG
52686871 TCGCGATCGA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 18 0.78
16 5 0.22
ACGTcount: A:0.51, C:0.13, G:0.26, T:0.10
Consensus pattern (15 bp):
AGATCAAGAGAAACG
Found at i:52689334 original size:48 final size:48
Alignment explanation
Indices: 52689272--52690239 Score: 1855
Period size: 48 Copynumber: 20.2 Consensus size: 48
52689262 GAAATTGATA
52689272 TATGAGATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATG
1 TATGAGATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATG
52689320 TATGAGATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATG
1 TATGAGATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATG
52689368 TATGAGATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATG
1 TATGAGATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATG
52689416 TATGAGATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATG
1 TATGAGATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATG
52689464 TATGAGATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATG
1 TATGAGATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATG
52689512 TATGAGATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATG
1 TATGAGATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATG
52689560 TATGAGATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATG
1 TATGAGATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATG
52689608 TATGAGATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATG
1 TATGAGATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATG
52689656 TATGAGATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATG
1 TATGAGATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATG
52689704 TATGAGATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATG
1 TATGAGATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATG
*
52689752 TATGAGATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATA
1 TATGAGATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATG
* *
52689800 TATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATA
1 TATGAGATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATG
*
52689848 TATGAGATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATA
1 TATGAGATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATG
* * *
52689896 TATGAGATATGTATATGTGGTAAAGCCGAATGGATAATGTGAAATATA
1 TATGAGATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATG
52689944 TATGAGATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATG
1 TATGAGATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATG
52689992 TATGAGATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATG
1 TATGAGATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATG
52690040 TATGAGATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATG
1 TATGAGATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATG
52690088 TATGAGATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATG
1 TATGAGATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATG
52690136 TATGAGATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATG
1 TATGAGATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATG
*
52690184 TATGAGATATGTATATGTGGTAAAGCTGAATGGCTAGTGTGAAATATG
1 TATGAGATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATG
*
52690232 TAGGAGAT
1 TATGAGAT
52690240 GTGTGTATAT
Statistics
Matches: 910, Mismatches: 10, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
48 910 1.00
ACGTcount: A:0.34, C:0.06, G:0.29, T:0.31
Consensus pattern (48 bp):
TATGAGATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATG
Found at i:52691558 original size:46 final size:46
Alignment explanation
Indices: 52691508--52691679 Score: 299
Period size: 46 Copynumber: 3.7 Consensus size: 46
52691498 TGGTTGAGCA
52691508 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
52691554 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
52691600 TCCAAACTCGTTGAGTCGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* *
52691646 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
52691680 GGGGCGGGTT
Statistics
Matches: 119, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
46 119 1.00
ACGTcount: A:0.22, C:0.22, G:0.27, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:52715141 original size:45 final size:44
Alignment explanation
Indices: 52715068--52715185 Score: 141
Period size: 45 Copynumber: 2.6 Consensus size: 44
52715058 GTGAGACAAG
* *
52715068 AGCTAGTATAAGACATGTCTGAGACATGCATCAGCCT-CGAGATGTA
1 AGCTAGTGTAAGACATGTCTGAGACATGCATC-GACTACGAG-T-TA
* *
52715114 AGC-AGTGTAAGACATGTTTGAGGCATGCATCGACTACGAGTTA
1 AGCTAGTGTAAGACATGTCTGAGACATGCATCGACTACGAGTTA
*
52715157 AGCTAGTGTAAGACCATGTCTGGGACATG
1 AGCTAGTGTAAGA-CATGTCTGAGACATG
52715186 GCATTGGCAA
Statistics
Matches: 62, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
43 5 0.08
44 13 0.21
45 41 0.66
46 3 0.05
ACGTcount: A:0.31, C:0.18, G:0.27, T:0.25
Consensus pattern (44 bp):
AGCTAGTGTAAGACATGTCTGAGACATGCATCGACTACGAGTTA
Found at i:52715939 original size:29 final size:29
Alignment explanation
Indices: 52715906--52715965 Score: 86
Period size: 29 Copynumber: 2.1 Consensus size: 29
52715896 CATAGGTAGG
52715906 CACATAGGCGTGTG-TCTAGGCCGTGTGTC
1 CACATAGGCGTGTGATC-AGGCCGTGTGTC
* *
52715935 CACATGGGCGTGTGATCCGGCCGTGTGTC
1 CACATAGGCGTGTGATCAGGCCGTGTGTC
52715964 CA
1 CA
52715966 TTGCACATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 26 0.93
30 2 0.07
ACGTcount: A:0.13, C:0.27, G:0.35, T:0.25
Consensus pattern (29 bp):
CACATAGGCGTGTGATCAGGCCGTGTGTC
Found at i:52722951 original size:19 final size:20
Alignment explanation
Indices: 52722912--52722958 Score: 62
Period size: 18 Copynumber: 2.4 Consensus size: 20
52722902 CTAAACCGAT
52722912 AACTTAAGAAATTTTTACAA
1 AACTTAAGAAATTTTTACAA
*
52722932 AACTT-AGAAA-TTTTACCA
1 AACTTAAGAAATTTTTACAA
52722950 AACTGTAAG
1 AACT-TAAG
52722959 GGTCACATGC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
18 11 0.46
19 6 0.25
20 7 0.29
ACGTcount: A:0.47, C:0.13, G:0.09, T:0.32
Consensus pattern (20 bp):
AACTTAAGAAATTTTTACAA
Found at i:52730418 original size:40 final size:40
Alignment explanation
Indices: 52730356--52730451 Score: 142
Period size: 40 Copynumber: 2.4 Consensus size: 40
52730346 AAGCCAAGTA
* * *
52730356 CCTTCGGGATTTA-ACCGGATATAGCT-ACTCGCTCAAATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
52730395 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
52730435 CCTTCGGGACTTAGCCC
1 CCTTCGGGACTTAGCCC
52730452 NNNNNNNNNN
Statistics
Matches: 52, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
39 13 0.25
40 39 0.75
ACGTcount: A:0.24, C:0.29, G:0.22, T:0.25
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:52741538 original size:43 final size:43
Alignment explanation
Indices: 52741483--52741654 Score: 174
Period size: 43 Copynumber: 4.0 Consensus size: 43
52741473 TAAGGATACA
*
52741483 ATGCCAACGTCCCAGACGTGGTCTTACATGTAATCAAATATCG
1 ATGCCAATGTCCCAGACGTGGTCTTACATGTAATCAAATATCG
* *
52741526 ATGCCATTGTCCCAGACAG-GGTCTTACACT-AAATCAAATAT-G
