Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr6
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: 56482370
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1659275 characters in sequence are not A, C, G, or T
File 77 of 172
Found at i:25545631 original size:27 final size:27
Alignment explanation
Indices: 25545558--25545640 Score: 89
Period size: 27 Copynumber: 3.1 Consensus size: 27
25545548 GTAACAGAGT
* *
25545558 CACCAAATACAAATAT-TGTGGTAGAGC
1 CACCAAA-ACAAATATATGTGGCAAAGC
* *
25545585 CACCAAAACAAATATTTGTGGCATAGC
1 CACCAAAACAAATATATGTGGCAAAGC
*
25545612 CACCAGAAACAGATA-ATGTGGCAAAGC
1 CACCA-AAACAAATATATGTGGCAAAGC
25545639 CA
1 CA
25545641 TTTAACAGAA
Statistics
Matches: 49, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
26 8 0.16
27 33 0.67
28 8 0.16
ACGTcount: A:0.42, C:0.22, G:0.18, T:0.18
Consensus pattern (27 bp):
CACCAAAACAAATATATGTGGCAAAGC
Found at i:25546284 original size:27 final size:26
Alignment explanation
Indices: 25546254--25546393 Score: 163
Period size: 27 Copynumber: 5.2 Consensus size: 26
25546244 GGCAAAATGG
* * * *
25546254 TAATTTTACCCCACAAGGGTATCTCGA
1 TAATTCTACCCTACAGGGGTATTTC-A
*
25546281 TAATTCTACCCTATAGGGGTATTTCA
1 TAATTCTACCCTACAGGGGTATTTCA
* *
25546307 TTATTTCTACCCTACAAGGGTATTTCA
1 -TAATTCTACCCTACAGGGGTATTTCA
*
25546334 GTAATTCTACCCTATAGGGGTATTTCA
1 -TAATTCTACCCTACAGGGGTATTTCA
25546361 GTAATTCTACCCTACAGGGGTATTTCAA
1 -TAATTCTACCCTACAGGGGTATTTC-A
25546389 TAATT
1 TAATT
25546394 TTGTAAATCG
Statistics
Matches: 98, Mismatches: 13, Indels: 4
0.85 0.11 0.03
Matches are distributed among these distances:
26 1 0.01
27 96 0.98
28 1 0.01
ACGTcount: A:0.28, C:0.21, G:0.15, T:0.36
Consensus pattern (26 bp):
TAATTCTACCCTACAGGGGTATTTCA
Found at i:25546408 original size:27 final size:27
Alignment explanation
Indices: 25546378--25546481 Score: 84
Period size: 27 Copynumber: 3.9 Consensus size: 27
25546368 TACCCTACAG
25546378 GGGTATTTCAATAATTTTGTAAATCGA
1 GGGTATTTCAATAATTTTGTAAATCGA
*** ** *
25546405 GGGTAAAACGGTAATTCTGTAAATCGA
1 GGGTATTTCAATAATTTTGTAAATCGA
** ** *
25546432 GGGTACTTT-GGTAATTTTACAAGTCGA
1 GGGTA-TTTCAATAATTTTGTAAATCGA
*
25546459 GGGTATTTCAATAATTTGGTAAA
1 GGGTATTTCAATAATTTTGTAAA
25546482 CTAAAGTATT
Statistics
Matches: 56, Mismatches: 19, Indels: 4
0.71 0.24 0.05
Matches are distributed among these distances:
26 3 0.05
27 53 0.95
ACGTcount: A:0.33, C:0.09, G:0.23, T:0.36
Consensus pattern (27 bp):
GGGTATTTCAATAATTTTGTAAATCGA
Found at i:25552726 original size:29 final size:29
Alignment explanation
Indices: 25552665--25552726 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 29
25552655 GGCCTCGTTT
* * *
25552665 TGTCCTCACGGGCAAGACACATGCCCTTT
1 TGTCCTCACGGGCAAGACACACGCCCGTG
**
25552694 TGTCCTCACGGGCAAGACACACGGGCGTG
1 TGTCCTCACGGGCAAGACACACGCCCGTG
25552723 TGTC
1 TGTC
25552727 TAGACCGTGT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.19, C:0.32, G:0.27, T:0.21
Consensus pattern (29 bp):
TGTCCTCACGGGCAAGACACACGCCCGTG
Found at i:25552881 original size:55 final size:55
Alignment explanation
Indices: 25552797--25552977 Score: 301
Period size: 55 Copynumber: 3.3 Consensus size: 55
25552787 GCACTTAAAA
* * * * *
25552797 TTTT-AAGTCATTGTTGTACACGAGTAGGCCACATGGGCGTGTGCCATGGCCGTG
1 TTTTAAAGTCAGTATTGTACACGGGCAGGCCACACGGGCGTGTGCCATGGCCGTG
25552851 TTTTAAAGTCAGTATTGTACACGGGCAGGCCACACGGGCGTGTGCCATGGCCGTG
1 TTTTAAAGTCAGTATTGTACACGGGCAGGCCACACGGGCGTGTGCCATGGCCGTG
25552906 TTTTAAAGTCAGTATTGTACACGGGCAGGCCACACGGGCGTGTGCCATGGCCGTG
1 TTTTAAAGTCAGTATTGTACACGGGCAGGCCACACGGGCGTGTGCCATGGCCGTG
*
25552961 TTTTAAAGTTAGTATTG
1 TTTTAAAGTCAGTATTG
25552978 CACATTAGAT
Statistics
Matches: 120, Mismatches: 6, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
54 4 0.03
55 116 0.97
ACGTcount: A:0.20, C:0.20, G:0.31, T:0.28
Consensus pattern (55 bp):
TTTTAAAGTCAGTATTGTACACGGGCAGGCCACACGGGCGTGTGCCATGGCCGTG
Found at i:25559315 original size:47 final size:45
Alignment explanation
Indices: 25559248--25559460 Score: 218
Period size: 47 Copynumber: 4.6 Consensus size: 45
25559238 CTTATGGGCT
*
25559248 AGTGTAAGACATGTCTGGGACATGCATCGGGCACATTATGAGTGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGGGCACA-GATGAGTGCC
* *
25559294 AGTGTAAGACAATGTCTGGGACATGGCATCGGTGTAGAGATGAGTGCC
1 AGTGTAAGAC-ATGTCTGGGACAT-GCATCGG-GCACAGATGAGTGCC
* * *
25559342 AGTGTAAGACATGTTTGGGACATGCATCGGCCTCGACGATGA-TAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGGGCAC-A-GATGAGT-GCC
* * *
25559389 AGTGTAAGACCTGTCTGGGACATGCATC-GGCTA-AGA-GTTGTGCT
1 AGTGTAAGACATGTCTGGGACATGCATCGGGC-ACAGATG-AGTGCC
* *
25559433 AGTGTAAGACATATCTAGGACATGCATC
1 AGTGTAAGACATGTCTGGGACATGCATC
25559461 AGCACGTATA
Statistics
Matches: 141, Mismatches: 17, Indels: 20
0.79 0.10 0.11
Matches are distributed among these distances:
43 1 0.01
44 29 0.21
45 2 0.01
46 21 0.15
47 59 0.42
48 26 0.18
49 3 0.02
ACGTcount: A:0.27, C:0.18, G:0.31, T:0.24
Consensus pattern (45 bp):
AGTGTAAGACATGTCTGGGACATGCATCGGGCACAGATGAGTGCC
Found at i:25559409 original size:94 final size:91
Alignment explanation
Indices: 25559248--25559460 Score: 252
Period size: 94 Copynumber: 2.3 Consensus size: 91
25559238 CTTATGGGCT
* **
25559248 AGTGTAAGACATGTCTGGGACATGCATCGGGCACATTATGAGTGCCAGTGTAAGACAATGTCTGG
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCACACGATGAGTGCCAGTGTAAGACAATGTCTGG
*
25559313 GACATGGCATCGG-TGTAGAGATGAGTGCC
66 GACAT-GCATCGGCT-AAGAG-T-AGTGCC
* * *
25559342 AGTGTAAGACATGTTTGGGACATGCATCGGCCTCGACGATGA-TAGCCAGTGTAAGAC-CTGTCT
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCAC-ACGATGAGT-GCCAGTGTAAGACAATGTCT
* *
25559405 GGGACATGCATCGGCTAAGAGTTGTGCT
64 GGGACATGCATCGGCTAAGAGTAGTGCC
* *
25559433 AGTGTAAGACATATCTAGGACATGCATC
1 AGTGTAAGACATGTCTGGGACATGCATC
25559461 AGCACGTATA
Statistics
Matches: 104, Mismatches: 12, Indels: 9
0.83 0.10 0.07
Matches are distributed among these distances:
91 29 0.28
92 1 0.01
93 11 0.11
94 45 0.43
95 18 0.17
ACGTcount: A:0.27, C:0.18, G:0.31, T:0.24
Consensus pattern (91 bp):
AGTGTAAGACATGTCTGGGACATGCATCGGCCACACGATGAGTGCCAGTGTAAGACAATGTCTGG
GACATGCATCGGCTAAGAGTAGTGCC
Found at i:25560441 original size:13 final size:13
Alignment explanation
Indices: 25560423--25560448 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
25560413 TGTGTGCCAT
25560423 GGCCATGTTTTAA
1 GGCCATGTTTTAA
25560436 GGCCATGTTTTAA
1 GGCCATGTTTTAA
25560449 AGTCAGTATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.15, G:0.23, T:0.38
Consensus pattern (13 bp):
GGCCATGTTTTAA
Found at i:25561856 original size:23 final size:24
Alignment explanation
Indices: 25561779--25561899 Score: 158
Period size: 24 Copynumber: 5.0 Consensus size: 24
25561769 GCTTTATCAT
*
25561779 ATAACTGGAGGCCT-AGCCTCTTTTA
1 ATAACTGG-GGCATAAGCC-CTTTTA
25561804 ATAACTGGGGCA-AAGCCCTTTTTTTA
1 ATAACTGGGGCATAAGCCC---TTTTA
*
25561830 ATAACTAGGGCATAAGCCC-TTTA
1 ATAACTGGGGCATAAGCCCTTTTA
25561853 ATAACTGGGGCATAAGCCCTTTTA
1 ATAACTGGGGCATAAGCCCTTTTA
25561877 ATAACTGGGGCATAAGCCCTTTT
1 ATAACTGGGGCATAAGCCCTTTT
25561900 GCACTTCCTC
Statistics
Matches: 87, Mismatches: 3, Indels: 13
0.84 0.03 0.13
Matches are distributed among these distances:
23 23 0.26
24 34 0.39
25 8 0.09
26 16 0.18
27 6 0.07
ACGTcount: A:0.28, C:0.21, G:0.20, T:0.31
Consensus pattern (24 bp):
ATAACTGGGGCATAAGCCCTTTTA
Found at i:25561888 original size:47 final size:47
Alignment explanation
Indices: 25561800--25561898 Score: 155
Period size: 47 Copynumber: 2.1 Consensus size: 47
25561790 CCTAGCCTCT
25561800 TTTAATAACTGGGGCAAAGCCCTTTTTTTAATAACTAGGGCATAAGCCC
1 TTTAATAACTGGGGCAAAGCCC--TTTTTAATAACTAGGGCATAAGCCC
*
25561849 TTTAATAACTGGGGCATAAGCCC-TTTTAATAACTGGGGCATAAGCCC
1 TTTAATAACTGGGGCA-AAGCCCTTTTTAATAACTAGGGCATAAGCCC
25561896 TTT
1 TTT
25561899 TGCACTTCCT
Statistics
Matches: 48, Mismatches: 1, Indels: 4
0.91 0.02 0.08
Matches are distributed among these distances:
47 26 0.54
49 16 0.33
50 6 0.12
ACGTcount: A:0.29, C:0.20, G:0.19, T:0.31
Consensus pattern (47 bp):
TTTAATAACTGGGGCAAAGCCCTTTTTAATAACTAGGGCATAAGCCC
Found at i:25561976 original size:20 final size:20
Alignment explanation
Indices: 25561953--25562015 Score: 108
Period size: 20 Copynumber: 3.1 Consensus size: 20
25561943 GAACATCTCG
*
25561953 TGTGCATATCTTACATATCA
1 TGTGCATATCATACATATCA
*
25561973 TGTGCATATCATACATGTCA
1 TGTGCATATCATACATATCA
25561993 TGTGCATATCATACATATCA
1 TGTGCATATCATACATATCA
25562013 TGT
1 TGT
25562016 TTATCAAAAT
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 40 1.00
ACGTcount: A:0.30, C:0.19, G:0.13, T:0.38
Consensus pattern (20 bp):
TGTGCATATCATACATATCA
Found at i:25562080 original size:25 final size:25
Alignment explanation
Indices: 25562052--25562099 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
25562042 ATATATAAAC
* * *
25562052 CCTAGGGGTATAATGGTCATTTTTA
1 CCTAGGGGCAAAACGGTCATTTTTA
25562077 CCTAGGGGCAAAACGGTCATTTT
1 CCTAGGGGCAAAACGGTCATTTT
25562100 CACATTATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (25 bp):
CCTAGGGGCAAAACGGTCATTTTTA
Found at i:25570539 original size:40 final size:40
Alignment explanation
Indices: 25570455--25570679 Score: 296
Period size: 40 Copynumber: 5.7 Consensus size: 40
25570445 TTGAATGATG
* * * *
25570455 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* * *
25570495 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
*
25570535 TCCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
25570574 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
25570614 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
25570655 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
25570680 AACGAGGAGC
Statistics
Matches: 165, Mismatches: 15, Indels: 10
0.87 0.08 0.05
Matches are distributed among these distances:
39 34 0.21
40 121 0.73
41 10 0.06
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:25570701 original size:119 final size:119
Alignment explanation
Indices: 25570455--25570712 Score: 283
Period size: 119 Copynumber: 2.2 Consensus size: 119
25570445 TTGAATGATG
* *
25570455 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATTT
1 TCCGGGTTAAGTCCCGAAGGCTTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATTT
* ** *
25570520 GTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTGGTGCGAGTTACTAAA
66 GTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTGACTAAA
* * * **
25570574 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCAT
1 TCCGGGTTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCAT
* * * *
25570637 TTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-GAGCTATA
64 TTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTGGAACGAGTGA-CTAAA
* *
25570694 TCC-GGTTAAATTCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
25570713 TACGTGATTT
Statistics
Matches: 117, Mismatches: 17, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
118 3 0.03
119 83 0.71
120 31 0.26
