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 128 of 276
Found at i:41347556 original size:57 final size:57
Alignment explanation
Indices: 41347487--41347673 Score: 286
Period size: 57 Copynumber: 3.2 Consensus size: 57
41347477 AAGTGAACAT
* *
41347487 AGGCACTGTGTGTGTGAGTTCCGTAACCGAGCACTGTGTGTGCGAGATC-GATTGTTG
1 AGGCACTGTGTGTGCGAGTTCCGTAACCGAGCACTGTGTGTGCAAGATCAG-TTGTTG
* *
41347544 AGGCACTGTGTGTGCGAGTTTCGTAACCGAGCACTGTGTGTGCAAGATCAGTTGTTA
1 AGGCACTGTGTGTGCGAGTTCCGTAACCGAGCACTGTGTGTGCAAGATCAGTTGTTG
*
41347601 AGGCACTGTGTGTGCGAGTTCCGTAACCAAGCACTGTGTGTGCAAGATCAGTTGTTG
1 AGGCACTGTGTGTGCGAGTTCCGTAACCGAGCACTGTGTGTGCAAGATCAGTTGTTG
*
41347658 GGGCACTAAGTGTGTG
1 AGGCACT--GTGTGTG
41347674 AAATGAGATC
Statistics
Matches: 119, Mismatches: 8, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
57 111 0.93
58 1 0.01
59 7 0.06
ACGTcount: A:0.20, C:0.18, G:0.34, T:0.29
Consensus pattern (57 bp):
AGGCACTGTGTGTGCGAGTTCCGTAACCGAGCACTGTGTGTGCAAGATCAGTTGTTG
Found at i:41350544 original size:93 final size:93
Alignment explanation
Indices: 41350385--41350570 Score: 336
Period size: 93 Copynumber: 2.0 Consensus size: 93
41350375 AGTTTTCATT
* * *
41350385 GTTCAAATGAAGACACGAGGATTATATCGTGTTACTGAAATAAACTACTATGAGCTTTGGGTATG
1 GTTCAAATGAAGACACAAGGATTATATCATGTTACTAAAATAAACTACTATGAGCTTTGGGTATG
41350450 GAATTACTTTGTAACACTGTGTTCTAGA
66 GAATTACTTTGTAACACTGTGTTCTAGA
*
41350478 GTTCAAATGGAGACACAAGGATTATATCATGTTACTAAAATAAACTACTATGAGCTTTGGGTATG
1 GTTCAAATGAAGACACAAGGATTATATCATGTTACTAAAATAAACTACTATGAGCTTTGGGTATG
41350543 GAATTACTTTGTAACACTGTGTTCTAGA
66 GAATTACTTTGTAACACTGTGTTCTAGA
41350571 ACCTGAAAGC
Statistics
Matches: 89, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 89 1.00
ACGTcount: A:0.33, C:0.13, G:0.20, T:0.33
Consensus pattern (93 bp):
GTTCAAATGAAGACACAAGGATTATATCATGTTACTAAAATAAACTACTATGAGCTTTGGGTATG
GAATTACTTTGTAACACTGTGTTCTAGA
Found at i:41352745 original size:28 final size:28
Alignment explanation
Indices: 41352705--41352783 Score: 104
Period size: 28 Copynumber: 2.8 Consensus size: 28
41352695 GCAATCAAAT
* * *
41352705 ATGGTACTCAGTGTACGAAATATTGAGA
1 ATGGCACTTAGTGTGCGAAATATTGAGA
*
41352733 ATGGCACTTAGTGTGCGAGATATTGAGA
1 ATGGCACTTAGTGTGCGAAATATTGAGA
* *
41352761 ATGACACTTAGTGTGCAAAATAT
1 ATGGCACTTAGTGTGCGAAATAT
41352784 CGAATGATTC
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 44 1.00
ACGTcount: A:0.34, C:0.11, G:0.25, T:0.29
Consensus pattern (28 bp):
ATGGCACTTAGTGTGCGAAATATTGAGA
Found at i:41355330 original size:6 final size:6
Alignment explanation
Indices: 41355319--41355356 Score: 60
Period size: 6 Copynumber: 6.3 Consensus size: 6
41355309 CATTCGTGCC
41355319 TTTCTT TTTCTT TTTCTT TTTCTT TTT-TT ATTTCTT TT
1 TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT -TTTCTT TT
41355357 ATTCATTCTT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
5 2 0.07
6 26 0.87
7 2 0.07
ACGTcount: A:0.03, C:0.13, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTCTT
Found at i:41357098 original size:19 final size:20
Alignment explanation
Indices: 41357061--41357098 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
41357051 ATAAGGTGGT
41357061 AAGATGATGAATGATGTTTA
1 AAGATGATGAATGATGTTTA
41357081 AAGATG-TGATAT-ATGTTT
1 AAGATGATGA-ATGATGTTT
41357099 TGGTGGTACC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.37, C:0.00, G:0.24, T:0.39
Consensus pattern (20 bp):
AAGATGATGAATGATGTTTA
Found at i:41380284 original size:43 final size:43
Alignment explanation
Indices: 41380214--41380334 Score: 113
Period size: 43 Copynumber: 2.8 Consensus size: 43
41380204 AACAAGTACA
* * * *
41380214 ATGCCGAAGTCTCAGAC-GTGGTTTTACATGTAATTC-AATATTG
1 ATGCCGATGTCCCAGACAG-GGTCTTACATGTAAATCAAATA-TG
** *
41380257 ATGCCTCTGTCCCAGACAGGGTCTTACACG-AAATCAAATATG
1 ATGCCGATGTCCCAGACAGGGTCTTACATGTAAATCAAATATG
* * *
41380299 ATGCCGATGTCCTAGACATGGTCTTATATGTAAATC
1 ATGCCGATGTCCCAGACAGGGTCTTACATGTAAATC
41380335 TCAATCGAGG
Statistics
Matches: 62, Mismatches: 13, Indels: 6
0.77 0.16 0.07
Matches are distributed among these distances:
42 30 0.48
43 31 0.50
44 1 0.02
ACGTcount: A:0.29, C:0.21, G:0.20, T:0.31
Consensus pattern (43 bp):
ATGCCGATGTCCCAGACAGGGTCTTACATGTAAATCAAATATG
Found at i:41381649 original size:43 final size:43
Alignment explanation
Indices: 41381579--41381699 Score: 113
Period size: 43 Copynumber: 2.8 Consensus size: 43
41381569 AACAAGTACA
* * * *
41381579 ATGCCGAAGTCTCAGAC-GTGGTTTTACATGTAATTC-AATATTG
1 ATGCCGATGTCCCAGACAG-GGTCTTACATGTAAATCAAATA-TG
** *
41381622 ATGCCTCTGTCCCAGACAGGGTCTTACACG-AAATCAAATATG
1 ATGCCGATGTCCCAGACAGGGTCTTACATGTAAATCAAATATG
* * *
41381664 ATGCCGATGTCCTAGACATGGTCTTATATGTAAATC
1 ATGCCGATGTCCCAGACAGGGTCTTACATGTAAATC
41381700 TCAATCGAGG
Statistics
Matches: 62, Mismatches: 13, Indels: 6
0.77 0.16 0.07
Matches are distributed among these distances:
42 30 0.48
43 31 0.50
44 1 0.02
ACGTcount: A:0.29, C:0.21, G:0.20, T:0.31
Consensus pattern (43 bp):
ATGCCGATGTCCCAGACAGGGTCTTACATGTAAATCAAATATG
Found at i:41392745 original size:25 final size:26
Alignment explanation
Indices: 41392702--41392750 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
41392692 AAGAATTTAA
41392702 AATTTTATTTTTAAATTTTTAAGAAT
1 AATTTTATTTTTAAATTTTTAAGAAT
*
41392728 AATTTTATTTTT-ATTTTTTAAGA
1 AATTTTATTTTTAAATTTTTAAGA
41392751 GTACTAACAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 10 0.45
26 12 0.55
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.61
Consensus pattern (26 bp):
AATTTTATTTTTAAATTTTTAAGAAT
Found at i:41399515 original size:22 final size:22
Alignment explanation
Indices: 41399488--41399532 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
41399478 TAACAAGAAC
41399488 ATAGCAACAAAACAGTAAAAAA
1 ATAGCAACAAAACAGTAAAAAA
*
41399510 ATAGCAACAAAATAGTAAAAAA
1 ATAGCAACAAAACAGTAAAAAA
41399532 A
1 A
41399533 GTAATTTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.69, C:0.11, G:0.09, T:0.11
Consensus pattern (22 bp):
ATAGCAACAAAACAGTAAAAAA
Found at i:41401274 original size:22 final size:21
Alignment explanation
Indices: 41401245--41401303 Score: 66
Period size: 22 Copynumber: 2.7 Consensus size: 21
41401235 TACATAAAAT
41401245 TATT-AAATATTAAATATTAAA
1 TATTAAAATATTAAATA-TAAA
*
41401266 TATTAAAATAATATAATATAAA
1 TATTAAAATATTA-AATATAAA
*
41401288 TATTTAAAAAATTAAA
1 TA-TTAAAATATTAAA
41401304 AATAGTATGA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
21 4 0.12
22 15 0.47
23 13 0.41
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (21 bp):
TATTAAAATATTAAATATAAA
Found at i:41401306 original size:7 final size:7
Alignment explanation
Indices: 41401245--41401291 Score: 60
Period size: 7 Copynumber: 6.6 Consensus size: 7
41401235 TACATAAAAT
41401245 TATTAAA
1 TATTAAA
41401252 TATTAAA
1 TATTAAA
41401259 TATTAAA
1 TATTAAA
41401266 TATTAAAA
1 TATT-AAA
*
41401274 TAATATAA
1 TATTA-AA
41401282 TA-TAAA
1 TATTAAA
41401288 TATT
1 TATT
41401292 TAAAAAATTA
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
6 4 0.11
7 22 0.61
8 10 0.28
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (7 bp):
TATTAAA
Found at i:41402380 original size:10 final size:10
Alignment explanation
Indices: 41402365--41402409 Score: 65
Period size: 10 Copynumber: 4.5 Consensus size: 10
41402355 AATTTTAGCT
41402365 TTTATCTTTA
1 TTTATCTTTA
41402375 TTTATCTTTA
1 TTTATCTTTA
*
41402385 ATTATCTTTA
1 TTTATCTTTA
41402395 TTTAT-TTGTA
1 TTTATCTT-TA
41402405 TTTAT
1 TTTAT
41402410 TTTCTAGAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
9 2 0.06
10 30 0.94
ACGTcount: A:0.22, C:0.07, G:0.02, T:0.69
Consensus pattern (10 bp):
TTTATCTTTA
Found at i:41409368 original size:34 final size:34
Alignment explanation
Indices: 41409325--41409393 Score: 120
Period size: 34 Copynumber: 2.0 Consensus size: 34
41409315 ATGTTTTTTC
* *
41409325 GGAAGAGCTTCCTGGATTTCCTCCGAATCGTGAA
1 GGAAGAGCTTCCTGGATTACCTCCGAATCGGGAA
41409359 GGAAGAGCTTCCTGGATTACCTCCGAATCGGGAA
1 GGAAGAGCTTCCTGGATTACCTCCGAATCGGGAA
41409393 G
1 G
41409394 TTGAGTTTGG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.25, C:0.23, G:0.29, T:0.23
Consensus pattern (34 bp):
GGAAGAGCTTCCTGGATTACCTCCGAATCGGGAA
Found at i:41413309 original size:38 final size:38
Alignment explanation
Indices: 41413258--41413333 Score: 143
Period size: 38 Copynumber: 2.0 Consensus size: 38
41413248 ACTGTGCTAA
*
41413258 TCAATTGTAGGACATCGGACGAGATCTCAGTAGCAGTC
1 TCAATTGTAGGACATCGGAAGAGATCTCAGTAGCAGTC
41413296 TCAATTGTAGGACATCGGAAGAGATCTCAGTAGCAGTC
1 TCAATTGTAGGACATCGGAAGAGATCTCAGTAGCAGTC
41413334 GTCGCGAATC
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.30, C:0.20, G:0.26, T:0.24
Consensus pattern (38 bp):
TCAATTGTAGGACATCGGAAGAGATCTCAGTAGCAGTC
Found at i:41432984 original size:40 final size:40
Alignment explanation
Indices: 41432929--41433149 Score: 349
Period size: 40 Copynumber: 5.6 Consensus size: 40
41432919 TATTCGAATG
41432929 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTATTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTATTGACT
41432969 ATATCCGGGCTAAGTCCCGAA-GCATTTGTGCTATTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTATTGACT
* *
41433008 ACATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTATTGACT
* *
41433048 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTATTGACC
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTATTGACT
* *
41433088 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTA-TTGACT
*
41433128 ATATCCGGG-TAAATCCCGAAGG
1 ATATCCGGGCTAAGTCCCGAAGG
41433150 TACTTGGGTT
Statistics
Matches: 167, Mismatches: 12, Indels: 5
0.91 0.07 0.03
Matches are distributed among these distances:
39 49 0.29
40 115 0.69
41 3 0.02
ACGTcount: A:0.23, C:0.24, G:0.26, T:0.27
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTATTGACT
Found at i:41433062 original size:79 final size:79
Alignment explanation
Indices: 41432931--41433148 Score: 341
Period size: 79 Copynumber: 2.8 Consensus size: 79
41432921 TTCGAATGAT
*
41432931 ATCCGGGCTAAGTCCCGAAGGCATTTGTGCTATTGACTATATCCGGGCTAAGTCCCGAAGCATTT
1 ATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTCCCGAAGCATTT
*
41432996 GTGCTATTGACTAC
66 GTGCTATTGACCAC
*
41433010 ATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTCCCGAAGGCTTT
1 ATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTCCCGAA-GCATT
*
41433075 TGTGCTATTGACCAT
65 TGTGCTATTGACCAC
* * *
41433090 ATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CTATATCCGGG-TAAATCCCGAAG
1 ATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAG-TGACTATATCCGGGCTAAGTCCCGAAG
41433149 GTACTTGGGT
Statistics
Matches: 130, Mismatches: 7, Indels: 5
0.92 0.05 0.04
Matches are distributed among these distances:
78 1 0.01
79 68 0.52
80 59 0.45
81 2 0.02
ACGTcount: A:0.23, C:0.24, G:0.26, T:0.27
Consensus pattern (79 bp):
ATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTCCCGAAGCATTT
GTGCTATTGACCAC
Found at i:41433145 original size:119 final size:119
Alignment explanation
Indices: 41432929--41433149 Score: 356
Period size: 119 Copynumber: 1.9 Consensus size: 119
41432919 TATTCGAATG
* *
41432929 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTATTGACTATATCCGGGCTAAGTCCCGAAGCAT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTATTGACCATATCCGGGCTAAGACCCGAAGCAT
* *
41432994 TTGTGCTATTGACTACATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
66 TTGTGCGATTGACTACATCCGGGCTAAATCCCGAAGGCATTTGTGCTAGTGACT
*
41433048 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTATTGACCATATCCGGGCTAAGACCCGAAGGCA
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTATTGACCATATCCGGGCTAAGACCCGAA-GCA