1 ATGCCAATGTCCCAGAC-GTGGTCTTACA-TGTAATCAAATATCG
** * *
52741568 ATGCCAATGTCCCAGATATGGTCTTACACGTAAATCATAA-GTCG
1 ATGCCAATGTCCCAGACGTGGTCTTACATGT-AATCA-AATATCG
* * *
52741612 ATGCTAACGTCCCAGACGTGGTCTTACATGATAA-CACATATCG
1 ATGCCAATGTCCCAGACGTGGTCTTACATG-TAATCAAATATCG
52741655 GATCCTATGT
Statistics
Matches: 104, Mismatches: 16, Indels: 18
0.75 0.12 0.13
Matches are distributed among these distances:
42 26 0.25
43 45 0.43
44 32 0.31
45 1 0.01
ACGTcount: A:0.31, C:0.24, G:0.18, T:0.26
Consensus pattern (43 bp):
ATGCCAATGTCCCAGACGTGGTCTTACATGTAATCAAATATCG
Found at i:52748467 original size:29 final size:29
Alignment explanation
Indices: 52748434--52748499 Score: 105
Period size: 29 Copynumber: 2.3 Consensus size: 29
52748424 ATATGAAACA
* *
52748434 GGCCATATAAATGTGATTTGGGTCTAATG
1 GGCCATATAAAGGTGATTTGGGCCTAATG
*
52748463 GGCCATATACAGGTGATTTGGGCCTAATG
1 GGCCATATAAAGGTGATTTGGGCCTAATG
52748492 GGCCATAT
1 GGCCATAT
52748500 GTATATGATT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.26, C:0.15, G:0.29, T:0.30
Consensus pattern (29 bp):
GGCCATATAAAGGTGATTTGGGCCTAATG
Found at i:52748508 original size:29 final size:29
Alignment explanation
Indices: 52748434--52748531 Score: 92
Period size: 29 Copynumber: 3.4 Consensus size: 29
52748424 ATATGAAACA
* *
52748434 GGCCATATAAATG-TGATTTGGGTCTAATG
1 GGCCATATACA-GATGATTTGGGCCTAATG
*
52748463 GGCCATATACAGGTGATTTGGGCCTAATG
1 GGCCATATACAGATGATTTGGGCCTAATG
** * *
52748492 GGCCATATGTATATGA-TTGGGCTTAATG
1 GGCCATATACAGATGATTTGGGCCTAATG
* *
52748520 GGCTAGATACAG
1 GGCCATATACAG
52748532 GTATGTGAAA
Statistics
Matches: 56, Mismatches: 12, Indels: 3
0.79 0.17 0.04
Matches are distributed among these distances:
28 19 0.34
29 37 0.66
ACGTcount: A:0.27, C:0.13, G:0.30, T:0.31
Consensus pattern (29 bp):
GGCCATATACAGATGATTTGGGCCTAATG
Found at i:52750735 original size:43 final size:43
Alignment explanation
Indices: 52750674--52750832 Score: 187
Period size: 43 Copynumber: 3.7 Consensus size: 43
52750664 CAATGCCATA
* * * *
52750674 TCCCAGATATGGTCTTACATGTTATCACATATCGATTCCATTG
1 TCCCAGACATGGTCTTACATGTAATCACATATCAATTCCAATG
* * *
52750717 TCCCAGACAGGGTCTTACATGAAATCGA-ATAACAATTCCAATG
1 TCCCAGACATGGTCTTACATGTAATC-ACATATCAATTCCAATG
** *
52750760 TCCCAGACATGGTCTTACACATAATCACA-ATACAATGCCAATG
1 TCCCAGACATGGTCTTACATGTAATCACATAT-CAATTCCAATG
*
52750803 TCCCAGACATGGTCTTACATGTAGTCACAT
1 TCCCAGACATGGTCTTACATGTAATCACAT
52750833 CTAGATAACC
Statistics
Matches: 96, Mismatches: 16, Indels: 7
0.81 0.13 0.06
Matches are distributed among these distances:
42 2 0.02
43 93 0.97
44 1 0.01
ACGTcount: A:0.32, C:0.25, G:0.14, T:0.28
Consensus pattern (43 bp):
TCCCAGACATGGTCTTACATGTAATCACATATCAATTCCAATG
Found at i:52754173 original size:93 final size:93
Alignment explanation
Indices: 52754061--52754232 Score: 308
Period size: 93 Copynumber: 1.8 Consensus size: 93
52754051 GCCCATAAGT
* *
52754061 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
52754126 CGAGCTCGGATGCCTAGTTACATCTCTC
66 CGAGCTCGGATGCCTAGTTACATCTCTC
*
52754154 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
*
52754219 CGAGTTCGGATGCC
66 CGAGCTCGGATGCC
52754233 CAAACATCCT
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.27, C:0.30, G:0.22, T:0.21
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGCTCGGATGCCTAGTTACATCTCTC
Found at i:52754228 original size:46 final size:46
Alignment explanation
Indices: 52754053--52754228 Score: 214
Period size: 46 Copynumber: 3.8 Consensus size: 46
52754043 TGTAACCCGC
* *