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.25
Consensus pattern (119 bp):
TCCGGGTTAAGTCCCGAAGGCTTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATTT
GTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTGACTAAA
Found at i:25574726 original size:14 final size:15
Alignment explanation
Indices: 25574709--25574737 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
25574699 GCACGAAAAT
25574709 TTCACACAT-ATAAA
1 TTCACACATAATAAA
25574723 TTCACACATAATAAA
1 TTCACACATAATAAA
25574738 CACTGAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.52, C:0.21, G:0.00, T:0.28
Consensus pattern (15 bp):
TTCACACATAATAAA
Found at i:25575074 original size:15 final size:15
Alignment explanation
Indices: 25575042--25575070 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
25575032 ATTTTTTATG
25575042 TTTATTATGTGTGAA
1 TTTATTATGTGTGAA
25575057 TTTA-TATGTGTGAA
1 TTTATTATGTGTGAA
25575071 ATTTTTGTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.28, C:0.00, G:0.21, T:0.52
Consensus pattern (15 bp):
TTTATTATGTGTGAA
Found at i:25576305 original size:41 final size:44
Alignment explanation
Indices: 25576178--25576309 Score: 130
Period size: 45 Copynumber: 3.0 Consensus size: 44
25576168 GGATTTCTGG
* *
25576178 TATGTGTTCTCGTGTAAGACCATGTTTGGGAC-GTTGGCATCGATA
1 TATGTGAT-TCGTGTAAGACCATGTTTAGGACAG-TGGCATCGATA
* * *
25576223 TATGTGGTTACGTGTAAGACCATGTTTTGGACA-TCGACATCG-TA
1 TATGTGATT-CGTGTAAGACCATGTTTAGGACAGT-GGCATCGATA
* *
25576267 T-T-TGATTCGTGTAAGACCTTGTCTAGGACAGTGGCATCGATA
1 TATGTGATTCGTGTAAGACCATGTTTAGGACAGTGGCATCGATA
25576309 T
1 T
25576310 GGGATAGCAT
Statistics
Matches: 74, Mismatches: 8, Indels: 13
0.78 0.08 0.14
Matches are distributed among these distances:
41 26 0.35
42 8 0.11
43 1 0.01
44 5 0.07
45 34 0.46
ACGTcount: A:0.23, C:0.16, G:0.27, T:0.35
Consensus pattern (44 bp):
TATGTGATTCGTGTAAGACCATGTTTAGGACAGTGGCATCGATA
Found at i:25589033 original size:40 final size:40
Alignment explanation
Indices: 25588966--25589222 Score: 333
Period size: 40 Copynumber: 6.5 Consensus size: 40
25588956 ACCCAAGTAT
*
25588966 CTTCGGGAT-TTAG-CCGGATATAACAACTCGCACAAATGC
1 CTTCGGG-TCTTAGCCCGGATATAGCAACTCGCACAAATGC
*
25589005 CCTCGGGTCTTAGCCCGGATATAGCAACTCGCACAAATGC
1 CTTCGGGTCTTAGCCCGGATATAGCAACTCGCACAAATGC
* * *
25589045 CTTCGGGTCTTAGCCCGGATATAATC-ACTAGCATAAATGC
1 CTTCGGGTCTTAGCCCGGATAT-AGCAACTCGCACAAATGC
*
25589085 CTTCGGGACTTAGCCCGGATATAGCAACTCGCACAAATGC
1 CTTCGGGTCTTAGCCCGGATATAGCAACTCGCACAAATGC
* * *
25589125 CTTCGGGTCTTAGCCCGGATATAATC-ACTAGCATAAATGC
1 CTTCGGGTCTTAGCCCGGATAT-AGCAACTCGCACAAATGC
* * *
25589165 CTTCGGGACATAGCCCGGATATAGCAACTCGCACAAATAC
1 CTTCGGGTCTTAGCCCGGATATAGCAACTCGCACAAATGC
* *
25589205 CTTCGGATCTTAGTCCGG
1 CTTCGGGTCTTAGCCCGG
25589223 TTATCATCCG
Statistics
Matches: 188, Mismatches: 24, Indels: 11
0.84 0.11 0.05
Matches are distributed among these distances:
38 1 0.01
39 14 0.07
40 169 0.90
41 4 0.02
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.23
Consensus pattern (40 bp):
CTTCGGGTCTTAGCCCGGATATAGCAACTCGCACAAATGC
Found at i:25589098 original size:80 final size:80
Alignment explanation
Indices: 25588966--25589222 Score: 403
Period size: 80 Copynumber: 3.2 Consensus size: 80
25588956 ACCCAAGTAT
* * * *
25588966 CTTCGGGAT-TTAG-CCGGATATAA-CAACTCGCACAAATGCCCTCGGGTCTTAGCCCGGATATA
1 CTTCGGG-TCTTAGCCCGGATATAATC-ACTAGCATAAATGCCTTCGGGACTTAGCCCGGATATA
25589028 GCAACTCGCACAAATGC
64 GCAACTCGCACAAATGC
25589045 CTTCGGGTCTTAGCCCGGATATAATCACTAGCATAAATGCCTTCGGGACTTAGCCCGGATATAGC
1 CTTCGGGTCTTAGCCCGGATATAATCACTAGCATAAATGCCTTCGGGACTTAGCCCGGATATAGC
25589110 AACTCGCACAAATGC
66 AACTCGCACAAATGC
*
25589125 CTTCGGGTCTTAGCCCGGATATAATCACTAGCATAAATGCCTTCGGGACATAGCCCGGATATAGC
1 CTTCGGGTCTTAGCCCGGATATAATCACTAGCATAAATGCCTTCGGGACTTAGCCCGGATATAGC
*
25589190 AACTCGCACAAATAC
66 AACTCGCACAAATGC
* *
25589205 CTTCGGATCTTAGTCCGG
1 CTTCGGGTCTTAGCCCGG
25589223 TTATCATCCG
Statistics
Matches: 167, Mismatches: 8, Indels: 5
0.93 0.04 0.03
Matches are distributed among these distances:
78 1 0.01
79 11 0.07
80 154 0.92
81 1 0.01
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.23
Consensus pattern (80 bp):
CTTCGGGTCTTAGCCCGGATATAATCACTAGCATAAATGCCTTCGGGACTTAGCCCGGATATAGC
AACTCGCACAAATGC
Found at i:25599294 original size:93 final size:93
Alignment explanation
Indices: 25599179--25599350 Score: 283
Period size: 93 Copynumber: 1.8 Consensus size: 93
25599169 GCCCATAAGT
* * *
25599179 GAACTCGGACTCAACTCAACGAGCTT-GGGCGTTCGCATTCATAAGTGAACTCAGACTCAACTCA
1 GAACTCGGACTCAACTCAACGAG-TTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCA
25599243 ACGAGCTCGGATGCCTAGTTACATCTCTC
65 ACGAGCTCGGATGCCTAGTTACATCTCTC
*
25599272 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCAA
*
25599337 CGAGTTCGGATGCC
66 CGAGCTCGGATGCC
25599351 CAAACACCCT
Statistics
Matches: 73, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
92 2 0.03
93 71 0.97
ACGTcount: A:0.28, C:0.29, G:0.21, T:0.22
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCAA
CGAGCTCGGATGCCTAGTTACATCTCTC
Found at i:25599341 original size:46 final size:46
Alignment explanation
Indices: 25599171--25599346 Score: 189
Period size: 46 Copynumber: 3.8 Consensus size: 46
25599161 TGTAACCCGC
* *
25599171 CCATAAGTGAACTCGGACTCAACTCAACGAGCTT-GGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAG-TTCGGACATTCGCAT
* * * *
25599217 TCATAAGTGAACTCAGACTCAACTCAACGAGCTCGG--ATGC-CTAGTT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGC-A--T
* ***
25599263 ACATCTCTCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGT-GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
25599310 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
25599347 TGCCCAAACA
Statistics
Matches: 106, Mismatches: 16, Indels: 16
0.77 0.12 0.12
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
45 1 0.01
46 65 0.61
47 31 0.29
49 4 0.04
50 1 0.01
ACGTcount: A:0.29, C:0.28, G:0.20, T:0.22
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:25599365 original size:46 final size:45
Alignment explanation
Indices: 25599222--25599365 Score: 107
Period size: 46 Copynumber: 3.1 Consensus size: 45
25599212 CGCATTCATA
* * * *
25599222 AGTGAACTCAGACTCAACTCAACGAGCTCGGATGCCTAGTTACATCTCT
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCCA---ACA-CCCT
* * * * *
25599271 --CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGC-A-TCCAT
1 AGTGAACTCGGACTCAACTCAACGAGTTCGG--ATGCCCAACACCCT
25599314 AAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCCAAACACCCT
1 -AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCC-AACACCCT
25599361 AGTGA
1 AGTGA
25599366 CATGTCACTT
Statistics
Matches: 73, Mismatches: 14, Indels: 19
0.69 0.13 0.18
Matches are distributed among these distances:
43 2 0.03
44 4 0.05
45 1 0.01
46 34 0.47
47 29 0.40
49 3 0.04
ACGTcount: A:0.30, C:0.30, G:0.19, T:0.21
Consensus pattern (45 bp):
AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCCAACACCCT
Found at i:25604113 original size:34 final size:34
Alignment explanation
Indices: 25604070--25604138 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
25604060 ATCGAGTTGC
25604070 TTTAGCCGAAATCCCTTTTGTTTTTCCCCTCATT
1 TTTAGCCGAAATCCCTTTTGTTTTTCCCCTCATT
25604104 TTTAGCCGAAATCCCTTTTGTTTTTCCCCTCATT
1 TTTAGCCGAAATCCCTTTTGTTTTTCCCCTCATT
25604138 T
1 T
25604139 GACTCTTTTG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.14, C:0.29, G:0.09, T:0.48
Consensus pattern (34 bp):
TTTAGCCGAAATCCCTTTTGTTTTTCCCCTCATT
Found at i:25607512 original size:30 final size:29
Alignment explanation
Indices: 25607471--25607532 Score: 97
Period size: 30 Copynumber: 2.1 Consensus size: 29
25607461 GGTATCCGAT
*
25607471 GCTAGTTAAATCGCACACTTAGTGCCAAA
1 GCTAGTTAAATCCCACACTTAGTGCCAAA
*
25607500 GCTAGTTTAAATCCCACATTTAGTGCCAAA
1 GCTAG-TTAAATCCCACACTTAGTGCCAAA
25607530 GCT
1 GCT
25607533 TTCGATTCAT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
29 5 0.17
30 25 0.83
ACGTcount: A:0.32, C:0.24, G:0.16, T:0.27
Consensus pattern (29 bp):
GCTAGTTAAATCCCACACTTAGTGCCAAA
Found at i:25617773 original size:193 final size:193
Alignment explanation
Indices: 25617444--25617829 Score: 763
Period size: 193 Copynumber: 2.0 Consensus size: 193
25617434 ATCTCAGGTA
25617444 ATTTAATTCTAATATACAAAGTCATGAATCAACTCAACCTTATAAGCCAATATTACTCCTTTAAT
1 ATTTAATTCTAATATACAAAGTCATGAATCAACTCAACCTTATAAGCCAATATTACTCCTTTAAT
25617509 CGATTATAGATAGTTAAAAATAATATCACAAACATATACACCTATATGGCCGAATATACCAAATT
66 CGATTATAGATAGTTAAAAATAATATCACAAACATATACACCTATATGGCCGAATATACCAAATT
*
25617574 AAATTTAACATTACCTATGTAATTACCTATAAGTTCTTGTACTTCAAATTTCATACATTTAAC
131 AAATTTAACATTACCTATGTAATTACCTATAAGTTCTTATACTTCAAATTTCATACATTTAAC
25617637 ATTTAATTCTAATATACAAAGTCATGAATCAACTCAACCTTATAAGCCAATATTACTCCTTTAAT
1 ATTTAATTCTAATATACAAAGTCATGAATCAACTCAACCTTATAAGCCAATATTACTCCTTTAAT
25617702 CGATTATAGATAGTTAAAAATAATATCACAAACATATACACCTATATGGCCGAATATACCAAATT
66 CGATTATAGATAGTTAAAAATAATATCACAAACATATACACCTATATGGCCGAATATACCAAATT
25617767 AAATTTAACATTACCTATGTAATTACCTATAAGTTCTTATACTTCAAATTTCATACATTTAAC
131 AAATTTAACATTACCTATGTAATTACCTATAAGTTCTTATACTTCAAATTTCATACATTTAAC
25617830 CTTTTAATGC
Statistics
Matches: 192, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
193 192 1.00
ACGTcount: A:0.41, C:0.18, G:0.06, T:0.35
Consensus pattern (193 bp):
ATTTAATTCTAATATACAAAGTCATGAATCAACTCAACCTTATAAGCCAATATTACTCCTTTAAT
CGATTATAGATAGTTAAAAATAATATCACAAACATATACACCTATATGGCCGAATATACCAAATT
AAATTTAACATTACCTATGTAATTACCTATAAGTTCTTATACTTCAAATTTCATACATTTAAC
Found at i:25619075 original size:33 final size:33
Alignment explanation
Indices: 25619038--25619102 Score: 130
Period size: 33 Copynumber: 2.0 Consensus size: 33
25619028 GCCAACTCAA
25619038 ATAAGCACTTAAACATCTAGCACACAGCTTTTT
1 ATAAGCACTTAAACATCTAGCACACAGCTTTTT
25619071 ATAAGCACTTAAACATCTAGCACACAGCTTTT
1 ATAAGCACTTAAACATCTAGCACACAGCTTTT
25619103 ACATTTTATG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.37, C:0.25, G:0.09, T:0.29
Consensus pattern (33 bp):
ATAAGCACTTAAACATCTAGCACACAGCTTTTT
Found at i:25623201 original size:5 final size:5
Alignment explanation
Indices: 25623191--25623247 Score: 55
Period size: 5 Copynumber: 11.0 Consensus size: 5
25623181 CTCTTGCCTC
*
25623191 TCTTT TCTTT T-TATT TCATTT TCTTT T-TCT TCTTT TGCTTTT TCTTT
1 TCTTT TCTTT TCT-TT TC-TTT TCTTT TCTTT TCTTT T-C-TTT TCTTT
25623238 TCTTT TCTTT
1 TCTTT TCTTT
25623248 ATTTTCTCTT
Statistics
Matches: 44, Mismatches: 2, Indels: 12
0.76 0.03 0.21
Matches are distributed among these distances:
4 4 0.09
5 29 0.66
6 6 0.14
7 5 0.11
ACGTcount: A:0.04, C:0.18, G:0.02, T:0.77
Consensus pattern (5 bp):
TCTTT
Found at i:25623231 original size:15 final size:14
Alignment explanation
Indices: 25623191--25623247 Score: 60
Period size: 16 Copynumber: 3.7 Consensus size: 14
25623181 CTCTTGCCTC
*
25623191 TCTTTTCTTTTTATT
1 TCTTTTCTTTTT-CT
25623206 TCATTTTCTTTTTCT
1 TC-TTTTCTTTTTCT
25623221 TCTTTTGCTTTTTCTTT