*
41433113 TTTGTGCGAGTTG-CTATATCCGGG-TAAATCCCGAAGG
65 TTTGTGCGA-TTGACTACATCCGGGCTAAATCCCGAAGG
41433150 TACTTGGGTT
Statistics
Matches: 94, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
119 70 0.74
120 21 0.22
121 3 0.03
ACGTcount: A:0.23, C:0.24, G:0.26, T:0.27
Consensus pattern (119 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTATTGACCATATCCGGGCTAAGACCCGAAGCAT
TTGTGCGATTGACTACATCCGGGCTAAATCCCGAAGGCATTTGTGCTAGTGACT
Found at i:41439303 original size:72 final size:72
Alignment explanation
Indices: 41439044--41439356 Score: 389
Period size: 73 Copynumber: 4.3 Consensus size: 72
41439034 AAAATCATAT
* * ** *
41439044 ATAAAAAACTATTAATAAAACTA-ATTTA-GTATAAATAAGTAGAACATAAATTTAATATCCAAA
1 ATAAACAACTATTGATAAAACTAGA-TTACACATAAATAAGTAGAACATAAATTCAATATCCAAA
*
41439107 AATCAAAC
65 AACCAAAC
* ** * * *
41439115 ATAAACAATTATTGATAAAACTAGCCCTA-AGCATAAATAATTAGACCATAAATTCGATATCCAA
1 ATAAACAACTATTGATAAAACTAG-ATTACA-CATAAATAAGTAGAACATAAATTCAATATCCAA
*
41439179 AGACCAAAC
64 AAACCAAAC
* * * * *
41439188 ATAAACAACTATTTGATAAAACTATATTACATATAAAAAAGTAGAATATAAATTCAATATCTAAA
1 ATAAACAACTA-TTGATAAAACTAGATTACACATAAATAAGTAGAACATAAATTCAATATCCAAA
41439253 AACCAAAC
65 AACCAAAC
*
41439261 ATAAACAACCATTGATAAAACTAGATTACACATAAATAAGTAGAACATAAATTCAATATCCAAAA
1 ATAAACAACTATTGATAAAACTAGATTACACATAAATAAGTAGAACATAAATTCAATATCCAAAA
41439326 ACCAAAC
66 ACCAAAC
*
41439333 ATAAATAACTATTGATAAAACTAG
1 ATAAACAACTATTGATAAAACTAG
41439357 TTTAGCATTG
Statistics
Matches: 204, Mismatches: 33, Indels: 9
0.83 0.13 0.04
Matches are distributed among these distances:
71 20 0.10
72 80 0.39
73 91 0.45
74 13 0.06
ACGTcount: A:0.55, C:0.14, G:0.06, T:0.25
Consensus pattern (72 bp):
ATAAACAACTATTGATAAAACTAGATTACACATAAATAAGTAGAACATAAATTCAATATCCAAAA
ACCAAAC
Found at i:41439808 original size:18 final size:18
Alignment explanation
Indices: 41439785--41439819 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
41439775 TCCATCAATG
* *
41439785 TGAACATCATTTGAAATA
1 TGAACACCATTTAAAATA
41439803 TGAACACCATTTAAAAT
1 TGAACACCATTTAAAAT
41439820 GTTAATATCA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.46, C:0.14, G:0.09, T:0.31
Consensus pattern (18 bp):
TGAACACCATTTAAAATA
Found at i:41442424 original size:15 final size:15
Alignment explanation
Indices: 41442404--41442436 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
41442394 AGAATGGGGC
41442404 CTAAGTAGGAATAAA
1 CTAAGTAGGAATAAA
41442419 CTAAGTAGGAATAAA
1 CTAAGTAGGAATAAA
41442434 CTA
1 CTA
41442437 GGTTTTCTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.52, C:0.09, G:0.18, T:0.21
Consensus pattern (15 bp):
CTAAGTAGGAATAAA
Found at i:41445851 original size:40 final size:39
Alignment explanation
Indices: 41445807--41445891 Score: 109
Period size: 40 Copynumber: 2.2 Consensus size: 39
41445797 TATTTCAAAC
* *
41445807 TTTTTTTATTTTT-TAATTAATGTTTTAAATTAATAAAT
1 TTTTTTTCTTTTTCTAATTAATCTTTTAAATTAATAAAT
* * *
41445845 ATTTTTTTCTTTTTCTAATTCATCTTTTTAATTAATAACT
1 -TTTTTTTCTTTTTCTAATTAATCTTTTAAATTAATAAAT
41445885 TTTTTTT
1 TTTTTTT
41445892 ATAAAATCAA
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
39 19 0.47
40 21 0.52
ACGTcount: A:0.27, C:0.06, G:0.01, T:0.66
Consensus pattern (39 bp):
TTTTTTTCTTTTTCTAATTAATCTTTTAAATTAATAAAT
Found at i:41455584 original size:14 final size:14
Alignment explanation
Indices: 41455557--41455591 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
41455547 ATCCCATTAA
* *
41455557 TAAATTAAATATTG
1 TAAATAAAAAATTG
41455571 TAAATAAAAAATTG
1 TAAATAAAAAATTG
41455585 TAAATAA
1 TAAATAA
41455592 TGAAAAAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.60, C:0.00, G:0.06, T:0.34
Consensus pattern (14 bp):
TAAATAAAAAATTG
Found at i:41458358 original size:104 final size:101
Alignment explanation
Indices: 41458176--41458449 Score: 314
Period size: 104 Copynumber: 2.6 Consensus size: 101
41458166 GAGCAGGGTT
* * * **
41458176 CACACAGGCAAGGACATGGGTGTGTGTCCAGGCCGTGTAACTCATTATTTATAATTTATAACCAC
1 CACAC-GGCAAGGACAT-GG-GTGTGTCCAGGCCGTGTAACTCACTGTTTATGATTTAGGACCAC
* * * * *
41458241 ATGGCCAGAGACATGGGCATGTGCCCAAGTTGTATGAGC
63 AAGGCCAGAGACATAGCCATGTGCCCAAGTCGTATAAGC
*
41458280 CACACGGGCAATGACATAGGCGTGTGTCCAGGCCGTGTAACTCACTGTTTATGATTTAGGACCAC
1 CACAC-GGCAAGGACAT-GG-GTGTGTCCAGGCCGTGTAACTCACTGTTTATGATTTAGGACCAC
* * * *
41458345 AAGGCCAGGGACATAGCCGTGTGCCTAGGTCGTATAAGC
63 AAGGCCAGAGACATAGCCATGTGCCCAAGTCGTATAAGC
* *
41458384 CATACGGCTAAGGATATGGGTGTGTGCCTAGGCCGTGTAACTCACTGTTTATGATTTAGGACCAC
1 CACACGGC-AAGGACATGGGTGTGT-CC-AGGCCGTGTAACTCACTGTTTATGATTTAGGACCAC
41458449 A
63 A
41458450 CAACTAGGGA
Statistics
Matches: 146, Mismatches: 21, Indels: 6
0.84 0.12 0.03
Matches are distributed among these distances:
102 6 0.04
103 7 0.05
104 133 0.91
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (101 bp):
CACACGGCAAGGACATGGGTGTGTCCAGGCCGTGTAACTCACTGTTTATGATTTAGGACCACAAG
GCCAGAGACATAGCCATGTGCCCAAGTCGTATAAGC
Found at i:41458487 original size:104 final size:103
Alignment explanation
Indices: 41458176--41458538 Score: 281
Period size: 104 Copynumber: 3.5 Consensus size: 103
41458166 GAGCAGGGTT
* * * * * **
41458176 CACACAGGCAAGGACATGGGTGTGTGTCCAGGCCGTGTAACTCATTATTTATAATTTATAACCAC
1 CACACAGGAAAGGACACGGGTGTGTG-CCAGGCCGTGTAACTCACTGTTTATGATTTAGGACCAC
* * * * * * ** *
41458241 ATGGCCAGAGACATGGGCA-TGTGCCCAAGTTGTATGAGC
65 AAGACCAGGGACAT-AGCAGTGTGCCTAGGACGTATAAGC
* * * *
41458280 CACACGGGCAATGACATAGGCGTGTGT-CCAGGCCGTGTAACTCACTGTTTATGATTTAGGACCA
1 CACACAGGAAAGGACA-CGG-GTGTGTGCCAGGCCGTGTAACTCACTGTTTATGATTTAGGACCA
* * *
41458344 CAAGGCCAGGGACATAGCCGTGTGCCTAGGTCGTATAAGC
64 CAAGACCAGGGACATAGCAGTGTGCCTAGGACGTATAAGC
* * * *
41458384 CATAC-GGCTAAGGATATGGGTGTGTGCCTAGGCCGTGTAACTCACTGTTTATGATTTAGGACCA
1 CACACAGG-AAAGGACACGGGTGTGTGCC-AGGCCGTGTAACTCACTGTTTATGATTTAGGACCA
* *
41458448 CACA-ACTAGGGACAT-G-AGTGTACGCCTA-GACAGTGTAAGC
64 CA-AGACCAGGGACATAGCAGTGT--GCCTAGGAC-GTATAAGC
* * * *
41458488 CACACAGGAAAGGACACGGGTGTATGCCCAAGCCGTGTGACTCGCTGTTTA
1 CACACAGGAAAGGACACGGGTGTGTG-CCAGGCCGTGTAACTCACTGTTTA
41458539 CAATTTAAAA
Statistics
Matches: 213, Mismatches: 34, Indels: 24
0.79 0.13 0.09
Matches are distributed among these distances:
102 10 0.05
103 11 0.05
104 179 0.84
105 7 0.03
106 6 0.03
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.23
Consensus pattern (103 bp):
CACACAGGAAAGGACACGGGTGTGTGCCAGGCCGTGTAACTCACTGTTTATGATTTAGGACCACA
AGACCAGGGACATAGCAGTGTGCCTAGGACGTATAAGC
Found at i:41459714 original size:10 final size:11
Alignment explanation
Indices: 41459696--41459753 Score: 63
Period size: 10 Copynumber: 5.7 Consensus size: 11
41459686 TAAATTCTAA
41459696 AAGATAAATAC
1 AAGATAAATAC
41459707 AA-ATAAAT-C
1 AAGATAAATAC
*
41459716 AAGATAATTA-
1 AAGATAAATAC
41459726 AAGATAAATA-
1 AAGATAAATAC
*
41459736 AGGATAAATA-
1 AAGATAAATAC
41459746 AAGATAAA
1 AAGATAAA
41459754 AGCTAAAATT
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
9 3 0.07
10 36 0.88
11 2 0.05
ACGTcount: A:0.66, C:0.03, G:0.10, T:0.21
Consensus pattern (11 bp):
AAGATAAATAC
Found at i:41459719 original size:20 final size:19
Alignment explanation
Indices: 41459696--41459753 Score: 73
Period size: 20 Copynumber: 2.9 Consensus size: 19
41459686 TAAATTCTAA
41459696 AAGATAAATACAA-ATAAAT
1 AAGATAAATA-AAGATAAAT
*
41459715 CAAGATAATTAAAGATAAAT
1 -AAGATAAATAAAGATAAAT
41459735 AAGGATAAATAAAGATAAA
1 AA-GATAAATAAAGATAAA
41459754 AGCTAAAATT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
19 4 0.12
20 30 0.88
ACGTcount: A:0.66, C:0.03, G:0.10, T:0.21
Consensus pattern (19 bp):
AAGATAAATAAAGATAAAT
Found at i:41459731 original size:30 final size:30
Alignment explanation
Indices: 41459695--41459752 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
41459685 TTAAATTCTA
*
41459695 AAAGATAAATACA-AATAAATCAAGATAATT
1 AAAGATAAATA-AGAATAAATAAAGATAATT
*
41459725 AAAGATAAATAAGGATAAATAAAGATAA
1 AAAGATAAATAAGAATAAATAAAGATAA
41459753 AAGCTAAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 1 0.04
30 24 0.96
ACGTcount: A:0.66, C:0.03, G:0.10, T:0.21
Consensus pattern (30 bp):
AAAGATAAATAAGAATAAATAAAGATAATT
Found at i:41460426 original size:3 final size:3
Alignment explanation
Indices: 41460420--41460451 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
41460410 CTTCTTCTTC
*
41460420 TTA TTA TTA TTA TCA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
41460452 GCTTAAGAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:41460620 original size:99 final size:101
Alignment explanation
Indices: 41460438--41460636 Score: 285
Period size: 99 Copynumber: 2.0 Consensus size: 101
41460428 ATTATCATTA
* *
41460438 TTATTATTATTATTGCTTAAGAATATATTGAACCTTTTGAAGCGAAGAGAGATGACAGCCAAGCA
1 TTATTATTATTATTGCTTAAGAACATATCGAACCTTTTGAAGCGAAGAGAGATGACAGCCAAGCA
* *
41460503 CCCCACCCCAGTTGCTCAGCCCAACATACTCCTAAT
66 CCCCACCCCAGTTACTCAGCCCAACAAACTCCTAAT
* * * * *
41460539 TTATTA-TATT-TTTCTTAAGAACATATCGGACCTTTTGACGTGAAGAGAGATGACAGCTAAGCA
1 TTATTATTATTATTGCTTAAGAACATATCGAACCTTTTGAAGCGAAGAGAGATGACAGCCAAGCA
* *
41460602 CCCCACCCCGGTTACTCAGCCCAACAAATTCCTAA
66 CCCCACCCCAGTTACTCAGCCCAACAAACTCCTAA
41460637 AAAAATTTAT
Statistics
Matches: 87, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
99 77 0.89
100 4 0.05
101 6 0.07
ACGTcount: A:0.32, C:0.25, G:0.15, T:0.28
Consensus pattern (101 bp):
TTATTATTATTATTGCTTAAGAACATATCGAACCTTTTGAAGCGAAGAGAGATGACAGCCAAGCA
CCCCACCCCAGTTACTCAGCCCAACAAACTCCTAAT
Found at i:41461481 original size:16 final size:15
Alignment explanation
Indices: 41461460--41461491 Score: 55
Period size: 16 Copynumber: 2.1 Consensus size: 15
41461450 GCAAAGGAAG
41461460 GTTCAGCAGTGGTAC
1 GTTCAGCAGTGGTAC
41461475 NGTTCAGCAGTGGTAC
1 -GTTCAGCAGTGGTAC
41461491 G
1 G
41461492 GCTTTTAGTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 1 0.06
16 15 0.94
ACGTcount: A:0.19, C:0.19, G:0.34, T:0.25
Consensus pattern (15 bp):
GTTCAGCAGTGGTAC
Found at i:41461807 original size:15 final size:14
Alignment explanation
Indices: 41461787--41461817 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
41461777 ATCTAAACAA
41461787 AATAAAATAATAAAT
1 AATAAAATAA-AAAT
41461802 AATAAAATAAAAAT
1 AATAAAATAAAAAT
41461816 AA
1 AA
41461818 AAATTGGGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.38
15 10 0.62
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (14 bp):
AATAAAATAAAAAT
Found at i:41463245 original size:33 final size:33
Alignment explanation
Indices: 41463203--41463280 Score: 120
Period size: 33 Copynumber: 2.4 Consensus size: 33
41463193 TTGTTTCCTT
* *
41463203 TTGGAAATCAAGAGTTTGTCGTAGTATTTGCTG
1 TTGGAAATCAAGAGTTTGCCGTAGTATCTGCTG
* *
41463236 TTGGAAATCAACAGTTTGCCGTTGTATCTGCTG
1 TTGGAAATCAAGAGTTTGCCGTAGTATCTGCTG
41463269 TTGGAAATCAAG
1 TTGGAAATCAAG
41463281 CACATTAGCT
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 40 1.00
ACGTcount: A:0.26, C:0.13, G:0.26, T:0.36
Consensus pattern (33 bp):
TTGGAAATCAAGAGTTTGCCGTAGTATCTGCTG
Found at i:41480620 original size:21 final size:21
Alignment explanation
Indices: 41480596--41480635 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
41480586 GAAATTTTAA
41480596 ATAATTATTA-ATATTTTTTGT
1 ATAATTATTAGAT-TTTTTTGT
*
41480617 ATAATTTTTAGATTTTTTT
1 ATAATTATTAGATTTTTTT
41480636 AGTTTTGAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 15 0.88
22 2 0.12
ACGTcount: A:0.30, C:0.00, G:0.05, T:0.65
Consensus pattern (21 bp):
ATAATTATTAGATTTTTTTGT
Found at i:41483359 original size:27 final size:28
Alignment explanation
Indices: 41483307--41483359 Score: 99
Period size: 28 Copynumber: 1.9 Consensus size: 28
