Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D05
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: 64368997
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1610000 characters in sequence are not A, C, G, or T
File 76 of 208
Found at i:27280901 original size:28 final size:28
Alignment explanation
Indices: 27280867--27280924 Score: 80
Period size: 28 Copynumber: 2.1 Consensus size: 28
27280857 CATTCACATG
*
27280867 TTTTAAAGCTTTTCATATTTTTCTGAAT
1 TTTTAAAGCTTTTCAGATTTTTCTGAAT
** *
27280895 TTTTAAATTTTTTGAGATTTTTCTGAAT
1 TTTTAAAGCTTTTCAGATTTTTCTGAAT
27280923 TT
1 TT
27280925 GTTTTGATAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.24, C:0.07, G:0.09, T:0.60
Consensus pattern (28 bp):
TTTTAAAGCTTTTCAGATTTTTCTGAAT
Found at i:27280938 original size:22 final size:22
Alignment explanation
Indices: 27280904--27280946 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
27280894 TTTTTAAATT
*
27280904 TTTTGAG-ATTTTTCTGAATTTG
1 TTTTGAGAATTTTTGT-AATTTG
*
27280926 TTTTGATAATTTTTGTAATTT
1 TTTTGAGAATTTTTGTAATTT
27280947 CACTTTTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 11 0.61
23 7 0.39
ACGTcount: A:0.21, C:0.02, G:0.14, T:0.63
Consensus pattern (22 bp):
TTTTGAGAATTTTTGTAATTTG
Found at i:27293370 original size:21 final size:21
Alignment explanation
Indices: 27293344--27293389 Score: 92
Period size: 21 Copynumber: 2.2 Consensus size: 21
27293334 AAATTGAACC
27293344 CAATAAAACATCGCAGAAGCA
1 CAATAAAACATCGCAGAAGCA
27293365 CAATAAAACATCGCAGAAGCA
1 CAATAAAACATCGCAGAAGCA
27293386 CAAT
1 CAAT
27293390 TGGTGTTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.52, C:0.24, G:0.13, T:0.11
Consensus pattern (21 bp):
CAATAAAACATCGCAGAAGCA
Found at i:27297738 original size:43 final size:43
Alignment explanation
Indices: 27297666--27297868 Score: 227
Period size: 43 Copynumber: 4.7 Consensus size: 43
27297656 TGATAAGTGC
* *
27297666 TTTCGTGTAAGACCACTTCTAGGG-CGATGGCATCGATTTGTAT
1 TTTCATGTAAGACCACGTCT-GGGACGATGGCATCGATTTGTAT
* * *
27297709 TTTCATGTAAGACCACGTCTGTGATGATGGCATCAATTTGTAT
1 TTTCATGTAAGACCACGTCTGGGACGATGGCATCGATTTGTAT
*
27297752 TTTCGTGTAAGACCACGTCTGGGACGATGGCATCGATTTGTATT
1 TTTCATGTAAGACCACGTCTGGGACGATGGCATCGATTTGTA-T
* * * *
27297796 TTTGA-GTAAGACC-CTGTTTGGGAC-AGTGGCATCGATGTGCGA-
1 TTTCATGTAAGACCAC-GTCTGGGACGA-TGGCATCGATTTG-TAT
*
27297838 TTACATGTAAGACCACGTCTGGGACGATGGC
1 TTTCATGTAAGACCACGTCTGGGACGATGGC
27297869 GTTGTATGAA
Statistics
Matches: 135, Mismatches: 17, Indels: 16
0.80 0.10 0.10
Matches are distributed among these distances:
42 7 0.05
43 121 0.90
44 7 0.05
ACGTcount: A:0.23, C:0.18, G:0.27, T:0.32
Consensus pattern (43 bp):
TTTCATGTAAGACCACGTCTGGGACGATGGCATCGATTTGTAT
Found at i:27302330 original size:109 final size:109
Alignment explanation
Indices: 27302139--27302556 Score: 764
Period size: 109 Copynumber: 3.8 Consensus size: 109
27302129 TTTCTAATTG
*
27302139 AGGCAATGTTTTACGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATTTTTCT
1 AGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATTTTTCT
27302204 CGTTCAACCAAATAGCTAAATATCCTTTCAAAAATTATAAAATA
66 CGTTCAACCAAATAGCTAAATATCCTTTCAAAAATTATAAAATA
27302248 AGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATTTTTCT
1 AGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATTTTTCT
27302313 CGTTCAACCAAATAGCTAAATATCCTTTCAAAAATTATAAAATA
66 CGTTCAACCAAATAGCTAAATATCCTTTCAAAAATTATAAAATA
* *
27302357 AGTCAATGTTTCGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATTTTTCT
1 AGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATTTTTCT
* * * *
27302422 CGTTCAACCAAATAGCTTAATATCCTTTTAAAATTTTTAAAATA
66 CGTTCAACCAAATAGCTAAATATCCTTTCAAAAATTATAAAATA
27302466 AGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATTTTTCT
1 AGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATTTTTCT
*
27302531 CGTTCAACCAAATAGCTAAACATCCT
66 CGTTCAACCAAATAGCTAAATATCCT
27302557 CTTGAATTTT
Statistics
Matches: 298, Mismatches: 11, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
109 298 1.00
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Consensus pattern (109 bp):
AGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATTTTTCT
CGTTCAACCAAATAGCTAAATATCCTTTCAAAAATTATAAAATA
Found at i:27306179 original size:18 final size:17
Alignment explanation
Indices: 27306158--27306191 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
27306148 GTCTAAAATA
27306158 TATATATTTAATAAAAAG
1 TATAT-TTTAATAAAAAG
*
27306176 TATATTTTATTAAAAA
1 TATATTTTAATAAAAA
27306192 TAAAAATATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (17 bp):
TATATTTTAATAAAAAG
Found at i:27306201 original size:40 final size:37
Alignment explanation
Indices: 27306095--27306216 Score: 118
Period size: 40 Copynumber: 3.1 Consensus size: 37
27306085 GGCCCGACCC
*
27306095 ATATTTGATTAAAAATAAAAATATATATATTTAATAT
1 ATATTTGATTAAAAATAAAAATATATATATTTAAAAT
* *
27306132 ATAATTCTGATTAAAAGTCTAAAATATATATATTTAATAAAAAGT
1 AT-ATT-TGATTAAAAAT-AAAAATATATATA-TT--T-AAAA-T
* * *
27306177 ATATTTTATTAAAAATAAAAATATATGTATTTAACAT
1 ATATTTGATTAAAAATAAAAATATATATATTTAAAAT
27306214 ATA
1 ATA
27306217 ATTCAGGTCG
Statistics
Matches: 69, Mismatches: 8, Indels: 16
0.74 0.09 0.17
Matches are distributed among these distances:
37 6 0.09
38 6 0.09
39 11 0.16
40 12 0.17
41 4 0.06
42 11 0.16
43 10 0.14
44 6 0.09
45 3 0.04
ACGTcount: A:0.52, C:0.02, G:0.04, T:0.41
Consensus pattern (37 bp):
ATATTTGATTAAAAATAAAAATATATATATTTAAAAT
Found at i:27308388 original size:25 final size:24
Alignment explanation
Indices: 27308366--27308413 Score: 60
Period size: 26 Copynumber: 1.9 Consensus size: 24
27308356 AATGTTTACA
*
27308366 ATTTTTGTTAATTTGACTCTTTATTC
1 ATTTTTGTTAATTTAAC-CTTTA-TC
*
27308392 TTTTTTGTTAATTTAACCTTTA
1 ATTTTTGTTAATTTAACCTTTA
27308414 AAAGAGGCAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
25 5 0.25
26 15 0.75
ACGTcount: A:0.21, C:0.10, G:0.06, T:0.62
Consensus pattern (24 bp):
ATTTTTGTTAATTTAACCTTTATC
Found at i:27308771 original size:28 final size:26
Alignment explanation
Indices: 27308740--27308804 Score: 69
Period size: 27 Copynumber: 2.4 Consensus size: 26
27308730 AAGTTAAATG
27308740 TAAATTTAACTAAAAAATAAATTAAA-AC
1 TAAATTTAA--AAAAAA-AAATTAAAGAC
* *
27308768 TAAATTGAGAAAAAAAATATTAAAGAC
1 TAAATTTA-AAAAAAAAAATTAAAGAC
27308795 TAAATTTAAA
1 TAAATTTAAA
27308805 GTTATAGCTA
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
26 9 0.28
27 15 0.47
28 7 0.22
29 1 0.03
ACGTcount: A:0.63, C:0.05, G:0.05, T:0.28
Consensus pattern (26 bp):
TAAATTTAAAAAAAAAAATTAAAGAC
Found at i:27309584 original size:30 final size:30
Alignment explanation
Indices: 27309543--27309610 Score: 79
Period size: 29 Copynumber: 2.3 Consensus size: 30
27309533 AACCAAAAAA
*
27309543 GGCCGGTTTTTTTCAA-AATTTACCGAAATG
1 GGCCAGTTTTTTT-AATAATTTACCGAAATG
* *
27309573 GGCCAG-TTTTTTAATTATTTACCGGAATG
1 GGCCAGTTTTTTTAATAATTTACCGAAATG
27309602 GGCCA-TTTT
1 GGCCAGTTTT
27309611 CCGCGAAATC
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
28 2 0.06
29 26 0.79
30 5 0.15
ACGTcount: A:0.24, C:0.16, G:0.21, T:0.40
Consensus pattern (30 bp):
GGCCAGTTTTTTTAATAATTTACCGAAATG
Found at i:27325261 original size:31 final size:30
Alignment explanation
Indices: 27325188--27325269 Score: 94
Period size: 31 Copynumber: 2.7 Consensus size: 30
27325178 AATGTATAAT
*
27325188 TATATACAT-AAACTTTAATTTGGTGCAAT
1 TATATACATGAAACTTTAATTTGGTGCAAA
* * * *
27325217 TATACACGTGAAACTCTAATTATGGTTCAAA
1 TATATACATGAAACTTTAATT-TGGTGCAAA
*
27325248 TATATACTTGAAACTTTAATTT
1 TATATACATGAAACTTTAATTT
27325270 TGATTTAATC
Statistics
Matches: 43, Mismatches: 8, Indels: 3
0.80 0.15 0.06
Matches are distributed among these distances:
29 7 0.16
30 11 0.26
31 25 0.58
ACGTcount: A:0.38, C:0.12, G:0.10, T:0.40
Consensus pattern (30 bp):
TATATACATGAAACTTTAATTTGGTGCAAA
Found at i:27325446 original size:30 final size:29
Alignment explanation
Indices: 27325412--27325470 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 29
27325402 TAATTGGATC
*
27325412 AAATCAATATTTCATGTATAAAATTACACA
1 AAATCAA-AGTTCATGTATAAAATTACACA
27325442 AAATCAAAGTTCATGTATAAAATTACACA
1 AAATCAAAGTTCATGTATAAAATTACACA
27325471 TTATACCATA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
29 21 0.75
30 7 0.25
ACGTcount: A:0.51, C:0.14, G:0.05, T:0.31
Consensus pattern (29 bp):
AAATCAAAGTTCATGTATAAAATTACACA
Found at i:27326909 original size:27 final size:30
Alignment explanation
Indices: 27326846--27326911 Score: 75
Period size: 32 Copynumber: 2.2 Consensus size: 30
27326836 AATCTTAAAA
* *
27326846 TTATATATTAATTTTAATTTAATGGTGTAAT
1 TTATATATAAATTTTAATTT-ATGGTGTAAG
27326877 TGTATATATAAATTTTAA-TT-TGGTG-AAG
1 T-TATATATAAATTTTAATTTATGGTGTAAG
27326905 TTATATA
1 TTATATA
27326912 CGTGAAACTC
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
27 6 0.19
28 3 0.09
29 5 0.16
31 3 0.09
32 15 0.47
ACGTcount: A:0.36, C:0.00, G:0.12, T:0.52
Consensus pattern (30 bp):
TTATATATAAATTTTAATTTATGGTGTAAG
Found at i:27329690 original size:13 final size:13
Alignment explanation
Indices: 27329674--27329723 Score: 55
Period size: 13 Copynumber: 3.7 Consensus size: 13
27329664 AATAATTTTT
27329674 AATTAAAATTATA
1 AATTAAAATTATA
*
27329687 AATTAAAATAATA
1 AATTAAAATTATA
* *
27329700 ATTCTAAAAATTATC
1 AAT-T-AAAATTATA
27329715 AATTAAAAT
1 AATTAAAAT
27329724 GTTATTAAGC
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
13 19 0.63
14 2 0.07
15 9 0.30
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (13 bp):
AATTAAAATTATA
Found at i:27331417 original size:30 final size:31
Alignment explanation
Indices: 27331373--27331442 Score: 81
Period size: 31 Copynumber: 2.3 Consensus size: 31
27331363 GTAATTGTAT
* *
27331373 ACAT-AAACTTTAATT-TGGTGCAATTATAC
1 ACATGAAACTCTAATTATGGTGCAAATATAC
* *
27331402 ACATGAAACTCTAATTATGGTTCAAATATAT
1 ACATGAAACTCTAATTATGGTGCAAATATAC
*
27331433 ACTTGAAACT
1 ACATGAAACT
27331443 TTGATTTTGA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
29 4 0.12
30 10 0.29
31 20 0.59
ACGTcount: A:0.40, C:0.14, G:0.10, T:0.36
Consensus pattern (31 bp):
ACATGAAACTCTAATTATGGTGCAAATATAC
Found at i:27332143 original size:18 final size:18
Alignment explanation
Indices: 27332122--27332159 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