52754053 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
*
52754099 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG--ATGC-CTAGTT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGC-A--T
* *** *
52754145 ACATCTCTCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGT-GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
*
52754192 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGA
52754229 TGCCCAAACA
Statistics
Matches: 111, Mismatches: 12, Indels: 14
0.81 0.09 0.10
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
46 70 0.63
47 32 0.29
49 4 0.04
50 1 0.01
ACGTcount: A:0.28, C:0.30, G:0.21, T:0.21
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
Found at i:52761810 original size:49 final size:49
Alignment explanation
Indices: 52761738--52761864 Score: 145
Period size: 49 Copynumber: 2.6 Consensus size: 49
52761728 GGATAAGTTA
* *
52761738 TCGATGCCATGTCCCAAATATGGTCTTACAATAGCTATC-ATCAT-TGAGG
1 TCGATGCCATGTCCCAGACATGGTCTTACAATAGCTATCGAT-ATATG-GG
* * *
52761787 TCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCGTATATATGTG
1 TCGATGCCATGTCCCAGACATGGTCTTACAATAGCTATCG-ATATATGGG
*
52761837 TTGATG-CATGTCCCAGACAT-GTCTTACA
1 TCGATGCCATGTCCCAGACATGGTCTTACA
52761865 CTAACACAAC
Statistics
Matches: 69, Mismatches: 6, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
48 8 0.12
49 49 0.71
50 8 0.12
51 4 0.06
ACGTcount: A:0.25, C:0.24, G:0.19, T:0.31
Consensus pattern (49 bp):
TCGATGCCATGTCCCAGACATGGTCTTACAATAGCTATCGATATATGGG
Found at i:52763924 original size:43 final size:42
Alignment explanation
Indices: 52763877--52763983 Score: 144
Period size: 43 Copynumber: 2.5 Consensus size: 42
52763867 TGTGATTGCA
* *
52763877 TGTAAGACCATGCCTGGGACATTGGCAT-TGTATTTTGATTACG
1 TGTAAGACCATGTCTGGGACATTGGCATAT-TA-TTCGATTACG
*
52763920 TGTAAGACCATGTCTGGGACATTGGCATCATTATTCGATTTCG
1 TGTAAGACCATGTCTGGGACATTGGCAT-ATTATTCGATTACG
*
52763963 TGTAAGACCCTGTCTGGGACA
1 TGTAAGACCATGTCTGGGACA
52763984 GTAGTATCGA
Statistics
Matches: 58, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
43 55 0.95
44 2 0.03
45 1 0.02
ACGTcount: A:0.23, C:0.19, G:0.25, T:0.33
Consensus pattern (42 bp):
TGTAAGACCATGTCTGGGACATTGGCATATTATTCGATTACG
Found at i:52768565 original size:27 final size:27
Alignment explanation
Indices: 52768535--52768712 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
52768525 ATATTGAGTC
* * * *
52768535 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
52768562 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
52768589 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
52768617 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
52768644 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
52768671 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
52768698 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
52768713 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:52768674 original size:82 final size:81
Alignment explanation
Indices: 52768556--52768711 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
52768546 TGCTATATAA
* *
52768556 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
52768621 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
52768638 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
52768702 CACTTAGTGC
65 CACTTAGTGC
52768712 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:52776755 original size:27 final size:27
Alignment explanation
Indices: 52776725--52776902 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