1 TCTTTT-CTTTTTC--T
25623238 TCTTTTCTTT
1 TCTTTTCTTT
25623248 ATTTTCTCTT
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
14 4 0.11
15 12 0.32
16 14 0.38
17 7 0.19
ACGTcount: A:0.04, C:0.18, G:0.02, T:0.77
Consensus pattern (14 bp):
TCTTTTCTTTTTCT
Found at i:25623257 original size:21 final size:20
Alignment explanation
Indices: 25623189--25623258 Score: 63
Period size: 20 Copynumber: 3.4 Consensus size: 20
25623179 GCCTCTTGCC
25623189 TCTCTTTTCTTTTTATTTCATTT
1 TCTCTTTTC-TTTT-TTT-ATTT
**
25623212 TCT-TTTTCTTCTTTTGCTTT
1 TCTCTTTTCTT-TTTTTATTT
25623232 T-TCTTTTCTTTTCTTTATTT
1 TCTCTTTTCTTTT-TTTATTT
25623252 TCTCTTT
1 TCTCTTT
25623259 ACAAGAATGT
Statistics
Matches: 39, Mismatches: 4, Indels: 10
0.74 0.08 0.19
Matches are distributed among these distances:
19 3 0.08
20 17 0.44
21 9 0.23
22 7 0.18
23 3 0.08
ACGTcount: A:0.04, C:0.19, G:0.01, T:0.76
Consensus pattern (20 bp):
TCTCTTTTCTTTTTTTATTT
Found at i:25624127 original size:13 final size:11
Alignment explanation
Indices: 25624109--25624175 Score: 73
Period size: 11 Copynumber: 5.6 Consensus size: 11
25624099 GCACAAATCT
25624109 TTTTTTTTGAAA
1 TTTTTTTTG-AA
25624121 CTTTTTTTTGAA
1 -TTTTTTTTGAA
25624133 TTTTTTTTCG-A
1 TTTTTTTT-GAA
25624144 TTTTTTTTCCGAA
1 TTTTTTTT--GAA
25624157 TTTTTTTTTGAA
1 -TTTTTTTTGAA
25624169 TTTTTTT
1 TTTTTTT
25624176 ATACTTGTAT
Statistics
Matches: 50, Mismatches: 0, Indels: 10
0.83 0.00 0.17
Matches are distributed among these distances:
11 24 0.48
12 8 0.16
13 10 0.20
14 8 0.16
ACGTcount: A:0.15, C:0.06, G:0.07, T:0.72
Consensus pattern (11 bp):
TTTTTTTTGAA
Found at i:25624137 original size:12 final size:12
Alignment explanation
Indices: 25624108--25624175 Score: 84
Period size: 12 Copynumber: 5.6 Consensus size: 12
25624098 TGCACAAATC
25624108 TTTTTTTTTGAAA
1 TTTTTTTTTG-AA
*
25624121 CTTTTTTTTGAA
1 TTTTTTTTTGAA
*
25624133 TTTTTTTTCG-A
1 TTTTTTTTTGAA
*
25624144 TTTTTTTTCCGAA
1 TTTTTTTT-TGAA
25624157 TTTTTTTTTGAA
1 TTTTTTTTTGAA
25624169 TTTTTTT
1 TTTTTTT
25624176 ATACTTGTAT
Statistics
Matches: 49, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
11 9 0.18
12 22 0.45
13 18 0.37
ACGTcount: A:0.15, C:0.06, G:0.07, T:0.72
Consensus pattern (12 bp):
TTTTTTTTTGAA
Found at i:25625894 original size:30 final size:30
Alignment explanation
Indices: 25625798--25625882 Score: 98
Period size: 30 Copynumber: 2.8 Consensus size: 30
25625788 TACACTAAAA
*
25625798 TGAGCTAAGCTTTAGCTCATGAGCTAAAGT
1 TGAGCTAAGATTTAGCTCATGAGCTAAAGT
* * * * *
25625828 TGAGCTGAGATTAAACTCCTAAGCTAAAGT
1 TGAGCTAAGATTTAGCTCATGAGCTAAAGT
* *
25625858 TGAGCTAAGGTTTAGCTCGTGAGCT
1 TGAGCTAAGATTTAGCTCATGAGCT
25625883 GAATATGAGC
Statistics
Matches: 43, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
30 43 1.00
ACGTcount: A:0.29, C:0.16, G:0.25, T:0.29
Consensus pattern (30 bp):
TGAGCTAAGATTTAGCTCATGAGCTAAAGT
Found at i:25629337 original size:20 final size:20
Alignment explanation
Indices: 25629271--25629331 Score: 104
Period size: 20 Copynumber: 3.0 Consensus size: 20
25629261 ATTTTGATAA
*
25629271 ACATGGTATGTATGATATGC
1 ACATGATATGTATGATATGC
*
25629291 ACATGACATGTATGATATGC
1 ACATGATATGTATGATATGC
25629311 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
25629331 A
1 A
25629332 TGTGATGTAA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.34, C:0.11, G:0.21, T:0.33
Consensus pattern (20 bp):
ACATGATATGTATGATATGC
Found at i:25629466 original size:23 final size:23
Alignment explanation
Indices: 25629388--25629531 Score: 234
Period size: 24 Copynumber: 6.1 Consensus size: 23
25629378 AGGAAGTGAA
*
25629388 AAAGGGCTTATGCCCCAGTTATCA
1 AAAGGGCTTATGCCCCAGTTAT-T
*
25629412 AAAGGGCTTATGCCCCAGTTATCA
1 AAAGGGCTTATGCCCCAGTTAT-T
25629436 AAAGGGCTTATGCCCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATT
25629459 AAAGGGCTTATGCCCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATT
25629482 AAAGGGCTTATGCCCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATT
*
25629505 AAAAGGGCTTTTGCCCCAGTTATT
1 -AAAGGGCTTATGCCCCAGTTATT
25629529 AAA
1 AAA
25629532 AGAGGCTAGG
Statistics
Matches: 117, Mismatches: 2, Indels: 3
0.96 0.02 0.02
Matches are distributed among these distances:
23 49 0.42
24 68 0.58
ACGTcount: A:0.28, C:0.22, G:0.21, T:0.28
Consensus pattern (23 bp):
AAAGGGCTTATGCCCCAGTTATT
Found at i:25629510 original size:47 final size:47
Alignment explanation
Indices: 25629388--25629531 Score: 245
Period size: 47 Copynumber: 3.1 Consensus size: 47
25629378 AGGAAGTGAA
* *
25629388 AAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATCA
1 AAAGGGCTTATGCCCCAGTTATTAAAAGGGCTTATGCCCCAGTTAT-T
25629436 AAAGGGCTTATGCCCCAGTTATT-AAAGGGCTTATGCCCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATTAAAAGGGCTTATGCCCCAGTTATT
*
25629482 AAAGGGCTTATGCCCCAGTTATTAAAAGGGCTTTTGCCCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATTAAAAGGGCTTATGCCCCAGTTATT
25629529 AAA
1 AAA
25629532 AGAGGCTAGG
Statistics
Matches: 92, Mismatches: 3, Indels: 3
0.94 0.03 0.03
Matches are distributed among these distances:
46 23 0.25
47 47 0.51
48 22 0.24
ACGTcount: A:0.28, C:0.22, G:0.21, T:0.28
Consensus pattern (47 bp):
AAAGGGCTTATGCCCCAGTTATTAAAAGGGCTTATGCCCCAGTTATT
Found at i:25629784 original size:31 final size:31
Alignment explanation
Indices: 25629746--25629809 Score: 92
Period size: 31 Copynumber: 2.1 Consensus size: 31
25629736 CGTTTACAGT
25629746 AAAGGCTTCAGCCCAGTAATATGAAATATGA
1 AAAGGCTTCAGCCCAGTAATATGAAATATGA
** **
25629777 AAAGGCTTTGGCCCAGTGTTATGAAATATGA
1 AAAGGCTTCAGCCCAGTAATATGAAATATGA
25629808 AA
1 AA
25629810 TATGAAAAGG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.39, C:0.14, G:0.22, T:0.25
Consensus pattern (31 bp):
AAAGGCTTCAGCCCAGTAATATGAAATATGA
Found at i:25632411 original size:30 final size:29
Alignment explanation
Indices: 25632368--25632431 Score: 110
Period size: 30 Copynumber: 2.2 Consensus size: 29
25632358 CAAGTAGCCG
25632368 AAGCTAGTTAAATCACACACTTAGTGCCA
1 AAGCTAGTTAAATCACACACTTAGTGCCA
*
25632397 AAGCTAGTTTAAATCGCACACTTAGTGCCA
1 AAGCTAG-TTAAATCACACACTTAGTGCCA
25632427 AAGCT
1 AAGCT
25632432 TCTGATTCAT
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
29 7 0.21
30 26 0.79
ACGTcount: A:0.36, C:0.23, G:0.16, T:0.25
Consensus pattern (29 bp):
AAGCTAGTTAAATCACACACTTAGTGCCA
Found at i:25638360 original size:40 final size:40
Alignment explanation
Indices: 25638305--25638457 Score: 236
Period size: 40 Copynumber: 3.8 Consensus size: 40
25638295 GCATGAGCAT
25638305 TTGATATATCCGGGCTAAGACCCGAAGGCAATTATGCAAG
1 TTGATATATCCGGGCTAAGACCCGAAGGCAATTATGCAAG
25638345 TTGATATATCCGGGCTAAGACCCGAAGGCAATTATGCAAG
1 TTGATATATCCGGGCTAAGACCCGAAGGCAATTATGCAAG
* * *
25638385 TTGATATATCCGAGCTAAGACCCGAAGGC-ATTCGTGCGAG
1 TTGATATATCCGGGCTAAGACCCGAAGGCAATT-ATGCAAG
* * *
25638425 TTGCTATACCCGGGTTAAGACCCGAAGGCAATT
1 TTGATATATCCGGGCTAAGACCCGAAGGCAATT
25638458 GTGCTTGNNN
Statistics
Matches: 104, Mismatches: 7, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
39 3 0.03
40 98 0.94
41 3 0.03
ACGTcount: A:0.30, C:0.22, G:0.25, T:0.23
Consensus pattern (40 bp):
TTGATATATCCGGGCTAAGACCCGAAGGCAATTATGCAAG
Found at i:25642363 original size:70 final size:70
Alignment explanation
Indices: 25642280--25642415 Score: 236
Period size: 70 Copynumber: 1.9 Consensus size: 70
25642270 TGATGATGAT
* * * *
25642280 GATTGTTTGAGGTTTAGAAGTCGGTTGTGTGTTCCAAGGAATTCAGGACTCATTTCGATGATTCT
1 GATTGTTTGAGGTTCAGAAGTCGGTTGTGCGTTCCAAGAAATTCAGAACTCATTTCGATGATTCT
25642345 GTGAC
66 GTGAC
25642350 GATTGTTTGAGGTTCAGAAGTCGGTTGTGCGTTCCAAGAAATTCAGAACTCATTTCGATGATTCT
1 GATTGTTTGAGGTTCAGAAGTCGGTTGTGCGTTCCAAGAAATTCAGAACTCATTTCGATGATTCT
25642415 G
66 G
25642416 AACGAAGCTC
Statistics
Matches: 62, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
70 62 1.00
ACGTcount: A:0.23, C:0.14, G:0.27, T:0.36
Consensus pattern (70 bp):
GATTGTTTGAGGTTCAGAAGTCGGTTGTGCGTTCCAAGAAATTCAGAACTCATTTCGATGATTCT
GTGAC
Found at i:25642803 original size:258 final size:258
Alignment explanation
Indices: 25642346--25642819 Score: 903
Period size: 258 Copynumber: 1.8 Consensus size: 258
25642336 GATGATTCTG
25642346 TGACGATTGTTTGAGGTTCAGAAGTCGGTTGTGCGTTCCAAGAAATTCAGAACTCATTTCGATGA
1 TGACGATTGTTTGAGGTTCAGAAGTCGGTTGTGCGTTCCAAGAAATTCAGAACTCATTTCGATGA
25642411 TTCTGAACGAAGCTCATTGTAGCCGAATGTCAATTCACCCGGGGAGTACGAAAATGTACAACGAT
66 TTCTGAACGAAGCTCATTGTAGCCGAATGTCAATTCACCCGGGGAGTACGAAAATGTACAACGAT
*
25642476 TTGAAACGTTGGTTTTGGTGGCATGGTATGAAACGAGACATCTCCGACTTTGTTTCGAGATGTTT
131 TTGAAACGTCGGTTTTGGTGGCATGGTATGAAACGAGACATCTCCGACTTTGTTTCGAGATGTTT
*
25642541 AATATGTCAACAAGTTAAAGCTGAATGTATTCCGAATATGGAATCCGAATTTCAAATTGATGA
196 AATATGTCAACAAGTGAAAGCTGAATGTATTCCGAATATGGAATCCGAATTTCAAATTGATGA
25642604 TGACGATTGTTTGAGGTTCAGAAGTCGGTTGTGCGTTCCAAGAAATTCAGAACTCATTTCGATGA
1 TGACGATTGTTTGAGGTTCAGAAGTCGGTTGTGCGTTCCAAGAAATTCAGAACTCATTTCGATGA
25642669 TTCTGAACGAAGCTCATTGTAGCCGAATGTCAATTCACCCGGGGAGTACGAAAATGTACAACGAT
66 TTCTGAACGAAGCTCATTGTAGCCGAATGTCAATTCACCCGGGGAGTACGAAAATGTACAACGAT
* * *
25642734 TTGAAACGTCGGTTTTGGTGGCATGGTATGAAACGGGACATCTCTGACTTTGTTTTGAGATGTTT
131 TTGAAACGTCGGTTTTGGTGGCATGGTATGAAACGAGACATCTCCGACTTTGTTTCGAGATGTTT
25642799 AATATGTCAACAAGTGAAAGC
196 AATATGTCAACAAGTGAAAGC
25642820 GGAACATCAA
Statistics
Matches: 211, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
258 211 1.00
ACGTcount: A:0.29, C:0.16, G:0.24, T:0.30
Consensus pattern (258 bp):
TGACGATTGTTTGAGGTTCAGAAGTCGGTTGTGCGTTCCAAGAAATTCAGAACTCATTTCGATGA
TTCTGAACGAAGCTCATTGTAGCCGAATGTCAATTCACCCGGGGAGTACGAAAATGTACAACGAT
TTGAAACGTCGGTTTTGGTGGCATGGTATGAAACGAGACATCTCCGACTTTGTTTCGAGATGTTT
AATATGTCAACAAGTGAAAGCTGAATGTATTCCGAATATGGAATCCGAATTTCAAATTGATGA
Found at i:25645852 original size:40 final size:40
Alignment explanation
Indices: 25645797--25646113 Score: 492
Period size: 40 Copynumber: 7.9 Consensus size: 40
25645787 GCATGAGCAT
* *
25645797 TTGATATATCCGGGCTAAGACCTGAAGGCATTTGTGCAAG
1 TTGATATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAG
25645837 TTGATATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAG
1 TTGATATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAG
25645877 TTGATATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAG
1 TTGATATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAG
* *
25645917 TTGATAAATCCGGGCTAAGACCCGGAGGCATTTGTGCGAG
1 TTGATATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAG
*
25645957 TTGATATATCCGGGCTAAAACCCGAAGGCATTTGTGCGAG
1 TTGATATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAG
* * *
25645997 TTGATAAATCCGGGCTAAGACCCGAAGGCAATTATG-GAAG
1 TTGATATATCCGGGCTAAGACCCGAAGGCATTTGTGCG-AG
* *
25646037 TTGGTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAG
1 TTGATATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAG
* * * *
25646077 TTGCTATACCCGGGTTAAGACCCGAAGGCAATTGTGC
1 TTGATATATCCGGGCTAAGACCCGAAGGCATTTGTGC
25646114 TTGCGGTTAT
Statistics