27332112 CTTCTACCCT
27332122 TTCCCCTTTCCCTTCCCC
1 TTCCCCTTTCCCTTCCCC
*
27332140 TTCCCTTTTCCCTTCCCC
1 TTCCCCTTTCCCTTCCCC
27332158 TT
1 TT
27332160 GGATTGCAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.00, C:0.55, G:0.00, T:0.45
Consensus pattern (18 bp):
TTCCCCTTTCCCTTCCCC
Found at i:27332253 original size:25 final size:25
Alignment explanation
Indices: 27332219--27332268 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
27332209 CAGGTAAGGC
*
27332219 TCCTTCTTCTTCTTCCGTTTTTCAT
1 TCCTTCTTCTTCTTCCGTTCTTCAT
* *
27332244 TCCTTTTTCTTCTTCTGTTCTTCAT
1 TCCTTCTTCTTCTTCCGTTCTTCAT
27332269 CTTCTCTTCT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.04, C:0.30, G:0.04, T:0.62
Consensus pattern (25 bp):
TCCTTCTTCTTCTTCCGTTCTTCAT
Found at i:27335632 original size:15 final size:15
Alignment explanation
Indices: 27335593--27335645 Score: 52
Period size: 15 Copynumber: 3.2 Consensus size: 15
27335583 GAACATTTGG
27335593 AATTTAATTAGATAAAA
1 AATTT-ATTA-ATAAAA
27335610 AACTTTTATTAATAAAA
1 AA--TTTATTAATAAAA
*
27335627 AATTTATTTATAAATA
1 AATTTATTAATAAA-A
27335643 AAT
1 AAT
27335646 CATTGCAATA
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
15 11 0.34
16 4 0.12
17 10 0.31
18 4 0.12
19 3 0.09
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.42
Consensus pattern (15 bp):
AATTTATTAATAAAA
Found at i:27335719 original size:22 final size:20
Alignment explanation
Indices: 27335676--27335714 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
27335666 TAATTTAAAA
27335676 TATAAAAATTTATTAATATG
1 TATAAAAATTTATTAATATG
*
27335696 TATATAAATTTATTAATAT
1 TATAAAAATTTATTAATAT
27335715 ATGTAAAAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (20 bp):
TATAAAAATTTATTAATATG
Found at i:27335837 original size:20 final size:20
Alignment explanation
Indices: 27335812--27335851 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
27335802 AATATTTTCC
*
27335812 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
27335832 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
27335852 TCATTTTACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:27335857 original size:34 final size:35
Alignment explanation
Indices: 27335800--27335866 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
27335790 CAAACACTAG
*
27335800 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
*
27335835 AAAACATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
27335867 CATTTTACTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.46, C:0.13, G:0.09, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:27335858 original size:14 final size:14
Alignment explanation
Indices: 27335835--27335874 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
27335825 ACAGAAAAGT
*
27335835 AAAACATTTTCCAG
1 AAAACATTTTACAG
* *
27335849 AAATCATTTTACGG
1 AAAACATTTTACAG
27335863 AAAACATTTTAC
1 AAAACATTTTAC
27335875 TGCCAATCAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.42, C:0.17, G:0.07, T:0.33
Consensus pattern (14 bp):
AAAACATTTTACAG
Found at i:27340652 original size:8 final size:8
Alignment explanation
Indices: 27340639--27340675 Score: 56
Period size: 8 Copynumber: 4.6 Consensus size: 8
27340629 CTGTCAAATT
27340639 TTATAAAA
1 TTATAAAA
27340647 TTATAAAA
1 TTATAAAA
*
27340655 TTATATAA
1 TTATAAAA
*
27340663 TAATAAAA
1 TTATAAAA
27340671 TTATA
1 TTATA
27340676 TTTTAAACCT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
8 25 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (8 bp):
TTATAAAA
Found at i:27341301 original size:29 final size:29
Alignment explanation
Indices: 27341269--27341324 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
27341259 AGCAAATGAT
*
27341269 AAATT-AATATCTATAATAATCTAATATCC
1 AAATTCAATATCTATAA-AAACTAATATCC
* *
27341298 AAATTCATTATTTATAAAAACTAATAT
1 AAATTCAATATCTATAAAAACTAATAT
27341325 AATTTTAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
29 14 0.61
30 9 0.39
ACGTcount: A:0.50, C:0.11, G:0.00, T:0.39
Consensus pattern (29 bp):
AAATTCAATATCTATAAAAACTAATATCC
Found at i:27348987 original size:68 final size:68
Alignment explanation
Indices: 27348855--27348984 Score: 187
Period size: 68 Copynumber: 1.9 Consensus size: 68
27348845 AAAGTCTTAA
*
27348855 CTGCTCATAACATCATGGTGGGGTATAACAGATTGTTACTAATAAAAATGAAAACGCTAGAAAAG
1 CTGCTCATAACATCATGGTGGGGTATAAAAGATTGTTACTAATAAAAATGAAAACGCTAGAAAAG
27348920 TGT
66 TGT
* *
27348923 CTGCTCA-AATCATTATGGTGGGGTGTAAAAGATTGTTACTAA-AAAAA-GAAAACG-TCAGAAA
1 CTGCTCATAA-CATCATGGTGGGGTATAAAAGATTGTTACTAATAAAAATGAAAACGCT-AGAAA
27348984 A
64 A
27348985 AAGAAGTAGT
Statistics
Matches: 57, Mismatches: 3, Indels: 6
0.86 0.05 0.09
Matches are distributed among these distances:
65 1 0.02
66 13 0.23
67 7 0.12
68 36 0.63
ACGTcount: A:0.42, C:0.12, G:0.21, T:0.25
Consensus pattern (68 bp):
CTGCTCATAACATCATGGTGGGGTATAAAAGATTGTTACTAATAAAAATGAAAACGCTAGAAAAG
TGT
Found at i:27353682 original size:20 final size:20
Alignment explanation
Indices: 27353657--27353694 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
27353647 ATTATTTAAA
27353657 TAAATA-TATAAAACAAATCT
1 TAAATATTATAAAA-AAATCT
27353677 TAAATATTATAAAAAAAT
1 TAAATATTATAAAAAAAT
27353695 ATAAAAATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.63, C:0.05, G:0.00, T:0.32
Consensus pattern (20 bp):
TAAATATTATAAAAAAATCT
Found at i:27360372 original size:87 final size:84
Alignment explanation
Indices: 27360262--27360419 Score: 246
Period size: 87 Copynumber: 1.8 Consensus size: 84
27360252 CTTTTTGTTT
* *
27360262 CACTCAATTGGGTATTTGAACTTTCAAAATGCATCAAAAA-AGCCCTCAAATCTTTTCAAAAAAA
1 CACTCAATTGGGTACTTGAACTTTCAAAATGCATCAAAAAGA-CCCTCAAA-C--TTAAAAAAAA
*
27360326 GCAATTAAGCGCTTACTATTTTG
62 ACAATTAAGCGCTTACTATTTTG
27360349 CACTCAATTGGGTACTTGAACTTTCAAAATGCATCAAAAAGACCCTCAAACTTAAAAAAAAACAA
1 CACTCAATTGGGTACTTGAACTTTCAAAATGCATCAAAAAGACCCTCAAACTTAAAAAAAAACAA
27360414 TTAAGC
66 TTAAGC
27360420 CCCTACTTTT
Statistics
Matches: 67, Mismatches: 3, Indels: 5
0.89 0.04 0.07
Matches are distributed among these distances:
84 18 0.27
86 1 0.01
87 47 0.70
88 1 0.01
ACGTcount: A:0.42, C:0.20, G:0.11, T:0.27
Consensus pattern (84 bp):
CACTCAATTGGGTACTTGAACTTTCAAAATGCATCAAAAAGACCCTCAAACTTAAAAAAAAACAA
TTAAGCGCTTACTATTTTG
Found at i:27360840 original size:37 final size:37
Alignment explanation
Indices: 27360771--27360842 Score: 92
Period size: 38 Copynumber: 1.9 Consensus size: 37
27360761 GGGTTATTAA
* * *
27360771 TTTTTTATGATTTTTTATAAAATTTTACAATTTTTTAT
1 TTTTTTACGATTTTTTAAAAAATTCTA-AATTTTTTAT
27360809 TTTTTTACGATTTTTATAAAAAATTCT-AATTTTT
1 TTTTTTACGATTTTT-TAAAAAATTCTAAATTTTT
27360843 AATAAATTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
37 7 0.23
38 14 0.47
39 9 0.30
ACGTcount: A:0.31, C:0.04, G:0.03, T:0.62
Consensus pattern (37 bp):
TTTTTTACGATTTTTTAAAAAATTCTAAATTTTTTAT
Found at i:27362106 original size:80 final size:84
Alignment explanation
Indices: 27361973--27362146 Score: 250
Period size: 80 Copynumber: 2.1 Consensus size: 84
27361963 TGGCCCACTC
* *
27361973 AAAATGAAAATTTTCAATTCAGTCTTATTATAAATAAAAAATCTATAAATT-A-ATGTAGTGAAA
1 AAAATAAAAATTTTCAATTCAGTCTTATTATAAATAAAAAATCTATAAATTAATATGTAGTAAAA
* * *
27362036 TTATATTTT-AGTC-CCTT
66 TTACATTTTAACTCTCCTA
*
27362053 AAAATAAAAATTTTCAATTCAGTCTTCTTATAAATAGAAAAAT-TATAAATTAATATGTAGTAAA
1 AAAATAAAAATTTTCAATTCAGTCTTATTATAAATA-AAAAATCTATAAATTAATATGTAGTAAA
27362117 ATTACATTTTAACTCTCCTA
65 ATTACATTTTAACTCTCCTA
27362137 AAAATAAAAA
1 AAAATAAAAA
27362147 ATATCTATTT
Statistics
Matches: 83, Mismatches: 6, Indels: 6
0.87 0.06 0.06
Matches are distributed among these distances:
80 42 0.51
81 7 0.08
82 18 0.22
83 3 0.04
84 13 0.16
ACGTcount: A:0.48, C:0.09, G:0.06, T:0.37
Consensus pattern (84 bp):
AAAATAAAAATTTTCAATTCAGTCTTATTATAAATAAAAAATCTATAAATTAATATGTAGTAAAA
TTACATTTTAACTCTCCTA
Found at i:27365985 original size:36 final size:36
Alignment explanation
Indices: 27365938--27366010 Score: 146
Period size: 36 Copynumber: 2.0 Consensus size: 36
27365928 GTGCATTTGC
27365938 TTTGTAGCATGAAATTTGAACTTAATTTTAGTGATT
1 TTTGTAGCATGAAATTTGAACTTAATTTTAGTGATT
27365974 TTTGTAGCATGAAATTTGAACTTAATTTTAGTGATT
1 TTTGTAGCATGAAATTTGAACTTAATTTTAGTGATT
27366010 T
1 T
27366011 ACTCCAAACC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.30, C:0.05, G:0.16, T:0.48
Consensus pattern (36 bp):
TTTGTAGCATGAAATTTGAACTTAATTTTAGTGATT
Found at i:27366267 original size:32 final size:32
Alignment explanation
Indices: 27366194--27366268 Score: 96
Period size: 32 Copynumber: 2.3 Consensus size: 32
27366184 TCATATTTTT
**
27366194 AAAACTAAAAATTAATGAATAATTAAAAAATA
1 AAAACTAAAAATTAATGAATAACGAAAAAATA
** * *
27366226 AAATTTAAAAATTAATGAATAACGAATAATTA
1 AAAACTAAAAATTAATGAATAACGAAAAAATA
27366258 AAAACTAAAAA
1 AAAACTAAAAA
27366269 AATAAAGAGA
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.67, C:0.04, G:0.04, T:0.25
Consensus pattern (32 bp):
AAAACTAAAAATTAATGAATAACGAAAAAATA
Found at i:27367172 original size:20 final size:21
Alignment explanation
Indices: 27367147--27367188 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
27367137 ATAATTTTTT
27367147 ATTTTTAATAATGTTT-TAAA
1 ATTTTTAATAATGTTTATAAA
*
27367167 ATTTTTAATAGTGTTTATAAA
1 ATTTTTAATAATGTTTATAAA
27367188 A
1 A
27367189 ATAAAATACA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 15 0.75
21 5 0.25
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.52
Consensus pattern (21 bp):
ATTTTTAATAATGTTTATAAA
Found at i:27367314 original size:31 final size:31
Alignment explanation
Indices: 27367270--27367328 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
27367260 GTAGTATTTG
**
27367270 TTTTTTTTCTAAATTTTGTATAA-ATTTTAAA
1 TTTTTTTAATAAATTTTGTA-AACATTTTAAA
27367301 TTTTTTTAATAAATTTTGTAAACATTTT
1 TTTTTTTAATAAATTTTGTAAACATTTT
27367329 CATATTATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 2 0.08
31 23 0.92
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.61
Consensus pattern (31 bp):
TTTTTTTAATAAATTTTGTAAACATTTTAAA
Found at i:27369955 original size:16 final size:18
Alignment explanation
Indices: 27369922--27369958 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
27369912 TGTAATGTTT
*
27369922 TATATCATATTATTTTTA
1 TATATCATATTATATTTA
27369940 TATATCATA-TA-ATTTA
1 TATATCATATTATATTTA
27369956 TAT