52776715 ATATTGAGTC
* * * *
52776725 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
52776752 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
52776779 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
52776807 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
52776834 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
52776861 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
52776888 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
52776903 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:52776864 original size:82 final size:81
Alignment explanation
Indices: 52776746--52776901 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
52776736 TGCTATATAA
* *
52776746 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
52776811 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
52776828 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
52776892 CACTTAGTGC
65 CACTTAGTGC
52776902 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:52778767 original size:37 final size:36
Alignment explanation
Indices: 52778714--52778789 Score: 93
Period size: 37 Copynumber: 2.1 Consensus size: 36
52778704 ATTCTAAAAA
*
52778714 TAATATTATTTTAATAGT-TTAATATTAAATTTAAT-T
1 TAATATTATCTTAATAGTATT-ATATT-AATTTAATGT
*
52778750 TAATACTTATCTTAATAGTATTTTATTAATTTAATGT
1 TAATA-TTATCTTAATAGTATTATATTAATTTAATGT
52778787 TAA
1 TAA
52778790 AATGATTATT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
36 13 0.37
37 20 0.57
38 2 0.06
ACGTcount: A:0.39, C:0.03, G:0.04, T:0.54
Consensus pattern (36 bp):
TAATATTATCTTAATAGTATTATATTAATTTAATGT
Found at i:52779341 original size:37 final size:36
Alignment explanation
Indices: 52779288--52779363 Score: 93
Period size: 37 Copynumber: 2.1 Consensus size: 36
52779278 ATTCTAAAAA
*
52779288 TAATATTATTTTAATAGT-TTAATATTAAATTTAAT-T
1 TAATATTATCTTAATAGTATT-ATATT-AATTTAATGT
*
52779324 TAATACTTATCTTAATAGTATTTTATTAATTTAATGT
1 TAATA-TTATCTTAATAGTATTATATTAATTTAATGT
52779361 TAA
1 TAA
52779364 AATGATTATT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
36 13 0.37
37 20 0.57
38 2 0.06
ACGTcount: A:0.39, C:0.03, G:0.04, T:0.54
Consensus pattern (36 bp):
TAATATTATCTTAATAGTATTATATTAATTTAATGT
Found at i:52779488 original size:574 final size:574
Alignment explanation
Indices: 52778400--52779549 Score: 2300
Period size: 574 Copynumber: 2.0 Consensus size: 574
52778390 TTAGCCTATC
52778400 ATATTTTGCCATATCTCATGTTGATCCCTATTTAATAATTCCTCATGAAATTGGCGAAATTAGGG
1 ATATTTTGCCATATCTCATGTTGATCCCTATTTAATAATTCCTCATGAAATTGGCGAAATTAGGG
52778465 AATGAAACTTCCACATATGCATGTACACACATAATAAACGTAGAATATAACAATTAATTATTTTC
66 AATGAAACTTCCACATATGCATGTACACACATAATAAACGTAGAATATAACAATTAATTATTTTC
52778530 ATAACTCGGTTTTGTGGTCCCGAAACCACTTCCCGACTAGGGTCAATTTTGGGCTGTCACAAAAA
131 ATAACTCGGTTTTGTGGTCCCGAAACCACTTCCCGACTAGGGTCAATTTTGGGCTGTCACAAAAA
52778595 ACGAGTTGTTACATCCGGTAGGTGACAATGGTTGGTCTTTGGTGGTTGAGTAGTGGAAGAGTTAC
196 ACGAGTTGTTACATCCGGTAGGTGACAATGGTTGGTCTTTGGTGGTTGAGTAGTGGAAGAGTTAC
52778660 ACTCCTACTTGGACTCTACCAGAGAATTCGATTTCATATTAATTATTCTAAAAATAATATTATTT
261 ACTCCTACTTGGACTCTACCAGAGAATTCGATTTCATATTAATTATTCTAAAAATAATATTATTT
52778725 TAATAGTTTAATATTAAATTTAATTTAATACTTATCTTAATAGTATTTTATTAATTTAATGTTAA
326 TAATAGTTTAATATTAAATTTAATTTAATACTTATCTTAATAGTATTTTATTAATTTAATGTTAA
52778790 AATGATTATTCTAATATTAAATTTAATTTAATGTTTATCTTGTAGATAAACATTCTATTATTTTA
391 AATGATTATTCTAATATTAAATTTAATTTAATGTTTATCTTGTAGATAAACATTCTATTATTTTA
52778855 ATAAGATATAATATAGTATTTAATCTAATATTTATCTTGATAAATATTATATTAATTTAATATTA