Matches: 254, Mismatches: 21, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
39 1 0.00
40 252 0.99
41 1 0.00
ACGTcount: A:0.26, C:0.20, G:0.29, T:0.24
Consensus pattern (40 bp):
TTGATATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAG
Found at i:25647962 original size:46 final size:46
Alignment explanation
Indices: 25647912--25648078 Score: 162
Period size: 46 Copynumber: 3.6 Consensus size: 46
25647902 AGCATCTGAG
* *
25647912 CTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCAAATGTCCGAA
1 CTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAAAGTCCGAA
* * * *
25647958 CTCGTTGAGTTGAGTCTGAGTTC-GTGA--GATGTAACTAAGCATCCGAA
1 CTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAA--AAG--TCCGAA
* * * *
25648005 CTCGTTGAGTTGAGTCCGAGTTCATTTATGGATGCGAACG-CCCAA
1 CTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAAAGTCCGAA
*
25648050 GCTCATTGAGTTGAGTCCGAGTTCACTTA
1 -CTCGTTGAGTTGAGTCCGAGTTCACTTA
25648079 GGGGCGGGTT
Statistics
Matches: 100, Mismatches: 13, Indels: 16
0.78 0.10 0.12
Matches are distributed among these distances:
43 6 0.06
45 8 0.08
46 49 0.49
47 28 0.28
48 4 0.04
50 5 0.05
ACGTcount: A:0.23, C:0.19, G:0.26, T:0.31
Consensus pattern (46 bp):
CTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAAAGTCCGAA
Found at i:25648061 original size:93 final size:93
Alignment explanation
Indices: 25647902--25648073 Score: 247
Period size: 93 Copynumber: 1.8 Consensus size: 93
25647892 AGGATGGTTG
* * * * * *
25647902 AGCATCTGAGCTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCAAATGTCCGAACTCGTTGAG
1 AGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGTCCCAACTCATTGAG
*
25647967 TTGAGTCTGAGTTCGTGAGATGTAACTA
66 TTGAGTCCGAGTTCGTGAGATGTAACTA
* *
25647995 AGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCATTTATGGATGCGAACG-CCCAAGCTCATTGA
1 AGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGTCCCAA-CTCATTGA
25648059 GTTGAGTCCGAGTTC
65 GTTGAGTCCGAGTTC
25648074 ACTTAGGGGC
Statistics
Matches: 69, Mismatches: 9, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
92 4 0.06
93 65 0.94
ACGTcount: A:0.23, C:0.19, G:0.27, T:0.30
Consensus pattern (93 bp):
AGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGTCCCAACTCATTGAG
TTGAGTCCGAGTTCGTGAGATGTAACTA
Found at i:25648340 original size:19 final size:20
Alignment explanation
Indices: 25648303--25648340 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
25648293 ATAAGGTGAT
25648303 AAGATGATGAATGATGTTTA
1 AAGATGATGAATGATGTTTA
25648323 AAGATG-TGATAT-ATGTTT
1 AAGATGATGA-ATGATGTTT
25648341 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:25649500 original size:28 final size:28
Alignment explanation
Indices: 25649453--25649514 Score: 97
Period size: 28 Copynumber: 2.2 Consensus size: 28
25649443 AAATTAACCC
*
25649453 TAGGGGTATAAAGGTCATTTTGCATACA
1 TAGGGGTATAAAGGTAATTTTGCATACA
* *
25649481 TAGGGGTATAATGGTAATTTTGCATGCA
1 TAGGGGTATAAAGGTAATTTTGCATACA
25649509 TAGGGG
1 TAGGGG
25649515 CATTCTAGTA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.29, C:0.08, G:0.31, T:0.32
Consensus pattern (28 bp):
TAGGGGTATAAAGGTAATTTTGCATACA
Found at i:25650603 original size:12 final size:13
Alignment explanation
Indices: 25650584--25650616 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
25650574 GGGTTCGGCT
25650584 ATGGAGAAGGAAG
1 ATGGAGAAGGAAG
*
25650597 A-GGAGAAGGTAG
1 ATGGAGAAGGAAG
25650609 ATGGAGAA
1 ATGGAGAA
25650617 AAAGAAATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.45, C:0.00, G:0.45, T:0.09
Consensus pattern (13 bp):
ATGGAGAAGGAAG
Found at i:25652661 original size:29 final size:28
Alignment explanation
Indices: 25652626--25652695 Score: 70
Period size: 29 Copynumber: 2.4 Consensus size: 28
25652616 GGTCCCTAGA
* *
25652626 AATCCATATTTTTCATTTATTTCACAATTT
1 AATCCATATTTTACA--CATTTCACAATTT
25652656 AA-CCATGAATTTTACACATTTCACAATTT
1 AATCCAT--ATTTTACACATTTCACAATTT
*
25652685 AATCCCTATTT
1 AATCCATATTT
25652696 GGACATTTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
28 4 0.12
29 18 0.53
30 5 0.15
31 7 0.21
ACGTcount: A:0.33, C:0.20, G:0.01, T:0.46
Consensus pattern (28 bp):
AATCCATATTTTACACATTTCACAATTT
Found at i:25659524 original size:27 final size:27
Alignment explanation
Indices: 25659494--25659670 Score: 185
Period size: 27 Copynumber: 6.5 Consensus size: 27
25659484 AAATTGTACA
* *
25659494 GCACTAAGGGTGCGATTTGACTATGTT
1 GCACTAAGTGTGCGATTTGACTATGTG
** *
25659521 GCACTAAGTGTGCGAAATGAATATGAT-
1 GCACTAAGTGTGCGATTTGACTATG-TG
* * *
25659548 GCACTAAGTGTGCGAATTGACCATGCG
1 GCACTAAGTGTGCGATTTGACTATGTG
25659575 GCACTAAGTGTGCGAGTTTGACTATGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTG
* * *
25659603 GCACTAAGTGTGCAATTTGATTATGTA
1 GCACTAAGTGTGCGATTTGACTATGTG
* * * *
25659630 GCACTAAGTGTGCGAGTTGATTATATA
1 GCACTAAGTGTGCGATTTGACTATGTG
*
25659657 GCACTGAGTGTGCG
1 GCACTAAGTGTGCG
25659671 GACTCGATAT
Statistics
Matches: 129, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 105 0.81
28 24 0.19
ACGTcount: A:0.27, C:0.15, G:0.29, T:0.30
Consensus pattern (27 bp):
GCACTAAGTGTGCGATTTGACTATGTG
Found at i:25659607 original size:82 final size:81
Alignment explanation
Indices: 25659494--25659649 Score: 226
Period size: 82 Copynumber: 1.9 Consensus size: 81
25659484 AAATTGTACA
*
25659494 GCACTAAGGGTGCGATTTGACTATGTTGCACTAAGTGTGCGAA-ATGAATATG-ATGCACTAAGT
1 GCACTAAGGGTGCGATTTGACTATGTGGCACTAAGTGTGC-AATATGAATATGTA-GCACTAAGT
25659557 GTGCGAATTGACCATGCG
64 GTGCGAATTGACCATGCG
* * *
25659575 GCACTAAGTGTGCGAGTTTGACTATGTGGCACTAAGTGTGCAATTTGATTATGTAGCACTAAGTG
1 GCACTAAGGGTGCGA-TTTGACTATGTGGCACTAAGTGTGCAATATGAATATGTAGCACTAAGTG
*
25659640 TGCGAGTTGA
65 TGCGAATTGA
25659650 TTATATAGCA
Statistics
Matches: 67, Mismatches: 5, Indels: 5
0.87 0.06 0.06
Matches are distributed among these distances:
81 16 0.24
82 50 0.75
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.29, T:0.29
Consensus pattern (81 bp):
GCACTAAGGGTGCGATTTGACTATGTGGCACTAAGTGTGCAATATGAATATGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:25659661 original size:82 final size:81
Alignment explanation
Indices: 25659490--25659670 Score: 222
Period size: 82 Copynumber: 2.2 Consensus size: 81
25659480 GATTAAATTG
* *
25659490 TACAGCACTAAGGGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTGGCACTAAGTGTGCGAAATGAATATGATGCACTAA
25659555 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * * *
25659571 TGCGGCACTAAGTGTGCGAGTTTGACTATGTGGCACTAAGTGTGC-AATTTGATTATG-TAGCAC
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTGGCACTAAGTGTGCGAA-ATGAATATGAT-GCAC
* **
25659634 TAAGTGTGCGAGTTGATTA
63 TAAGTGTGCGAATTGACCA
* *
25659653 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
25659671 GACTCGATAT
Statistics
Matches: 84, Mismatches: 13, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
81 19 0.23
82 65 0.77
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTGGCACTAAGTGTGCGAAATGAATATGATGCACTAA
GTGTGCGAATTGACCA
Found at i:25663673 original size:19 final size:17
Alignment explanation
Indices: 25663643--25663686 Score: 52
Period size: 19 Copynumber: 2.5 Consensus size: 17
25663633 ATGAAATTTT
*
25663643 AAATAGTATTATGAGATA
1 AAATATTATTATGAGA-A
*
25663661 AAATTATTATTATTAGAA
1 AAA-TATTATTATGAGAA
25663679 AAATATTA
1 AAATATTA
25663687 CTGTAAGTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
17 5 0.22
18 7 0.30
19 11 0.48
ACGTcount: A:0.52, C:0.00, G:0.09, T:0.39
Consensus pattern (17 bp):
AAATATTATTATGAGAA
Found at i:25666077 original size:20 final size:20
Alignment explanation
Indices: 25666054--25666111 Score: 107
Period size: 20 Copynumber: 2.9 Consensus size: 20
25666044 TAAACATGGT
25666054 ATGTATGATATGCACATGAC
1 ATGTATGATATGCACATGAC
*
25666074 ATGTATGATATGCACATGAT
1 ATGTATGATATGCACATGAC
25666094 ATGTATGATATGCACATG
1 ATGTATGATATGCACATG
25666112 GTGTATTCAT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.34, C:0.12, G:0.21, T:0.33
Consensus pattern (20 bp):
ATGTATGATATGCACATGAC
Found at i:25666094 original size:11 final size:11
Alignment explanation
Indices: 25666058--25666111 Score: 53
Period size: 11 Copynumber: 5.3 Consensus size: 11
25666048 CATGGTATGT
25666058 ATGATATGCAC
1 ATGATATGCAC
* *
25666069 ATGACATG--T
1 ATGATATGCAC
25666078 ATGATATGCAC
1 ATGATATGCAC
*
25666089 ATGATATG--T
1 ATGATATGCAC
25666098 ATGATATGCAC
1 ATGATATGCAC
25666109 ATG
1 ATG
25666112 GTGTATTCAT
Statistics
Matches: 33, Mismatches: 6, Indels: 8
0.70 0.13 0.17
Matches are distributed among these distances:
9 15 0.45
11 18 0.55
ACGTcount: A:0.35, C:0.13, G:0.20, T:0.31
Consensus pattern (11 bp):
ATGATATGCAC
Found at i:25666192 original size:23 final size:23
Alignment explanation
Indices: 25666162--25666234 Score: 119
Period size: 23 Copynumber: 3.1 Consensus size: 23
25666152 AAGAAGTACA
25666162 AAAGGGCTTATGCCCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATT
25666185 AAAGGGCTTATGCCCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATT
* *
25666208 AAAATGGCTTTTGCCCCAGTTATT
1 -AAAGGGCTTATGCCCCAGTTATT
25666232 AAA
1 AAA
25666235 AGAGGCTAGG
Statistics
Matches: 47, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
23 26 0.55
24 21 0.45
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.32
Consensus pattern (23 bp):
AAAGGGCTTATGCCCCAGTTATT
Found at i:25666251 original size:25 final size:24
Alignment explanation
Indices: 25666161--25666255 Score: 131
Period size: 24 Copynumber: 4.0 Consensus size: 24
25666151 GAAGAAGTAC
25666161 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
25666185 -AAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
* *
25666208 AAAATGGCTTTTGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
*
25666232 AAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTATGCC-CCAGTTAT
25666256 ATGATAAAGC
Statistics
Matches: 63, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
23 23 0.37
24 29 0.46
25 11 0.17
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.29
Consensus pattern (24 bp):
AAAAGGGCTTATGCCCCAGTTATT
Found at i:25669253 original size:21 final size:21
Alignment explanation
Indices: 25669227--25669268 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
25669217 ATATAGCCAG
25669227 GTAAGTTCATAGTATTAAATT
1 GTAAGTTCATAGTATTAAATT
25669248 GTAAGTTCATAGTATTAAATT
1 GTAAGTTCATAGTATTAAATT
25669269 TTATAATTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.38, C:0.05, G:0.14, T:0.43
Consensus pattern (21 bp):
GTAAGTTCATAGTATTAAATT
Found at i:25669369 original size:20 final size:20
Alignment explanation
Indices: 25669336--25669448 Score: 59
Period size: 20 Copynumber: 5.2 Consensus size: 20
25669326 GTAAATTCTA
* *
25669336 CCCTGATTGCACTTACGTAC
1 CCCTGTTTGTACTTACGTAC
*
25669356 CCCTGTTTGTACTTCGGTACTTAC
1 CCCTGTTTGTAC-T---TACGTAC
25669380 GTGCCCCTGTTTGTACTT-CGGTAC
1 ---CC-CTGTTTGTACTTAC-GTAC
* * * *
25669404 CCCTGATTGCACTTACATGC
1 CCCTGTTTGTACTTACGTAC
25669424 CCCTGTTTGTACTT-CAGTAC