1 TAT
27369959 CACATAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 7 0.39
17 2 0.11
18 9 0.50
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (18 bp):
TATATCATATTATATTTA
Found at i:27376063 original size:29 final size:29
Alignment explanation
Indices: 27376013--27376068 Score: 71
Period size: 29 Copynumber: 1.9 Consensus size: 29
27376003 CAAATAGGGA
27376013 TTAAATTGAGAAATATGAAAAT-TATGTG
1 TTAAATTGAGAAATATGAAAATGTATGTG
*
27376041 TTAAATGTGAGAAAT-TGTGAAATGTATG
1 TTAAAT-TGAGAAATATG-AAAATGTATG
27376069 GGCTGCTATA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
28 8 0.33
29 12 0.50
30 4 0.17
ACGTcount: A:0.43, C:0.00, G:0.21, T:0.36
Consensus pattern (29 bp):
TTAAATTGAGAAATATGAAAATGTATGTG
Found at i:27376531 original size:25 final size:25
Alignment explanation
Indices: 27376503--27376572 Score: 86
Period size: 25 Copynumber: 2.8 Consensus size: 25
27376493 ATATCGATTC
*
27376503 CAGCTCTTATGAGCTTACCGATACT
1 CAGCTCATATGAGCTTACCGATACT
* * *
27376528 CAGCTCGTATGAGCTTACCGTTATT
1 CAGCTCATATGAGCTTACCGATACT
* *
27376553 CAGCTCAGAGGAGCTTACCG
1 CAGCTCATATGAGCTTACCG
27376573 TTTATCGCTC
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 39 1.00
ACGTcount: A:0.23, C:0.27, G:0.21, T:0.29
Consensus pattern (25 bp):
CAGCTCATATGAGCTTACCGATACT
Found at i:27376573 original size:25 final size:25
Alignment explanation
Indices: 27376503--27376590 Score: 83
Period size: 25 Copynumber: 3.6 Consensus size: 25
27376493 ATATCGATTC
* * *
27376503 CAGCTCTTATGAGCTTACCGATACT
1 CAGCTCGTAGGAGCTTACCGTTACT
* *
27376528 CAGCTCGTATGAGCTTACCGTTATT
1 CAGCTCGTAGGAGCTTACCGTTACT
27376553 CAGCTCAG-AGGAGCTTACCGTTTA-T
1 CAGCTC-GTAGGAGCTTACCG-TTACT
*
27376578 C-GCTCGTATGAGC
1 CAGCTCGTAGGAGC
27376591 ATATGTGCGT
Statistics
Matches: 55, Mismatches: 5, Indels: 7
0.82 0.07 0.10
Matches are distributed among these distances:
23 1 0.02
24 9 0.16
25 41 0.75
26 4 0.07
ACGTcount: A:0.22, C:0.26, G:0.22, T:0.31
Consensus pattern (25 bp):
CAGCTCGTAGGAGCTTACCGTTACT
Found at i:27377854 original size:43 final size:43
Alignment explanation
Indices: 27377806--27377892 Score: 156
Period size: 43 Copynumber: 2.0 Consensus size: 43
27377796 ACGGGTATGG
*
27377806 ACACGGGCTGGGACACGGCCGTGTGTCCCCATTTTGAATGCCT
1 ACACGGGCTGGGACACGGCCGTGTGTCCCCATTTTAAATGCCT
*
27377849 ACACGGGCTGGGACACGTCCGTGTGTCCCCATTTTAAATGCCT
1 ACACGGGCTGGGACACGGCCGTGTGTCCCCATTTTAAATGCCT
27377892 A
1 A
27377893 TTTTGAAAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.18, C:0.30, G:0.28, T:0.24
Consensus pattern (43 bp):
ACACGGGCTGGGACACGGCCGTGTGTCCCCATTTTAAATGCCT
Found at i:27381405 original size:15 final size:16
Alignment explanation
Indices: 27381375--27381406 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
27381365 TTATATTATA
27381375 AAAATATTATTAAATT
1 AAAATATTATTAAATT
27381391 AAAATATTA-TAAATT
1 AAAATATTATTAAATT
27381406 A
1 A
27381407 TATTAATTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
AAAATATTATTAAATT
Found at i:27381410 original size:25 final size:26
Alignment explanation
Indices: 27381367--27381419 Score: 74
Period size: 24 Copynumber: 2.1 Consensus size: 26
27381357 TTCTTGATTT
27381367 ATATTATAAAAATATTATTAAATTAAA
1 ATATTATAAAAATATTATT-AATTAAA
*
27381394 ATATTAT-AAATTA-TATTAATTAAA
1 ATATTATAAAAATATTATTAATTAAA
27381418 AT
1 AT
27381420 TAAGATAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
24 9 0.36
25 4 0.16
26 5 0.20
27 7 0.28
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (26 bp):
ATATTATAAAAATATTATTAATTAAA
Found at i:27381427 original size:25 final size:22
Alignment explanation
Indices: 27381377--27381434 Score: 53
Period size: 24 Copynumber: 2.4 Consensus size: 22
27381367 ATATTATAAA
**
27381377 AATATTATTAAATTAAAATATTAT
1 AATA-TATT-AATTAAAATAAGAT
27381401 AAATTATATTAATTAAAATTAAGAT
1 -AA-TATATTAATTAAAA-TAAGAT
27381426 AATATATTA
1 AATATATTA
27381435 TAGAAAACAA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
23 7 0.24
24 10 0.34
25 10 0.34
26 2 0.07
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (22 bp):
AATATATTAATTAAAATAAGAT
Found at i:27381434 original size:28 final size:27
Alignment explanation
Indices: 27381378--27381436 Score: 66
Period size: 28 Copynumber: 2.1 Consensus size: 27
27381368 TATTATAAAA
27381378 ATATTATTAAATTAAAATATTATAAATT
1 ATATTATTAAATTAAAATA-TATAAATT
* *
27381406 ATATTAATTAAAATTAAGATA-ATATATT
1 ATATT-ATT-AAATTAAAATATATAAATT
27381434 ATA
1 ATA
27381437 GAAAACAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
28 14 0.52
29 3 0.11
30 10 0.37
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (27 bp):
ATATTATTAAATTAAAATATATAAATT
Found at i:27381657 original size:15 final size:16
Alignment explanation
Indices: 27381632--27381661 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
27381622 TAAGTAAGTA
27381632 AAACAAAAAGAAAAAG
1 AAACAAAAAGAAAAAG
27381648 AAAC-AAAAGAAAAA
1 AAACAAAAAGAAAAA
27381662 CAGCAAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.83, C:0.07, G:0.10, T:0.00
Consensus pattern (16 bp):
AAACAAAAAGAAAAAG
Found at i:27382635 original size:23 final size:21
Alignment explanation
Indices: 27382601--27382686 Score: 86
Period size: 21 Copynumber: 4.0 Consensus size: 21
27382591 GCTTTGCCGA
*
27382601 TCAGACACTTTATGTGTCGTAT
1 TCAGGCAC-TTATGTGTCGTAT
*
27382623 CTCAGGCATTTTATGTGTCGTA-
1 -TCAGGCA-CTTATGTGTCGTAT
**
27382645 TCAGGCACCTCGTGTGTCGT-T
1 TCAGGCA-CTTATGTGTCGTAT
27382666 TCAGGCACTTATGTGTCGTAT
1 TCAGGCACTTATGTGTCGTAT
27382687 ACTGATCAGG
Statistics
Matches: 52, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
20 10 0.19
21 24 0.46
23 18 0.35
ACGTcount: A:0.17, C:0.21, G:0.23, T:0.38
Consensus pattern (21 bp):
TCAGGCACTTATGTGTCGTAT
Found at i:27388496 original size:15 final size:16
Alignment explanation
Indices: 27388466--27388497 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
27388456 TTATATTATA
27388466 AAAATATTATTAAATT
1 AAAATATTATTAAATT
27388482 AAAATATTA-TAAATT
1 AAAATATTATTAAATT
27388497 A
1 A
27388498 TTTTAATTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
AAAATATTATTAAATT
Found at i:27388510 original size:24 final size:27
Alignment explanation
Indices: 27388458--27388510 Score: 76
Period size: 24 Copynumber: 2.1 Consensus size: 27
27388448 TTCTTGATTT
27388458 ATATTATAAAAATATTATTAAATTAAA
1 ATATTATAAAAATATTATTAAATTAAA
*
27388485 ATATTAT-AAATTATT-TT-AATTAAA
1 ATATTATAAAAATATTATTAAATTAAA
27388509 AT
1 AT
27388511 TAAGATAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
24 9 0.36
25 2 0.08
26 7 0.28
27 7 0.28
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (27 bp):
ATATTATAAAAATATTATTAAATTAAA
Found at i:27389696 original size:22 final size:23
Alignment explanation
Indices: 27389659--27389702 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
27389649 GATTTGCCGA
*
27389659 TCAGGCACTTTATGTGTCGTATC
1 TCAGACACTTTATGTGTCGTATC
27389682 TCAGACAC-TTATGTGTCGTAT
1 TCAGACACTTTATGTGTCGTAT
27389703 ACTGATCAGG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 13 0.65
23 7 0.35
ACGTcount: A:0.20, C:0.20, G:0.20, T:0.39
Consensus pattern (23 bp):
TCAGACACTTTATGTGTCGTATC
Found at i:27392928 original size:33 final size:32
Alignment explanation
Indices: 27392852--27392962 Score: 91
Period size: 33 Copynumber: 3.4 Consensus size: 32
27392842 CATAGTCCAA
* **
27392852 CTATGGTCTTACA-CATGCATTGCCATGGCCCAG
1 CTATGGTCTTACATCA-G-AATGCCATAACCCAG
* * *
27392885 CCATGATCTTACATTC-GTAGTGCCATAACCCAG
1 CTATGGTCTTACA-TCAG-AATGCCATAACCCAG
* *
27392918 TTATGGTCTTATCATCAGAATGCCATAGCCCAG
1 CTATGGTCTTA-CATCAGAATGCCATAACCCAG
27392951 CTATGGTCTTAC
1 CTATGGTCTTAC
27392963 TTATAAATAC
Statistics
Matches: 62, Mismatches: 12, Indels: 9
0.75 0.14 0.11
Matches are distributed among these distances:
32 1 0.02
33 57 0.92
34 3 0.05
35 1 0.02
ACGTcount: A:0.24, C:0.28, G:0.18, T:0.30
Consensus pattern (32 bp):
CTATGGTCTTACATCAGAATGCCATAACCCAG
Found at i:27393013 original size:101 final size:101
Alignment explanation
Indices: 27392839--27393097 Score: 315
Period size: 101 Copynumber: 2.6 Consensus size: 101
27392829 GTTTTCTTTG
* * * * * * * * *
27392839 TGCCATAGTCCAACTATGGTCTTACACAT--GCATTGCCATGGCCCAGCCATGATCTTACATTCG
1 TGCCATAGCCCAACTATGGTATTACATATAAACACTGCCATGGTCCAACCATGGTCTTACATTCA
* * *
27392902 TAGTGCCATAACCCAGTTATGGTCTTATCATCAGAA
66 AAGTGCCATAACCCAGTTATGGTATTATCATCAAAA
* * * * *
27392938 TGCCATAGCCCAGCTATGGTCTTACTTATAAATACTGCCATGGTCCAACCATGGTCTTACGTTCA
1 TGCCATAGCCCAACTATGGTATTACATATAAACACTGCCATGGTCCAACCATGGTCTTACATTCA
* * *
27393003 AAGTGTCATAACCCAGTTATGGTATTTTCATTAAAA
66 AAGTGCCATAACCCAGTTATGGTATTATCATCAAAA
*
27393039 TGCCATAGCCCAACTATGGTATTACATATAAACATTGCCATGGTCCAACCATGGTCTTA
1 TGCCATAGCCCAACTATGGTATTACATATAAACACTGCCATGGTCCAACCATGGTCTTA
27393098 TCCGTCAATT
Statistics
Matches: 135, Mismatches: 23, Indels: 2
0.84 0.14 0.01
Matches are distributed among these distances:
99 25 0.19
101 110 0.81
ACGTcount: A:0.28, C:0.25, G:0.16, T:0.31
Consensus pattern (101 bp):
TGCCATAGCCCAACTATGGTATTACATATAAACACTGCCATGGTCCAACCATGGTCTTACATTCA
AAGTGCCATAACCCAGTTATGGTATTATCATCAAAA
Found at i:27397417 original size:11 final size:11
Alignment explanation
Indices: 27397357--27397417 Score: 54
Period size: 11 Copynumber: 5.3 Consensus size: 11
27397347 AATCAAAAAA
27397357 GAAAAAGAAAG
1 GAAAAAGAAAG
27397368 GAAAAGCAAGAAA-
1 G-AAA--AAGAAAG
27397381 GAAAAAGAAA-
1 GAAAAAGAAAG
27397391 GAGAAAAGAAATG
1 GA-AAAAGAAA-G
*
27397404 GAAAAGGAAAG
1 GAAAAAGAAAG
27397415 GAA
1 GAA
27397418 TACGTTAACT
Statistics
Matches: 43, Mismatches: 1, Indels: 12
0.77 0.02 0.21
Matches are distributed among these distances:
10 8 0.19
11 13 0.30
12 13 0.30
13 3 0.07
14 6 0.14
ACGTcount: A:0.69, C:0.02, G:0.28, T:0.02
Consensus pattern (11 bp):
GAAAAAGAAAG
Found at i:27399770 original size:43 final size:43
Alignment explanation
Indices: 27399718--27399825 Score: 123
Period size: 43 Copynumber: 2.6 Consensus size: 43
27399708 CGTGTATTAC
* *
27399718 TTTCC-GTTTAGCTCTTACGAGCTTCTATTTAACTCATAT-GAG
1 TTTCCTGTTTAGCTCTTACGAGCTTCTATTCAACCCATATAG-G
* * *
27399760 TTTCCTGTTTAGCTCTTTCGAGCTTCTGTTCAACCCTTATAGG
1 TTTCCTGTTTAGCTCTTACGAGCTTCTATTCAACCCATATAGG
* *
27399803 TTT-CTATTCAGCTCTTACGAGCT
1 TTTCCTGTTTAGCTCTTACGAGCT
27399826 ACTGTTCAGC
Statistics