456 ATAAGATATAATATAGTATTTAATCTAATATTTATCTTGATAAATATTATATTAATTTAATATTA
52778920 AAGTAATTAAGTTTAATCATAGTTAAACTCTCTAAACTCTCCCTATATAAAGAG
521 AAGTAATTAAGTTTAATCATAGTTAAACTCTCTAAACTCTCCCTATATAAAGAG
52778974 ATATTTTGCCATATCTCATGTTGATCCCTATTTAATAATTCCTCATGAAATTGGCGAAATTAGGG
1 ATATTTTGCCATATCTCATGTTGATCCCTATTTAATAATTCCTCATGAAATTGGCGAAATTAGGG
52779039 AATGAAACTTCCACATATGCATGTACACACATAATAAACGTAGAATATAACAATTAATTATTTTC
66 AATGAAACTTCCACATATGCATGTACACACATAATAAACGTAGAATATAACAATTAATTATTTTC
52779104 ATAACTCGGTTTTGTGGTCCCGAAACCACTTCCCGACTAGGGTCAATTTTGGGCTGTCACAAAAA
131 ATAACTCGGTTTTGTGGTCCCGAAACCACTTCCCGACTAGGGTCAATTTTGGGCTGTCACAAAAA
52779169 ACGAGTTGTTACATCCGGTAGGTGACAATGGTTGGTCTTTGGTGGTTGAGTAGTGGAAGAGTTAC
196 ACGAGTTGTTACATCCGGTAGGTGACAATGGTTGGTCTTTGGTGGTTGAGTAGTGGAAGAGTTAC
52779234 ACTCCTACTTGGACTCTACCAGAGAATTCGATTTCATATTAATTATTCTAAAAATAATATTATTT
261 ACTCCTACTTGGACTCTACCAGAGAATTCGATTTCATATTAATTATTCTAAAAATAATATTATTT
52779299 TAATAGTTTAATATTAAATTTAATTTAATACTTATCTTAATAGTATTTTATTAATTTAATGTTAA
326 TAATAGTTTAATATTAAATTTAATTTAATACTTATCTTAATAGTATTTTATTAATTTAATGTTAA
52779364 AATGATTATTCTAATATTAAATTTAATTTAATGTTTATCTTGTAGATAAACATTCTATTATTTTA
391 AATGATTATTCTAATATTAAATTTAATTTAATGTTTATCTTGTAGATAAACATTCTATTATTTTA
52779429 ATAAGATATAATATAGTATTTAATCTAATATTTATCTTGATAAATATTATATTAATTTAATATTA
456 ATAAGATATAATATAGTATTTAATCTAATATTTATCTTGATAAATATTATATTAATTTAATATTA
52779494 AAGTAATTAAGTTTAATCATAGTTAAACTCTCTAAACTCTCCCTATATAAAGAG
521 AAGTAATTAAGTTTAATCATAGTTAAACTCTCTAAACTCTCCCTATATAAAGAG
52779548 AT
1 AT
52779550 TCTTGGGTCA
Statistics
Matches: 576, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
574 576 1.00
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.39
Consensus pattern (574 bp):
ATATTTTGCCATATCTCATGTTGATCCCTATTTAATAATTCCTCATGAAATTGGCGAAATTAGGG
AATGAAACTTCCACATATGCATGTACACACATAATAAACGTAGAATATAACAATTAATTATTTTC
ATAACTCGGTTTTGTGGTCCCGAAACCACTTCCCGACTAGGGTCAATTTTGGGCTGTCACAAAAA
ACGAGTTGTTACATCCGGTAGGTGACAATGGTTGGTCTTTGGTGGTTGAGTAGTGGAAGAGTTAC
ACTCCTACTTGGACTCTACCAGAGAATTCGATTTCATATTAATTATTCTAAAAATAATATTATTT
TAATAGTTTAATATTAAATTTAATTTAATACTTATCTTAATAGTATTTTATTAATTTAATGTTAA
AATGATTATTCTAATATTAAATTTAATTTAATGTTTATCTTGTAGATAAACATTCTATTATTTTA
ATAAGATATAATATAGTATTTAATCTAATATTTATCTTGATAAATATTATATTAATTTAATATTA
AAGTAATTAAGTTTAATCATAGTTAAACTCTCTAAACTCTCCCTATATAAAGAG
Found at i:52784294 original size:20 final size:20
Alignment explanation
Indices: 52784240--52784327 Score: 59
Period size: 20 Copynumber: 4.4 Consensus size: 20
52784230 CTTGTACGGG
* *
52784240 TTTGCAATTTGGTGCCTCTA
1 TTTGCACTTCGGTGCCTCTA
* * * *
52784260 TGTGCACATCAGTGCCTCTT
1 TTTGCACTTCGGTGCCTCTA
* *
52784280 TTTGCACTTCGGTGCTTCTG
1 TTTGCACTTCGGTGCCTCTA
* * **
52784300 TGTACACTTCGGTATCTCTA
1 TTTGCACTTCGGTGCCTCTA
*
52784320 ATTGCACT
1 TTTGCACT
52784328 ACAGTGTCTC
Statistics
Matches: 48, Mismatches: 20, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.15, C:0.25, G:0.19, T:0.41
Consensus pattern (20 bp):
TTTGCACTTCGGTGCCTCTA
Found at i:52790405 original size:40 final size:40
Alignment explanation
Indices: 52790244--52790402 Score: 212
Period size: 40 Copynumber: 4.0 Consensus size: 40
52790234 CTTTGATTTT
* * * * *
52790244 AAGCTATCTCAAATCACACACTAAATGTCATATATAGCCG
1 AAGCTATGTCGAATCGCACACTAAGTGCCATATATAGCCG
52790284 AAGCTATGTCGAATCGCACACTAAGTGCCATATATAGCCG
1 AAGCTATGTCGAATCGCACACTAAGTGCCATATATAGCCG
* *
52790324 AAACTATGTCAAATCGCACACTAAGTGCCATATATAGCC-
1 AAGCTATGTCGAATCGCACACTAAGTGCCATATATAGCCG
* * *