41483297 ATGTGCGAGG
41483307 CCCCTCATGTGAACCCCTATAGGTGAGT
1 CCCCTCATGTGAACCCCTATAGGTGAGT
41483335 CCCCTCATGTGAA-CCCTATAGGTGA
1 CCCCTCATGTGAACCCCTATAGGTGA
41483360 ACCCCCTATT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
27 12 0.48
28 13 0.52
ACGTcount: A:0.23, C:0.32, G:0.21, T:0.25
Consensus pattern (28 bp):
CCCCTCATGTGAACCCCTATAGGTGAGT
Found at i:41483365 original size:27 final size:28
Alignment explanation
Indices: 41483307--41483366 Score: 95
Period size: 27 Copynumber: 2.2 Consensus size: 28
41483297 ATGTGCGAGG
**
41483307 CCCCTCATGTGAACCCCTATAGGTGAGT
1 CCCCTCATGTGAACCCCTATAGGTGAAC
41483335 CCCCTCATGTGAA-CCCTATAGGTGAAC
1 CCCCTCATGTGAACCCCTATAGGTGAAC
41483362 CCCCT
1 CCCCT
41483367 ATTGCGAACC
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
27 17 0.57
28 13 0.43
ACGTcount: A:0.22, C:0.37, G:0.18, T:0.23
Consensus pattern (28 bp):
CCCCTCATGTGAACCCCTATAGGTGAAC
Found at i:41483375 original size:27 final size:27
Alignment explanation
Indices: 41483307--41483377 Score: 81
Period size: 27 Copynumber: 2.6 Consensus size: 27
41483297 ATGTGCGAGG
* **
41483307 CCCCTCATGTGAACCCCTATAGGTGAGT
1 CCCCTCATGCGAA-CCCTATAGGTGAAC
*
41483335 CCCCTCATGTGAACCCTATAGGTGAAC
1 CCCCTCATGCGAACCCTATAGGTGAAC
41483362 CCCCT-ATTGCGAACCC
1 CCCCTCA-TGCGAACCC
41483378 ATATGCAAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
26 1 0.03
27 25 0.64
28 13 0.33
ACGTcount: A:0.23, C:0.37, G:0.18, T:0.23
Consensus pattern (27 bp):
CCCCTCATGCGAACCCTATAGGTGAAC
Found at i:41485860 original size:39 final size:39
Alignment explanation
Indices: 41485806--41486020 Score: 403
Period size: 39 Copynumber: 5.5 Consensus size: 39
41485796 TAATGGAGAA
*
41485806 TTATATCCGGGCTAAGTCCCAAAGGCATTCGTGCTGGTG
1 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
41485845 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
1 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
* *
41485884 TTATATCCGGGCTAAGTCCCGAACGCATTCGTGTTGGTG
1 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
41485923 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
1 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
41485962 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
1 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
41486001 TTATATCCGGGCTAAGTCCC
1 TTATATCCGGGCTAAGTCCC
41486021 TTATATCCGG
Statistics
Matches: 171, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 171 1.00
ACGTcount: A:0.19, C:0.24, G:0.29, T:0.29
Consensus pattern (39 bp):
TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
Found at i:41486012 original size:117 final size:117
Alignment explanation
Indices: 41485806--41486706 Score: 1191
Period size: 117 Copynumber: 7.5 Consensus size: 117
41485796 TAATGGAGAA
* * *
41485806 TTATATCCGGGCTAAGTCCCAAAGGCATTCGTGCTGGTGTTATATCCGGGCTAAGTCCCGAAGGC
1 TTATATCCGGGCTAAGTCCCGAACGCATTCGTGCTGGTGTTATATCCGGGCTAAGTCCCGAACGC
*
41485871 ATTCGTGCTGGTGTTATATCCGGGCTAAGTCCCGAACGCATTCGTGTTGGTG
66 ATTCGTGTTGGTGTTATATCCGGGCTAAGTCCCGAACGCATTCGTGTTGGTG
* *
41485923 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTGTTATATCCGGGCTAAGTCCCGAAGGC
1 TTATATCCGGGCTAAGTCCCGAACGCATTCGTGCTGGTGTTATATCCGGGCTAAGTCCCGAACGC
* * * ** **
41485988 ATTCGTGCTGGTGTTATATCCGGGCTAAGTCCCTTATATCCGGGCTAAGTC-TCGAAGGCA
66 ATTCGTGTTGGTGTTATATCCGGGCTAAGTCCC-GA-A--C--GC--ATTCGT-GTTGGTG
* * * * ** ** * * *
41486048 TTCGT-GCTGGTGTTATA-T-CCGGGCTAAGTCCCGAAGGCATTCGTGTTGGTGTTATATCCGGG
1 TT-ATATCCGG-GCTA-AGTCCCGAACGCA-T-TCG--TGC--TGGTGTT------ATATCCGGG
41486110 CTAAGTCCCGAACGCATTCGTGTTGGTGTTATATCCGGGCTAAGTCCCGAACGCATTCGTGTTGG
51 CTAAGTCCCGAACGCATTCGTGTTGGTGTTATATCCGGGCTAAGTCCCGAACGCATTCGTGTTGG
41486175 TG
116 TG
*
41486177 TTATATCCGGGCTAAGTCCCGAACGCATTCGTGTTGGTGTTATATCCGGGCTAAGTCCCGAACGC
1 TTATATCCGGGCTAAGTCCCGAACGCATTCGTGCTGGTGTTATATCCGGGCTAAGTCCCGAACGC
41486242 ATTCGTGTTGGTGTTATATCCGGGCTAAGTCCCGAACGCATTCGTGTTGGTG
66 ATTCGTGTTGGTGTTATATCCGGGCTAAGTCCCGAACGCATTCGTGTTGGTG
*
41486294 TTATATCCGGGCTAAGTCCCGAACGCATTCGTGTTGGTGTTATATCCGGGCTAAGTCCCGAACGC
1 TTATATCCGGGCTAAGTCCCGAACGCATTCGTGCTGGTGTTATATCCGGGCTAAGTCCCGAACGC
41486359 ATTCGTGTTGGTGTTATATCCGGGCTAAGTCCCGAACGCATTCGTGTTGGTG
66 ATTCGTGTTGGTGTTATATCCGGGCTAAGTCCCGAACGCATTCGTGTTGGTG
*
41486411 TTATATCCGGGCTAAGTCCCGAACGCATTCGTGTTGGTGTTATATCCGGGCTAAGTCCCGAACGC
1 TTATATCCGGGCTAAGTCCCGAACGCATTCGTGCTGGTGTTATATCCGGGCTAAGTCCCGAACGC
41486476 ATTCGTGTTGGTGTTATATCCGGGCTAAGTCCCGAACGCATTCGTGTTGGTG
66 ATTCGTGTTGGTGTTATATCCGGGCTAAGTCCCGAACGCATTCGTGTTGGTG
*
41486528 TTATATCCGGGCTAAGTCCCGAACGCATTCGTGTTGGTGTTATATCCGGGCTAAGTCCCGAACGC
1 TTATATCCGGGCTAAGTCCCGAACGCATTCGTGCTGGTGTTATATCCGGGCTAAGTCCCGAACGC
* *
41486593 ATTCGTGTTGGTGTTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
66 ATTCGTGTTGGTGTTATATCCGGGCTAAGTCCCGAACGCATTCGTGTTGGTG
* *** * * *
41486645 TTAAATCCGGGCTAAAGTCCCGCGGGC-TTTGTGCTAGTATTATATCCGGGCTTAAAGTCCCG
1 TTATATCCGGGCT-AAGTCCCGAACGCATTCGTGCTGGTGTTATATCCGGGC-T-AAGTCCCG
41486707 CATGCTTTAT
Statistics
Matches: 704, Mismatches: 49, Indels: 60
0.87 0.06 0.07
Matches are distributed among these distances:
117 554 0.79
118 12 0.02
119 9 0.01
121 1 0.00
123 8 0.01
124 1 0.00
125 16 0.02
126 6 0.01
127 6 0.01
128 6 0.01
129 18 0.03
130 1 0.00
131 8 0.01
133 1 0.00
135 1 0.00
136 1 0.00
137 55 0.08
ACGTcount: A:0.18, C:0.23, G:0.29, T:0.30
Consensus pattern (117 bp):
TTATATCCGGGCTAAGTCCCGAACGCATTCGTGCTGGTGTTATATCCGGGCTAAGTCCCGAACGC
ATTCGTGTTGGTGTTATATCCGGGCTAAGTCCCGAACGCATTCGTGTTGGTG
Found at i:41486026 original size:20 final size:20
Alignment explanation
Indices: 41486001--41486038 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
41485991 CGTGCTGGTG
41486001 TTATATCCGGGCTAAGTCCC
1 TTATATCCGGGCTAAGTCCC
41486021 TTATATCCGGGCTAAGTC
1 TTATATCCGGGCTAAGTC
41486039 TCGAAGGCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.21, C:0.26, G:0.21, T:0.32
Consensus pattern (20 bp):
TTATATCCGGGCTAAGTCCC
Found at i:41486054 original size:59 final size:59
Alignment explanation
Indices: 41485962--41486079 Score: 227
Period size: 59 Copynumber: 2.0 Consensus size: 59
41485952 CGTGCTGGTG
41485962 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTGTTATATCCGGGCTAAGTCCC
1 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTGTTATATCCGGGCTAAGTCCC
*
41486021 TTATATCCGGGCTAAGTCTCGAAGGCATTCGTGCTGGTGTTATATCCGGGCTAAGTCCC
1 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTGTTATATCCGGGCTAAGTCCC
41486080 GAAGGCATTC
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
59 58 1.00
ACGTcount: A:0.19, C:0.25, G:0.27, T:0.30
Consensus pattern (59 bp):
TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTGTTATATCCGGGCTAAGTCCC
Found at i:41486092 original size:98 final size:98
Alignment explanation
Indices: 41485923--41486118 Score: 374
Period size: 98 Copynumber: 2.0 Consensus size: 98
41485913 CGTGTTGGTG
41485923 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTGTTATATCCGGGCTAAGTCCCGAAGGC
1 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTGTTATATCCGGGCTAAGTCCCGAAGGC
41485988 ATTCGTGCTGGTGTTATATCCGGGCTAAGTCCC
66 ATTCGTGCTGGTGTTATATCCGGGCTAAGTCCC
*
41486021 TTATATCCGGGCTAAGTCTCGAAGGCATTCGTGCTGGTGTTATATCCGGGCTAAGTCCCGAAGGC
1 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTGTTATATCCGGGCTAAGTCCCGAAGGC
*
41486086 ATTCGTGTTGGTGTTATATCCGGGCTAAGTCCC
66 ATTCGTGCTGGTGTTATATCCGGGCTAAGTCCC
41486119 GAACGCATTC
Statistics
Matches: 96, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
98 96 1.00
ACGTcount: A:0.18, C:0.23, G:0.29, T:0.30
Consensus pattern (98 bp):
TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTGTTATATCCGGGCTAAGTCCCGAAGGC
ATTCGTGCTGGTGTTATATCCGGGCTAAGTCCC
Found at i:41486130 original size:137 final size:137
Alignment explanation
Indices: 41485884--41486157 Score: 494
Period size: 137 Copynumber: 2.0 Consensus size: 137
41485874 CGTGCTGGTG
*
41485884 TTATATCCGGGCTAAGTCCCGAACGCATTCGTGTTGGTGTTATATCCGGGCTAAGTCCCGAAGGC
1 TTATATCCGGGCTAAGTCCCGAACGCATTCGTGCTGGTGTTATATCCGGGCTAAGTCCCGAAGGC
*
41485949 ATTCGTGCTGGTGTTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTGTTATATCCGGGCT
66 ATTCGTGCTGGTGTTATATCCGGGCTAAGTCCCGAACGCATTCGTGCTGGTGTTATATCCGGGCT
41486014 AAGTCCC
131 AAGTCCC
* *
41486021 TTATATCCGGGCTAAGTCTCGAAGGCATTCGTGCTGGTGTTATATCCGGGCTAAGTCCCGAAGGC
1 TTATATCCGGGCTAAGTCCCGAACGCATTCGTGCTGGTGTTATATCCGGGCTAAGTCCCGAAGGC
* *
41486086 ATTCGTGTTGGTGTTATATCCGGGCTAAGTCCCGAACGCATTCGTGTTGGTGTTATATCCGGGCT
66 ATTCGTGCTGGTGTTATATCCGGGCTAAGTCCCGAACGCATTCGTGCTGGTGTTATATCCGGGCT
41486151 AAGTCCC
131 AAGTCCC
41486158 GAACGCATTC
Statistics
Matches: 131, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
137 131 1.00
ACGTcount: A:0.18, C:0.23, G:0.28, T:0.30
Consensus pattern (137 bp):
TTATATCCGGGCTAAGTCCCGAACGCATTCGTGCTGGTGTTATATCCGGGCTAAGTCCCGAAGGC
ATTCGTGCTGGTGTTATATCCGGGCTAAGTCCCGAACGCATTCGTGCTGGTGTTATATCCGGGCT
AAGTCCC
Found at i:41486696 original size:39 final size:39
Alignment explanation
Indices: 41486021--41486666 Score: 1220
Period size: 39 Copynumber: 16.5 Consensus size: 39
41486011 GCTAAGTCCC
* * *
41486021 TTATATCCGGGCTAAGTCTCGAAGGCATTCGTGCTGGTG
1 TTATATCCGGGCTAAGTCCCGAACGCATTCGTGTTGGTG
*
41486060 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGTTGGTG
1 TTATATCCGGGCTAAGTCCCGAACGCATTCGTGTTGGTG
41486099 TTATATCCGGGCTAAGTCCCGAACGCATTCGTGTTGGTG
1 TTATATCCGGGCTAAGTCCCGAACGCATTCGTGTTGGTG
41486138 TTATATCCGGGCTAAGTCCCGAACGCATTCGTGTTGGTG
1 TTATATCCGGGCTAAGTCCCGAACGCATTCGTGTTGGTG
41486177 TTATATCCGGGCTAAGTCCCGAACGCATTCGTGTTGGTG
1 TTATATCCGGGCTAAGTCCCGAACGCATTCGTGTTGGTG
41486216 TTATATCCGGGCTAAGTCCCGAACGCATTCGTGTTGGTG
1 TTATATCCGGGCTAAGTCCCGAACGCATTCGTGTTGGTG
41486255 TTATATCCGGGCTAAGTCCCGAACGCATTCGTGTTGGTG
1 TTATATCCGGGCTAAGTCCCGAACGCATTCGTGTTGGTG
41486294 TTATATCCGGGCTAAGTCCCGAACGCATTCGTGTTGGTG
1 TTATATCCGGGCTAAGTCCCGAACGCATTCGTGTTGGTG
41486333 TTATATCCGGGCTAAGTCCCGAACGCATTCGTGTTGGTG
1 TTATATCCGGGCTAAGTCCCGAACGCATTCGTGTTGGTG
41486372 TTATATCCGGGCTAAGTCCCGAACGCATTCGTGTTGGTG
1 TTATATCCGGGCTAAGTCCCGAACGCATTCGTGTTGGTG
41486411 TTATATCCGGGCTAAGTCCCGAACGCATTCGTGTTGGTG
1 TTATATCCGGGCTAAGTCCCGAACGCATTCGTGTTGGTG
41486450 TTATATCCGGGCTAAGTCCCGAACGCATTCGTGTTGGTG
1 TTATATCCGGGCTAAGTCCCGAACGCATTCGTGTTGGTG
41486489 TTATATCCGGGCTAAGTCCCGAACGCATTCGTGTTGGTG
1 TTATATCCGGGCTAAGTCCCGAACGCATTCGTGTTGGTG
41486528 TTATATCCGGGCTAAGTCCCGAACGCATTCGTGTTGGTG
1 TTATATCCGGGCTAAGTCCCGAACGCATTCGTGTTGGTG
41486567 TTATATCCGGGCTAAGTCCCGAACGCATTCGTGTTGGTG
1 TTATATCCGGGCTAAGTCCCGAACGCATTCGTGTTGGTG
* *
41486606 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
1 TTATATCCGGGCTAAGTCCCGAACGCATTCGTGTTGGTG
*
41486645 TTAAATCCGGGCTAAAGTCCCG
1 TTATATCCGGGCT-AAGTCCCG
41486667 CGGGCTTTGT
Statistics
Matches: 600, Mismatches: 6, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
39 592 0.99
40 8 0.01
ACGTcount: A:0.18, C:0.23, G:0.28, T:0.30
Consensus pattern (39 bp):
TTATATCCGGGCTAAGTCCCGAACGCATTCGTGTTGGTG
Found at i:41489597 original size:42 final size:42
Alignment explanation
Indices: 41489538--41489621 Score: 168
Period size: 42 Copynumber: 2.0 Consensus size: 42
41489528 AGAACAATAG
41489538 CATCAGTCATCATGTCAGACCTAAAATTCAAAAATAAAAAAT
1 CATCAGTCATCATGTCAGACCTAAAATTCAAAAATAAAAAAT
41489580 CATCAGTCATCATGTCAGACCTAAAATTCAAAAATAAAAAAT
1 CATCAGTCATCATGTCAGACCTAAAATTCAAAAATAAAAAAT
41489622 TAACTCACAC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.50, C:0.19, G:0.07, T:0.24
Consensus pattern (42 bp):
CATCAGTCATCATGTCAGACCTAAAATTCAAAAATAAAAAAT
Found at i:41495312 original size:46 final size:46
Alignment explanation
Indices: 41495245--41495559 Score: 399