Matches: 56, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
42 22 0.39
43 33 0.59
44 1 0.02
ACGTcount: A:0.18, C:0.24, G:0.15, T:0.44
Consensus pattern (43 bp):
TTTCCTGTTTAGCTCTTACGAGCTTCTATTCAACCCATATAGG
Found at i:27399788 original size:21 final size:21
Alignment explanation
Indices: 27399723--27399789 Score: 64
Period size: 21 Copynumber: 3.1 Consensus size: 21
27399713 ATTACTTTCC
*
27399723 GTTTAGCTCTTACGAGCTTCT
1 GTTTAGCTCTTTCGAGCTTCT
* * * *
27399744 ATTTAACTCATAT-GAGTTTCCT
1 GTTTAGCTC-TTTCGAGCTT-CT
27399766 GTTTAGCTCTTTCGAGCTTCT
1 GTTTAGCTCTTTCGAGCTTCT
27399787 GTT
1 GTT
27399790 CAACCCTTAT
Statistics
Matches: 34, Mismatches: 9, Indels: 6
0.69 0.18 0.12
Matches are distributed among these distances:
21 19 0.56
22 15 0.44
ACGTcount: A:0.16, C:0.21, G:0.16, T:0.46
Consensus pattern (21 bp):
GTTTAGCTCTTTCGAGCTTCT
Found at i:27404982 original size:9 final size:9
Alignment explanation
Indices: 27404956--27405051 Score: 58
Period size: 9 Copynumber: 10.8 Consensus size: 9
27404946 ATTTAAGATT
27404956 TTATT-TAA
1 TTATTATAA
27404964 GTTATATATAA
1 -TTAT-TATAA
*
27404975 ATATTAT-A
1 TTATTATAA
27404983 TGTA-TATAA
1 T-TATTATAA
27404992 TTATTATAA
1 TTATTATAA
*
27405001 TTATTAAACA
1 TTATTATA-A
**
27405011 TTATTATGG
1 TTATTATAA
27405020 TT-TTAT-A
1 TTATTATAA
*
27405027 TTATTATTA
1 TTATTATAA
* *
27405036 CTATTATTA
1 TTATTATAA
27405045 TTATTAT
1 TTATTAT
27405052 TAAATAAACC
Statistics
Matches: 70, Mismatches: 9, Indels: 16
0.74 0.09 0.17
Matches are distributed among these distances:
7 2 0.03
8 14 0.20
9 40 0.57
10 11 0.16
11 3 0.04
ACGTcount: A:0.39, C:0.02, G:0.04, T:0.55
Consensus pattern (9 bp):
TTATTATAA
Found at i:27406282 original size:15 final size:15
Alignment explanation
Indices: 27406262--27406301 Score: 71
Period size: 15 Copynumber: 2.7 Consensus size: 15
27406252 AAGTTATGCA
*
27406262 ATTTATTATGAAATG
1 ATTTATCATGAAATG
27406277 ATTTATCATGAAATG
1 ATTTATCATGAAATG
27406292 ATTTATCATG
1 ATTTATCATG
27406302 TGGTTAATTC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.38, C:0.05, G:0.12, T:0.45
Consensus pattern (15 bp):
ATTTATCATGAAATG
Found at i:27407822 original size:19 final size:18
Alignment explanation
Indices: 27407773--27407822 Score: 50
Period size: 18 Copynumber: 2.8 Consensus size: 18
27407763 AATCGTGTCG
*
27407773 TTCATTTTCAAAATATTA
1 TTCAATTTCAAAATATTA
*
27407791 TT-TATTT-ACAAATCATTA
1 TTCAATTTCA-AAAT-ATTA
27407809 TTCAATTTCAAAAT
1 TTCAATTTCAAAAT
27407823 GTTTTATTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 7
0.71 0.09 0.20
Matches are distributed among these distances:
16 1 0.04
17 7 0.28
18 8 0.32
19 8 0.32
20 1 0.04
ACGTcount: A:0.40, C:0.12, G:0.00, T:0.48
Consensus pattern (18 bp):
TTCAATTTCAAAATATTA
Found at i:27409514 original size:37 final size:37
Alignment explanation
Indices: 27409450--27409606 Score: 199
Period size: 37 Copynumber: 4.0 Consensus size: 37
27409440 TACGTATGAT
*
27409450 CACTTATCAC-TTGTCCCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
*
27409486 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
27409523 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGC
1 CACTTATCACTTTGTCTCTTGATCAGATAA--GT-G-T--AGC
*
27409566 TATCACTTATCACTTTGTCTCTTGATCAGATAAGTATAGC
1 ---CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
27409606 C
1 C
27409607 GAAGCTATCA
Statistics
Matches: 107, Mismatches: 4, Indels: 19
0.82 0.03 0.15
Matches are distributed among these distances:
36 10 0.09
37 54 0.50
39 2 0.02
40 4 0.04
41 1 0.01
42 1 0.01
43 3 0.03
44 2 0.02
46 30 0.28
ACGTcount: A:0.26, C:0.22, G:0.15, T:0.37
Consensus pattern (37 bp):
CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
Found at i:27409576 original size:46 final size:46
Alignment explanation
Indices: 27409523--27409893 Score: 409
Period size: 46 Copynumber: 7.6 Consensus size: 46
27409513 TAAGTGTAGC
* **
27409523 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
* *
27409569 CACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
27409615 CACTTATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCTAT
1 CACTTATCAC---T---TTGTCACTTGATCAGATAAGTGTAGCCGAAG----CTAT
*
27409671 CACTTATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTAT
1 CACTTATCAC--T----TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
*
27409723 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
* * *
27409769 AACTTATCACTTTATCACTTGATCAGATAAGTATAGCCGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
* ** *
27409815 TACTTATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCAC--T----TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
*
27409867 CACTTATCACTTTATCACTTGATCAGA
1 CACTTATCACTTTGTCACTTGATCAGA
27409894 AGTACTCAAA
Statistics
Matches: 290, Mismatches: 18, Indels: 34
0.85 0.05 0.10
Matches are distributed among these distances:
46 154 0.53
48 1 0.00
49 1 0.00
50 2 0.01
52 82 0.28
55 3 0.01
56 47 0.16
ACGTcount: A:0.29, C:0.22, G:0.14, T:0.35
Consensus pattern (46 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
Found at i:27409696 original size:56 final size:55
Alignment explanation
Indices: 27409566--27409723 Score: 225
Period size: 56 Copynumber: 2.9 Consensus size: 55
27409556 TAGCTAAAGC
* *
27409566 TATCACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAG----CTATCACT
1 TATCACTT-TCAC-TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCTATCACT
27409619 TATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCTATCACT
1 TATCAC-TTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCTATCACT
*
27409675 TATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTATC
1 TATCACTTT-CACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATC
27409724 ACTTATCACT
Statistics
Matches: 96, Mismatches: 3, Indels: 9
0.89 0.03 0.08
Matches are distributed among these distances:
52 29 0.30
53 10 0.10
54 2 0.02
55 3 0.03
56 52 0.54
ACGTcount: A:0.27, C:0.23, G:0.15, T:0.35
Consensus pattern (55 bp):
TATCACTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCTATCACT
Found at i:27409864 original size:98 final size:97
Alignment explanation
Indices: 27409523--27409893 Score: 455
Period size: 98 Copynumber: 3.7 Consensus size: 97
27409513 TAAGTGTAGC
* * * * *
27409523 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCTCT
1 CACTT-TCAC-TTGTCACTTGATCAGATAAGTGTAGCCAAAGCTATAACTTATCACTTTATCACT
27409588 TGATCAGATAAGTATAGCCGAAGCTATCACTTAT
64 TGATCAGATAAGTATAGCCGAAGCTATCACTTAT
*
27409622 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCTATCACTTATCACTTTCCA
1 CAC-TTTCACTTGTCACTTGATCAGATAAGTGTAGCCAAAGCTA--TA--ACTTATCACTTT--A
* *
27409687 CTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTATCACTTAT
59 ----TCACTTGATCAGATAAGTATAGCCGAAGCTATCACTTAT
* *
27409730 CAC--T---TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATAACTTATCACTTTATCACTTG
1 CACTTTCACTTGTCACTTGATCAGATAAGTGTAGCCAAAGCTATAACTTATCACTTTATCACTTG
*
27409790 ATCAGATAAGTATAGCCGAAGCTATTACTTAT
66 ATCAGATAAGTATAGCCGAAGCTATCACTTAT
* **
27409822 CACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTATCACTT
1 CACTTT-CACTTGTCACTTGATCAGATAAGTGTAGCCAAAGCTATAACTTATCACTTTATCACTT
27409887 GATCAGA
65 GATCAGA
27409894 AGTACTCAAA
Statistics
Matches: 238, Mismatches: 17, Indels: 35
0.82 0.06 0.12
Matches are distributed among these distances:
92 39 0.16
94 1 0.00
96 1 0.00
98 100 0.42
99 7 0.03
100 5 0.02
102 45 0.19
105 1 0.00
108 39 0.16
ACGTcount: A:0.29, C:0.22, G:0.14, T:0.35
Consensus pattern (97 bp):
CACTTTCACTTGTCACTTGATCAGATAAGTGTAGCCAAAGCTATAACTTATCACTTTATCACTTG
ATCAGATAAGTATAGCCGAAGCTATCACTTAT
Found at i:27417450 original size:18 final size:19
Alignment explanation
Indices: 27417429--27417464 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
27417419 AATCAAACTC
27417429 AAATAAAAAAATC-ATTTT
1 AAATAAAAAAATCGATTTT
*
27417447 AAATTAAAAAATCGATTT
1 AAATAAAAAAATCGATTT
27417465 AATAGAAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.58, C:0.06, G:0.03, T:0.33
Consensus pattern (19 bp):
AAATAAAAAAATCGATTTT
Found at i:27421073 original size:24 final size:24
Alignment explanation
Indices: 27421037--27421082 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
27421027 ATTATTCATT
27421037 ATATTATTGAATT-TTTCATTTTAA
1 ATATTATTGAATTATTT-ATTTTAA
* *
27421061 ATATTTTTTAATTATTTATTTT
1 ATATTATTGAATTATTTATTTT
27421083 TTTATAAAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 16 0.84
25 3 0.16
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.65
Consensus pattern (24 bp):
ATATTATTGAATTATTTATTTTAA
Found at i:27421893 original size:19 final size:20
Alignment explanation
Indices: 27421869--27421906 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
27421859 ATATTTATTT
27421869 TTTTAA-TATGATATAAATA
1 TTTTAATTATGATATAAATA
*
27421888 TTTTAATTATGATTTAAAT
1 TTTTAATTATGATATAAAT
27421907 TGTTAAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (20 bp):
TTTTAATTATGATATAAATA
Found at i:27421912 original size:19 final size:19
Alignment explanation
Indices: 27421871--27421912 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 19
27421861 ATTTATTTTT
*
27421871 TTAATATGATATAAATATT
1 TTAATATGATATAAATATG
*
27421890 TTAATTATGATTTAAAT-TG
1 TTAA-TATGATATAAATATG
27421909 TTAA
1 TTAA
27421913 ATAAAATCAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 9 0.45
20 11 0.55
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (19 bp):
TTAATATGATATAAATATG
Found at i:27422254 original size:14 final size:15
Alignment explanation
Indices: 27422235--27422267 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
27422225 TTGTATTGTA
27422235 TTAAATATTTT-TTT
1 TTAAATATTTTATTT
*
27422249 TTAAATTTTTTATTT
1 TTAAATATTTTATTT
27422264 TTAA
1 TTAA
27422268 TCTATCTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 10 0.59
15 7 0.41
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (15 bp):
TTAAATATTTTATTT
Found at i:27422470 original size:31 final size:31
Alignment explanation
Indices: 27422416--27422492 Score: 91
Period size: 31 Copynumber: 2.5 Consensus size: 31
27422406 GTTACAAAAT
* *
27422416 AATCATTAAACTATTCGAAAGTTTTCATTTA
1 AATCACTAAACTATTCGAAAGTTTTCAGTTA
* * * *
27422447 AGTCACTAAATTATTTGAAAGTTTTTAGTTA
1 AATCACTAAACTATTCGAAAGTTTTCAGTTA
*
27422478 AATCACTAGACTATT