1 CCCTGTTTGTACTTAC-GTAC
25669444 CCCTG
1 CCCTG
25669449 ATTGCACATC
Statistics
Matches: 70, Mismatches: 12, Indels: 22
0.67 0.12 0.21
Matches are distributed among these distances:
19 1 0.01
20 41 0.59
21 4 0.06
23 1 0.01
24 10 0.14
27 3 0.04
28 10 0.14
ACGTcount: A:0.14, C:0.33, G:0.18, T:0.35
Consensus pattern (20 bp):
CCCTGTTTGTACTTACGTAC
Found at i:25669386 original size:28 final size:28
Alignment explanation
Indices: 25669346--25669403 Score: 107
Period size: 28 Copynumber: 2.1 Consensus size: 28
25669336 CCCTGATTGC
25669346 ACTTACGTACCCCTGTTTGTACTTCGGT
1 ACTTACGTACCCCTGTTTGTACTTCGGT
*
25669374 ACTTACGTGCCCCTGTTTGTACTTCGGT
1 ACTTACGTACCCCTGTTTGTACTTCGGT
25669402 AC
1 AC
25669404 CCCTGATTGC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.14, C:0.29, G:0.19, T:0.38
Consensus pattern (28 bp):
ACTTACGTACCCCTGTTTGTACTTCGGT
Found at i:25669429 original size:40 final size:40
Alignment explanation
Indices: 25669374--25669479 Score: 160
Period size: 40 Copynumber: 2.6 Consensus size: 40
25669364 GTACTTCGGT
*
25669374 ACTTACGTGCCCCTGTTTGTACTTCGGTACCCCTGATTGC
1 ACTTACGTGCCCCTGTTTGTACTTCAGTACCCCTGATTGC
*
25669414 ACTTACATGCCCCTGTTTGTACTTCAGTACCCCTGATTGC
1 ACTTACGTGCCCCTGTTTGTACTTCAGTACCCCTGATTGC
* *
25669454 ACAT-CGGTGCCCCTGTTTGAACTTCA
1 ACTTAC-GTGCCCCTGTTTGTACTTCA
25669480 ATGCTCTTAC
Statistics
Matches: 60, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
39 1 0.02
40 59 0.98
ACGTcount: A:0.16, C:0.32, G:0.18, T:0.34
Consensus pattern (40 bp):
ACTTACGTGCCCCTGTTTGTACTTCAGTACCCCTGATTGC
Found at i:25669466 original size:20 final size:20
Alignment explanation
Indices: 25669380--25669478 Score: 83
Period size: 20 Copynumber: 5.0 Consensus size: 20
25669370 CGGTACTTAC
* *
25669380 GTGCCCCTGTTTGTACTTCG
1 GTGCCCCTGATTGCACTTCG
*
25669400 GTACCCCTGATTGCACTTAC-
1 GTGCCCCTGATTGCACTT-CG
* * * *
25669420 ATGCCCCTGTTTGTACTTCA
1 GTGCCCCTGATTGCACTTCG
* *
25669440 GTACCCCTGATTGCACATCG
1 GTGCCCCTGATTGCACTTCG
* *
25669460 GTGCCCCTGTTTGAACTTC
1 GTGCCCCTGATTGCACTTC
25669479 AATGCTCTTA
Statistics
Matches: 60, Mismatches: 17, Indels: 4
0.74 0.21 0.05
Matches are distributed among these distances:
19 1 0.02
20 58 0.97
21 1 0.02
ACGTcount: A:0.14, C:0.32, G:0.19, T:0.34
Consensus pattern (20 bp):
GTGCCCCTGATTGCACTTCG
Found at i:25669987 original size:29 final size:29
Alignment explanation
Indices: 25669945--25670005 Score: 122
Period size: 29 Copynumber: 2.1 Consensus size: 29
25669935 AAATTTATTT
25669945 TAATATTATTCTAAGTGTTTACAGCATGA
1 TAATATTATTCTAAGTGTTTACAGCATGA
25669974 TAATATTATTCTAAGTGTTTACAGCATGA
1 TAATATTATTCTAAGTGTTTACAGCATGA
25670003 TAA
1 TAA
25670006 CATATATGTG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.36, C:0.10, G:0.13, T:0.41
Consensus pattern (29 bp):
TAATATTATTCTAAGTGTTTACAGCATGA
Found at i:25671211 original size:29 final size:28
Alignment explanation
Indices: 25671168--25671222 Score: 92
Period size: 29 Copynumber: 1.9 Consensus size: 28
25671158 AGATATACCA
25671168 ATTTGGCTTCGGGCCATGAATATCAGTTG
1 ATTTGGCTTCGGGCCATG-ATATCAGTTG
*
25671197 ATTTGGCTTCTGGCCATGATATCAGT
1 ATTTGGCTTCGGGCCATGATATCAGT
25671223 GCTTCAGATG
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
28 8 0.32
29 17 0.68
ACGTcount: A:0.20, C:0.18, G:0.25, T:0.36
Consensus pattern (28 bp):
ATTTGGCTTCGGGCCATGATATCAGTTG
Found at i:25673058 original size:23 final size:23
Alignment explanation
Indices: 25673032--25673091 Score: 102
Period size: 23 Copynumber: 2.6 Consensus size: 23
25673022 AGTTCATAAG
* *
25673032 AGCTTACTGTTTCAGCTTATTGA
1 AGCTTACCGATTCAGCTTATTGA
25673055 AGCTTACCGATTCAGCTTATTGA
1 AGCTTACCGATTCAGCTTATTGA
25673078 AGCTTACCGATTCA
1 AGCTTACCGATTCA
25673092 ACTCAATAGA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.25, C:0.22, G:0.17, T:0.37
Consensus pattern (23 bp):
AGCTTACCGATTCAGCTTATTGA
Found at i:25673104 original size:23 final size:23
Alignment explanation
Indices: 25673008--25673131 Score: 94
Period size: 23 Copynumber: 5.3 Consensus size: 23
25672998 CAGCTAGTAT
* *
25673008 GAGCTTACCGATTTAGTTC-ATAA
1 GAGCTTACCGATTCAGCTCAAT-A
* * * *
25673031 GAGCTTACTGTTTCAGCT-TATT
1 GAGCTTACCGATTCAGCTCAATA
* *
25673053 GAAGCTTACCGATTCAGCT-TATT
1 G-AGCTTACCGATTCAGCTCAATA
*
25673076 GAAGCTTACCGATTCAACTCAATA
1 G-AGCTTACCGATTCAGCTCAATA
25673100 GAGCTTACC-ATTTTCAGCTCAATA
1 GAGCTTACCGA--TTCAGCTCAATA
25673124 GAGCTTAC
1 GAGCTTAC
25673132 TGTTCATCAG
Statistics
Matches: 85, Mismatches: 11, Indels: 9
0.81 0.10 0.09
Matches are distributed among these distances:
22 2 0.02
23 61 0.72
24 22 0.26
ACGTcount: A:0.28, C:0.22, G:0.16, T:0.34
Consensus pattern (23 bp):
GAGCTTACCGATTCAGCTCAATA
Found at i:25675546 original size:140 final size:140
Alignment explanation
Indices: 25675307--25675563 Score: 433
Period size: 140 Copynumber: 1.8 Consensus size: 140
25675297 AAAGAATATC
* *
25675307 TTGAATTGAAGCAAGGACGTATGTTAGTCACAGAATATGAAAGAAAGTTTCTACGACTCAGCAAA
1 TTGAATTAAAGCAAGGACGTATGTCAGTCACAGAATATGAAAGAAAGTTTCTACGACTCAGCAAA
* *
25675372 TATGTAACGCCCCAATCCCCAAATCCCTGATAAAATTATTTTTTTGTCTTTGCTTCAATTCAAGA
66 TATGTAACACCCCAATCCCCAAATCCCTGATAAAATTATTTTTATGTCTTTGCTTCAATTCAAGA
25675437 AAATAATTTA
131 AAATAATTTA
* *
25675447 TTGAATTAAAGCAAGGACGTATGTCAGTCACTGAATATGAAAGAAAGTTTGTACGACTCAGCAAA
1 TTGAATTAAAGCAAGGACGTATGTCAGTCACAGAATATGAAAGAAAGTTTCTACGACTCAGCAAA
* * *
25675512 TATGTAACACGCCAATCCCTAAATCCCTGATAAAATTATTTTTATGTGTTTG
66 TATGTAACACCCCAATCCCCAAATCCCTGATAAAATTATTTTTATGTCTTTG
25675564 TGATGTGAAA
Statistics
Matches: 108, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
140 108 1.00
ACGTcount: A:0.36, C:0.17, G:0.16, T:0.31
Consensus pattern (140 bp):
TTGAATTAAAGCAAGGACGTATGTCAGTCACAGAATATGAAAGAAAGTTTCTACGACTCAGCAAA
TATGTAACACCCCAATCCCCAAATCCCTGATAAAATTATTTTTATGTCTTTGCTTCAATTCAAGA
AAATAATTTA
Found at i:25680201 original size:27 final size:26
Alignment explanation
Indices: 25680161--25680211 Score: 75
Period size: 27 Copynumber: 1.9 Consensus size: 26
25680151 CTCGCTGCAA
*
25680161 TCTGGTGGCCTCGTCACATATATCTAT
1 TCTGGTGACCTCGTCACA-ATATCTAT
*
25680188 TCTGGTGACTTCGTCACAATATCT
1 TCTGGTGACCTCGTCACAATATCT
25680212 GGTAGCCTCA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 6 0.27
27 16 0.73
ACGTcount: A:0.20, C:0.25, G:0.18, T:0.37
Consensus pattern (26 bp):
TCTGGTGACCTCGTCACAATATCTAT
Found at i:25682328 original size:38 final size:38
Alignment explanation
Indices: 25682277--25682352 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
25682267 GTAGAAAGAC
25682277 AGAATCGTGAGAAAGATCAGAACCGTTTTAGGAGAGAT
1 AGAATCGTGAGAAAGATCAGAACCGTTTTAGGAGAGAT
25682315 AGAATCGTGAGAAAGATCAGAACCGTTTTAGGAGAGAT
1 AGAATCGTGAGAAAGATCAGAACCGTTTTAGGAGAGAT
25682353 TCAGGACTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.39, C:0.11, G:0.29, T:0.21
Consensus pattern (38 bp):
AGAATCGTGAGAAAGATCAGAACCGTTTTAGGAGAGAT
Found at i:25682352 original size:21 final size:21
Alignment explanation
Indices: 25682290--25682352 Score: 71
Period size: 21 Copynumber: 3.2 Consensus size: 21
25682280 ATCGTGAGAA
25682290 AGATCAGAACCGTTTTAGGAG
1 AGATCAGAACCGTTTTAGGAG
* * *
25682311 AGAT-AGAATCG--TGA-GAA
1 AGATCAGAACCGTTTTAGGAG
25682328 AGATCAGAACCGTTTTAGGAG
1 AGATCAGAACCGTTTTAGGAG
25682349 AGAT
1 AGAT
25682353 TCAGGACTTT
Statistics
Matches: 32, Mismatches: 6, Indels: 8
0.70 0.13 0.17
Matches are distributed among these distances:
17 6 0.19
18 8 0.25
20 8 0.25
21 10 0.31
ACGTcount: A:0.38, C:0.11, G:0.29, T:0.22
Consensus pattern (21 bp):
AGATCAGAACCGTTTTAGGAG
Found at i:25687419 original size:27 final size:26
Alignment explanation
Indices: 25687375--25687426 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
25687365 CTCGCTGCAA
*
25687375 TCTGGTGGCCTCGCCACATATATCTGT
1 TCTGGTGACCTCGCCACA-ATATCTGT
* *
25687402 TCTGGTGACTTCGTCACAATATCTG
1 TCTGGTGACCTCGCCACAATATCTG
25687427 GCAGCCTCGC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.17, C:0.27, G:0.21, T:0.35
Consensus pattern (26 bp):
TCTGGTGACCTCGCCACAATATCTGT
Found at i:25687517 original size:27 final size:26
Alignment explanation
Indices: 25687465--25687524 Score: 75
Period size: 27 Copynumber: 2.3 Consensus size: 26
25687455 CCACATATAT
*
25687465 ATATCTGTTCTGGTGGCCTAGCCACA
1 ATATCTGTTCTGGTGACCTAGCCACA
* * *
25687491 ATATCTGTATCTGGTGACTTCGTCACA
1 ATATCTGT-TCTGGTGACCTAGCCACA
25687518 ATATCTG
1 ATATCTG
25687525 GCAGCCTCGC
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 8 0.28
27 21 0.72
ACGTcount: A:0.22, C:0.23, G:0.20, T:0.35
Consensus pattern (26 bp):
ATATCTGTTCTGGTGACCTAGCCACA
Found at i:25697799 original size:18 final size:18
Alignment explanation
Indices: 25697757--25697799 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
25697747 GCCCATTCCG
* *
25697757 AAGTATATATATATACAT
1 AAGTATGTATATATACAC
25697775 ATA-TATGTATATATACAC
1 A-AGTATGTATATATACAC
25697793 AAGTATG
1 AAGTATG
25697800 CCCATTCGGG
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
17 1 0.05
18 19 0.90
19 1 0.05
ACGTcount: A:0.47, C:0.07, G:0.09, T:0.37
Consensus pattern (18 bp):
AAGTATGTATATATACAC
Found at i:25698306 original size:56 final size:56
Alignment explanation
Indices: 25698244--25698477 Score: 303
Period size: 56 Copynumber: 4.2 Consensus size: 56
25698234 GAGATTGGCG
* *
25698244 CTAAGTGTGCGGGTTTAAAT-TGTGCAGCACTAAGTGTGCGA-ATTGACTATGTAGCA
1 CTAAGTGTGCGAGTTTGAATATGT--AGCACTAAGTGTGCGAGATTGACTATGTAGCA
* * *
25698300 CTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGAGTTTGACTATGTAGAA
1 CTAAGTGTGCGAGTTTGAATATGTAGCACTAAGTGTGCGAGATTGACTATGTAGCA
* * * *
25698356 CCAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGAGCTTGATTATGTAGCA
1 CTAAGTGTGCGAGTTTGAATATGTAGCACTAAGTGTGCGAGATTGACTATGTAGCA
* * * *
25698412 CTAAGTGTGCGAGTTTGATTATATAGCACTAAGTGTGCGAG-TTGATTATATAGCA
1 CTAAGTGTGCGAGTTTGAATATGTAGCACTAAGTGTGCGAGATTGACTATGTAGCA
*
25698467 CTGAGTGTGCG
1 CTAAGTGTGCG
25698478 GACTTATTAT
Statistics
Matches: 162, Mismatches: 14, Indels: 5
0.90 0.08 0.03
Matches are distributed among these distances:
55 39 0.24
56 120 0.74
57 3 0.02
ACGTcount: A:0.26, C:0.14, G:0.29, T:0.32
Consensus pattern (56 bp):
CTAAGTGTGCGAGTTTGAATATGTAGCACTAAGTGTGCGAGATTGACTATGTAGCA
Found at i:25698326 original size:28 final size:28
Alignment explanation
Indices: 25698269--25698477 Score: 314
Period size: 28 Copynumber: 7.5 Consensus size: 28
25698259 TAAATTGTGC
*
25698269 AGCACTAAGTGTGCGA-ATTGACTATGT
1 AGCACTAAGTGTGCGAGTTTGACTATGT
25698296 AGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGAGTTTGACTATGT
25698324 AGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGAGTTTGACTATGT
* *
25698352 AGAACCAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGAGTTTGACTATGT
* *
25698380 AGCACTAAGTGTGCGAGCTTGATTATGT
1 AGCACTAAGTGTGCGAGTTTGACTATGT
* *
25698408 AGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCGAGTTTGACTATGT
* *
25698436 AGCACTAAGTGTGCGAG-TTGATTATAT
1 AGCACTAAGTGTGCGAGTTTGACTATGT
*