Period size: 46 Copynumber: 6.8 Consensus size: 46
41495235 TGTAACCCAC
* * * * *
41495245 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCAT
* *
41495291 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-ATTTGCAT
* *
41495341 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCAT
* *
41495384 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-ATTTGCAT
* *
41495434 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCAT
41495477 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCAT
41495523 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
41495560 TGCTCAACCA
Statistics
Matches: 234, Mismatches: 21, Indels: 28
0.83 0.07 0.10
Matches are distributed among these distances:
43 12 0.05
44 4 0.02
45 4 0.02
46 138 0.59
47 58 0.25
48 4 0.02
49 4 0.02
50 10 0.04
ACGTcount: A:0.29, C:0.28, G:0.20, T:0.22
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCAT
Found at i:41495364 original size:93 final size:93
Alignment explanation
Indices: 41495252--41495559 Score: 489
Period size: 93 Copynumber: 3.3 Consensus size: 93
41495242 CACCCATAAG
* * * *
41495252 CGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCATAAGTGAACTCGGACTCAACTCA
41495317 ACGAGTTCGGATGCCTAGTTACATCTCA
66 ACGAGTTCGGATGCCTAGTTACATCTCA
41495345 CGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCATAAGTGAACTCGGACTCAACTCA
41495410 ACGAGTTCGGATGCCTAGTTACATCTCA
66 ACGAGTTCGGATGCCTAGTTACATCTCA
41495438 CGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCATAAGTGAACTCGGACTCAACTCA
* * *
41495503 ACGAGTTCGGA---C-ATTTGCATCCATAA
66 ACGAGTTCGGATGCCTAGTTACAT-C-TCA
*
41495529 GTGAACTCGGACTCAACTCAACGAGTTCGGA
1 -CGAACTCGGACTCAACTCAACGAGTTCGGA
41495560 TGCTCAACCA
Statistics
Matches: 204, Mismatches: 8, Indels: 7
0.93 0.04 0.03
Matches are distributed among these distances:
89 6 0.03
90 2 0.01
91 2 0.01
92 29 0.14
93 165 0.81
ACGTcount: A:0.29, C:0.28, G:0.20, T:0.22
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATCTCA
Found at i:41495495 original size:139 final size:138
Alignment explanation
Indices: 41495299--41495562 Score: 433
Period size: 139 Copynumber: 1.9 Consensus size: 138
41495289 ATCCATAAGT
*
41495299 GAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACATCTCACGAACTCGGACTCAACTCA
1 GAACTCGGACTCAACTCAACGAGTTCGGA--CCTAGTTACATCTAACGAACTCGGACTCAACTCA
41495364 ACGAGTTCGGACATTTGCATCCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGT
64 ACGAGTTCGGACATTTGCATCCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGT
41495429 TACATCTCAC
129 TACATCTCAC
* * *
41495439 GAACTCGGACTCAACTCAACGAGTTCGGA-C-ATTTGCATCCATAAGTGAACTCGGACTCAACTC
1 GAACTCGGACTCAACTCAACGAGTTCGGACCTAGTTACAT-C-TAA-CGAACTCGGACTCAACTC
41495502 AACGAGTTCGGACATTTGCATCCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGC
63 AACGAGTTCGGACATTTGCATCCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGC
41495563 TCAACCATCC
Statistics
Matches: 117, Mismatches: 4, Indels: 7
0.91 0.03 0.05
Matches are distributed among these distances:
136 6 0.05
137 2 0.02
138 2 0.02
139 78 0.67
140 29 0.25
ACGTcount: A:0.29, C:0.28, G:0.20, T:0.23
Consensus pattern (138 bp):
GAACTCGGACTCAACTCAACGAGTTCGGACCTAGTTACATCTAACGAACTCGGACTCAACTCAAC
GAGTTCGGACATTTGCATCCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTA
CATCTCAC
Found at i:41506836 original size:29 final size:29
Alignment explanation
Indices: 41506790--41506856 Score: 80
Period size: 29 Copynumber: 2.3 Consensus size: 29
41506780 CTTACATTGT
* *
41506790 GAACCCTACTTGTTTGAAATCCTAGGTGC
1 GAACCCTACTTGTATGAAACCCTAGGTGC
* * *
41506819 GAACCCTGCTTGTATGAACCCCTAGGTGT
1 GAACCCTACTTGTATGAAACCCTAGGTGC
*
41506848 GCACCCTAC
1 GAACCCTAC
41506857 CTGAGCGAAC
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.22, C:0.30, G:0.21, T:0.27
Consensus pattern (29 bp):
GAACCCTACTTGTATGAAACCCTAGGTGC
Found at i:41516257 original size:47 final size:47
Alignment explanation
Indices: 41516203--41516426 Score: 205
Period size: 47 Copynumber: 4.8 Consensus size: 47
41516193 TCGGTAAGGT
* *
41516203 GTCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCAT-ATTTCAA
1 GTCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCATCATCTC-A
* *
41516250 GTCGATGCTATGTCCCAAACATGGTCTTACACT-GAC-CATCATCTCGTA
1 GTCGATGCCATGTCCCAGACATGGTCTTACACTAG-CTCATCATCTC--A
* * * *
41516298 GCCGATG-CATGTCCCAGACAT-GTCTTACACTAGTTTA-CGTCTCGA
1 GTCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCATCATCTC-A
* * *
41516343 GGCTGATG-CATGTCCCAGACAT-GTCTTACACTAGCAC-TCGTCTCA
1 GTC-GATGCCATGTCCCAGACATGGTCTTACACTAGCTCATCATCTCA
*
41516388 GTGCCGATGCCATGTCCAAGACATGGTCTTACACTAGCT
1 GT--CGATGCCATGTCCCAGACATGGTCTTACACTAGCT
41516427 TCCACAATGT
Statistics
Matches: 148, Mismatches: 18, Indels: 21
0.79 0.10 0.11
Matches are distributed among these distances:
45 5 0.03
46 59 0.40
47 64 0.43
48 20 0.14
ACGTcount: A:0.23, C:0.29, G:0.20, T:0.28
Consensus pattern (47 bp):
GTCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCATCATCTCA
Found at i:41516341 original size:46 final size:47
Alignment explanation
Indices: 41516205--41516470 Score: 185
Period size: 46 Copynumber: 5.7 Consensus size: 47
41516195 GGTAAGGTGT
* * * * *
41516205 CGATGCCATGTCCCAGACATGGTCTTACACTGGCTCATA--TTTC-AAGT
1 CGATG-CATGTCCCAGACAT-GTCTTACACTAGCT-TTACGTCTCGTAGC
* ** *
41516252 CGATGCTATGTCCCAAACATGGTCTTACACT-GACCAT-CATCTCGTAGC
1 CGATGC-ATGTCCCAGACAT-GTCTTACACTAG-CTTTACGTCTCGTAGC
41516300 CGATGCATGTCCCAGACATGTCTTACACTAG-TTTACGTCTCG-AGGC
1 CGATGCATGTCCCAGACATGTCTTACACTAGCTTTACGTCTCGTA-GC
* **
41516346 TGATGCATGTCCCAGACATGTCTTACACTAGCACT-CGTCTCAGT-GC
1 CGATGCATGTCCCAGACATGTCTTACACTAGCTTTACGTCTC-GTAGC
* * ** *
41516392 CGATGCCATGTCCAAGACATGGTCTTACACTAGCTTCCAC-AAT-GTGGC
1 CGATG-CATGTCCCAGACAT-GTCTTACACTAGCTT-TACGTCTCGTAGC
* *
41516440 CAATGCATGTTCCAGACATGTCTTACACTAG
1 CGATGCATGTCCCAGACATGTCTTACACTAG
41516471 TACACACAAG
Statistics
Matches: 181, Mismatches: 22, Indels: 33
0.77 0.09 0.14
Matches are distributed among these distances:
45 2 0.01
46 76 0.42
47 74 0.41
48 27 0.15
49 1 0.01
50 1 0.01
ACGTcount: A:0.24, C:0.29, G:0.19, T:0.28
Consensus pattern (47 bp):
CGATGCATGTCCCAGACATGTCTTACACTAGCTTTACGTCTCGTAGC
Found at i:41516449 original size:47 final size:44
Alignment explanation
Indices: 41516348--41516470 Score: 124
Period size: 47 Copynumber: 2.6 Consensus size: 44
41516338 CTCGAGGCTG
* *
41516348 ATGCATGTCCCAGACATGTCTTACACTAGCACTCGTCTCAGTGCCG
1 ATGCATGT-CCAGACATGTCTTACACTAGCACTCG-CACAGTGCCA
*
41516394 ATGCCATGTCCAAGACATGGTCTTACACTAGC-TTC-CACAATGTGGCCA
1 ATG-CATGTCC-AGACAT-GTCTTACACTAGCACTCGCAC-A-GT-GCCA
41516442 ATGCATGTTCCAGACATGTCTTACACTAG
1 ATGCATG-TCCAGACATGTCTTACACTAG
41516471 TACACACAAG
Statistics
Matches: 67, Mismatches: 3, Indels: 14
0.80 0.04 0.17
Matches are distributed among these distances:
45 2 0.03
46 18 0.27
47 25 0.37
48 22 0.33
ACGTcount: A:0.25, C:0.29, G:0.19, T:0.27
Consensus pattern (44 bp):
ATGCATGTCCAGACATGTCTTACACTAGCACTCGCACAGTGCCA
Found at i:41517180 original size:12 final size:12
Alignment explanation
Indices: 41517163--41517187 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
41517153 AAAAAATGTA
41517163 AAAATCATCAAG
1 AAAATCATCAAG
41517175 AAAATCATCAAG
1 AAAATCATCAAG
41517187 A
1 A
41517188 TCACTTACAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.60, C:0.16, G:0.08, T:0.16
Consensus pattern (12 bp):
AAAATCATCAAG
Found at i:41523706 original size:46 final size:46
Alignment explanation
Indices: 41523620--41523838 Score: 200
Period size: 46 Copynumber: 4.7 Consensus size: 46
41523610 GTAAGGTGTC
41523620 GATGCCATGTCCCAGACATGGTCTTACACT-GAC-TATCATCTCGTAGCT
1 GATG-CATGTCCCAGACAT-GTCTTACACTAG-CTTA-CATCTCGTAGCT
* *
41523668 GATGCATGTCCCAAACATGTCTTACACTGGCTTACATCTCG-AGGCT
1 GATGCATGTCCCAGACATGTCTTACACTAGCTTACATCTCGTA-GCT
* *
41523714 GATGCATGTCCCAGACATGTCTTACACTAGCACT-CGTCTCAGT-G-T
1 GATGCATGTCCCAGACATGTCTTACACTAGC-TTACATCTC-GTAGCT
* * * * *
41523759 CGGTGCCATGTCCCAGACATAGTCTTACACTAGCTTCCATAAT-GTGGCC
1 -GATG-CATGTCCCAGACAT-GTCTTACACTAGCTTACAT-CTCGTAGCT
*
41523808 GATGCATGTCCCAGAAATGTCTTACACTAGC
1 GATGCATGTCCCAGACATGTCTTACACTAGC
41523839 ACATACAAGT
Statistics
Matches: 146, Mismatches: 12, Indels: 28
0.78 0.06 0.15
Matches are distributed among these distances:
45 2 0.01
46 72 0.49
47 48 0.33
48 23 0.16
49 1 0.01
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.28
Consensus pattern (46 bp):
GATGCATGTCCCAGACATGTCTTACACTAGCTTACATCTCGTAGCT
Found at i:41524517 original size:12 final size:12
Alignment explanation
Indices: 41524500--41524524 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
41524490 CAAAAATGTA
41524500 AAAATCATCAAG
1 AAAATCATCAAG
41524512 AAAATCATCAAG
1 AAAATCATCAAG
41524524 A
1 A
41524525 TCACTTACAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.60, C:0.16, G:0.08, T:0.16
Consensus pattern (12 bp):
AAAATCATCAAG
Found at i:41525399 original size:44 final size:45
Alignment explanation
Indices: 41525313--41525410 Score: 135
Period size: 44 Copynumber: 2.2 Consensus size: 45
41525303 ATTGTTTGGG
41525313 AAGCAATATTCACGTAGAGGTACAAAAAACAAAACAAATGTATGGA
1 AAGCAATATTCACGTAGAGGTA-AAAAAACAAAACAAATGTATGGA
* * ** *
41525359 AAGCAATATTCATGTGGAGGT-AAAAAACAAAACATGTGTATGGG
1 AAGCAATATTCACGTAGAGGTAAAAAAACAAAACAAATGTATGGA
41525403 AAGCAATA
1 AAGCAATA
41525411 CGTGGGGATC
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
44 28 0.60
46 19 0.40
ACGTcount: A:0.49, C:0.11, G:0.20, T:0.19
Consensus pattern (45 bp):
AAGCAATATTCACGTAGAGGTAAAAAAACAAAACAAATGTATGGA
Found at i:41527865 original size:10 final size:10
Alignment explanation
Indices: 41527850--41527882 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
41527840 AGGTGTTCAT
*
41527850 GGGCCGGGCC
1 GGGCCGAGCC
41527860 GGGCCGAGCC
1 GGGCCGAGCC
41527870 GGGCCGAGCC
1 GGGCCGAGCC
41527880 GGG
1 GGG
41527883 TTCGGGTCAG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.06, C:0.36, G:0.58, T:0.00
Consensus pattern (10 bp):
GGGCCGAGCC
Found at i:41528234 original size:30 final size:31
Alignment explanation
Indices: 41528176--41528239 Score: 105
Period size: 31 Copynumber: 2.1 Consensus size: 31
41528166 ACTTAACAAG
41528176 CAAATGCTTCTAAAATAATAATAAAAATTAA
1 CAAATGCTTCTAAAATAATAATAAAAATTAA
41528207 CAAATGCCTT-TAAAATAATAA-AAAAATTAA
1 CAAATG-CTTCTAAAATAATAATAAAAATTAA
41528237 CAA
1 CAA
41528240 TAAAATAAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
30 12 0.38
31 17 0.53
32 3 0.09
ACGTcount: A:0.59, C:0.11, G:0.03, T:0.27
Consensus pattern (31 bp):
CAAATGCTTCTAAAATAATAATAAAAATTAA
Found at i:41529866 original size:5 final size:5
Alignment explanation
Indices: 41529848--41529882 Score: 61
Period size: 5 Copynumber: 6.8 Consensus size: 5
41529838 CTAATTTAAC
41529848 ATAAA ATCAAA ATAAA ATAAA ATAAA ATAAA ATAA
1 ATAAA AT-AAA ATAAA ATAAA ATAAA ATAAA ATAA
41529883 GATTTTTTCC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
5 24 0.83
6 5 0.17
ACGTcount: A:0.77, C:0.03, G:0.00, T:0.20
Consensus pattern (5 bp):
ATAAA
Found at i:41541363 original size:47 final size:47
Alignment explanation
Indices: 41541311--41541406 Score: 183
Period size: 47 Copynumber: 2.0 Consensus size: 47
41541301 CCGTGACTAA
41541311 ATGAGTTTATAATTAATAGGTGAAAAGCTGGAATTTAATTATAAATC
1 ATGAGTTTATAATTAATAGGTGAAAAGCTGGAATTTAATTATAAATC
*
41541358 ATGAGTTTATAATTAATAGGTGAAAAGTTGGAATTTAATTATAAATC
1 ATGAGTTTATAATTAATAGGTGAAAAGCTGGAATTTAATTATAAATC
41541405 AT
1 AT
41541407 TTGAGCCCTA
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 48 1.00
ACGTcount: A:0.43, C:0.03, G:0.17, T:0.38
Consensus pattern (47 bp):