1 AATCACTAAACTATT
27422493 AAGGTTTTTC
Statistics
Matches: 37, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.38, C:0.12, G:0.09, T:0.42
Consensus pattern (31 bp):
AATCACTAAACTATTCGAAAGTTTTCAGTTA
Found at i:27426885 original size:42 final size:42
Alignment explanation
Indices: 27426826--27426913 Score: 167
Period size: 42 Copynumber: 2.1 Consensus size: 42
27426816 GGTAATCTTC
*
27426826 GTAATTTTATATGTTGATGACATTCTACTCATTGGGAATGAT
1 GTAATATTATATGTTGATGACATTCTACTCATTGGGAATGAT
27426868 GTAATATTATATGTTGATGACATTCTACTCATTGGGAATGAT
1 GTAATATTATATGTTGATGACATTCTACTCATTGGGAATGAT
27426910 GTAA
1 GTAA
27426914 GGACATTGTC
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.31, C:0.09, G:0.19, T:0.41
Consensus pattern (42 bp):
GTAATATTATATGTTGATGACATTCTACTCATTGGGAATGAT
Found at i:27433027 original size:16 final size:16
Alignment explanation
Indices: 27433003--27433039 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
27432993 CCTATTGCTC
*
27433003 TATCTAAATATGTGCA
1 TATCAAAATATGTGCA
27433019 TATCAAAATATGTGCA
1 TATCAAAATATGTGCA
27433035 TATCA
1 TATCA
27433040 TTGAAAGTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.41, C:0.14, G:0.11, T:0.35
Consensus pattern (16 bp):
TATCAAAATATGTGCA
Found at i:27437239 original size:12 final size:12
Alignment explanation
Indices: 27437222--27437246 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
27437212 ACCAGTCTCT
27437222 TTCTTCTTTTTC
1 TTCTTCTTTTTC
27437234 TTCTTCTTTTTC
1 TTCTTCTTTTTC
27437246 T
1 T
27437247 CCACCAAAGC
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:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (12 bp):
TTCTTCTTTTTC
Found at i:27441193 original size:20 final size:20
Alignment explanation
Indices: 27441160--27441207 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
27441150 CTTTTCCATG
27441160 CATTTAATGCATTTT-TCCTA
1 CATTTAATGCATTTTCT-CTA
** *
27441180 CATTTAATTTATTTTCTCTC
1 CATTTAATGCATTTTCTCTA
27441200 CATTTAAT
1 CATTTAAT
27441208 CCTTAAAACA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 23 0.96
21 1 0.04
ACGTcount: A:0.25, C:0.19, G:0.02, T:0.54
Consensus pattern (20 bp):
CATTTAATGCATTTTCTCTA
Found at i:27445446 original size:31 final size:32
Alignment explanation
Indices: 27445401--27445463 Score: 94
Period size: 31 Copynumber: 2.0 Consensus size: 32
27445391 TTCCCAAAAG
*
27445401 AAAATTTACCAAGCCACAAACCAA-AAATAATT
1 AAAAATTACCAAGCCA-AAACCAATAAATAATT
27445433 AAAAATTA-CAAGCCAAAACCAATAAATAATT
1 AAAAATTACCAAGCCAAAACCAATAAATAATT
27445464 CATAATACTT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
30 7 0.24
31 15 0.52
32 7 0.24
ACGTcount: A:0.59, C:0.19, G:0.03, T:0.19
Consensus pattern (32 bp):
AAAAATTACCAAGCCAAAACCAATAAATAATT
Found at i:27451712 original size:40 final size:39
Alignment explanation
Indices: 27451654--27451738 Score: 109
Period size: 40 Copynumber: 2.2 Consensus size: 39
27451644 TGTTCAGTTT
* *
27451654 TTATGAGCTTCTGTTGGCGTGTTTC-AGGTGGACCAACTC
1 TTATGAACTTCTGTTGGCGTATTTCGA-GTGGACCAACTC
* *
27451693 TTATGAACTTTTGTTTGGCGTATTTCGATTGGACCAACTC
1 TTATGAACTTCTG-TTGGCGTATTTCGAGTGGACCAACTC
27451733 TTATGA
1 TTATGA
27451739 GATTCTATCT
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
39 11 0.28
40 28 0.70
41 1 0.03
ACGTcount: A:0.19, C:0.18, G:0.24, T:0.40
Consensus pattern (39 bp):
TTATGAACTTCTGTTGGCGTATTTCGAGTGGACCAACTC
Found at i:27454616 original size:47 final size:47
Alignment explanation
Indices: 27454555--27455231 Score: 1165
Period size: 47 Copynumber: 14.4 Consensus size: 47
27454545 CAGCCAAGAC
27454555 AGTGTATATGTGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 AGTGTATATGTGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
*
27454602 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 AGTGTATATGTGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
27454649 AGTGTATATGTGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 AGTGTATATGTGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
27454696 AGTGTATATGTGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 AGTGTATATGTGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
27454743 AGTGTATATGTGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 AGTGTATATGTGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
* *
27454790 AGTGTATATGTGTGATAAGGCCTAATAGCCGATGTGATGAATTTGAA
1 AGTGTATATGTGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
27454837 AGTGTATATGTGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 AGTGTATATGTGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
*
27454884 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 AGTGTATATGTGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
*
27454931 AGTGTATATCTGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 AGTGTATATGTGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
*
27454978 AGTGTATATGTGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
1 AGTGTATATGTGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
*
27455025 AGTGTATATGTGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
1 AGTGTATATGTGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
* *
27455072 AGTGTATATATGTAATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 AGTGTATATGTGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
*
27455119 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 AGTGTATATGTGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
* * * * * * * *
27455166 AGTGTATATATGTGACAGGGCCGAGTGGCCAACGTGATGGATGTGAA
1 AGTGTATATGTGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
* **
27455213 AGTGCATAAATGTGATAAG
1 AGTGTATATGTGTGATAAG
27455232 TCCCGAAGGG
Statistics
Matches: 605, Mismatches: 25, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 605 1.00
ACGTcount: A:0.31, C:0.09, G:0.31, T:0.29
Consensus pattern (47 bp):
AGTGTATATGTGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
Found at i:27455406 original size:37 final size:37
Alignment explanation
Indices: 27455350--27455428 Score: 115
Period size: 37 Copynumber: 2.1 Consensus size: 37
27455340 CCGAGCTCTA
* *
27455350 AAGACCCGATGACTACGTGTGG-GAATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAG-ATTATGTCCGGGT
*
27455387 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
27455424 AAGAC
1 AAGAC
27455429 TTCGTAATAA
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
37 37 0.97
38 1 0.03
ACGTcount: A:0.25, C:0.19, G:0.30, T:0.25
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:27458667 original size:10 final size:10
Alignment explanation
Indices: 27458652--27458677 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
27458642 TAATTACTTC
27458652 AATTCATTTT
1 AATTCATTTT
27458662 AATTCATTTT
1 AATTCATTTT
27458672 AATTCA
1 AATTCA
27458678 CCTTTAGAGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.35, C:0.12, G:0.00, T:0.54
Consensus pattern (10 bp):
AATTCATTTT
Found at i:27459414 original size:22 final size:20
Alignment explanation
Indices: 27459374--27459415 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
27459364 AAAGATGATA
*
27459374 CTTTTCTCTTCTTTTTTTTT
1 CTTTTCTCTTCTTTGTTTTT
27459394 CTTTTCTCTCTCTTTAGTTTTT
1 CTTTTCTCT-TCTTT-GTTTTT
27459416 ATGTTTTAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 9 0.47
21 5 0.26
22 5 0.26
ACGTcount: A:0.02, C:0.21, G:0.02, T:0.74
Consensus pattern (20 bp):
CTTTTCTCTTCTTTGTTTTT
Found at i:27467204 original size:37 final size:37
Alignment explanation
Indices: 27467150--27467240 Score: 164
Period size: 37 Copynumber: 2.5 Consensus size: 37
27467140 TTTAAGTGAT
* *
27467150 AATTAAGATAGAATTATTAAATGAGAATAGTTTATTA
1 AATTAAAATAGAGTTATTAAATGAGAATAGTTTATTA
27467187 AATTAAAATAGAGTTATTAAATGAGAATAGTTTATTA
1 AATTAAAATAGAGTTATTAAATGAGAATAGTTTATTA
27467224 AATTAAAATAGAGTTAT
1 AATTAAAATAGAGTTAT
27467241 CACTTAACTA
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
37 52 1.00
ACGTcount: A:0.49, C:0.00, G:0.13, T:0.37
Consensus pattern (37 bp):
AATTAAAATAGAGTTATTAAATGAGAATAGTTTATTA
Found at i:27467205 original size:19 final size:19
Alignment explanation
Indices: 27467150--27467240 Score: 96
Period size: 18 Copynumber: 4.9 Consensus size: 19
27467140 TTTAAGTGAT
* *
27467150 AATTAAGATAGAATTATTA
1 AATTAAAATAGAGTTATTA
* * *
27467169 AATGAGAATAG-TTTATTA
1 AATTAAAATAGAGTTATTA
27467187 AATTAAAATAGAGTTATTA
1 AATTAAAATAGAGTTATTA
* * *
27467206 AATGAGAATAG-TTTATTA
1 AATTAAAATAGAGTTATTA
27467224 AATTAAAATAGAGTTAT
1 AATTAAAATAGAGTTAT
27467241 CACTTAACTA
Statistics
Matches: 57, Mismatches: 13, Indels: 4
0.77 0.18 0.05
Matches are distributed among these distances:
18 30 0.53
19 27 0.47
ACGTcount: A:0.49, C:0.00, G:0.13, T:0.37
Consensus pattern (19 bp):
AATTAAAATAGAGTTATTA
Found at i:27467950 original size:27 final size:29
Alignment explanation
Indices: 27467887--27467952 Score: 93
Period size: 29 Copynumber: 2.3 Consensus size: 29
27467877 TTTTTTTGGT
*
27467887 ATATTTTAGTAAATAAAAATATATATATA
1 ATATTTTGGTAAATAAAAATATATATATA
27467916 ATATTTTGGTAAATAAAAA-A-AGT-TATA
1 ATATTTTGGTAAATAAAAATATA-TATATA
27467943 ATATTTTGGT
1 ATATTTTGGT
27467953 TATTTTTTAT
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
27 15 0.43
28 2 0.06
29 18 0.51
ACGTcount: A:0.48, C:0.00, G:0.09, T:0.42
Consensus pattern (29 bp):
ATATTTTGGTAAATAAAAATATATATATA
Found at i:27468228 original size:18 final size:20
Alignment explanation
Indices: 27468194--27468230 Score: 60
Period size: 18 Copynumber: 1.9 Consensus size: 20
27468184 TTTCTCAAAA
27468194 TTAAAAATCATTAAAATTAT
1 TTAAAAATCATTAAAATTAT
27468214 TTAAAAAT-A-TAAAATTA
1 TTAAAAATCATTAAAATTA
27468231 AAAATATATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 8 0.47
19 1 0.06
20 8 0.47
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (20 bp):
TTAAAAATCATTAAAATTAT
Found at i:27474572 original size:50 final size:50
Alignment explanation
Indices: 27474472--27474710 Score: 219
Period size: 50 Copynumber: 4.7 Consensus size: 50
27474462 AAAGAGATCT
*
27474472 CATGTAAGACCATGTCTCGGACATGACATTGGCATCATTGAGATTATGAGAGGTCC
1 CATGTAAGACCATGTCTGGGACATGACATTGGCA-C--TGAG---ATGAGAGGTCC
**
27474528 CATGTAAGACCATGTCTGGGACATGATGTTGGCACTGAGATGAGAGGTCC
1 CATGTAAGACCATGTCTGGGACATGACATTGGCACTGAGATGAGAGGTCC
** * * * * **
27474578 CGCGTAAGACCATGTCTGGGACATGGCATGGGCACCGATATGAGAACTCC