52790363 AATGCTATGTCGAATCGTACACTAAGTGCCACAAATAGCC
1 AA-GCTATGTCGAATCGCACACTAAGTGCCATATATAGCC
52790403 AATTTGTTGT
Statistics
Matches: 106, Mismatches: 12, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
39 2 0.02
40 104 0.98
ACGTcount: A:0.36, C:0.25, G:0.15, T:0.23
Consensus pattern (40 bp):
AAGCTATGTCGAATCGCACACTAAGTGCCATATATAGCCG
Found at i:52800376 original size:28 final size:28
Alignment explanation
Indices: 52800344--52800397 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
52800334 ATACTGTTGA
*
52800344 ATACTCAATGTCT-AGCACACTAAGTGCC
1 ATACTCAATATCTCA-CACACTAAGTGCC
*
52800372 ATACTCGATATCTCACACACTAAGTG
1 ATACTCAATATCTCACACACTAAGTG
52800398 TCGTACATAG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
28 22 0.96
29 1 0.04
ACGTcount: A:0.33, C:0.28, G:0.13, T:0.26
Consensus pattern (28 bp):
ATACTCAATATCTCACACACTAAGTGCC
Found at i:52800448 original size:40 final size:40
Alignment explanation
Indices: 52800387--52800522 Score: 182
Period size: 40 Copynumber: 3.4 Consensus size: 40
52800377 CGATATCTCA
* * * * *
52800387 CACACTAAGTGTCGTACATAGCTGAAGCTATCTCAAATCG
1 CACACTAAGTGCCATAAATAGCCGAAGCTATGTCAAATCG
* *
52800427 CACACTAAGTTCCATAAATAGCCGAAGCTATGTCGAATCG
1 CACACTAAGTGCCATAAATAGCCGAAGCTATGTCAAATCG
* * *
52800467 CACACTAAGTGCCACATATAGCCAAAGCTATGTCAAATCG
1 CACACTAAGTGCCATAAATAGCCGAAGCTATGTCAAATCG
52800507 CACACTAAGTGCCATA
1 CACACTAAGTGCCATA
52800523 TATTGTCGTC
Statistics
Matches: 83, Mismatches: 13, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 83 1.00
ACGTcount: A:0.35, C:0.26, G:0.16, T:0.22
Consensus pattern (40 bp):
CACACTAAGTGCCATAAATAGCCGAAGCTATGTCAAATCG
Found at i:52802047 original size:79 final size:78
Alignment explanation
Indices: 52801945--52802167 Score: 272
Period size: 79 Copynumber: 2.8 Consensus size: 78
52801935 GCTCCTCGTT
* *
52801945 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
1 CAAATGCCTTCGGG-CTTAGCCCGG-TATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGG
*
52802010 ATTTAGTAACTCGCA
64 AATTAGTAACTCGCA
* *
52802025 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGG-CTTAGCCCGGA
1 CAAATGCCTTCGGGCTTAGCCCGGTA-TAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGA
*
52802089 ATTAGTATCTCGCA
65 ATTAGTAACTCGCA
* * * * *
52802103 CAAATGCCTTCGGATCTTAGTCCGGATATTGTCACTTAGCAC-AA-GCCTTCGGGACTTAGCCCG
1 CAAATGCCTTCGG-GCTTAGCCCGG-TATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGCCCG
52802166 GA
63 GA
52802168 CATCATTCAA
Statistics
Matches: 125, Mismatches: 13, Indels: 11
0.84 0.09 0.07
Matches are distributed among these distances:
78 45 0.36
79 60 0.48
80 20 0.16
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (78 bp):
CAAATGCCTTCGGGCTTAGCCCGGTATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGAA
TTAGTAACTCGCA
Found at i:52802062 original size:39 final size:40
Alignment explanation
Indices: 52801945--52802167 Score: 280
Period size: 39 Copynumber: 5.7 Consensus size: 40
52801935 GCTCCTCGTT
* *
52801945 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGTAACTCGCA
* *
52801985 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCA
*
52802025 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCA
*
52802064 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCA
* * *
52802103 CAAATGCCTTC-GGATCTTAGTCCGGATATT-GTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGA-ATTAGTAAC-TCGCA
52802144 C-AA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
52802168 CATCATTCAA
Statistics