ATGAGTTTATAATTAATAGGTGAAAAGCTGGAATTTAATTATAAATC
Found at i:41541739 original size:8 final size:9
Alignment explanation
Indices: 41541726--41541761 Score: 51
Period size: 8 Copynumber: 4.3 Consensus size: 9
41541716 GAGTTGAGAA
41541726 AATT-ATTT
1 AATTAATTT
41541734 AATT-ATTT
1 AATTAATTT
41541742 AATTAATTT
1 AATTAATTT
41541751 -ATTAATTT
1 AATTAATTT
41541759 AAT
1 AAT
41541762 ATGTTTACTG
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
8 20 0.77
9 6 0.23
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (9 bp):
AATTAATTT
Found at i:41542714 original size:18 final size:18
Alignment explanation
Indices: 41542691--41542727 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
41542681 GTCCAACAGG
41542691 CCTATGTGTAAATTTCGA
1 CCTATGTGTAAATTTCGA
41542709 CCTATGTGTAAATTTCGA
1 CCTATGTGTAAATTTCGA
41542727 C
1 C
41542728 GCTTCAATTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.27, C:0.19, G:0.16, T:0.38
Consensus pattern (18 bp):
CCTATGTGTAAATTTCGA
Found at i:41545587 original size:21 final size:21
Alignment explanation
Indices: 41545553--41545594 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
41545543 CATGTTAAGT
*
41545553 GTCAAATTAAAATTATCATGG
1 GTCAAATTAAAATTATAATGG
**
41545574 GTCAAATTGGAATTATAATGG
1 GTCAAATTAAAATTATAATGG
41545595 ACTAAAATAG
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:0.40, C:0.07, G:0.19, T:0.33
Consensus pattern (21 bp):
GTCAAATTAAAATTATAATGG
Found at i:41556939 original size:42 final size:42
Alignment explanation
Indices: 41556826--41556943 Score: 121
Period size: 43 Copynumber: 2.8 Consensus size: 42
41556816 CGGAAAGCTC
* ** *
41556826 ATACAATGCCAACATCCTAGATGTGGTCTTACATGTAATCAA
1 ATACAATGCCAACGTCCTAGACATGGTCTTACATGAAATCAA
* * * *
41556868 AAATCAATGCC-ACTGTCCCAGGCAGGGTCTTACATGAAATCAA
1 ATA-CAATGCCAAC-GTCCTAGACATGGTCTTACATGAAATCAA
* *
41556911 ATACGATGCCAACGTCCTAGACCTGGTCTTACA
1 ATACAATGCCAACGTCCTAGACATGGTCTTACA
41556944 CATAAATTGT
Statistics
Matches: 59, Mismatches: 14, Indels: 6
0.75 0.18 0.08
Matches are distributed among these distances:
42 26 0.44
43 33 0.56
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (42 bp):
ATACAATGCCAACGTCCTAGACATGGTCTTACATGAAATCAA
Found at i:41562151 original size:24 final size:25
Alignment explanation
Indices: 41562123--41562186 Score: 78
Period size: 24 Copynumber: 2.6 Consensus size: 25
41562113 TCAACCGAAT
* * *
41562123 TCGCACACATAGTGCTA-ATTAAGC
1 TCGCACACATAGTGCCATACTAAAC
*
41562147 TCGCACACATACTGCCATACTAAAC
1 TCGCACACATAGTGCCATACTAAAC
41562172 -CGCACACATAGTGCC
1 TCGCACACATAGTGCC
41562187 TAAAATTTTC
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
24 29 0.85
25 5 0.15
ACGTcount: A:0.33, C:0.33, G:0.14, T:0.20
Consensus pattern (25 bp):
TCGCACACATAGTGCCATACTAAAC
Found at i:41562237 original size:24 final size:24
Alignment explanation
Indices: 41562210--41562255 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
41562200 CATGCATCGA
41562210 CATTCAAATCT-GCACACATAGTGC
1 CATT-AAATCTCGCACACATAGTGC
* *
41562234 CATTTAATTTCGCACACATAGT
1 CATTAAATCTCGCACACATAGT
41562256 TCCAATGTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 4 0.21
24 15 0.79
ACGTcount: A:0.33, C:0.26, G:0.11, T:0.30
Consensus pattern (24 bp):
CATTAAATCTCGCACACATAGTGC
Found at i:41564558 original size:23 final size:23
Alignment explanation
Indices: 41564514--41564559 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
41564504 ATGTGGAGGG
*
41564514 AATCAAGGAGAGGATTGGGGAGA
1 AATCAAGGAGAGGATTAGGGAGA
*
41564537 AATCAAGGAGAGGATTATGGAGA
1 AATCAAGGAGAGGATTAGGGAGA
41564560 GATTTTAGGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.41, C:0.04, G:0.39, T:0.15
Consensus pattern (23 bp):
AATCAAGGAGAGGATTAGGGAGA
Found at i:41566029 original size:26 final size:26
Alignment explanation
Indices: 41565972--41566034 Score: 83
Period size: 26 Copynumber: 2.4 Consensus size: 26
41565962 TTTAGTCTTT
41565972 ATACTGATTACTGGCAGCTTTGCTGC
1 ATACTGATTACTGGCAGCTTTGCTGC
* *
41565998 ACTACTG-TTATTGGCAGCTTTGCTGTG
1 A-TACTGATTACTGGCAGCTTTGCTG-C
41566025 ATACTGATTA
1 ATACTGATTA
41566035 GTGCCACAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
26 23 0.72
27 9 0.28
ACGTcount: A:0.21, C:0.19, G:0.22, T:0.38
Consensus pattern (26 bp):
ATACTGATTACTGGCAGCTTTGCTGC
Found at i:41570697 original size:6 final size:6
Alignment explanation
Indices: 41570687--41570753 Score: 55
Period size: 6 Copynumber: 11.2 Consensus size: 6
41570677 CATAAAAAGC
* * * * *
41570687 AAAATA GAAATA AAAATA AAAAT- AAGATA AAAGATA AAAGTA AAGAGA
1 AAAATA AAAATA AAAATA AAAATA AAAATA AAA-ATA AAAATA AAAATA
* *
41570735 AACATA AACATA AAAATA A
1 AAAATA AAAATA AAAATA A
41570754 CCAGACTCAA
Statistics
Matches: 48, Mismatches: 11, Indels: 4
0.76 0.17 0.06
Matches are distributed among these distances:
5 4 0.08
6 38 0.79
7 6 0.12
ACGTcount: A:0.73, C:0.03, G:0.09, T:0.15
Consensus pattern (6 bp):
AAAATA
Found at i:41570699 original size:18 final size:17
Alignment explanation
Indices: 41570664--41570707 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
41570654 TCAAAATAGG
**
41570664 AAAACAAAATAGTCATA
1 AAAACAAAATAGAAATA
41570681 AAAAGCAAAATAGAAATA
1 AAAA-CAAAATAGAAATA
*
41570699 AAAATAAAA
1 AAAACAAAA
41570708 ATAAGATAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
17 8 0.35
18 15 0.65
ACGTcount: A:0.73, C:0.07, G:0.07, T:0.14
Consensus pattern (17 bp):
AAAACAAAATAGAAATA
Found at i:41572395 original size:25 final size:25
Alignment explanation
Indices: 41572367--41572414 Score: 96
Period size: 25 Copynumber: 1.9 Consensus size: 25
41572357 TAATGAGTAA
41572367 GCTAGAAATAAAATAATAAATAATG
1 GCTAGAAATAAAATAATAAATAATG
41572392 GCTAGAAATAAAATAATAAATAA
1 GCTAGAAATAAAATAATAAATAA
41572415 GGAATAAAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.62, C:0.04, G:0.10, T:0.23
Consensus pattern (25 bp):
GCTAGAAATAAAATAATAAATAATG
Found at i:41578181 original size:27 final size:26
Alignment explanation
Indices: 41578159--41578300 Score: 160
Period size: 27 Copynumber: 5.3 Consensus size: 26
41578149 CTTGTAGTGA
*
41578159 AAAATGACCGTAATGCCCCTGTAAAGT
1 AAAATGACCGTAATGCCCCTGT-AGGT
* * *
41578186 AAAATGACCATAATACCCCTATAGGAT
1 AAAATGACCGTAATGCCCCTGTAGG-T
** *
41578213 AAAATGACTATGATGCCCCTGTAAGGT
1 AAAATGACCGTAATGCCCCTGT-AGGT
*
41578240 AAAATGACCGTAATTCCCCTGTAGGGT
1 AAAATGACCGTAATGCCCCTGTA-GGT
41578267 AAAATGACCGTAATGCCCCTGTAGGGT
1 AAAATGACCGTAATGCCCCTGTA-GGT
41578294 -AAATGAC
1 AAAATGAC
41578301 AATTATGCCT
Statistics
Matches: 99, Mismatches: 13, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
26 10 0.10
27 86 0.87
28 3 0.03
ACGTcount: A:0.36, C:0.21, G:0.20, T:0.23
Consensus pattern (26 bp):
AAAATGACCGTAATGCCCCTGTAGGT
Found at i:41578248 original size:81 final size:80
Alignment explanation
Indices: 41578159--41578309 Score: 212
Period size: 81 Copynumber: 1.9 Consensus size: 80
41578149 CTTGTAGTGA
*
41578159 AAAATGACCGTAATGCCCCTGTAAAGTAAAATGACCATAATACCCCTATAGGATAAAATGACTAT
1 AAAATGACCGTAATGCCCCTGTAAAGTAAAATGACCATAATACCCCTATAGGAT-AAATGACAAT
41578224 GATGCCCCTGTAAGGT
65 GATGCCCCTGTAAGGT
* ** * * * * *
41578240 AAAATGACCGTAATTCCCCTGTAGGGTAAAATGACCGTAATGCCCCTGTAGGGTAAATGACAATT
1 AAAATGACCGTAATGCCCCTGTAAAGTAAAATGACCATAATACCCCTATAGGATAAATGACAATG
41578305 ATGCC
66 ATGCC
41578310 TTTATATTCT
Statistics
Matches: 61, Mismatches: 9, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
80 14 0.23
81 47 0.77
ACGTcount: A:0.36, C:0.21, G:0.19, T:0.24
Consensus pattern (80 bp):
AAAATGACCGTAATGCCCCTGTAAAGTAAAATGACCATAATACCCCTATAGGATAAATGACAATG
ATGCCCCTGTAAGGT
Found at i:41578295 original size:54 final size:54
Alignment explanation
Indices: 41578131--41578300 Score: 200
Period size: 54 Copynumber: 3.2 Consensus size: 54
41578121 CCCCAATTTT
* * * * *
41578131 TAAAATTACCAAAATACCCTTGTAGTGA-AAAATGACCGTAATGCCCCTGTAAAG
1 TAAAATGACCATAATACCCCTATAG-GATAAAATGACCGTAATGCCCCTGTAAGG
** *
41578185 TAAAATGACCATAATACCCCTATAGGATAAAATGACTATGATGCCCCTGTAAGG
1 TAAAATGACCATAATACCCCTATAGGATAAAATGACCGTAATGCCCCTGTAAGG
* * * * *
41578239 TAAAATGACCGTAATTCCCCTGTAGGGTAAAATGACCGTAATGCCCCTGTAGGG
1 TAAAATGACCATAATACCCCTATAGGATAAAATGACCGTAATGCCCCTGTAAGG
41578293 T-AAATGAC
1 TAAAATGAC
41578301 AATTATGCCT
Statistics
Matches: 99, Mismatches: 16, Indels: 3
0.84 0.14 0.03
Matches are distributed among these distances:
53 9 0.09
54 90 0.91
ACGTcount: A:0.37, C:0.21, G:0.18, T:0.24
Consensus pattern (54 bp):
TAAAATGACCATAATACCCCTATAGGATAAAATGACCGTAATGCCCCTGTAAGG
Found at i:41581877 original size:119 final size:120
Alignment explanation
Indices: 41581654--41581921 Score: 423
Period size: 119 Copynumber: 2.2 Consensus size: 120
41581644 TATTTGGATG
*
41581654 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAACCGGGCTAAGTCCCGAAGGCA
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTATAACCGGGCTAAGTCCCGAAGGCA
* * * *
41581719 TTTGTGTGAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTTGTGTGAGTTACT
66 TTTGTGCGAGCTACTATATCCGGGCCAAGTCCCGAAGGCATTTGTGCGAGTTACT
* *
41581774 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTA-ATTCCGGGCTAAG-CCCGAAGGC
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTATA-ACCGGGCTAAGTCCCGAAGGC
* *
41581837 ATTTGTGCGAGCTACTATATTCGGGCCAAGTCCTGAAGGCATTTGTGCGAGTTACT
65 ATTTGTGCGAGCTACTATATCCGGGCCAAGTCCCGAAGGCATTTGTGCGAGTTACT
*
41581893 ATAACCGGGCTAAGTCTCGAAGGCATTTG
1 ATAACCGGGCTAAGTCCCGAAGGCATTTG
41581922 AGCAAGTAGC
Statistics
Matches: 137, Mismatches: 10, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
119 88 0.64
120 49 0.36
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (120 bp):
ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTATAACCGGGCTAAGTCCCGAAGGCA
TTTGTGCGAGCTACTATATCCGGGCCAAGTCCCGAAGGCATTTGTGCGAGTTACT
Found at i:41581935 original size:40 final size:40
Alignment explanation
Indices: 41581654--41581921 Score: 405
Period size: 40 Copynumber: 6.7 Consensus size: 40
41581644 TATTTGGATG
41581654 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
*
41581694 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGTGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
* *
41581734 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGTGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
* *
41581774 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
* *
41581814 A-ATTCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGCTACT
1 ATA-ACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
** * *
41581853 ATATTCGGGCCAAGTCCTGAAGGCATTTGTGCGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
*
41581893 ATAACCGGGCTAAGTCTCGAAGGCATTTG
1 ATAACCGGGCTAAGTCCCGAAGGCATTTG
41581922 AGCAAGTAGC
Statistics
Matches: 206, Mismatches: 19, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
39 33 0.16
40 173 0.84
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (40 bp):
ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
Found at i:41581940 original size:119 final size:120
Alignment explanation
Indices: 41581654--41581953 Score: 421
Period size: 119 Copynumber: 2.5 Consensus size: 120
41581644 TATTTGGATG
* *
41581654 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAACCGGGCTAAGTCCCGAAGGC
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCAAG-TAGCTATATCCGGGCTAAGTCCCGAAGGC
* * * *
41581718 ATTTGTGTGAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTTGTGTGAGTTACT
65 ATTTGTGCGAGCTACTATATCCGGGCCAAGTCCCGAAGGCATTTGTGCGAGTTACT
*
41581774 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCTAGT-GACTA-ATTCCGGGCTAAG-CCCGAAGG
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTAG-CTATA-TCCGGGCTAAGTCCCGAAGG