1 CATGTAAGACCATGTCTGGGACATGACATTGGCACTGAGATGAGAGGTCC
* * * * * * * **
27474628 CATGTAAGACCATATCTGGGATATGACATTGGTAGT-ACAGGAAACATCC
1 CATGTAAGACCATGTCTGGGACATGACATTGGCACTGAGATGAGAGGTCC
* *
27474677 CATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 CATGTAAGACCATGTCTGGGACATGACATTGGCA
27474711 TGTTATTATC
Statistics
Matches: 151, Mismatches: 32, Indels: 7
0.79 0.17 0.04
Matches are distributed among these distances:
49 37 0.25
50 78 0.52
53 4 0.03
55 1 0.01
56 31 0.21
ACGTcount: A:0.28, C:0.21, G:0.28, T:0.24
Consensus pattern (50 bp):
CATGTAAGACCATGTCTGGGACATGACATTGGCACTGAGATGAGAGGTCC
Found at i:27479483 original size:21 final size:21
Alignment explanation
Indices: 27479453--27479495 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
27479443 TACACATAAA
* *
27479453 TTAATTTTTATAATTTAACTT
1 TTAATATTTATAATATAACTT
27479474 TTAATATTTATAATATAACTT
1 TTAATATTTATAATATAACTT
27479495 T
1 T
27479496 AGAATTTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.37, C:0.05, G:0.00, T:0.58
Consensus pattern (21 bp):
TTAATATTTATAATATAACTT
Found at i:27480574 original size:21 final size:22
Alignment explanation
Indices: 27480544--27480598 Score: 78
Period size: 21 Copynumber: 2.6 Consensus size: 22
27480534 AACAGCGGTG
27480544 GCGGTGAGATTAGG-TACTGTA
1 GCGGTGAGATTAGGATACTGTA
*
27480565 GCGGTAAGATT-GGATACTGTA
1 GCGGTGAGATTAGGATACTGTA
*
27480586 GCAGTGAGATTAG
1 GCGGTGAGATTAG
27480599 AAATAATGGT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
20 2 0.07
21 26 0.90
22 1 0.03
ACGTcount: A:0.27, C:0.09, G:0.36, T:0.27
Consensus pattern (22 bp):
GCGGTGAGATTAGGATACTGTA
Found at i:27480855 original size:20 final size:20
Alignment explanation
Indices: 27480818--27480856 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
27480808 TTTAATAAAC
* * *
27480818 TATATAATCAATTTAAATTA
1 TATATAATAAAATAAAATTA
27480838 TATATAATAAAATAAAATT
1 TATATAATAAAATAAAATT
27480857 TTATCTAATT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (20 bp):
TATATAATAAAATAAAATTA
Found at i:27480896 original size:24 final size:25
Alignment explanation
Indices: 27480845--27480896 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
27480835 TTATATATAA
* *
27480845 TAAAATAAAATTTTATCTAATTTTT
1 TAAAATAAAATTGTATCTAATTTAT
* *
27480870 TAAAATAAAGTTGTA-CTTATTTAT
1 TAAAATAAAATTGTATCTAATTTAT
27480894 TAA
1 TAA
27480897 CTATATTTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
24 10 0.43
25 13 0.57
ACGTcount: A:0.44, C:0.04, G:0.04, T:0.48
Consensus pattern (25 bp):
TAAAATAAAATTGTATCTAATTTAT
Found at i:27481017 original size:15 final size:16
Alignment explanation
Indices: 27480985--27481027 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
27480975 TATATTTATT
27480985 AAATTATATAAAATTAA
1 AAATTAT-TAAAATTAA
*
27481002 ATATTATTAAAA-TAA
1 AAATTATTAAAATTAA
*
27481017 AAAGTATTAAA
1 AAATTATTAAA
27481028 TAAGTATAGT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
15 12 0.52
16 5 0.22
17 6 0.26
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (16 bp):
AAATTATTAAAATTAA
Found at i:27483812 original size:20 final size:19
Alignment explanation
Indices: 27483774--27483812 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
27483764 TTTTTAAAAA
*
27483774 TTCAATATTTTCGTTTTTT
1 TTCAATATTTTCGTCTTTT
*
27483793 TTCAATTATTTTTGTCTTTT
1 TTCAA-TATTTTCGTCTTTT
27483813 ATATAAACTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.15, C:0.10, G:0.05, T:0.69
Consensus pattern (19 bp):
TTCAATATTTTCGTCTTTT
Found at i:27489492 original size:232 final size:232
Alignment explanation
Indices: 27489080--27489545 Score: 878
Period size: 232 Copynumber: 2.0 Consensus size: 232
27489070 AATGAAGCTG
*
27489080 AGTAAGTTCGACGAGATAAACAAAATTCTTACCGAACTAACTATAATAAATCAAATAATAAAAAT
1 AGTAACTTCGACGAGATAAACAAAATTCTTACCGAACTAACTATAATAAATCAAATAATAAAAAT
*
27489145 CATTCAAGACAACTCCCTTTCATTCACAACTTCAATCGATAAATACATTTGTATTCAAATCAATA
66 CATTCAAGACAACTCCCTTTCATTCACAACTTCAATCGACAAATACATTTGTATTCAAATCAATA
*
27489210 CAAAAATAAATAATTTGTCTTTCAAATTCATTAAATAAATCACCTTACCGAGATTTTTCCATTTG
131 CAAAAATAAATAATATGTCTTTCAAATTCATTAAATAAATCACCTTACCGAGATTTTTCCATTTG
*
27489275 AAGAATGACTTATGGGTAAGAGTACATCATCAACAGA
196 AAGAATGACTTACGGGTAAGAGTACATCATCAACAGA
27489312 AGTAACTTCGACGAGATAAACAAAATTCTTACCGAACTAACTATAATAAATCAAATAATAAAAAT
1 AGTAACTTCGACGAGATAAACAAAATTCTTACCGAACTAACTATAATAAATCAAATAATAAAAAT
*
27489377 CATTCAAGACAACTCCCTTTCATTCACAACTTCAATCGACAAATATATTTGTATTCAAATCAATA
66 CATTCAAGACAACTCCCTTTCATTCACAACTTCAATCGACAAATACATTTGTATTCAAATCAATA
27489442 CAAAAATAAATAATATGTCTTTCAAATTCATTAAATAAATCACCTTACCGAGATTTTTCCATTTG
131 CAAAAATAAATAATATGTCTTTCAAATTCATTAAATAAATCACCTTACCGAGATTTTTCCATTTG
*
27489507 AAGAATGACTTACGGGTAAGAGTACATCGTCAACAGA
196 AAGAATGACTTACGGGTAAGAGTACATCATCAACAGA
27489544 AG
1 AG
27489546 CTTACGGGTA
Statistics
Matches: 228, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
232 228 1.00
ACGTcount: A:0.43, C:0.18, G:0.09, T:0.30
Consensus pattern (232 bp):
AGTAACTTCGACGAGATAAACAAAATTCTTACCGAACTAACTATAATAAATCAAATAATAAAAAT
CATTCAAGACAACTCCCTTTCATTCACAACTTCAATCGACAAATACATTTGTATTCAAATCAATA
CAAAAATAAATAATATGTCTTTCAAATTCATTAAATAAATCACCTTACCGAGATTTTTCCATTTG
AAGAATGACTTACGGGTAAGAGTACATCATCAACAGA
Found at i:27489553 original size:31 final size:31
Alignment explanation
Indices: 27489515--27489578 Score: 119
Period size: 31 Copynumber: 2.1 Consensus size: 31
27489505 TGAAGAATGA
*
27489515 CTTACGGGTAAGAGTACATCGTCAACAGAAG
1 CTTACGGGTAACAGTACATCGTCAACAGAAG
27489546 CTTACGGGTAACAGTACATCGTCAACAGAAG
1 CTTACGGGTAACAGTACATCGTCAACAGAAG
27489577 CT
1 CT
27489579 CATAAGAGCT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.34, C:0.22, G:0.23, T:0.20
Consensus pattern (31 bp):
CTTACGGGTAACAGTACATCGTCAACAGAAG
Found at i:27500274 original size:35 final size:35
Alignment explanation
Indices: 27500199--27500276 Score: 86
Period size: 35 Copynumber: 2.2 Consensus size: 35
27500189 TAAACGTCAT
*
27500199 GCCAAAACATCAATACTTCTTTCAATTGAAATCCC
1 GCCACAACATCAATACTTCTTTCAATTGAAATCCC
* * * * *
27500234 ACCACAACATCGATACTTTTTTC-ATTTAACGTCCC
1 GCCACAACATCAATACTTCTTTCAATTGAA-ATCCC
27500269 GCCACAAC
1 GCCACAAC
27500277 GCTAATATTT
Statistics
Matches: 35, Mismatches: 7, Indels: 2
0.80 0.16 0.05
Matches are distributed among these distances:
34 5 0.14
35 30 0.86
ACGTcount: A:0.33, C:0.32, G:0.06, T:0.28
Consensus pattern (35 bp):
GCCACAACATCAATACTTCTTTCAATTGAAATCCC
Found at i:27505119 original size:54 final size:53
Alignment explanation
Indices: 27505056--27505162 Score: 153
Period size: 54 Copynumber: 2.0 Consensus size: 53
27505046 AATGATGATG
* * *
27505056 ATAACCTAACATAATATTAACTCCCCCAAACTTATACCTACTCCTATAT-ATATA
1 ATAACCTAACATAATATTAACT--ACCAAACTTATACCTACACATATATAATATA
*
27505110 ATAACCTAACATAATATTAACTACCAAACTTATGCCTACACATATATAATATA
1 ATAACCTAACATAATATTAACTACCAAACTTATACCTACACATATATAATATA
27505163 TTATTATTAT
Statistics
Matches: 48, Mismatches: 4, Indels: 3
0.87 0.07 0.05
Matches are distributed among these distances:
52 21 0.44
53 5 0.10
54 22 0.46
ACGTcount: A:0.44, C:0.24, G:0.01, T:0.31
Consensus pattern (53 bp):
ATAACCTAACATAATATTAACTACCAAACTTATACCTACACATATATAATATA
Found at i:27505169 original size:3 final size:3
Alignment explanation
Indices: 27505161--27505186 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
27505151 ATATATAATA
27505161 TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TA
27505187 CCTCTCTCTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:27510893 original size:14 final size:14
Alignment explanation
Indices: 27510874--27510900 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
27510864 GAGAAATTAA
27510874 AATATAATTTTATT
1 AATATAATTTTATT
27510888 AATATAATTTTAT
1 AATATAATTTTAT
27510901 CAATTTTGAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (14 bp):
AATATAATTTTATT
Found at i:27517289 original size:34 final size:34
Alignment explanation
Indices: 27517247--27517316 Score: 140
Period size: 34 Copynumber: 2.1 Consensus size: 34
27517237 GATCCTTCAT
27517247 TCATCATTCTACAAGGTATTTATAGGGAAAGAGA
1 TCATCATTCTACAAGGTATTTATAGGGAAAGAGA
27517281 TCATCATTCTACAAGGTATTTATAGGGAAAGAGA
1 TCATCATTCTACAAGGTATTTATAGGGAAAGAGA
27517315 TC
1 TC
27517317 TGTTGTCTAG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.37, C:0.13, G:0.20, T:0.30
Consensus pattern (34 bp):
TCATCATTCTACAAGGTATTTATAGGGAAAGAGA
Found at i:27522888 original size:23 final size:24
Alignment explanation
Indices: 27522845--27522890 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
27522835 TATTATTTTA
*
27522845 TGTTAATAATTATTATTTAATTAG
1 TGTTAATAATTATTATATAATTAG
27522869 TGTT-ATAATTA-TATGATAATTA
1 TGTTAATAATTATTAT-ATAATTA
27522891 AAAGTAAACT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 3 0.15
23 13 0.65
24 4 0.20
ACGTcount: A:0.39, C:0.00, G:0.09, T:0.52
Consensus pattern (24 bp):
TGTTAATAATTATTATATAATTAG
Found at i:27526935 original size:43 final size:43
Alignment explanation
Indices: 27526886--27526970 Score: 152
Period size: 43 Copynumber: 2.0 Consensus size: 43
27526876 CACACCTGTG
*
27526886 TGGCTAGGCTGTCTGTCTCACACGGTCTAGAGACACGCCCGTA
1 TGGCTAGGCTGTCTGTCTCACACGGTCGAGAGACACGCCCGTA
*
27526929 TGGCTAGGCTGTGTGTCTCACACGGTCGAGAGACACGCCCGT
1 TGGCTAGGCTGTCTGTCTCACACGGTCGAGAGACACGCCCGT
27526971 GTCTCAAGCC
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 40 1.00
ACGTcount: A:0.18, C:0.29, G:0.31, T:0.22
Consensus pattern (43 bp):
TGGCTAGGCTGTCTGTCTCACACGGTCGAGAGACACGCCCGTA
Found at i:27529225 original size:21 final size:21
Alignment explanation
Indices: 27529201--27529242 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
27529191 TTTTTTAATT
*
27529201 AATTAACTAACAAAACGTTAA
1 AATTAACTAACAAAACATTAA
**
27529222 AATTTTCTAACAAAACATTAA
1 AATTAACTAACAAAACATTAA
27529243 TACTATCTTA
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:0.55, C:0.14, G:0.02, T:0.29
Consensus pattern (21 bp):
AATTAACTAACAAAACATTAA
Found at i:27532126 original size:17 final size:18
Alignment explanation
Indices: 27532092--27532126 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
27532082 GCCGAAATAC
*
27532092 AAATTAACCCTCAGCCCA
1 AAATTAACCCTCAACCCA
27532110 AAATTAACCCT-AACCCA
1 AAATTAACCCTCAACCCA