25698463 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
25698478 GACTTATTAT
Statistics
Matches: 171, Mismatches: 10, Indels: 2
0.93 0.05 0.01
Matches are distributed among these distances:
27 40 0.23
28 131 0.77
ACGTcount: A:0.27, C:0.14, G:0.28, T:0.31
Consensus pattern (28 bp):
AGCACTAAGTGTGCGAGTTTGACTATGT
Found at i:25705963 original size:18 final size:18
Alignment explanation
Indices: 25705921--25705963 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
25705911 GCCCATTCTG
* *
25705921 AAGTATATATATATACAT
1 AAGTATGTATATATACAC
25705939 ATA-TATGTATATATACAC
1 A-AGTATGTATATATACAC
25705957 AAGTATG
1 AAGTATG
25705964 CCCATTCGGG
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
17 1 0.05
18 19 0.90
19 1 0.05
ACGTcount: A:0.47, C:0.07, G:0.09, T:0.37
Consensus pattern (18 bp):
AAGTATGTATATATACAC
Found at i:25706452 original size:29 final size:28
Alignment explanation
Indices: 25706408--25706502 Score: 104
Period size: 27 Copynumber: 3.4 Consensus size: 28
25706398 GAGATTGGCG
* *
25706408 CTAAGTGTGCGGGTTTAAATTGT-TCAGCA
1 CTAAGTGTGCGAGTTT-AATTATAT-AGCA
*
25706437 CTAAGTGTGCGAGTTTGATTATATAGCA
1 CTAAGTGTGCGAGTTTAATTATATAGCA
* *
25706465 CTAAGTGTGCGAG-TTGATTTTATAGCA
1 CTAAGTGTGCGAGTTTAATTATATAGCA
*
25706492 CTGAGTGTGCG
1 CTAAGTGTGCG
25706503 GACTTAATAT
Statistics
Matches: 60, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
27 23 0.38
28 21 0.35
29 16 0.27
ACGTcount: A:0.24, C:0.13, G:0.28, T:0.35
Consensus pattern (28 bp):
CTAAGTGTGCGAGTTTAATTATATAGCA
Found at i:25706489 original size:27 final size:28
Alignment explanation
Indices: 25706433--25706502 Score: 115
Period size: 27 Copynumber: 2.5 Consensus size: 28
25706423 TAAATTGTTC
25706433 AGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCGAGTTTGATTATAT
*
25706461 AGCACTAAGTGTGCGAG-TTGATTTTAT
1 AGCACTAAGTGTGCGAGTTTGATTATAT
*
25706488 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
25706503 GACTTAATAT
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
27 23 0.57
28 17 0.43
ACGTcount: A:0.26, C:0.13, G:0.29, T:0.33
Consensus pattern (28 bp):
AGCACTAAGTGTGCGAGTTTGATTATAT
Found at i:25706515 original size:27 final size:27
Alignment explanation
Indices: 25706433--25706515 Score: 87
Period size: 27 Copynumber: 3.0 Consensus size: 27
25706423 TAAATTGTTC
* *
25706433 AGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCGA-CTTGAATATAT
* * *
25706461 AGCACTAAGTGTGCGAGTTGATTTTAT
1 AGCACTAAGTGTGCGACTTGAATATAT
*
25706488 AGCACTGAGTGTGCGGACTT-AATATAT
1 AGCACTAAGTGTGC-GACTTGAATATAT
25706515 A
1 A
25706516 TATTTTTGAA
Statistics
Matches: 48, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
27 28 0.58
28 20 0.42
ACGTcount: A:0.29, C:0.12, G:0.25, T:0.34
Consensus pattern (27 bp):
AGCACTAAGTGTGCGACTTGAATATAT
Found at i:25714678 original size:27 final size:27
Alignment explanation
Indices: 25714648--25714825 Score: 137
Period size: 27 Copynumber: 6.6 Consensus size: 27
25714638 ATATTGAGTC
* *
25714648 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
* * * *
25714675 CGCACATTTAGTGCCACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
* *
25714702 CGCACACTTAGTGCTACATAGTCAAACC
1 CGCACACTTAGTGCTACATAATC-AACT
** ** *
25714730 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
* **
25714757 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAATCAACT
* *
25714784 CGCACACTTAGTGCAACA-AAGT-AGAAT
1 CGCACACTTAGTGCTACATAA-TCA-ACT
25714811 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
25714826 GTACAATTTA
Statistics
Matches: 121, Mismatches: 25, Indels: 10
0.78 0.16 0.06
Matches are distributed among these distances:
26 2 0.02
27 96 0.79
28 23 0.19
ACGTcount: A:0.30, C:0.28, G:0.16, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:25714760 original size:55 final size:54
Alignment explanation
Indices: 25714648--25714825 Score: 164
Period size: 54 Copynumber: 3.3 Consensus size: 54
25714638 ATATTGAGTC
* * * * *
25714648 CGCACACTCAGTGCTATATAATCAACTCGCACATTTAGTGCCACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACCCGCACACTTAGTGCCACATAATCAAAT
* * ** *
25714702 CGCACACTTAGTGCTACATAGTCAAACCCGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATC-AACCCGCACACTTAGTGCCACATAATCAAAT
* *** *
25714757 CGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACA-AAGT-AGAAT
1 CGCACACTTAGTGCTA-CATAATCAACCCGCACACTTAGTGCCACATAA-TCA-AAT
25714811 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
25714826 GTACAATTTA
Statistics
Matches: 100, Mismatches: 19, Indels: 9
0.78 0.15 0.07
Matches are distributed among these distances:
53 1 0.01
54 55 0.55
55 44 0.44
ACGTcount: A:0.30, C:0.28, G:0.16, T:0.26
Consensus pattern (54 bp):
CGCACACTTAGTGCTACATAATCAACCCGCACACTTAGTGCCACATAATCAAAT
Found at i:25719196 original size:15 final size:14
Alignment explanation
Indices: 25719178--25719225 Score: 53
Period size: 15 Copynumber: 3.4 Consensus size: 14
25719168 TTTTGAATGA
25719178 AAATTTTCCGATCTG
1 AAATTTT-CGATCTG
* *
25719193 AAATTTTGGA-ATG
1 AAATTTTCGATCTG
25719206 AAATTTTTCGATCTG
1 AAA-TTTTCGATCTG
25719221 AAATT
1 AAATT
25719226 CAGTCTCCTT
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
13 5 0.19
14 10 0.37
15 12 0.44
ACGTcount: A:0.33, C:0.10, G:0.15, T:0.42
Consensus pattern (14 bp):
AAATTTTCGATCTG
Found at i:25719209 original size:28 final size:29
Alignment explanation
Indices: 25719167--25719225 Score: 93
Period size: 28 Copynumber: 2.1 Consensus size: 29
25719157 CTTTTGCACT
*
25719167 TTTTTGAATGAAAATTTTCCGATCTGAAA
1 TTTTGGAATGAAAATTTTCCGATCTGAAA
*
25719196 TTTTGGAATG-AAATTTTTCGATCTGAAA
1 TTTTGGAATGAAAATTTTCCGATCTGAAA
25719224 TT
1 TT
25719226 CAGTCTCCTT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
28 19 0.68
29 9 0.32
ACGTcount: A:0.32, C:0.08, G:0.15, T:0.44
Consensus pattern (29 bp):
TTTTGGAATGAAAATTTTCCGATCTGAAA
Found at i:25719213 original size:29 final size:28
Alignment explanation
Indices: 25719167--25719225 Score: 91
Period size: 29 Copynumber: 2.1 Consensus size: 28
25719157 CTTTTGCACT
*
25719167 TTTTTGAATGAAAATTTTCCGATCTGAAA
1 TTTTGGAATGAAAATTTT-CGATCTGAAA
*
25719196 TTTTGGAATGAAATTTTTCGATCTGAAA
1 TTTTGGAATGAAAATTTTCGATCTGAAA
25719224 TT
1 TT
25719226 CAGTCTCCTT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
28 12 0.43
29 16 0.57
ACGTcount: A:0.32, C:0.08, G:0.15, T:0.44
Consensus pattern (28 bp):
TTTTGGAATGAAAATTTTCGATCTGAAA
Found at i:25723906 original size:27 final size:26
Alignment explanation
Indices: 25723866--25723971 Score: 95
Period size: 27 Copynumber: 3.9 Consensus size: 26
25723856 AGGAAGCGTC
*
25723866 CTGGTGGCTATGCCACAATCATCTGAT
1 CTGGTGGCTCTGCCACAAT-ATCTGAT
* *
25723893 CTGGTGGCTCTGCCACATATTTCTGTT
1 CTGGTGGCTCTGCCACA-ATATCTGAT
* * *
25723920 CTGGTGGCTCTACCACGATTATCTATAT
1 CTGGTGGCTCTGCCAC-AATATCT-GAT
* * *
25723948 CTGGTGACTCTGTCACATTATCTG
1 CTGGTGGCTCTGCCACAATATCTG
25723972 TTCTAGCAGC
Statistics
Matches: 64, Mismatches: 12, Indels: 7
0.77 0.14 0.08
Matches are distributed among these distances:
27 47 0.73
28 17 0.27
ACGTcount: A:0.18, C:0.25, G:0.21, T:0.36
Consensus pattern (26 bp):
CTGGTGGCTCTGCCACAATATCTGAT
Found at i:25733543 original size:9 final size:9
Alignment explanation
Indices: 25733524--25733552 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
25733514 CAAAAAGACC
25733524 TCTTC-TTT
1 TCTTCTTTT
25733532 TCTTCTTTT
1 TCTTCTTTT
25733541 TCTTCTTTT
1 TCTTCTTTT
25733550 TCT
1 TCT
25733553 CCTTGCTTAC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 5 0.25
9 15 0.75
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (9 bp):
TCTTCTTTT
Found at i:25738147 original size:68 final size:63
Alignment explanation
Indices: 25738000--25738147 Score: 174
Period size: 63 Copynumber: 2.3 Consensus size: 63
25737990 ATATAGTTCG
* *
25738000 GCTCTCTTGTACACATGGTGAACACTTAGTACCACCCATGTGACCTAGCCAGTTTATCTCGTA
1 GCTCTCTTGTACACATGGTGAACACATAGTACCACCCATGCGACCTAGCCAGTTTATCTCGTA
* * *
25738063 GCTCTCTTGT-CTACATGGTGTACACATAGTATCACCCATGCGACCTAGCTACA-TCATAATGTC
1 GCTCTCTTGTAC-ACATGGTGAACACATAGTACCACCCATGCGACCTAGC--CAGT--T--TATC
25738126 TCGTA
59 TCGTA
25738131 GCTCTCTTGTACACATG
1 GCTCTCTTGTACACATG
25738148 ATGTGCACTC
Statistics
Matches: 72, Mismatches: 5, Indels: 11
0.82 0.06 0.12
Matches are distributed among these distances:
62 1 0.01
63 43 0.60
64 1 0.01
65 2 0.03
66 1 0.01
68 23 0.32
69 1 0.01
ACGTcount: A:0.24, C:0.28, G:0.17, T:0.31
Consensus pattern (63 bp):
GCTCTCTTGTACACATGGTGAACACATAGTACCACCCATGCGACCTAGCCAGTTTATCTCGTA
Found at i:25738176 original size:68 final size:68
Alignment explanation
Indices: 25738056--25738184 Score: 163
Period size: 68 Copynumber: 1.9 Consensus size: 68
25738046 AGCCAGTTTA
* * * *
25738056 TCTCGTAGCTCTCTTGTCTACATGGTGTACACATAGTATCACCCATGCGACCTAGCTACATCATA
1 TCTCGTAGCTCTCTTGTCTACATGATGTACACATAGCACCACACATGCGACCTAGCTACATCATA
25738121 ATG
66 ATG
* * *
25738124 TCTCGTAGCTCTCTTGTAC-ACATGATGTGCAC-TCAGCACCATACATGTGACCTAGCTACAT
1 TCTCGTAGCTCTCTTGT-CTACATGATGTACACAT-AGCACCACACATGCGACCTAGCTACAT
25738185 ACCATCTGTA
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
67 1 0.02
68 50 0.96
69 1 0.02
ACGTcount: A:0.25, C:0.29, G:0.16, T:0.30
Consensus pattern (68 bp):
TCTCGTAGCTCTCTTGTCTACATGATGTACACATAGCACCACACATGCGACCTAGCTACATCATA
ATG
Found at i:25740049 original size:40 final size:40
Alignment explanation
Indices: 25739877--25740042 Score: 253
Period size: 40 Copynumber: 4.2 Consensus size: 40
25739867 AACCCAAGTA
* * *
25739877 CCTTCGGGATTTAG-CCGGATATAGCAACTCGCATAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
*
25739916 CCTTCGAGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
**
25739956 CCTTCGGGACTTAGCCTAGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* *
25739996 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
25740036 CCTTCGG
1 CCTTCGG
25740043 ATCTTAGTCC
Statistics
Matches: 115, Mismatches: 11, Indels: 1
0.91 0.09 0.01
Matches are distributed among these distances:
39 12 0.10
40 103 0.90
ACGTcount: A:0.28, C:0.27, G:0.22, T:0.24
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:25742163 original size:29 final size:28
Alignment explanation
Indices: 25742127--25742182 Score: 67
Period size: 29 Copynumber: 2.0 Consensus size: 28
25742117 TCATTAACTC
*
25742127 AAACTTTGGAAAATTACAATTTTGCCCT
1 AAACTTTGCAAAATTACAATTTTGCCCT
* * *
25742155 AAACTTTTGCATATTTACACTTTTGCCC
1 AAAC-TTTGCAAAATTACAATTTTGCCC
25742183 CTAGGCTCGG
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
28 4 0.17
29 19 0.83
ACGTcount: A:0.30, C:0.21, G:0.09, T:0.39
Consensus pattern (28 bp):
AAACTTTGCAAAATTACAATTTTGCCCT
Found at i:25745132 original size:11 final size:11
Alignment explanation
Indices: 25745106--25745138 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
25745096 GGGATTGATT
25745106 TGTAAAAA-TA
1 TGTAAAAATTA
25745116 -GTAAAAATTA
1 TGTAAAAATTA
25745126 TGTAAAAATTA
1 TGTAAAAATTA
25745137 TG