* *
41581836 CATTTGTGCGAGCTACTATATTCGGGCCAAGTCCTGAAGGCATTTGTGCGAGTTACT
64 CATTTGTGCGAGCTACTATATCCGGGCCAAGTCCCGAAGGCATTTGTGCGAGTTACT
* * * *
41581893 ATAACCGGGCTAAGTCTCGAAGGCATTTGAGCAAGTAGCTATATCC-GGCTAAATTCCGAAG
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTAGCTATATCCGGGCTAAGTCCCGAAG
41581954 ATACTTGGTT
Statistics
Matches: 161, Mismatches: 13, Indels: 13
0.86 0.07 0.07
Matches are distributed among these distances:
118 6 0.04
119 106 0.66
120 49 0.30
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.26
Consensus pattern (120 bp):
ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTAGCTATATCCGGGCTAAGTCCCGAAGGCA
TTTGTGCGAGCTACTATATCCGGGCCAAGTCCCGAAGGCATTTGTGCGAGTTACT
Found at i:41587523 original size:49 final size:48
Alignment explanation
Indices: 41587375--41587549 Score: 140
Period size: 49 Copynumber: 3.6 Consensus size: 48
41587365 TAAGATGCCA
* * * **
41587375 ATGCCAGGTCCCAGACATGGTTTTACACTGGCTAACA-C-ATTAAAGTCG
1 ATGCCATGTCCCAGACA-GGTCTTACACTGGCTATCATCTATT-GGGTCG
* * * * * * * * *
41587423 ATGTCATGTCCCAGATAAGTCTTACACTGACTTTTATTTATCGAGGCCG
1 ATGCCATGTCCCAGACAGGTCTTACACTGGCTATCATCTATTG-GGTCG
*
41587472 ATGCCATGTCCCAGACAGGTCTTACACTGGCTCTCATCTATTGGTGTCG
1 ATGCCATGTCCCAGACAGGTCTTACACTGGCTATCATCTATTGG-GTCG
*
41587521 ATGTCATGTCCCA-AGCAGGTCTTACACTG
1 ATGCCATGTCCCAGA-CAGGTCTTACACTG
41587550 ACACACAGCA
Statistics
Matches: 98, Mismatches: 24, Indels: 9
0.75 0.18 0.07
Matches are distributed among these distances:
47 13 0.13
48 16 0.16
49 69 0.70
ACGTcount: A:0.24, C:0.26, G:0.21, T:0.30
Consensus pattern (48 bp):
ATGCCATGTCCCAGACAGGTCTTACACTGGCTATCATCTATTGGGTCG
Found at i:41587543 original size:98 final size:97
Alignment explanation
Indices: 41587375--41587551 Score: 232
Period size: 98 Copynumber: 1.8 Consensus size: 97
41587365 TAAGATGCCA
* *
41587375 ATGCCAGGTCCCAGACATGGTTTTACACTGGCTAACACATTAAAGTCGATGTCATGTCCCAGATA
1 ATGCCAGGTCCCAGACATGGTCTTACACTGGCTAACACATTAAAGTCGATGTCATGTCCCAGACA
41587440 AGTCTTACACTGACTTTTATTTATCGAGGCCG
66 AGTCTTACACTGACTTTTATTTATCGAGGCCG
* ** ***
41587472 ATGCCATGTCCCAGACA-GGTCTTACACTGGCTCTCATCTATTGGTGTCGATGTCATGTCCCA-A
1 ATGCCAGGTCCCAGACATGGTCTTACACTGGCTAACA-C-ATTAAAGTCGATGTCATGTCCCAGA
*
41587535 GCAGGTCTTACACTGAC
64 -CAAGTCTTACACTGAC
41587552 ACACAGCAAG
Statistics
Matches: 68, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
96 16 0.24
97 18 0.26
98 34 0.50
ACGTcount: A:0.24, C:0.26, G:0.20, T:0.29
Consensus pattern (97 bp):
ATGCCAGGTCCCAGACATGGTCTTACACTGGCTAACACATTAAAGTCGATGTCATGTCCCAGACA
AGTCTTACACTGACTTTTATTTATCGAGGCCG
Found at i:41597100 original size:44 final size:44
Alignment explanation
Indices: 41597048--41597149 Score: 161
Period size: 44 Copynumber: 2.3 Consensus size: 44
41597038 TGAGTTATCG
**
41597048 TGTAAGACCACGTCTGGGATGTTGGCAT-GAACTTATGATTTACA
1 TGTAAGACCACGTCTGGGACATTGGCATCG-ACTTATGATTTACA
*
41597092 TGTAAGACCACGTCTGGGACATTGGCATCGACTTATGGTTTACA
1 TGTAAGACCACGTCTGGGACATTGGCATCGACTTATGATTTACA
41597136 TGTAAGACCACGTC
1 TGTAAGACCACGTC
41597150 AATTTGGTAA
Statistics
Matches: 54, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
44 53 0.98
45 1 0.02
ACGTcount: A:0.26, C:0.20, G:0.25, T:0.29
Consensus pattern (44 bp):
TGTAAGACCACGTCTGGGACATTGGCATCGACTTATGATTTACA
Found at i:41615783 original size:20 final size:20
Alignment explanation
Indices: 41615755--41615792 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
41615745 CTAGGAAATA
41615755 TGTGATCTGAGCTCATGAGT
1 TGTGATCTGAGCTCATGAGT
* *
41615775 TGTGGTCTGAGTTCATGA
1 TGTGATCTGAGCTCATGA
41615793 TATATGTGAC
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:0.18, C:0.13, G:0.32, T:0.37
Consensus pattern (20 bp):
TGTGATCTGAGCTCATGAGT
Found at i:41616031 original size:50 final size:50
Alignment explanation
Indices: 41615951--41616142 Score: 262
Period size: 50 Copynumber: 3.9 Consensus size: 50
41615941 CCGTGAGTAA
* * * *
41615951 TGAGATCCCATATAAGACCATGTTTAGGACAAGGCATTGGCATCGATATG
1 TGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGATATG
41616001 TGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGATATG
1 TGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGATATG
* * * *
41616051 TGAAATCCCATGTAGGACCATGTCTGGGTCATGGCATTGGCATCGGTATG
1 TGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGATATG
* * * *
41616101 T--GATCCCATGTAAGACCATATCTGAGATATGGCCTTGGCATC
1 TGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATC
41616143 TTATTATGTG
Statistics
Matches: 127, Mismatches: 15, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
48 34 0.27
50 93 0.73
ACGTcount: A:0.27, C:0.20, G:0.26, T:0.27
Consensus pattern (50 bp):
TGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGATATG
Found at i:41617359 original size:21 final size:21
Alignment explanation
Indices: 41617322--41617361 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
41617312 AATCATTAAA
*
41617322 TTGATGTTATGATATGTGTCT
1 TTGATGTTATGAAATGTGTCT
41617343 TTGATGTGTAT-AAATGTGT
1 TTGATGT-TATGAAATGTGT
41617362 AAGGGATTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 14 0.82
22 3 0.18
ACGTcount: A:0.23, C:0.03, G:0.25, T:0.50
Consensus pattern (21 bp):
TTGATGTTATGAAATGTGTCT
Found at i:41620279 original size:16 final size:16
Alignment explanation
Indices: 41620258--41620291 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
41620248 CCTATGACCA
41620258 AAGCTGGAAAAGATTC
1 AAGCTGGAAAAGATTC
41620274 AAGCTGGAAAAGATTC
1 AAGCTGGAAAAGATTC
41620290 AA
1 AA
41620292 TCTTTGTTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.47, C:0.12, G:0.24, T:0.18
Consensus pattern (16 bp):
AAGCTGGAAAAGATTC
Found at i:41621584 original size:20 final size:21
Alignment explanation
Indices: 41621556--41621613 Score: 64
Period size: 20 Copynumber: 2.7 Consensus size: 21
41621546 CAAGCTGGAG
41621556 TTAATTTGTCTTAGC-CGAAT
1 TTAATTTGTCTTAGCTCGAAT
* *
41621576 TTAAGTTGTCCTAGCTATCGAAT
1 TTAATTTGTCTTAGC--TCGAAT
41621599 TTAATTTGTCCTTAG
1 TTAATTTGT-CTTAG
41621614 GATTGACTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
20 13 0.43
23 13 0.43
24 4 0.13
ACGTcount: A:0.24, C:0.16, G:0.16, T:0.45
Consensus pattern (21 bp):
TTAATTTGTCTTAGCTCGAAT
Found at i:41626534 original size:41 final size:41
Alignment explanation
Indices: 41626487--41626576 Score: 144
Period size: 41 Copynumber: 2.2 Consensus size: 41
41626477 TATTGCATTC
* * *
41626487 ATATTTTCTACCTTTAAGTTTAACTATCTTTTCCAACAATA
1 ATATTTTCTACCTCTAAGTGTAACGATCTTTTCCAACAATA
*
41626528 ATATTTTCTACCTCTAAGTGTAACGATCTTTTCCAACATTA
1 ATATTTTCTACCTCTAAGTGTAACGATCTTTTCCAACAATA
41626569 ATATTTTC
1 ATATTTTC
41626577 CCTTGCTTTC
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 45 1.00
ACGTcount: A:0.30, C:0.20, G:0.04, T:0.46
Consensus pattern (41 bp):
ATATTTTCTACCTCTAAGTGTAACGATCTTTTCCAACAATA
Found at i:41628707 original size:15 final size:15
Alignment explanation
Indices: 41628687--41628722 Score: 72
Period size: 15 Copynumber: 2.4 Consensus size: 15
41628677 TTAAAATTTA
41628687 CTGTGACTACATAAT
1 CTGTGACTACATAAT
41628702 CTGTGACTACATAAT
1 CTGTGACTACATAAT
41628717 CTGTGA
1 CTGTGA
41628723 GGAAAATAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.33
Consensus pattern (15 bp):
CTGTGACTACATAAT
Found at i:41628823 original size:39 final size:40
Alignment explanation
Indices: 41628769--41628949 Score: 194
Period size: 40 Copynumber: 4.6 Consensus size: 40
41628759 AAACCAAGTA
* * * *
41628769 CCTTCGGAATTTAGCCGGATT-TAGCT-ACTTGCTCAAATG
1 CCTTCGGGACTTAGCCGGATTATAG-TAACTCGCACAAATG
*
41628808 CCTTCTGGACTTAGCCCGG-TTATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAG-CCGGATTATAGTAACTCGCACAAATG
*
41628848 CCTTCGGGACTTAGCC-CAGTTATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCGGA-TTATAGTAACTCGCACAAATG
* * *
41628888 CCTTCGGG-CTTAGCCCGGAAT-TAGTCACTAGCACAAATG
1 CCTTCGGGACTTAG-CCGGATTATAGTAACTCGCACAAATG
*
41628927 CCTTCGGGACTTAGCCCGATTAT
1 CCTTCGGGACTTAGCCGGATTAT
41628950 CATCCGAATA
Statistics
Matches: 120, Mismatches: 13, Indels: 17
0.80 0.09 0.11
Matches are distributed among these distances:
39 50 0.42
40 69 0.57
41 1 0.01
ACGTcount: A:0.24, C:0.27, G:0.21, T:0.28
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCGGATTATAGTAACTCGCACAAATG
Found at i:41628851 original size:40 final size:40
Alignment explanation
Indices: 41628802--41628949 Score: 219
Period size: 40 Copynumber: 3.7 Consensus size: 40
41628792 GCTACTTGCT
*
41628802 CAAATGCCTTCTGGACTTAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
*
41628842 CAAATGCCTTCGGGACTTAGCCCAGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
* * *
41628882 CAAATGCCTTCGGG-CTTAGCCCGG-AATTAGTCACTAGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTA-TAGTAACTCGCA
*
41628921 CAAATGCCTTCGGGACTTAGCCCGATTAT
1 CAAATGCCTTCGGGACTTAGCCCGGTTAT
41628950 CATCCGAATA
Statistics
Matches: 97, Mismatches: 8, Indels: 6
0.87 0.07 0.05
Matches are distributed among these distances:
38 1 0.01
39 33 0.34
40 62 0.64
41 1 0.01
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
Found at i:41636898 original size:40 final size:40
Alignment explanation
Indices: 41636854--41637082 Score: 431
Period size: 40 Copynumber: 5.7 Consensus size: 40
41636844 GCTACTTGCT
*
41636854 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCACA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
* *
41636894 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCACA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
41636934 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
41636974 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
41637014 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
41637054 CAAATGCCTTCGGGACTTAGCCCGGTTAT
1 CAAATGCCTTCGGGACTTAGCCCGGTTAT
41637083 CATCCAAATA
Statistics
Matches: 186, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 186 1.00
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
Found at i:41663675 original size:40 final size:39
Alignment explanation
Indices: 41663643--41663874 Score: 320
Period size: 40 Copynumber: 5.8 Consensus size: 39
41663633 CCAGCATGAT
* * * *
41663643 TGCTCTTCAGGACCTAGCCCGGATATAACACCAGCACGAA
1 TGCTCTTC-GGACTTAGCCCGGATACATCACTAGCACGAA
** * *
41663683 TGCTCTTCGGGGTCTAGCACGGATATATCACTAGCACGAA
1 TGCTCTTCGGACT-TAGCCCGGATACATCACTAGCACGAA
*
41663723 TGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAA
1 TGCTCTTCGG-ACTTAGCCCGGATACATCACTAGCACGAA
*
41663763 TGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAA
1 TGCTCTTCGG-ACTTAGCCCGGATACATCACTAGCACGAA
41663803 TGCTCTTCGAGACTTAGCCCGGATACATCACTAGCACGAA
1 TGCTCTTCG-GACTTAGCCCGGATACATCACTAGCACGAA
41663843 TGCTCTTCGGGACTTAGCCCGGATACATCACT
1 TGCTCTTC-GGACTTAGCCCGGATACATCACT
41663875 CTCAATTCTC
Statistics
Matches: 176, Mismatches: 12, Indels: 8
0.90 0.06 0.04
Matches are distributed among these distances:
39 2 0.01
40 171 0.97
41 3 0.02
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (39 bp):
TGCTCTTCGGACTTAGCCCGGATACATCACTAGCACGAA
Found at i:41665363 original size:47 final size:47
Alignment explanation
Indices: 41665289--41665979 Score: 1094
Period size: 47 Copynumber: 14.6 Consensus size: 47
41665279 CCCTTCGGGA
* * *
41665289 CTTATCACATTTATACACTTTCACATTCATCGCATCGGCCATTAGGG
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
41665336 CTTATCACATATATACACTTTCCCATTCATCACATCGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
41665383 CTTATCACATATTTACACTTTCACATTCATCGCATCGGCCATTAGGG
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
41665430 CTTATCACATATATACACTTTCCCATTCATCACATCGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