27532127 CCAAACTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.43, C:0.37, G:0.03, T:0.17
Consensus pattern (18 bp):
AAATTAACCCTCAACCCA
Found at i:27540475 original size:18 final size:18
Alignment explanation
Indices: 27540454--27540494 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
27540444 ACCGGAAATT
*
27540454 TTTTTAAAAACACGAGGA
1 TTTTTAAAAACACGAAGA
*
27540472 TTTTTGAAAACACGAAGA
1 TTTTTAAAAACACGAAGA
27540490 TTTTT
1 TTTTT
27540495 TTTTTTAACG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.39, C:0.10, G:0.15, T:0.37
Consensus pattern (18 bp):
TTTTTAAAAACACGAAGA
Found at i:27540584 original size:16 final size:16
Alignment explanation
Indices: 27540563--27540649 Score: 75
Period size: 16 Copynumber: 5.2 Consensus size: 16
27540553 AAAAAATATA
27540563 AAAAATTTTAAAACAC
1 AAAAATTTTAAAACAC
*
27540579 AAAAATTTGTGAAACAC
1 AAAAATTT-TAAAACAC
* *
27540596 GAGAATTATTGAAAACAC
1 AAAAATT-TT-AAAACAC
* *
27540614 GAAAAATTTGAAAATAC
1 -AAAAATTTTAAAACAC
* *
27540631 GAAAATTTAAAAACAC
1 AAAAATTTTAAAACAC
27540647 AAA
1 AAA
27540650 TTTTTTTTTA
Statistics
Matches: 55, Mismatches: 12, Indels: 8
0.73 0.16 0.11
Matches are distributed among these distances:
16 23 0.42
17 19 0.35
18 8 0.15
19 5 0.09
ACGTcount: A:0.59, C:0.10, G:0.09, T:0.22
Consensus pattern (16 bp):
AAAAATTTTAAAACAC
Found at i:27540678 original size:23 final size:21
Alignment explanation
Indices: 27540639--27540685 Score: 76
Period size: 23 Copynumber: 2.1 Consensus size: 21
27540629 ACGAAAATTT
27540639 AAAAACACAAATTTTTTTTTA
1 AAAAACACAAATTTTTTTTTA
27540660 AAAAACACGACAATTTTTTTTTA
1 AAAAACAC-A-AATTTTTTTTTA
27540683 AAA
1 AAA
27540686 CATAAAAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 8 0.33
22 1 0.04
23 15 0.62
ACGTcount: A:0.49, C:0.11, G:0.02, T:0.38
Consensus pattern (21 bp):
AAAAACACAAATTTTTTTTTA
Found at i:27540704 original size:110 final size:112
Alignment explanation
Indices: 27540568--27540767 Score: 275
Period size: 110 Copynumber: 1.8 Consensus size: 112
27540558 ATATAAAAAA
* * *
27540568 TTTTAAAACACAAAAATTTGTGAAACACGAGAATTAT-TGAAAACACGAAAAAT-TTGAAAATAC
1 TTTTAAAACAAAAAAATTTGTAAAACACGAGAATT-TGTG-AAACACGAAAAATGTTGAAAACAC
*
27540631 GAAAA-TTTAAAAACAC-AAATTTTTTTTTAAAAAACACGACAATTTTT
64 GAAAATTTTAAAAACACGAAAATTTTTTTTAAAAAACACGACAATTTTT
* *
27540678 TTTTAAAACATAAAAAATTT-TAAAACACGAGAATTTGTGAAACACGAGAATTGTTGAAAACACG
1 TTTTAAAACA-AAAAAATTTGTAAAACACGAGAATTTGTGAAACACGAAAAATGTTGAAAACACG
*
27540742 AAAATTTTGAAAACACGAAAATTTTT
65 AAAATTTTAAAAACACGAAAATTTTT
27540768 GAAACATAGA
Statistics
Matches: 78, Mismatches: 7, Indels: 8
0.84 0.08 0.09
Matches are distributed among these distances:
109 12 0.15
110 40 0.51
111 18 0.23
112 8 0.10
ACGTcount: A:0.50, C:0.10, G:0.10, T:0.29
Consensus pattern (112 bp):
TTTTAAAACAAAAAAATTTGTAAAACACGAGAATTTGTGAAACACGAAAAATGTTGAAAACACGA
AAATTTTAAAAACACGAAAATTTTTTTTAAAAAACACGACAATTTTT
Found at i:27540718 original size:127 final size:129
Alignment explanation
Indices: 27540533--27540765 Score: 380
Period size: 127 Copynumber: 1.8 Consensus size: 129
27540523 AAAATTTTTG
*
27540533 AAACACGACAATCTTTTTTAAAAAAATATAAAAAATTTTAAAACACAAAAATTTGTGAAACACGA
1 AAACACGACAATCTTTTTTAAAAAAACATAAAAAATTTTAAAACACAAAAATTTGTGAAACACGA
*
27540598 GAATTATTGAAAACACGAAAAATTTGAAAATACGAAAATTTAAAAACACAAATTTTTTTTTAAA
66 GAATTATTGAAAACACGAAAAATTTGAAAACACGAAAATTTAAAAACACAAATTTTTTTTTAAA
** * *
27540662 AAACACGACAAT-TTTTTT-TTAAAACATAAAAAATTTTAAAACACGAGAATTTGTGAAACACGA
1 AAACACGACAATCTTTTTTAAAAAAACATAAAAAATTTTAAAACACAAAAATTTGTGAAACACGA
* *
27540725 GAATTGTTGAAAACACGAAAATTTTGAAAACACGAAAATTT
66 GAATTATTGAAAACACGAAAAATTTGAAAACACGAAAATTT
27540766 TTGAAACATA
Statistics
Matches: 96, Mismatches: 8, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
127 78 0.81
128 6 0.06
129 12 0.12
ACGTcount: A:0.52, C:0.11, G:0.09, T:0.28
Consensus pattern (129 bp):
AAACACGACAATCTTTTTTAAAAAAACATAAAAAATTTTAAAACACAAAAATTTGTGAAACACGA
GAATTATTGAAAACACGAAAAATTTGAAAACACGAAAATTTAAAAACACAAATTTTTTTTTAAA
Found at i:27540740 original size:18 final size:17
Alignment explanation
Indices: 27540691--27540801 Score: 111
Period size: 17 Copynumber: 6.4 Consensus size: 17
27540681 TAAAACATAA
27540691 AAAATTTT-AAAACACG
1 AAAATTTTGAAAACACG
*
27540707 AGAATTTGTG-AAACACG
1 AAAATTT-TGAAAACACG
*
27540724 AGAATTGTTGAAAACACG
1 AAAATT-TTGAAAACACG
27540742 AAAATTTTGAAAACACG
1 AAAATTTTGAAAACACG
*
27540759 AAAATTTTTG-AAACATAG
1 AAAA-TTTTGAAAACA-CG
*
27540777 AAATTTTTAGAAAAACACG
1 AAAATTTT-G-AAAACACG
27540796 AAAATT
1 AAAATT
27540802 AGAAATTTTT
Statistics
Matches: 80, Mismatches: 6, Indels: 15
0.79 0.06 0.15
Matches are distributed among these distances:
16 6 0.08
17 40 0.50
18 23 0.29
19 6 0.08
20 5 0.06
ACGTcount: A:0.50, C:0.10, G:0.14, T:0.26
Consensus pattern (17 bp):
AAAATTTTGAAAACACG
Found at i:27540748 original size:35 final size:35
Alignment explanation
Indices: 27540564--27540801 Score: 118
Period size: 35 Copynumber: 6.7 Consensus size: 35
27540554 AAAAATATAA
*
27540564 AAAATTTT-AAAACACAAAAATT-TGTG-AAACACG
1 AAAATTTTGAAAACACGAAAATTGT-TGAAAACACG
* * *
27540597 AGAATTATTGAAAACACGAAAAAT-TTGAAAATACG
1 AAAATT-TTGAAAACACGAAAATTGTTGAAAACACG
* * * *
27540632 AAAA-TTTAAAAACAC-AAATTTTTTTTTAAAAAACACG
1 AAAATTTTGAAAACACGAAA---ATTGTT-GAAAACACG
* * **
27540669 ACAATTTTTTTTTAAAACATAAAAAATT-TT-AAAACACG
1 A-AA---ATTTTGAAAACA-CGAAAATTGTTGAAAACACG
* *
27540707 AGAATTTGTG-AAACACGAGAATTGTTGAAAACACG
1 AAAATTT-TGAAAACACGAAAATTGTTGAAAACACG
* *
27540742 AAAATTTTGAAAACACGAAAATTTTTG-AAACATAG
1 AAAATTTTGAAAACACGAAAATTGTTGAAAACA-CG
*
27540777 AAATTTTTAGAAAAACACGAAAATT
1 AAAATTTT-G-AAAACACGAAAATT
27540802 AGAAATTTTT
Statistics
Matches: 158, Mismatches: 25, Indels: 40
0.71 0.11 0.18
Matches are distributed among these distances:
32 3 0.02
33 19 0.12
34 22 0.14
35 61 0.39
36 3 0.02
37 23 0.15
38 11 0.07
40 2 0.01
41 2 0.01
42 9 0.06
44 3 0.02
ACGTcount: A:0.52, C:0.10, G:0.10, T:0.28
Consensus pattern (35 bp):
AAAATTTTGAAAACACGAAAATTGTTGAAAACACG
Found at i:27540755 original size:52 final size:53
Alignment explanation
Indices: 27540691--27540801 Score: 147
Period size: 52 Copynumber: 2.1 Consensus size: 53
27540681 TAAAACATAA
*
27540691 AAAATTTTAAAACACGAGAATTTGTGAAACACGAG-AATTGTT-G-AAAACACG
1 AAAATTTTAAAACACGAAAATTTGTGAAACA-GAGAAATTGTTAGAAAAACACG
* * *
27540742 AAAATTTTGAAAACACGAAAATTTTTGAAACATAGAAATTTTTAGAAAAACACG
1 AAAATTTT-AAAACACGAAAATTTGTGAAACAGAGAAATTGTTAGAAAAACACG
27540796 AAAATT
1 AAAATT
27540802 AGAAATTTTT
Statistics
Matches: 52, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
51 10 0.19
52 27 0.52
53 1 0.02
54 14 0.27
ACGTcount: A:0.50, C:0.10, G:0.14, T:0.26
Consensus pattern (53 bp):
AAAATTTTAAAACACGAAAATTTGTGAAACAGAGAAATTGTTAGAAAAACACG
Found at i:27540784 original size:127 final size:126
Alignment explanation
Indices: 27540533--27540843 Score: 360
Period size: 127 Copynumber: 2.4 Consensus size: 126
27540523 AAAATTTTTG
** * * *
27540533 AAACACGACAATCTTTTTTAAAAAAATATAAAAAATTTTAAAACACAAAAATTTGTGAAACACGA
1 AAACACGACAAT-TTTTTT-TTAAAACATAAAAAATTTTAAAACACGAGAATTTGTGAAACACGA
* *
27540598 GAATTATTGAAAACACGAAAAATTTGAAAATACGAAAATTTAAAAACACAAATTTTTTTTTA-AA
64 GAATTATTGAAAACACGAAAAATTTGAAAACACGAAAATTTAAAAACACAAA--TATTTTTAGAA
27540662 AAACACGACAATTTTTTTTTAAAACATAAAAAATTTTAAAACACGAGAATTTGTGAAACACGAGA
1 AAACACGACAATTTTTTTTTAAAACATAAAAAATTTTAAAACACGAGAATTTGTGAAACACGAGA
* * ** *
27540727 ATTGTTGAAAACACGAAAATTTTGAAAACACGAAAATTTTTGAAACATAGAA-ATTTTTAGAA
66 ATTATTGAAAACACGAAAAATTTGAAAACACGAAAA-TTTAAAAACACA-AATATTTTTAGAA
* * *
27540789 AAACACGAAAATTAGAAATTTTTTT-TAAC-TAGAAAATTTTAAAACACGAGAATTT
1 AAACACGACAATT-----TTTTTTTAAAACATAAAAAATTTTAAAACACGAGAATTT
27540844 TTTTTTAAAA
Statistics
Matches: 159, Mismatches: 15, Indels: 15
0.84 0.08 0.08
Matches are distributed among these distances:
126 6 0.04
127 89 0.56
128 15 0.09
129 14 0.09
130 25 0.16
131 3 0.02
132 7 0.04
ACGTcount: A:0.51, C:0.10, G:0.09, T:0.30
Consensus pattern (126 bp):
AAACACGACAATTTTTTTTTAAAACATAAAAAATTTTAAAACACGAGAATTTGTGAAACACGAGA
ATTATTGAAAACACGAAAAATTTGAAAACACGAAAATTTAAAAACACAAATATTTTTAGAA
Found at i:27541609 original size:18 final size:18
Alignment explanation
Indices: 27541588--27541631 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
27541578 GTTTGGGTTG
*
27541588 CGGGTCGGGTCACCGGAT
1 CGGGTCGGGTCACAGGAT
* *
27541606 CGGGTCGTGTCGCAGGAT
1 CGGGTCGGGTCACAGGAT
27541624 CGGGTCGG
1 CGGGTCGG
27541632 TTTGACCCGA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.09, C:0.25, G:0.48, T:0.18
Consensus pattern (18 bp):
CGGGTCGGGTCACAGGAT
Found at i:27541684 original size:6 final size:6
Alignment explanation
Indices: 27541674--27541750 Score: 59
Period size: 6 Copynumber: 12.3 Consensus size: 6
27541664 TATTTTTTAT
*
27541674 TTTTTCC TTTTTC -TTTTC TTTTTC TTTTTC TTTTTTC TTCTTCTCC TTCTTC
1 TTTTT-C TTTTTC TTTTTC TTTTTC TTTTTC -TTTTTC TT-TT-T-C TTTTTC
* * *
27541726 TTCTTC TTCTTC -TTTTC TTCTTC TT
1 TTTTTC TTTTTC TTTTTC TTTTTC TT
27541751 CACGAGCCCT
Statistics
Matches: 61, Mismatches: 3, Indels: 13
0.79 0.04 0.17
Matches are distributed among these distances:
5 9 0.15
6 33 0.54
7 14 0.23
8 2 0.03
9 3 0.05
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (6 bp):
TTTTTC
Found at i:27541716 original size:3 final size:3
Alignment explanation
Indices: 27541684--27541751 Score: 81
Period size: 3 Copynumber: 24.0 Consensus size: 3
27541674 TTTTTCCTTT
* * *
27541684 TTC TT- TTC TTT TTC TTT TTC TT- TT- TTC TTC TTC TCC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
27541729 TTC TTC TTC TT- TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC
27541752 ACGAGCCCTA
Statistics
Matches: 56, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
2 8 0.14
3 48 0.86
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (3 bp):
TTC
Found at i:27541887 original size:20 final size:20
Alignment explanation
Indices: 27541830--27541887 Score: 68
Period size: 20 Copynumber: 3.0 Consensus size: 20
27541820 TCGGAGGCTC
*
27541830 TCCTCTTC-TTCTC-CTTTC
1 TCCTCTTCTTTCTCTCTTTT
*
27541848 TCCTC-TCTTTCTCTCCTTT
1 TCCTCTTCTTTCTCTCTTTT
*
27541867 TCCTCTTCTTTTTCTCTTTT
1 TCCTCTTCTTTCTCTCTTTT
27541887 T
1 T
27541888 TTTATTTTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
17 2 0.06