1 TG
25745139 AAATAAGGGT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 7 0.33
10 2 0.10
11 12 0.57
ACGTcount: A:0.55, C:0.00, G:0.12, T:0.33
Consensus pattern (11 bp):
TGTAAAAATTA
Found at i:25745661 original size:38 final size:38
Alignment explanation
Indices: 25745591--25745679 Score: 108
Period size: 38 Copynumber: 2.3 Consensus size: 38
25745581 TTTATGCCGA
* *
25745591 TGTTATTTAGGCTTTGTGCCTAGTAGGATTTGTGCCAC
1 TGTTATTTAGGCTCTGTGCCTAATAGGATTTGTGCCAC
* *
25745629 TGTTATTTAGGCTCTGTGTCTAATA-GACTTTGTGCCAG
1 TGTTATTTAGGCTCTGTGCCTAATAGGA-TTTGTGCCAC
* *
25745667 TATTATGTAGGCT
1 TGTTATTTAGGCT
25745680 TTTTGCTGGT
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
37 2 0.05
38 42 0.95
ACGTcount: A:0.18, C:0.15, G:0.25, T:0.43
Consensus pattern (38 bp):
TGTTATTTAGGCTCTGTGCCTAATAGGATTTGTGCCAC
Found at i:25746135 original size:23 final size:23
Alignment explanation
Indices: 25746109--25746158 Score: 100
Period size: 23 Copynumber: 2.2 Consensus size: 23
25746099 GTAAGTAATG
25746109 AGATATAATGCTTGATTTGTGAT
1 AGATATAATGCTTGATTTGTGAT
25746132 AGATATAATGCTTGATTTGTGAT
1 AGATATAATGCTTGATTTGTGAT
25746155 AGAT
1 AGAT
25746159 TTTTGACATG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.32, C:0.04, G:0.22, T:0.42
Consensus pattern (23 bp):
AGATATAATGCTTGATTTGTGAT
Found at i:25746491 original size:12 final size:12
Alignment explanation
Indices: 25746474--25746499 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
25746464 GCAGTTACAC
25746474 GGCCTAGCACAT
1 GGCCTAGCACAT
25746486 GGCCTAGCACAT
1 GGCCTAGCACAT
25746498 GG
1 GG
25746500 GCGTGTGAGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.31, G:0.31, T:0.15
Consensus pattern (12 bp):
GGCCTAGCACAT
Found at i:25760164 original size:37 final size:37
Alignment explanation
Indices: 25760105--25760213 Score: 182
Period size: 37 Copynumber: 2.9 Consensus size: 37
25760095 AGCTCAGATG
* *
25760105 AAATCTCCACACGAAGTTATCGGGTCTTACCCAGACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCAGACA
*
25760142 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCAGACA
*
25760179 TAATCTCCACACGTAGTCATCGGGTCTTACCCAGA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCAGA
25760214 ATATATTTCC
Statistics
Matches: 67, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
37 67 1.00
ACGTcount: A:0.28, C:0.31, G:0.17, T:0.23
Consensus pattern (37 bp):
AAATCTCCACACGTAGTCATCGGGTCTTACCCAGACA
Found at i:25760484 original size:48 final size:48
Alignment explanation
Indices: 25760359--25761416 Score: 1994
Period size: 48 Copynumber: 22.0 Consensus size: 48
25760349 ACACATCGCC
*
25760359 TACATATTTCACAGTAGCCATTCGGCTTTACCACATATACATATCTCATA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTC--A
* * *
25760409 TATATATTTCACATT-GACCATTTGGCTTTACCACATATGCATATCTCA
1 TACATATTTCACATTAG-CCATTCGGCTTTACCACATATACATATCTCA
25760457 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTC--A
*
25760507 TATATATTTCACATT-GACCATTCGGCTTTACCACATATACATATCTCA
1 TACATATTTCACATTAG-CCATTCGGCTTTACCACATATACATATCTCA
25760555 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
25760603 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
25760651 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
25760699 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
25760747 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
25760795 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
25760843 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
25760891 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
25760939 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
25760987 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
25761035 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
25761083 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
25761131 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
25761179 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
25761227 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
25761275 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
25761323 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
*
25761371 TACATATTTCACATTAGCCATTCGGCTTTACCACGTATACATATCT
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCT
25761417 AATGCATCAA
Statistics
Matches: 992, Mismatches: 10, Indels: 14
0.98 0.01 0.01
Matches are distributed among these distances:
48 902 0.91
49 4 0.00
50 86 0.09
ACGTcount: A:0.31, C:0.27, G:0.07, T:0.36
Consensus pattern (48 bp):
TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
Found at i:25763881 original size:29 final size:30
Alignment explanation
Indices: 25763792--25763888 Score: 87
Period size: 28 Copynumber: 3.4 Consensus size: 30
25763782 TCTCATTTCA
* *
25763792 CACACTTAGTGCC-C-ACTGACCGATCTCG
1 CACACATAGTGCCTCAATTGACCGATCTCG
** * *
25763820 CACACATAGTG-CTCGGTTGA-AGAACTCG
1 CACACATAGTGCCTCAATTGACCGATCTCG
* *
25763848 TACACACAGTGCCTCAATT-ACCGATCTCG
1 CACACATAGTGCCTCAATTGACCGATCTCG
25763877 CACACATAGTGC
1 CACACATAGTGC
25763889 TCGGTTAAAG
Statistics
Matches: 52, Mismatches: 13, Indels: 7
0.72 0.18 0.10
Matches are distributed among these distances:
27 1 0.02
28 27 0.52
29 24 0.46
ACGTcount: A:0.27, C:0.33, G:0.19, T:0.22
Consensus pattern (30 bp):
CACACATAGTGCCTCAATTGACCGATCTCG
Found at i:25764110 original size:43 final size:43
Alignment explanation
Indices: 25764049--25764313 Score: 413
Period size: 43 Copynumber: 6.2 Consensus size: 43
25764039 CCTTGCTCGA
* *
25764049 ATCACCGGCACTAAGCCTGCTAGGCACGAAGACCCGAATACAC
1 ATCACCGGCACGAAGCCTGCTAGGCACGAAGGCCCGAATACAC
*
25764092 ATCACCGGCACGAAGCCTGCTAGGCACGAAGGCCCGAATACAT
1 ATCACCGGCACGAAGCCTGCTAGGCACGAAGGCCCGAATACAC
* * *
25764135 ATCACCTGCACGAAGCCTGCTAGGCACGAAGGCCTGAATACAT
1 ATCACCGGCACGAAGCCTGCTAGGCACGAAGGCCCGAATACAC
* *
25764178 ATCATCGGCACAAAGCCTGCTAGGCACGAAGGCCCGAATACAC
1 ATCACCGGCACGAAGCCTGCTAGGCACGAAGGCCCGAATACAC
* ** *
25764221 ATAATTGGCACGAAGCCTGCTAGGCACGAAGGCCCGAGTACAC
1 ATCACCGGCACGAAGCCTGCTAGGCACGAAGGCCCGAATACAC
*
25764264 ATCACCGGCACGAAGCCTGCTAGGCACGAAGGCCCCAATACAC
1 ATCACCGGCACGAAGCCTGCTAGGCACGAAGGCCCGAATACAC
25764307 ATCACCG
1 ATCACCG
25764314 AGTTTCATGC
Statistics
Matches: 203, Mismatches: 19, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 203 1.00
ACGTcount: A:0.31, C:0.33, G:0.24, T:0.12
Consensus pattern (43 bp):
ATCACCGGCACGAAGCCTGCTAGGCACGAAGGCCCGAATACAC
Found at i:25765717 original size:45 final size:45
Alignment explanation
Indices: 25765656--25765746 Score: 173
Period size: 45 Copynumber: 2.0 Consensus size: 45
25765646 TTTTTTAAAA
*
25765656 TTTTTGTCTCCCCTTGGCCGGCCACACACTTAAAAAGGGTCCAAT
1 TTTTTGTCTCCCCTTGGCCCGCCACACACTTAAAAAGGGTCCAAT
25765701 TTTTTGTCTCCCCTTGGCCCGCCACACACTTAAAAAGGGTCCAAT
1 TTTTTGTCTCCCCTTGGCCCGCCACACACTTAAAAAGGGTCCAAT
25765746 T
1 T
25765747 GCCCTTTAAA
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.22, C:0.32, G:0.16, T:0.30
Consensus pattern (45 bp):
TTTTTGTCTCCCCTTGGCCCGCCACACACTTAAAAAGGGTCCAAT
Found at i:25766856 original size:35 final size:35
Alignment explanation
Indices: 25766808--25766877 Score: 104
Period size: 35 Copynumber: 2.0 Consensus size: 35
25766798 AGAGGCCAAT
25766808 GAAGCCTTCTTCCAAATAATGAAAGAATAGTTTAC
1 GAAGCCTTCTTCCAAATAATGAAAGAATAGTTTAC
* ** *
25766843 GAAGCCTTTTTCCAGGTAATGAAAGAATGGTTTAC
1 GAAGCCTTCTTCCAAATAATGAAAGAATAGTTTAC
25766878 TGAGTATGAC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.36, C:0.16, G:0.19, T:0.30
Consensus pattern (35 bp):
GAAGCCTTCTTCCAAATAATGAAAGAATAGTTTAC
Found at i:25770834 original size:120 final size:119
Alignment explanation
Indices: 25770622--25770854 Score: 358
Period size: 120 Copynumber: 1.9 Consensus size: 119
25770612 AAGATATGCT
* * * *
25770622 TCGTTGTTGTGTTTTAAAGTTTGAAGGTAATCGGGAAAATATTTATCTTTTGTTGAATTTGCATA
1 TCGTTGTTGTGTTTTAAAGTTTGAAGGTAACCGGGAAAATATTTACCTTTAGTTGAATTCGCATA
* **
25770687 TAATAATAATTTTCAATCGAGCATAAAGATGGCGTCGTATGAAGCATTGTATCG
66 TAATAATAATTTTCAATCAAGCATAAAGATGGCACCGTATGAAGCATTGTATCG
**
25770741 TCGTTGTTGTGTTTTAGGGTTTGAAGGTAACCGGGAAAAATATTTACCTTTAGTTGAATTCGCAT
1 TCGTTGTTGTGTTTTAAAGTTTGAAGGTAACCGGG-AAAATATTTACCTTTAGTTGAATTCGCAT
* *
25770806 ATAATAATATTTTTCGATCAAGCATAAAGATGGCACCGTATGAAGCATT
65 ATAATAATAATTTTCAATCAAGCATAAAGATGGCACCGTATGAAGCATT
25770855 AGATGGTTGT
Statistics
Matches: 102, Mismatches: 11, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
119 32 0.31
120 70 0.69
ACGTcount: A:0.30, C:0.11, G:0.21, T:0.38
Consensus pattern (119 bp):
TCGTTGTTGTGTTTTAAAGTTTGAAGGTAACCGGGAAAATATTTACCTTTAGTTGAATTCGCATA
TAATAATAATTTTCAATCAAGCATAAAGATGGCACCGTATGAAGCATTGTATCG
Found at i:25773465 original size:57 final size:57
Alignment explanation
Indices: 25773358--25773496 Score: 147
Period size: 57 Copynumber: 2.4 Consensus size: 57
25773348 TATAGACAAT
* *
25773358 AGGATTACTAGTCCATGCTAAATCCTGTCTACAATATATACTCAATAGAGCTTAGTC
1 AGGATTACTAGTCCAGGCTAAATCCTGTCTACAACATATACTCAATAGAGCTTAGTC
* * * * *
25773415 AGGATTACTAGTCTAGGCTAAATCCTTTTTACGACATATGCTCTAA-AGAGCTT-GATC
1 AGGATTACTAGTCCAGGCTAAATCCTGTCTACAACATATACTC-AATAGAGCTTAG-TC
* * **
25773472 TGGATTTCCCGTCCAGGCTAAATCC
1 AGGATTACTAGTCCAGGCTAAATCC
25773497 AATCCATAAC
Statistics
Matches: 68, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
56 1 0.01
57 65 0.96
58 2 0.03
ACGTcount: A:0.29, C:0.22, G:0.17, T:0.32
Consensus pattern (57 bp):
AGGATTACTAGTCCAGGCTAAATCCTGTCTACAACATATACTCAATAGAGCTTAGTC
Found at i:25775274 original size:46 final size:48
Alignment explanation
Indices: 25775106--25775330 Score: 237
Period size: 47 Copynumber: 4.7 Consensus size: 48
25775096 CATAGGGTAT
* * *
25775106 AATGCTGATGCCATGTCCCAAACATGGTCTTACACTTGCTCTCACAT-T-
1 AATGCCGATGCCATGTCCCAGACAT-GTCTTACACTGGCTCT-ACATCTC
* * * *
25775154 AA-GTCGATTCCATGTCCCAGACATCGTCTTACACTGACTCTCACATATC
1 AATGCCGATGCCATGTCCCAGACAT-GTCTTACACTGGCTCT-ACATCTC
* * *
25775203 CATGTCGAAGCCATGTCCCAGACATGTCTTACACTGGCT-TACATCTC
1 AATGCCGATGCCATGTCCCAGACATGTCTTACACTGGCTCTACATCTC
* * * *
25775250 GAGGCCGATG-CATGTCCCAGACATGTCTTACAATAGCTCT-CATCTC
1 AATGCCGATGCCATGTCCCAGACATGTCTTACACTGGCTCTACATCTC
*
25775296 AATCCCGATGCCATGTCCCAGACATGTCTTACACT
1 AATGCCGATGCCATGTCCCAGACATGTCTTACACT
25775331 AGCGTACAAA
Statistics
Matches: 150, Mismatches: 22, Indels: 11
0.82 0.12 0.06
Matches are distributed among these distances:
46 39 0.26
47 73 0.49
48 4 0.03
49 14 0.09
50 20 0.13
ACGTcount: A:0.25, C:0.32, G:0.16, T:0.28
Consensus pattern (48 bp):
AATGCCGATGCCATGTCCCAGACATGTCTTACACTGGCTCTACATCTC
Found at i:25775328 original size:93 final size:95
Alignment explanation
Indices: 25775112--25775330 Score: 243
Period size: 93 Copynumber: 2.3 Consensus size: 95
25775102 GTATAATGCT
* * *
25775112 GATGCCATGTCCCAAACATGGTCTTACACTTGCTCTCACATTAAGTCGATTCCATGTCCCAGACA
1 GATGCCATGTCCCAGACAT-GTCTTACACTGGCTCTCACATTAAGCCGATTCCATGTCCCAGACA
* * **
25775177 TCGTCTTACACTGACTCTCACATATCCATGTC
65 TCGTCTTACAATGACTCT-ACATATCAATCCC