Matches: 167, Mismatches: 10, Indels: 13
0.88 0.05 0.07
Matches are distributed among these distances:
38 2 0.01
39 88 0.53
40 67 0.40
41 10 0.06
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCA
Found at i:52810539 original size:20 final size:20
Alignment explanation
Indices: 52810503--52810545 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
52810493 TTATGTTAAA
*
52810503 TAAATGGAATAGAAAGTAAG
1 TAAATGGAATAAAAAGTAAG
*
52810523 TAAATGGAA-AAACAAGTATG
1 TAAATGGAATAAA-AAGTAAG
52810543 TAA
1 TAA
52810546 GTAAAGTGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 2 0.10
20 18 0.90
ACGTcount: A:0.56, C:0.02, G:0.21, T:0.21
Consensus pattern (20 bp):
TAAATGGAATAAAAAGTAAG
Found at i:52813119 original size:3 final size:3
Alignment explanation
Indices: 52813111--52813156 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
52813101 TTCTCCACAC
52813111 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
52813157 GAGAGTGACT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:52825252 original size:61 final size:61
Alignment explanation
Indices: 52825125--52825414 Score: 222
Period size: 61 Copynumber: 4.8 Consensus size: 61
52825115 TAAATATTTG
* * * * ** * * * * *
52825125 CCACAAAGGCTTACCTTTCCAAAGTTTCGCCACAAAAGC-ATCTTTTACATTCAATACTCG
1 CCACAAAGGCTTTCATGTCCAGAGTTTTACCACAAAAGCTGTCCTTTACATCCAGTACTCA
* * * * * * *
52825185 CCACAAAGACTTTCTTGTTCAGAGATTTACCACAAAAGCTGTTCTTTACATCTAGTATTCA
1 CCACAAAGGCTTTCATGTCCAGAGTTTTACCACAAAAGCTGTCCTTTACATCCAGTACTCA
* * * * * * * *
52825246 CCACAAAGGCTTTCCTCTCCAGAGTTTTCCCATAAAGGTTGTCCTTTACATCCATTACTCG
1 CCACAAAGGCTTTCATGTCCAGAGTTTTACCACAAAAGCTGTCCTTTACATCCAGTACTCA
* * * * **
52825307 CCACAAAGGCTTTCATGTCCAGAGTTTTACCACAAAGGTTGTCATTTACATCCAATACTTG
1 CCACAAAGGCTTTCATGTCCAGAGTTTTACCACAAAAGCTGTCCTTTACATCCAGTACTCA
* * * * * * *
52825368 CCATAAAGGCTTTCTTGTCCAAAATTTTGCCATAAAGGCTGTCCTTT
1 CCACAAAGGCTTTCATGTCCAGAGTTTTACCACAAAAGCTGTCCTTT
52825415 TTTAGGTGTT
Statistics
Matches: 183, Mismatches: 46, Indels: 1
0.80 0.20 0.00
Matches are distributed among these distances:
60 30 0.16
61 153 0.84
ACGTcount: A:0.28, C:0.27, G:0.13, T:0.32
Consensus pattern (61 bp):
CCACAAAGGCTTTCATGTCCAGAGTTTTACCACAAAAGCTGTCCTTTACATCCAGTACTCA
Found at i:52825341 original size:122 final size:122
Alignment explanation
Indices: 52825125--52825414 Score: 300
Period size: 122 Copynumber: 2.4 Consensus size: 122
52825115 TAAATATTTG
* * * * * * * *
52825125 CCACAAAGGCTTACCTTTCC-AAAGTTTCGCCACAAAAGC-ATCTTTTACATTCAATACTCGCCA
1 CCACAAAGGCTTTCCTCTCCAAAATTTTC-CCATAAAGGCTGTCCTTTACATCCAATACTCGCCA
* * * *
52825188 CAAAGACTTTCTTGTTCAGAGATTTACCACAAAAGCTGTTC-TTTACATCTAGTA-TTCA
65 CAAAGACTTTCATGTCCAGAGATTTACCACAAAAGCTG-TCATTTACATCCAATACTT-A
* * * *
52825246 CCACAAAGGCTTTCCTCTCCAGAGTTTTCCCATAAAGGTTGTCCTTTACATCCATTACTCGCCAC
1 CCACAAAGGCTTTCCTCTCCAAAATTTTCCCATAAAGGCTGTCCTTTACATCCAATACTCGCCAC
* * * * *
52825311 AAAGGCTTTCATGTCCAGAGTTTTACCACAAAGGTTGTCATTTACATCCAATACTTG
66 AAAGACTTTCATGTCCAGAGATTTACCACAAAAGCTGTCATTTACATCCAATACTTA
* * * *
52825368 CCATAAAGGCTTTCTTGTCCAAAATTTTGCCATAAAGGCTGTCCTTT
1 CCACAAAGGCTTTCCTCTCCAAAATTTTCCCATAAAGGCTGTCCTTT
52825415 TTTAGGTGTT
Statistics
Matches: 137, Mismatches: 28, Indels: 7
0.80 0.16 0.04
Matches are distributed among these distances:
121 27 0.20
122 108 0.79
123 2 0.01
ACGTcount: A:0.28, C:0.27, G:0.13, T:0.32
Consensus pattern (122 bp):
CCACAAAGGCTTTCCTCTCCAAAATTTTCCCATAAAGGCTGTCCTTTACATCCAATACTCGCCAC
AAAGACTTTCATGTCCAGAGATTTACCACAAAAGCTGTCATTTACATCCAATACTTA
Done.