41665477 CTTATCACATATTTACACTTTCACATTCATCGCATCGGCCATTAGGG
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
41665524 CTTATCACATATATACACTTTCCCATTCATCACATCGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
41665571 CTTATCACATATTTACACTTTCACATTCATCGCATCGGCCATTAGGG
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
41665618 CTTATCACATATATACGCTTTCACATTCATCACATCGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
41665665 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
41665712 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
41665759 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
41665808 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
41665857 CTTATCACATATATATACAGTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
41665906 CTTATCACATATATACACTTTCACATCCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
41665953 CTTATCACATATATACACTTTCACATT
1 CTTATCACATATATACACTTTCACATT
41665980 TATTCAAATA
Statistics
Matches: 595, Mismatches: 47, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
47 453 0.76
49 142 0.24
ACGTcount: A:0.27, C:0.30, G:0.10, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:41668031 original size:27 final size:27
Alignment explanation
Indices: 41667958--41668071 Score: 113
Period size: 27 Copynumber: 4.2 Consensus size: 27
41667948 CTTACTGAAA
* ** ***
41667958 TACCCTCGACTTGTAAAATTACCAAAG
1 TACCCTCGATTTACAAAATTACCATTT
* * * *
41667985 TACCCTCGATTTATAGAATTATCGTTT
1 TACCCTCGATTTACAAAATTACCATTT
41668012 TACCCTCGATTTACAAAATTACCATTT
1 TACCCTCGATTTACAAAATTACCATTT
*
41668039 TACTCTC-AGTTTACAAAATTACCATTT
1 TACCCTCGA-TTTACAAAATTACCATTT
41668066 TACCCT
1 TACCCT
41668072 AATTGTGAAA
Statistics
Matches: 72, Mismatches: 14, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
26 1 0.01
27 71 0.99
ACGTcount: A:0.32, C:0.25, G:0.07, T:0.37
Consensus pattern (27 bp):
TACCCTCGATTTACAAAATTACCATTT
Found at i:41668183 original size:27 final size:27
Alignment explanation
Indices: 41668107--41668290 Score: 106
Period size: 27 Copynumber: 6.7 Consensus size: 27
41668097 TATAGGATAG
*
41668107 AATTACCAAAATACCACTAG-TTTG-AGA
1 AATTACCAAAATACC-CTTGATTTGTA-A
* * * **
41668134 AATTATCGAAATACTCTCAATTTGTAA
1 AATTACCAAAATACCCTTGATTTGTAA
**
41668161 AATTACCAAAATACCCTTGATTTACAA
1 AATTACCAAAATACCCTTGATTTGTAA
*
41668188 AATTA-CAGAAATACCCTTGACTTTTTTAAA
1 AATTACCA-AAATACCCTTGA--TTTGT-AA
* * * **
41668218 AATTA-TAAGAATACCATTGGTTTACAA
1 AATTACCAA-AATACCCTTGATTTGTAA
** *
41668245 AATTACTGAAATACCCTTGATTTGTAG
1 AATTACCAAAATACCCTTGATTTGTAA
* *
41668272 ATTTACCAAAACACCCTTG
1 AATTACCAAAATACCCTTG
41668291 TAGGATGAAA
Statistics
Matches: 120, Mismatches: 29, Indels: 16
0.73 0.18 0.10
Matches are distributed among these distances:
26 4 0.03
27 89 0.74
28 6 0.05
29 4 0.03
30 17 0.14
ACGTcount: A:0.41, C:0.18, G:0.09, T:0.33
Consensus pattern (27 bp):
AATTACCAAAATACCCTTGATTTGTAA
Found at i:41668736 original size:20 final size:20
Alignment explanation
Indices: 41668711--41668757 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
41668701 GTTGGGCCTT
41668711 AATGGGCAAGAATCGGGCCC
1 AATGGGCAAGAATCGGGCCC
**
41668731 AATGGGCTGGAATCGGGCCC
1 AATGGGCAAGAATCGGGCCC
41668751 AATGGGC
1 AATGGGC
41668758 TTTTGGGCCC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.26, C:0.23, G:0.38, T:0.13
Consensus pattern (20 bp):
AATGGGCAAGAATCGGGCCC
Found at i:41668758 original size:20 final size:20
Alignment explanation
Indices: 41668720--41668758 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
41668710 TAATGGGCAA
41668720 GAATCGGGCCCAATGGGCTG
1 GAATCGGGCCCAATGGGCTG
41668740 GAATCGGGCCCAATGGGCT
1 GAATCGGGCCCAATGGGCT
41668759 TTTGGGCCCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.21, C:0.26, G:0.38, T:0.15
Consensus pattern (20 bp):
GAATCGGGCCCAATGGGCTG
Found at i:41669136 original size:20 final size:19
Alignment explanation
Indices: 41669111--41669181 Score: 90
Period size: 20 Copynumber: 3.6 Consensus size: 19
41669101 GATATGATAT
*
41669111 ACATGATTGATATGATATGC
1 ACATGATTG-TATGAAATGC
*
41669131 ACATGATATGTATAAAATGC
1 ACATGAT-TGTATGAAATGC
41669151 ACATGAATTGTATGAAATGC
1 ACATG-ATTGTATGAAATGC
41669171 ACATGA-TGTAT
1 ACATGATTGTAT
41669182 TCATAAATGC
Statistics
Matches: 46, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
18 5 0.11
19 1 0.02
20 36 0.78
21 4 0.09
ACGTcount: A:0.39, C:0.10, G:0.18, T:0.32
Consensus pattern (19 bp):
ACATGATTGTATGAAATGC
Found at i:41669305 original size:52 final size:50
Alignment explanation
Indices: 41669227--41669349 Score: 185
Period size: 52 Copynumber: 2.4 Consensus size: 50
41669217 GAGGAAGTGC
*
41669227 AAAAGGGCTTATGGCCCAGTTTATTGAGAAGGGCTTATGCCCCAGTTTACCG
1 AAAAGGGCTTAT-GCCCAGTTTATTGAAAAGGGCTT-TGCCCCAGTTTACCG
*
41669279 AAAAGGGATTATGCCACAGTTTATTGAAAAGGGCTTTGCCCCAGTTTACCG
1 AAAAGGGCTTATGCC-CAGTTTATTGAAAAGGGCTTTGCCCCAGTTTACCG
41669330 AAAAGGGCTT-TGCCCCAGTT
1 AAAAGGGCTTATG-CCCAGTT
41669350 CTTAAAAGAG
Statistics
Matches: 66, Mismatches: 3, Indels: 6
0.88 0.04 0.08
Matches are distributed among these distances:
50 7 0.11
51 29 0.44
52 30 0.45
ACGTcount: A:0.27, C:0.21, G:0.25, T:0.27
Consensus pattern (50 bp):
AAAAGGGCTTATGCCCAGTTTATTGAAAAGGGCTTTGCCCCAGTTTACCG
Found at i:41669324 original size:25 final size:26
Alignment explanation
Indices: 41669227--41669349 Score: 160
Period size: 26 Copynumber: 4.8 Consensus size: 26
41669217 GAGGAAGTGC
* **
41669227 AAAAGGGCTTATGGCCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTACCG
*
41669253 AGAAGGGCTTATGCCCCAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTACCG
* * **
41669279 AAAAGGGATTATGCCACAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTACCG
41669305 AAAAGGGCTT-TGCCCCAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTACCG
41669330 AAAAGGGCTT-TGCCCCAGTT
1 AAAAGGGCTTATGCCCCAGTT
41669350 CTTAAAAGAG
Statistics
Matches: 84, Mismatches: 13, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
25 32 0.38
26 52 0.62
ACGTcount: A:0.27, C:0.21, G:0.25, T:0.27
Consensus pattern (26 bp):
AAAAGGGCTTATGCCCCAGTTTACCG
Found at i:41669554 original size:42 final size:42
Alignment explanation
Indices: 41669495--41669586 Score: 130
Period size: 42 Copynumber: 2.2 Consensus size: 42
41669485 TAGTCTCCCC
* * ** *
41669495 AAATGGGCTTGTATACATTCATTGGTATTTCATATGATATTG
1 AAATGGGCTTGCATACATCCATTGACATTACATATGATATTG
*
41669537 AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTG
1 AAATGGGCTTGCATACATCCATTGACATTACATATGATATTG
41669579 AAATGGGC
1 AAATGGGC
41669587 CTATAGGCCA
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.30, C:0.13, G:0.21, T:0.36
Consensus pattern (42 bp):
AAATGGGCTTGCATACATCCATTGACATTACATATGATATTG
Found at i:41669646 original size:31 final size:31
Alignment explanation
Indices: 41669610--41669719 Score: 184
Period size: 31 Copynumber: 3.5 Consensus size: 31
41669600 CGTTTACAGT
* *
41669610 AAAGGCTTCGGCCTAGTGAAATGATTTATGA
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
*
41669641 AAAGGCTTCGGCCCAATGATATGATTTATGA
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
41669672 AAAGGCTTCGGCCCAGTGATATGATTTATGA
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
*
41669703 AAAGGCTTCGGCTCAGT
1 AAAGGCTTCGGCCCAGT
41669720 AATCGTTAAA
Statistics
Matches: 74, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 74 1.00
ACGTcount: A:0.30, C:0.16, G:0.25, T:0.28
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTGATATGATTTATGA
Found at i:41672093 original size:27 final size:27
Alignment explanation
Indices: 41672063--41672160 Score: 80
Period size: 27 Copynumber: 3.6 Consensus size: 27
41672053 TGTAGGATAG
*
41672063 AATTACCAAAATACCACT-AGTTTG-AGA
1 AATTACCAAAATACC-CTCAATTTGTA-A
*
41672090 AATTA-CAGATATACCCTCAATTTGTAA
1 AATTACCA-AAATACCCTCAATTTGTAA
* *
41672117 AATTACCAAAATACCC-CTGATTTATAA
1 AATTACCAAAATACCCTC-AATTTGTAA
41672144 AATTA-CAGAAATACCCT
1 AATTACCA-AAATACCCT
41672161 TGACTTTTTA
Statistics
Matches: 59, Mismatches: 5, Indels: 13
0.77 0.06 0.17
Matches are distributed among these distances:
26 7 0.12
27 49 0.83
28 3 0.05
ACGTcount: A:0.44, C:0.20, G:0.07, T:0.29
Consensus pattern (27 bp):
AATTACCAAAATACCCTCAATTTGTAA
Found at i:41672187 original size:30 final size:28
Alignment explanation
Indices: 41672115--41672220 Score: 94
Period size: 27 Copynumber: 3.8 Consensus size: 28
41672105 CTCAATTTGT
* * *
41672115 AAAATTACCAAAATACCCCTGA-TTTAT
1 AAAATTACTAAAATACCCTTGAGTTTAA
*
41672142 AAAATTAC-AGAAATACCCTTGACTTTTTAA
1 AAAATTACTA-AAATACCCTTGA--GTTTAA
* *
41672172 AAAATTA-TAAGAATACCATTG-GTTTAC
1 AAAATTACTAA-AATACCCTTGAGTTTAA
41672199 AAAATTACTAAAATACCCTTGA
1 AAAATTACTAAAATACCCTTGA
41672221 TTTGTAGATT
Statistics
Matches: 65, Mismatches: 6, Indels: 15
0.76 0.07 0.17
Matches are distributed among these distances:
26 1 0.02
27 39 0.60
28 3 0.05
29 1 0.02
30 21 0.32
ACGTcount: A:0.45, C:0.17, G:0.07, T:0.31
Consensus pattern (28 bp):
AAAATTACTAAAATACCCTTGAGTTTAA
Found at i:41673073 original size:20 final size:20
Alignment explanation
Indices: 41673048--41673114 Score: 93
Period size: 20 Copynumber: 3.4 Consensus size: 20
41673038 GATATGATAT
*
41673048 ACATGAT-TGATATGATATGC
1 ACATGATATG-TATGAAATGC
41673068 ACATGATATGTAT-AAATTGC
1 ACATGATATGTATGAAA-TGC
41673088 ACATGATATGTATGAAATGC
1 ACATGATATGTATGAAATGC
41673108 ACATGAT
1 ACATGAT
41673115 GTATTCATAA
Statistics
Matches: 43, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
19 2 0.05
20 36 0.84
21 5 0.12
ACGTcount: A:0.39, C:0.10, G:0.18, T:0.33
Consensus pattern (20 bp):
ACATGATATGTATGAAATGC
Found at i:41673245 original size:52 final size:52
Alignment explanation
Indices: 41673164--41673325 Score: 242
Period size: 52 Copynumber: 3.2 Consensus size: 52
41673154 GAGGAAGTGC
* **
41673164 AAAAGGGCTTATACCCCAGTTTATAGAAAAGGGCTTATGCCCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTACCGAAAAGGGCTTATGCCCCAGTTTATTG
41673216 AAAAGGGCTTATGCCCCAGTTTACCGAAAAGGGCTTATGCCCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTACCGAAAAGGGCTTATGCCCCAGTTTATTG
* *
41673268 AAAAGGGCTT-TGCCCCAATTTACCGAAAATGGCTT-TGCCCCAG-TTATT-
1 AAAAGGGCTTATGCCCCAGTTTACCGAAAAGGGCTTATGCCCCAGTTTATTG
41673316 AAAAGAGGCT
1 AAAAG-GGCT
41673326 AGGCCTCCAA
Statistics
Matches: 104, Mismatches: 5, Indels: 5
0.91 0.04 0.04
Matches are distributed among these distances:
48 5 0.05
49 9 0.09
50 8 0.08
51 23 0.22
52 59 0.57
ACGTcount: A:0.30, C:0.22, G:0.22, T:0.27
Consensus pattern (52 bp):
AAAAGGGCTTATGCCCCAGTTTACCGAAAAGGGCTTATGCCCCAGTTTATTG
Found at i:41673289 original size:25 final size:26
Alignment explanation
Indices: 41673164--41673325 Score: 215
Period size: 26 Copynumber: 6.3 Consensus size: 26
41673154 GAGGAAGTGC
* *
41673164 AAAAGGGCTTATACCCCAGTTTATAG
1 AAAAGGGCTTATGCCCCAGTTTATTG
41673190 AAAAGGGCTTATGCCCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTATTG
**
41673216 AAAAGGGCTTATGCCCCAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTATTG
41673242 AAAAGGGCTTATGCCCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTATTG
* **
41673268 AAAAGGGCTT-TGCCCCAATTTACCG
1 AAAAGGGCTTATGCCCCAGTTTATTG
*
41673293 AAAATGGCTT-TGCCCCAG-TTATT-
1 AAAAGGGCTTATGCCCCAGTTTATTG
41673316 AAAAGAGGCT
1 AAAAG-GGCT
41673326 AGGCCTCCAA
Statistics
Matches: 121, Mismatches: 14, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
23 4 0.03
24 7 0.06
25 28 0.23
26 82 0.68
ACGTcount: A:0.30, C:0.22, G:0.22, T:0.27
Consensus pattern (26 bp):
AAAAGGGCTTATGCCCCAGTTTATTG
Found at i:41673517 original size:42 final size:42
Alignment explanation
Indices: 41673458--41673549 Score: 130