* * *
25775209 GAAGCCATGTCCCAGACATGTCTTACACTGGCT-T-ACATCTCGAGGCCGA-TGCATGTCCCAGA
1 GATGCCATGTCCCAGACATGTCTTACACTGGCTCTCACAT-T--AAGCCGATTCCATGTCCCAGA
*
25775271 CAT-GTCTTACAAT-AGCTCT-CATCTCAATCCC
63 CATCGTCTTACAATGA-CTCTACATATCAATCCC
25775302 GATGCCATGTCCCAGACATGTCTTACACT
1 GATGCCATGTCCCAGACATGTCTTACACT
25775331 AGCGTACAAA
Statistics
Matches: 106, Mismatches: 12, Indels: 12
0.82 0.09 0.09
Matches are distributed among these distances:
93 36 0.34
94 5 0.05
95 15 0.14
96 28 0.26
97 22 0.21
ACGTcount: A:0.25, C:0.32, G:0.16, T:0.28
Consensus pattern (95 bp):
GATGCCATGTCCCAGACATGTCTTACACTGGCTCTCACATTAAGCCGATTCCATGTCCCAGACAT
CGTCTTACAATGACTCTACATATCAATCCC
Found at i:25787013 original size:18 final size:18
Alignment explanation
Indices: 25786992--25787026 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
25786982 TTTTTCTTTT
25786992 TCAATTT-TTTTCTCAATC
1 TCAATTTCTTTTC-CAATC
25787010 TCAATTTCTTTTCCAAT
1 TCAATTTCTTTTCCAAT
25787027 TTTCTTTTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.23, C:0.23, G:0.00, T:0.54
Consensus pattern (18 bp):
TCAATTTCTTTTCCAATC
Found at i:25787921 original size:13 final size:13
Alignment explanation
Indices: 25787903--25787993 Score: 55
Period size: 12 Copynumber: 6.8 Consensus size: 13
25787893 AGACTCTTCA
25787903 CTTTTTTTTTCTT
1 CTTTTTTTTTCTT
25787916 CTTTTTTTTTAAC-T
1 CTTTTTTTTT--CTT
*
25787930 CGATTTTTTTGTCACTT
1 C--TTTTTTT-T-TCTT
*
25787947 CTTTTTTTTT-TG
1 CTTTTTTTTTCTT
*
25787959 CTTTTTTTTTC-A
1 CTTTTTTTTTCTT
**
25787971 CTTTTTTTTTGAT
1 CTTTTTTTTTCTT
25787984 -TTTTTTTTTC
1 CTTTTTTTTTC
25787994 AATCAATTTT
Statistics
Matches: 62, Mismatches: 7, Indels: 19
0.70 0.08 0.22
Matches are distributed among these distances:
12 30 0.48
13 10 0.16
14 3 0.05
15 8 0.13
16 8 0.13
17 3 0.05
ACGTcount: A:0.07, C:0.13, G:0.04, T:0.76
Consensus pattern (13 bp):
CTTTTTTTTTCTT
Found at i:25787962 original size:12 final size:12
Alignment explanation
Indices: 25787947--25787992 Score: 58
Period size: 12 Copynumber: 3.9 Consensus size: 12
25787937 TTTGTCACTT
25787947 CTTTTTTTTTTG
1 CTTTTTTTTTTG
**
25787959 CTTTTTTTTTCA
1 CTTTTTTTTTTG
25787971 C-TTTTTTTTTG
1 CTTTTTTTTTTG
*
25787982 ATTTTTTTTTT
1 CTTTTTTTTTT
25787993 CAATCAATTT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
11 8 0.29
12 20 0.71
ACGTcount: A:0.04, C:0.09, G:0.04, T:0.83
Consensus pattern (12 bp):
CTTTTTTTTTTG
Found at i:25787965 original size:11 final size:11
Alignment explanation
Indices: 25787949--25787991 Score: 59
Period size: 11 Copynumber: 3.8 Consensus size: 11
25787939 TGTCACTTCT
25787949 TTTTTTTTTGC
1 TTTTTTTTTGC
*
25787960 TTTTTTTTTCAC
1 TTTTTTTTT-GC
*
25787972 TTTTTTTTTGA
1 TTTTTTTTTGC
25787983 TTTTTTTTT
1 TTTTTTTTT
25787992 TCAATCAATT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
11 18 0.64
12 10 0.36
ACGTcount: A:0.05, C:0.07, G:0.05, T:0.84
Consensus pattern (11 bp):
TTTTTTTTTGC
Found at i:25787978 original size:41 final size:40
Alignment explanation
Indices: 25787900--25787993 Score: 104
Period size: 43 Copynumber: 2.4 Consensus size: 40
25787890 GCAAGACTCT
25787900 TCACTTTTTTTTTCTTCTTTTTTTTTAACTCGATTTTTTTG
1 TCACTTTTTTTTTCTTCTTTTTTTTTAACTC-ATTTTTTTG
* *
25787941 TCACTTCTTTTTTTTTTGCTTTTTTTTTCACT--TTTTTTT-
1 TCACTT-TTTTTTTCTT-CTTTTTTTTTAACTCATTTTTTTG
* *
25787980 TGATTTTTTTTTTC
1 TCACTTTTTTTTTC
25787994 AATCAATTTT
Statistics
Matches: 46, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
38 7 0.15
39 4 0.09
40 7 0.15
41 6 0.13
42 9 0.20
43 13 0.28
ACGTcount: A:0.07, C:0.14, G:0.04, T:0.74
Consensus pattern (40 bp):
TCACTTTTTTTTTCTTCTTTTTTTTTAACTCATTTTTTTG
Found at i:25787990 original size:27 final size:27
Alignment explanation
Indices: 25787933--25788019 Score: 72
Period size: 28 Copynumber: 3.2 Consensus size: 27
25787923 TTTAACTCGA
*
25787933 TTTTTTTGTCACTTCTTTTTTT--TTTGCT
1 TTTTTTTATCACTT-TTTTTTTGATTT--T
25787961 TTTTTTT-TCACTTTTTTTTTGATTTT
1 TTTTTTTATCACTTTTTTTTTGATTTT
* * * *
25787987 TTTTTTCAATCAATTTTTTTTCGAATTT
1 TTTTTT-TATCACTTTTTTTTTGATTTT
25788015 TTTTT
1 TTTTT
25788020 GATTTTTTTT
Statistics
Matches: 51, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
26 14 0.27
27 6 0.12
28 31 0.61
ACGTcount: A:0.10, C:0.10, G:0.05, T:0.75
Consensus pattern (27 bp):
TTTTTTTATCACTTTTTTTTTGATTTT
Found at i:25788024 original size:10 final size:11
Alignment explanation
Indices: 25787998--25788030 Score: 50
Period size: 10 Copynumber: 3.0 Consensus size: 11
25787988 TTTTTCAATC
25787998 AATTTTTTTTCG
1 AATTTTTTTT-G
25788010 AATTTTTTTTG
1 AATTTTTTTTG
25788021 -ATTTTTTTTG
1 AATTTTTTTTG
25788031 TTACTCCAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 10 0.48
11 1 0.05
12 10 0.48
ACGTcount: A:0.15, C:0.03, G:0.09, T:0.73
Consensus pattern (11 bp):
AATTTTTTTTG
Found at i:25789411 original size:30 final size:30
Alignment explanation
Indices: 25789340--25789422 Score: 89
Period size: 30 Copynumber: 2.7 Consensus size: 30
25789330 CTTTTGTTTC
* *
25789340 AATTTCTTTTTCATCTTCTTTTTCACTCTCA
1 AATTTCTTTTTCTTC-TCTTTTTCAATCTCA
25789371 AATTTC-TTTTCGTTCTCTTTTTCAATCTC-
1 AATTTCTTTTTC-TTCTCTTTTTCAATCTCA
* *
25789400 ATTTTCTTTTTCATTTTCTTTTT
1 AATTTCTTTTTC-TTCTCTTTTT
25789423 TCTTTTCAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
29 5 0.11
30 32 0.71
31 8 0.18
ACGTcount: A:0.13, C:0.22, G:0.01, T:0.64
Consensus pattern (30 bp):
AATTTCTTTTTCTTCTCTTTTTCAATCTCA
Found at i:25789422 original size:18 final size:18
Alignment explanation
Indices: 25789373--25789428 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
25789363 CACTCTCAAA
* *
25789373 TTTC-TTTTCGTTCTCTT
1 TTTCATTTTCATTTTCTT
* *
25789390 TTTCAATCTCATTTTCTT
1 TTTCATTTTCATTTTCTT
*
25789408 TTTCATTTTCTTTTTTCTT
1 TTTCATTTTC-ATTTTCTT
25789427 TT
1 TT
25789429 CAAAGGCTTT
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
17 4 0.13
18 17 0.57
19 9 0.30
ACGTcount: A:0.07, C:0.20, G:0.02, T:0.71
Consensus pattern (18 bp):
TTTCATTTTCATTTTCTT
Found at i:25789429 original size:12 final size:12
Alignment explanation
Indices: 25789398--25789422 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
25789388 TTTTTCAATC
25789398 TCATTTTCTTTT
1 TCATTTTCTTTT
25789410 TCATTTTCTTTT
1 TCATTTTCTTTT
25789422 T
1 T
25789423 TCTTTTCAAA
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:0.08, C:0.16, G:0.00, T:0.76
Consensus pattern (12 bp):
TCATTTTCTTTT
Found at i:25789440 original size:12 final size:12
Alignment explanation
Indices: 25789425--25789455 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
25789415 TTCTTTTTTC
25789425 TTTTCAAAGGCT
1 TTTTCAAAGGCT
25789437 TTTTCAAAGGCT
1 TTTTCAAAGGCT
25789449 TTTTCAA
1 TTTTCAA
25789456 GTTCTCTCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.26, C:0.16, G:0.13, T:0.45
Consensus pattern (12 bp):
TTTTCAAAGGCT
Found at i:25789513 original size:5 final size:5
Alignment explanation
Indices: 25789503--25789565 Score: 58
Period size: 5 Copynumber: 12.0 Consensus size: 5
25789493 CTCTTGCCTC
*
25789503 TCTTT TCTTT T-TATT TCATTT TCATTT TCTTT T-TCT TCTTT TGCTTT
1 TCTTT TCTTT TCT-TT TC-TTT TC-TTT TCTTT TCTTT TCTTT T-CTTT
25789550 TGCTTT TCTTT TCTTT
1 T-CTTT TCTTT TCTTT
25789566 ATTTTCTCTT
Statistics
Matches: 51, Mismatches: 2, Indels: 10
0.81 0.03 0.16
Matches are distributed among these distances:
4 4 0.08
5 25 0.49
6 21 0.41
7 1 0.02
ACGTcount: A:0.05, C:0.17, G:0.03, T:0.75
Consensus pattern (5 bp):
TCTTT
Found at i:25793915 original size:78 final size:78
Alignment explanation
Indices: 25793786--25793941 Score: 303
Period size: 78 Copynumber: 2.0 Consensus size: 78
25793776 ACCTTCGATC
*
25793786 GCAAGTGGGTGGTAGTCATTCGCGAACTTACCTTTTTCGAACAACCTAAAACACCTCTCGTTTGG
1 GCAAGTGGGTGGTAGTCATTCGCAAACTTACCTTTTTCGAACAACCTAAAACACCTCTCGTTTGG
25793851 AAGGTAATGTAGA
66 AAGGTAATGTAGA
25793864 GCAAGTGGGTGGTAGTCATTCGCAAACTTACCTTTTTCGAACAACCTAAAACACCTCTCGTTTGG
1 GCAAGTGGGTGGTAGTCATTCGCAAACTTACCTTTTTCGAACAACCTAAAACACCTCTCGTTTGG
25793929 AAGGTAATGTAGA
66 AAGGTAATGTAGA
25793942 TGGAATTGGA
Statistics
Matches: 77, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
78 77 1.00
ACGTcount: A:0.29, C:0.21, G:0.22, T:0.28
Consensus pattern (78 bp):
GCAAGTGGGTGGTAGTCATTCGCAAACTTACCTTTTTCGAACAACCTAAAACACCTCTCGTTTGG
AAGGTAATGTAGA
Found at i:25794159 original size:30 final size:30
Alignment explanation
Indices: 25794088--25794170 Score: 89
Period size: 30 Copynumber: 2.7 Consensus size: 30
25794078 CTTTTGTTTC
* *
25794088 AATTTCTTTTTCATCTTCTTTTTCACTCTCA
1 AATTTCTTTTTCTTC-TCTTTTTCAATCTCA
25794119 AATTTC-TTTTCGTTCTCTTTTTCAATCTC-
1 AATTTCTTTTTC-TTCTCTTTTTCAATCTCA
* *
25794148 ATTTTCTTTTTCATTTTCTTTTT
1 AATTTCTTTTTC-TTCTCTTTTT
25794171 ACTTTTCAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
29 5 0.11
30 32 0.71
31 8 0.18
ACGTcount: A:0.13, C:0.22, G:0.01, T:0.64
Consensus pattern (30 bp):
AATTTCTTTTTCTTCTCTTTTTCAATCTCA
Found at i:25794170 original size:18 final size:18
Alignment explanation
Indices: 25794121--25794176 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
25794111 CACTCTCAAA
* *
25794121 TTTC-TTTTCGTTCTCTT
1 TTTCATTTTCATTTTCTT
* *
25794138 TTTCAATCTCATTTTCTT
1 TTTCATTTTCATTTTCTT
*
25794156 TTTCATTTTCTTTTTACTT
1 TTTCATTTTCATTTT-CTT
25794175 TT
1 TT
25794177 CAAAGGCTTT
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
17 4 0.13
18 21 0.70
19 5 0.17
ACGTcount: A:0.09, C:0.20, G:0.02, T:0.70
Consensus pattern (18 bp):
TTTCATTTTCATTTTCTT
Found at i:25794177 original size:12 final size:12
Alignment explanation
Indices: 25794146--25794170 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
25794136 TTTTTCAATC
25794146 TCATTTTCTTTT
1 TCATTTTCTTTT
25794158 TCATTTTCTTTT
1 TCATTTTCTTTT
25794170 T
1 T
25794171 ACTTTTCAAA
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:0.08, C:0.16, G:0.00, T:0.76
Consensus pattern (12 bp):
TCATTTTCTTTT
Found at i:25794265 original size:21 final size:21
Alignment explanation
Indices: 25794241--25794292 Score: 77
Period size: 21 Copynumber: 2.4 Consensus size: 21
25794231 CTTGCCTCTC
25794241 TTTTCTTTTTATTTCATTTTCT
1 TTTTCTTTTT-TTTCATTTTCT
* *
25794263 TTTTCTTCTTTTTCTTTTTCT
1 TTTTCTTTTTTTTCATTTTCT
25794284 TTTTCTTTT
1 TTTTCTTTT
25794293 CTTTGTTTTC
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
21 18 0.67
22 9 0.33
ACGTcount: A:0.04, C:0.15, G:0.00, T:0.81
Consensus pattern (21 bp):
TTTTCTTTTTTTTCATTTTCT
Found at i:25794268 original size:6 final size:6
Alignment explanation
Indices: 25794252--25794296 Score: 53
Period size: 6 Copynumber: 8.2 Consensus size: 6
25794242 TTTCTTTTTA
*
25794252 TTTCAT TTTCTT TTTC-- -TTCTT TTTCTT TTTCTT TTTC-T TTTCTT
1 TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT
25794296 T
1 T
25794297 GTTTTCTCTT
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
3 3 0.09
5 5 0.15
6 26 0.76
ACGTcount: A:0.02, C:0.18, G:0.00, T:0.80
Consensus pattern (6 bp):
TTTCTT
Done.