Period size: 42 Copynumber: 2.2 Consensus size: 42
41673448 TAGTCTCCCC
* * ** *
41673458 AAATGGGCTTGCTTACATTCATTGGTATTTCATATGATATTG
1 AAATGGGCTTGCATACATCCATTGACATTACATATGATATTG
*
41673500 AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTG
1 AAATGGGCTTGCATACATCCATTGACATTACATATGATATTG
41673542 AAATGGGC
1 AAATGGGC
41673550 CTATGGGCCA
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.29, C:0.14, G:0.21, T:0.36
Consensus pattern (42 bp):
AAATGGGCTTGCATACATCCATTGACATTACATATGATATTG
Found at i:41673608 original size:31 final size:31
Alignment explanation
Indices: 41673573--41673742 Score: 249
Period size: 31 Copynumber: 5.5 Consensus size: 31
41673563 TGTTTACTGT
*
41673573 AAAGGCTTCGGCCCAGTGAAATGATTTATGA
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
41673604 AAAGGCTTCGGCCCAGTGATATGATTTATGA
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
*
41673635 AAAGGCTTCGGCCTAGTGATATGATTTATGA
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
* * *
41673666 AAAGGCTTCGGCCCAGT-A-ACCG-TTAAACG-
1 AAAGGCTTCGGCCCAGTGATA-TGATT-TATGA
41673695 AAAGGCTTCGGCCCAGTGATATGATTTATGA
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
41673726 AAAGGCTTCGGCCCAGT
1 AAAGGCTTCGGCCCAGT
41673743 AACCGTTAAA
Statistics
Matches: 124, Mismatches: 9, Indels: 12
0.86 0.06 0.08
Matches are distributed among these distances:
29 20 0.16
30 8 0.06
31 96 0.77
ACGTcount: A:0.29, C:0.19, G:0.26, T:0.26
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTGATATGATTTATGA
Found at i:41673708 original size:29 final size:29
Alignment explanation
Indices: 41673666--41673772 Score: 137
Period size: 29 Copynumber: 3.6 Consensus size: 29
41673656 TGATTTATGA
41673666 AAAGGCTTCGGCCCAGTAACCGTTAAACG
1 AAAGGCTTCGGCCCAGTAACCGTTAAACG
* * *
41673695 AAAGGCTTCGGCCCAGTGATA-TGATT-TATG
1 AAAGGCTTCGGCCCAGT-A-ACCG-TTAAACG
41673725 AAAAGGCTTCGGCCCAGTAACCGTTAAACG
1 -AAAGGCTTCGGCCCAGTAACCGTTAAACG
41673755 AAAGGCTTCGGCCCAGTA
1 AAAGGCTTCGGCCCAGTA
41673773 TATGTCAAGA
Statistics
Matches: 66, Mismatches: 6, Indels: 12
0.79 0.07 0.14
Matches are distributed among these distances:
29 38 0.58
30 8 0.12
31 20 0.30
ACGTcount: A:0.30, C:0.24, G:0.25, T:0.21
Consensus pattern (29 bp):
AAAGGCTTCGGCCCAGTAACCGTTAAACG
Found at i:41673723 original size:60 final size:60
Alignment explanation
Indices: 41673573--41673776 Score: 306
Period size: 60 Copynumber: 3.4 Consensus size: 60
41673563 TGTTTACTGT
* * * *
41673573 AAAGGCTTCGGCCCAGTGAAATGATTTATGAAAAGGCTTCGGCCCAGTGATA-TGATT-TATG
1 AAAGGCTTCGGCCCAGTGATATGATTTATGAAAAGGCTTCGGCCCAGT-A-ACCG-TTAAACG
*
41673634 AAAAGGCTTCGGCCTAGTGATATGATTTATGAAAAGGCTTCGGCCCAGTAACCGTTAAACG
1 -AAAGGCTTCGGCCCAGTGATATGATTTATGAAAAGGCTTCGGCCCAGTAACCGTTAAACG
41673695 AAAGGCTTCGGCCCAGTGATATGATTTATGAAAAGGCTTCGGCCCAGTAACCGTTAAACG
1 AAAGGCTTCGGCCCAGTGATATGATTTATGAAAAGGCTTCGGCCCAGTAACCGTTAAACG
41673755 AAAGGCTTCGGCCCAGT-ATATG
1 AAAGGCTTCGGCCCAGTGATATG
41673777 TCAAGACTAA
Statistics
Matches: 134, Mismatches: 6, Indels: 7
0.91 0.04 0.05
Matches are distributed among these distances:
59 5 0.04
60 79 0.59
61 4 0.03
62 46 0.34
ACGTcount: A:0.30, C:0.20, G:0.25, T:0.25
Consensus pattern (60 bp):
AAAGGCTTCGGCCCAGTGATATGATTTATGAAAAGGCTTCGGCCCAGTAACCGTTAAACG
Found at i:41675817 original size:104 final size:104
Alignment explanation
Indices: 41675677--41675884 Score: 346
Period size: 104 Copynumber: 2.0 Consensus size: 104
41675667 GTTGGGCGTC
* *
41675677 GGCTAAGAGTGCTCGGAGCGTAGATTAACTCCAGTCTCCTATCTGGTGTGTATTTCTCAGTACTC
1 GGCTAAGAGTGCTCGGAGCATAGATTAACTCCAGTCTCCTATCAGGTGTGTATTTCTCAGTACTC
41675742 TAGCTGTAGGATGGCTACTTCGGGCCGCGATGGGCCGAA
66 TAGCTGTAGGATGGCTACTTCGGGCCGCGATGGGCCGAA
* * **
41675781 GGCTAAGA-TGGCTCTGAGCATGGATTAACTTTAGTCTCCTATCAGGTGTGTATTTCTCAGTACT
1 GGCTAAGAGT-GCTCGGAGCATAGATTAACTCCAGTCTCCTATCAGGTGTGTATTTCTCAGTACT
41675845 CTAGCTGTAGGATGGCTACTTCGGGCCGCGATGGGCCGAA
65 CTAGCTGTAGGATGGCTACTTCGGGCCGCGATGGGCCGAA
41675885 AGGGGCCATG
Statistics
Matches: 97, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
103 1 0.01
104 96 0.99
ACGTcount: A:0.20, C:0.22, G:0.29, T:0.29
Consensus pattern (104 bp):
GGCTAAGAGTGCTCGGAGCATAGATTAACTCCAGTCTCCTATCAGGTGTGTATTTCTCAGTACTC
TAGCTGTAGGATGGCTACTTCGGGCCGCGATGGGCCGAA
Found at i:41676325 original size:27 final size:27
Alignment explanation
Indices: 41676093--41676349 Score: 132
Period size: 27 Copynumber: 9.6 Consensus size: 27
41676083 TTAGCTTACC
** *
41676093 AAATTACTGAAATACCCTCGACTTGTA
1 AAATTACCAAAATACCCTCGATTTGTA
* *
41676120 AAATTACCAAAGTACCCTCGATTTATA
1 AAATTACCAAAATACCCTCGATTTGTA
* * **** **
41676147 GAATTATCGTTTTACCCTCGATTTACA
1 AAATTACCAAAATACCCTCGATTTGTA
*** **
41676174 AAATTACCATTTTACCCTC-AGTTTACA
1 AAATTACCAAAATACCCTCGA-TTTGTA
* ***
41676201 AAATTACTATTTTACCCTCGA-TTGTA
1 AAATTACCAAAATACCCTCGATTTGTA
* * **
41676227 AAATTACTAAAATACCC-CTATAGGATA
1 AAATTACCAAAATACCCTCGATTTG-TA
* *
41676254 GAATTACCAAAATACCACT-GGTTTG-A
1 AAATTACCAAAATACC-CTCGATTTGTA
* *
41676280 GAAATTACCGAAATACCCTCAATTTGTA
1 -AAATTACCAAAATACCCTCGATTTGTA
**
41676308 AAATTACCAAAATACCCT-GATTTACA
1 AAATTACCAAAATACCCTCGATTTGTA
41676334 AAATTA-CAGAAATACC
1 AAATTACCA-AAATACC
41676350 TTTGGCTTTG
Statistics
Matches: 182, Mismatches: 38, Indels: 21
0.76 0.16 0.09
Matches are distributed among these distances:
25 4 0.02
26 40 0.22
27 133 0.73
28 5 0.03
ACGTcount: A:0.39, C:0.21, G:0.09, T:0.31
Consensus pattern (27 bp):
AAATTACCAAAATACCCTCGATTTGTA
Found at i:41676404 original size:27 final size:28
Alignment explanation
Indices: 41676328--41676406 Score: 74
Period size: 30 Copynumber: 2.8 Consensus size: 28
41676318 AATACCCTGA
* *
41676328 TTTACAAAATTACAGAAATACCTTTGGCTT
1 TTTACAAAATTACTGAAATACCATTGG--T
*
41676358 TGTTA-AAAATTA-TAAGAATACCATTGG-
1 T-TTACAAAATTACTGA-AATACCATTGGT
41676385 TTTACAAAATTACTGAAATACC
1 TTTACAAAATTACTGAAATACC
41676407 CTTGATTTGT
Statistics
Matches: 41, Mismatches: 4, Indels: 11
0.73 0.07 0.20
Matches are distributed among these distances:
26 3 0.07
27 14 0.34
28 2 0.05
29 1 0.02
30 18 0.44
31 3 0.07
ACGTcount: A:0.42, C:0.14, G:0.10, T:0.34
Consensus pattern (28 bp):
TTTACAAAATTACTGAAATACCATTGGT
Found at i:41677237 original size:20 final size:20
Alignment explanation
Indices: 41677223--41677278 Score: 94
Period size: 20 Copynumber: 2.8 Consensus size: 20
41677213 CATGATTGAG
*
41677223 ATGATATGCACATGATATGT
1 ATGAAATGCACATGATATGT
*
41677243 ATAAAATGCACATGATATGT
1 ATGAAATGCACATGATATGT
41677263 ATGAAATGCACATGAT
1 ATGAAATGCACATGAT
41677279 GTATTCATAA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.41, C:0.11, G:0.18, T:0.30
Consensus pattern (20 bp):
ATGAAATGCACATGATATGT
Found at i:41677451 original size:25 final size:26
Alignment explanation
Indices: 41677328--41677489 Score: 233
Period size: 26 Copynumber: 6.3 Consensus size: 26
41677318 GAGGAAGTGC
41677328 AAAAGGGCTTATGCCCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTATTG
41677354 AAAAGGGCTTATGCCCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTATTG
* * **
41677380 AAATGGGCTTATGCCCCAATTTACCG
1 AAAAGGGCTTATGCCCCAGTTTATTG
41677406 AAAAGGGCTTATGCCCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTATTG
*
41677432 AAAAGGGCTT-TGCCCCAGTTTATCG
1 AAAAGGGCTTATGCCCCAGTTTATTG
*
41677457 AAAAGGGCTT-TGCCCCTG-TTATT-
1 AAAAGGGCTTATGCCCCAGTTTATTG
41677480 AAAAGAGGCT
1 AAAAG-GGCT
41677490 AGGCCTCCAA
Statistics
Matches: 124, Mismatches: 11, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
23 5 0.04
24 8 0.06
25 31 0.25
26 80 0.65
ACGTcount: A:0.27, C:0.21, G:0.23, T:0.29
Consensus pattern (26 bp):
AAAAGGGCTTATGCCCCAGTTTATTG
Found at i:41677672 original size:42 final size:42
Alignment explanation
Indices: 41677613--41677704 Score: 139
Period size: 42 Copynumber: 2.2 Consensus size: 42
41677603 TAGTCTCCCC
* ** *
41677613 AAATGGGCTTGCATACATTCATTGGTATTTCATATGATATTG
1 AAATGGGCTTGCATACATCCATTGACATTACATATGATATTG
*
41677655 AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTG
1 AAATGGGCTTGCATACATCCATTGACATTACATATGATATTG
41677697 AAATGGGC
1 AAATGGGC
41677705 CTATGGGCCA
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.30, C:0.14, G:0.21, T:0.35
Consensus pattern (42 bp):
AAATGGGCTTGCATACATCCATTGACATTACATATGATATTG
Found at i:41677763 original size:31 final size:31
Alignment explanation
Indices: 41677728--41678023 Score: 547
Period size: 31 Copynumber: 9.5 Consensus size: 31
41677718 CGTTTACAGT
*
41677728 AAAGGCTTCGGCCCAGTGAAATGATTTATGA
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
41677759 AAAGGCTTCGGCCCAGTGATATGATTTATGA
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
*
41677790 AAAGGCTTCGGCCTAGTGATATGATTTATGA
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
41677821 AAAGGCTTCGGCCCAGTGATATGATTTATGA
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
*
41677852 AAAGGCTTCGGCCTAGTGATATGATTTATGA
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
41677883 AAAGGCTTCGGCCCAGTGATATGATTTATGA
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
*
41677914 AAAGGCTTCGGCCTAGTGATATGATTTATGA
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
41677945 AAAGGCTTCGGCCCAGTGATATGATTTATGA
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
*
41677976 AAAGGCTTCGGCCTAGTGATATGATTTATGA
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
41678007 AAAGGCTTCGGCCCAGT
1 AAAGGCTTCGGCCCAGT
41678024 AACCGTTAAA
Statistics
Matches: 256, Mismatches: 9, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 256 1.00
ACGTcount: A:0.29, C:0.16, G:0.26, T:0.29
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTGATATGATTTATGA
Found at i:41685766 original size:28 final size:28
Alignment explanation
Indices: 41685734--41685842 Score: 96
Period size: 28 Copynumber: 3.9 Consensus size: 28
41685724 TTACCAATAT
*
41685734 ATATGGCCCACTAAGCCCAATCTCTTTC
1 ATATGGCCCACTAAGCCCAATCACTTTC
* * *
41685762 ATATGGCCCATTAGGCCGAATCACATTT-
1 ATATGGCCCACTAAGCCCAATCAC-TTTC
* * * *
41685790 ATGTGGCCCATTAGGCCCAAATCACATTC
1 ATATGGCCCACTAAGCCC-AATCACTTTC
*
41685819 ATAT-GACCACTAAGCCCAAATCAC
1 ATATGGCCCACTAAGCCC-AATCAC
41685843 ATTTACAATC
Statistics
Matches: 67, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
28 55 0.82
29 12 0.18
ACGTcount: A:0.30, C:0.31, G:0.14, T:0.25
Consensus pattern (28 bp):
ATATGGCCCACTAAGCCCAATCACTTTC
Found at i:41687905 original size:11 final size:11
Alignment explanation
Indices: 41687889--41687913 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
41687879 ATATCTAGAA
41687889 TTCTCTTCATT
1 TTCTCTTCATT
41687900 TTCTCTTCATT
1 TTCTCTTCATT
41687911 TTC
1 TTC
41687914 ATCAGCTGGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.08, C:0.28, G:0.00, T:0.64
Consensus pattern (11 bp):
TTCTCTTCATT
Found at i:41689201 original size:25 final size:25
Alignment explanation
Indices: 41689168--41689216 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
41689158 AATAATTTGC
*
41689168 ATATTTGATATTGCCTAATAAATGA
1 ATATCTGATATTGCCTAATAAATGA
* *
41689193 ATATCTGATATTGCTTAGTAAATG
1 ATATCTGATATTGCCTAATAAATG
41689217 TCAAGCCAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.37, C:0.08, G:0.14, T:0.41
Consensus pattern (25 bp):
ATATCTGATATTGCCTAATAAATGA
Found at i:41689879 original size:10 final size:10
Alignment explanation
Indices: 41689864--41689891 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
41689854 ATATTACATG
41689864 TTTACTTTGT
1 TTTACTTTGT
41689874 TTTACTTTGT
1 TTTACTTTGT
41689884 TTTACTTT
1 TTTACTTT
41689892 TCCCCTTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.11, C:0.11, G:0.07, T:0.71
Consensus pattern (10 bp):
TTTACTTTGT
Done.