18 10 0.30
19 8 0.24
20 13 0.39
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (20 bp):
TCCTCTTCTTTCTCTCTTTT
Found at i:27542134 original size:29 final size:29
Alignment explanation
Indices: 27542101--27542217 Score: 94
Period size: 30 Copynumber: 3.9 Consensus size: 29
27542091 TGTAATTTTT
*
27542101 AGAAAATTTAGGATTAAAATGAAATTTAA
1 AGAAAATTTAGGGTTAAAATGAAATTTAA
* * *
27542130 TGAAAGTTTAGGGGTCT-AAGTGAAATTTAA
1 AGAAAATTTA-GGGT-TAAAATGAAATTTAA
* *
27542160 AGAAAGTTTAAGGGTCAAAATGAAATTT-A
1 AGAAAATTT-AGGGTTAAAATGAAATTTAA
* * *
27542189 GGAAAAGTTTAGGTGTCAAAATGCAATTT
1 AGAAAA-TTTAGG-GTTAAAATGAAATTT
27542218 TTATTTTTTA
Statistics
Matches: 72, Mismatches: 10, Indels: 11
0.77 0.11 0.12
Matches are distributed among these distances:
29 16 0.22
30 54 0.75
31 2 0.03
ACGTcount: A:0.44, C:0.03, G:0.21, T:0.31
Consensus pattern (29 bp):
AGAAAATTTAGGGTTAAAATGAAATTTAA
Found at i:27542156 original size:30 final size:30
Alignment explanation
Indices: 27542116--27542217 Score: 125
Period size: 30 Copynumber: 3.4 Consensus size: 30
27542106 ATTTAGGATT
*
27542116 AAAATGAAATTTAATGAAAGTTTAGGGGTC
1 AAAATGAAATTTAAAGAAAGTTTAGGGGTC
* * *
27542146 TAAGTGAAATTTAAAGAAAGTTTAAGGGTC
1 AAAATGAAATTTAAAGAAAGTTTAGGGGTC
* *
27542176 AAAATGAAATTT-AGGAAAAGTTTAGGTGTC
1 AAAATGAAATTTAAAG-AAAGTTTAGGGGTC
*
27542206 AAAATGCAATTT
1 AAAATGAAATTT
27542218 TTATTTTTTA
Statistics
Matches: 61, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
29 2 0.03
30 59 0.97
ACGTcount: A:0.44, C:0.04, G:0.22, T:0.30
Consensus pattern (30 bp):
AAAATGAAATTTAAAGAAAGTTTAGGGGTC
Found at i:27542621 original size:50 final size:50
Alignment explanation
Indices: 27542493--27542689 Score: 268
Period size: 50 Copynumber: 3.8 Consensus size: 50
27542483 CACGTGAGCC
* * *
27542493 AAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTGAAAACAGAATTTGCAA
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTG--AA-A-AA-TAGAAA
27542548 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAATAGAAA
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAATAGAAA
*
27542598 AAGGCTCAACTCACCTCTCGCAATATGAGTTGGTTTTTGAAAAATAGAAATTAA
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAATAG--A--AA
*
27542652 AAGGCTCAACTCACCTCTTGCAATATGAGTTGATTTTT
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT
27542690 TTTTTTGAAA
Statistics
Matches: 132, Mismatches: 6, Indels: 9
0.90 0.04 0.06
Matches are distributed among these distances:
50 50 0.38
51 2 0.02
52 2 0.02
53 2 0.02
54 38 0.29
55 38 0.29
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.31
Consensus pattern (50 bp):
AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAATAGAAA
Found at i:27542690 original size:105 final size:104
Alignment explanation
Indices: 27542493--27542689 Score: 324
Period size: 104 Copynumber: 1.9 Consensus size: 104
27542483 CACGTGAGCC
* *
27542493 AAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTGAAAACAGAATTTGCAAAAGGCTCAAC
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAACAGAAATT-CAAAAGGCTCAAC
27542558 TCACCTCTCGCAATATGAGTTGATTTTTGAAAAATAGAAA
65 TCACCTCTCGCAATATGAGTTGATTTTTGAAAAATAGAAA
* *
27542598 AAGGCTCAACTCACCTCTCGCAATATGAGTTGGTTTTTGAAAAATAGAAATT-AAAAGGCTCAAC
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTG-AAAACAGAAATTCAAAAGGCTCAAC
*
27542662 TCACCTCTTGCAATATGAGTTGATTTTT
65 TCACCTCTCGCAATATGAGTTGATTTTT
27542690 TTTTTTGAAA
Statistics
Matches: 86, Mismatches: 5, Indels: 3
0.91 0.05 0.03
Matches are distributed among these distances:
104 39 0.45
105 37 0.43
106 10 0.12
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.31
Consensus pattern (104 bp):
AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAACAGAAATTCAAAAGGCTCAACT
CACCTCTCGCAATATGAGTTGATTTTTGAAAAATAGAAA
Found at i:27542855 original size:79 final size:79
Alignment explanation
Indices: 27542717--27542874 Score: 241
Period size: 79 Copynumber: 2.0 Consensus size: 79
27542707 TTAAAAACAG
27542717 AAATTAAAACAGAATTGAAAAGACCTCAGCGTGTGGCCTGAGGCTCAACTCACCTCGCAATATGA
1 AAATTAAAACAGAATTGAAAAGACCTCAGCG-GTGGCCTGAGGCTCAACTCACCTCGCAATATGA
27542782 GTTGA-TTTGAAAAT
65 GTTGATTTTGAAAAT
* *
27542796 AAATTGAAACAGAAATTGAAAATACCTCAGC-GT-GCCTTGAGGCTCAACTCACTCTCGCAATAT
1 AAATTAAAACAG-AATTGAAAAGACCTCAGCGGTGGCC-TGAGGCTCAACTCAC-CTCGCAATAT
27542859 GAGTTGATTTTGAAAA
63 GAGTTGATTTTGAAAA
27542875 CAGAAATTGA
Statistics
Matches: 73, Mismatches: 2, Indels: 7
0.89 0.02 0.09
Matches are distributed among these distances:
77 3 0.04
78 17 0.23
79 28 0.38
80 25 0.34
ACGTcount: A:0.37, C:0.19, G:0.19, T:0.25
Consensus pattern (79 bp):
AAATTAAAACAGAATTGAAAAGACCTCAGCGGTGGCCTGAGGCTCAACTCACCTCGCAATATGAG
TTGATTTTGAAAAT
Found at i:27542995 original size:72 final size:72
Alignment explanation
Indices: 27542802--27543204 Score: 692
Period size: 72 Copynumber: 5.7 Consensus size: 72
27542792 AAATAAATTG
* * *
27542802 AAACAGAAATTGAAAATACCTCAGCGTGCCTTGAGGCTCAACTCA-CTCTCGCAATATGAGTTG-
1 AAACAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGA
27542865 ATTTTGA
66 ATTTTGA
27542872 AAACAGAAATTGAAAATACCTC-A-GTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGA
1 AAACAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGA
27542935 ATTTTGA
66 ATTTTGA
*
27542942 AAACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGA
1 AAACAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGA
27543007 ATTTTTGA
66 A-TTTTGA
*
27543015 AAACAGAAATTG-AAATACCTCAGCGTGTC-TGAGGCTCAACTCATTTCTCGCAATATGAGTTGA
1 AAACAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGA
27543078 ATTTTGA
66 ATTTTGA
*
27543085 AAACAGAAATTGAAAATACCTCAGCGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGA
1 AAACAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGA
27543150 ATTTTGA
66 ATTTTGA
*
27543157 AAACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTT
1 AAACAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCATTT
27543205 NNNNNNNNNN
Statistics
Matches: 318, Mismatches: 8, Indels: 12
0.94 0.02 0.04
Matches are distributed among these distances:
68 19 0.06
69 17 0.05
70 68 0.21
71 53 0.17
72 143 0.45
73 18 0.06
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.30
Consensus pattern (72 bp):
AAACAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGA
ATTTTGA
Found at i:27543055 original size:143 final size:142
Alignment explanation
Indices: 27542802--27543204 Score: 697
Period size: 143 Copynumber: 2.8 Consensus size: 142
27542792 AAATAAATTG
* *
27542802 AAACAGAAATTGAAAATACCTCAGCGTGCCTTGAGGCTCAACTCA-CTCTCGCAATATGAGTTG-
1 AAACAGAAATTGAAAATACCTCAGCGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGA
27542865 ATTTTGAAAACAGAAATTGAAAATACCTCA-GTGTCTTGAGGCTCAACTCATTTCTCGCAATATG
66 ATTTTGAAAACAGAAATTG-AAATACCTCACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATG
27542929 AGTTGAATTTTGA
130 AGTTGAATTTTGA
* *
27542942 AAACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGA
1 AAACAGAAATTGAAAATACCTCAGCGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGA
27543007 ATTTTTGAAAACAGAAATTGAAATACCTCAGCGTGTC-TGAGGCTCAACTCATTTCTCGCAATAT
66 A-TTTTGAAAACAGAAATTGAAATACCTCA-CGTGTCTTGAGGCTCAACTCATTTCTCGCAATAT
27543071 GAGTTGAATTTTGA
129 GAGTTGAATTTTGA
27543085 AAACAGAAATTGAAAATACCTCAGCGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGA
1 AAACAGAAATTGAAAATACCTCAGCGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGA
27543150 ATTTTGAAAACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTT
66 ATTTTGAAAACAGAAATTGAAA-TACCTC-ACGTGTCTTGAGGCTCAACTCATTT
27543205 NNNNNNNNNN
Statistics
Matches: 249, Mismatches: 6, Indels: 12
0.93 0.02 0.04
Matches are distributed among these distances:
140 42 0.17
141 17 0.07
142 32 0.13
143 135 0.54
144 23 0.09
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.30
Consensus pattern (142 bp):
AAACAGAAATTGAAAATACCTCAGCGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGA
ATTTTGAAAACAGAAATTGAAATACCTCACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGA
GTTGAATTTTGA
Found at i:27543155 original size:215 final size:213
Alignment explanation
Indices: 27542802--27543204 Score: 738
Period size: 215 Copynumber: 1.9 Consensus size: 213
27542792 AAATAAATTG
27542802 AAACAGAAATTGAAAATACCTCAGCGTGCCTTGAGGCTCAACTCACTCTCGCAATATGAGTTGAT
1 AAACAGAAATTGAAAATACCTCAGCGTGCCTTGAGGCTCAACTCACTCTCGCAATATGAGTTGAT
27542867 TTTGAAAACAGAAATTGAAAATACCTCAGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGT
66 TTTGAAAACAGAAATTGAAAATACCTCAGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGT
27542932 TGAATTTTGAAAACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAA
131 TGAATTTTGAAAACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAA
27542997 TATGAGTTGAATTTTTGA
196 TATGAGTTGAATTTTTGA
* *
27543015 AAACAGAAATTG-AAATACCTCAGCGTGTC-TGAGGCTCAACTCATTTCTCGCAATATGAGTTGA
1 AAACAGAAATTGAAAATACCTCAGCGTGCCTTGAGGCTCAACTCA-CTCTCGCAATATGAGTTG-
27543078 ATTTTGAAAACAGAAATTGAAAATACCTCAGCGTGTCTTGAGGCTCAACTCATTTCTCGCAATAT
64 ATTTTGAAAACAGAAATTGAAAATACCTCA--GTGTCTTGAGGCTCAACTCATTTCTCGCAATAT
27543143 GAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTT
127 GAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTT
27543205 NNNNNNNNNN
Statistics
Matches: 184, Mismatches: 2, Indels: 6
0.96 0.01 0.03
Matches are distributed among these distances:
211 14 0.08
212 33 0.18
213 42 0.23
215 95 0.52
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.30
Consensus pattern (213 bp):
AAACAGAAATTGAAAATACCTCAGCGTGCCTTGAGGCTCAACTCACTCTCGCAATATGAGTTGAT
TTTGAAAACAGAAATTGAAAATACCTCAGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGT
TGAATTTTGAAAACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAA
TATGAGTTGAATTTTTGA
Found at i:27555538 original size:18 final size:18
Alignment explanation
Indices: 27555517--27555557 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
27555507 ACCGGAAATT
*
27555517 TTTTTAAAAACACGAGGA
1 TTTTTAAAAACACGAAGA
*
27555535 TTTTTGAAAACACGAAGA
1 TTTTTAAAAACACGAAGA
27555553 TTTTT
1 TTTTT
27555558 TTTTTAACGC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.39, C:0.10, G:0.15, T:0.37
Consensus pattern (18 bp):
TTTTTAAAAACACGAAGA
Found at i:27555645 original size:16 final size:16
Alignment explanation
Indices: 27555624--27555710 Score: 75
Period size: 16 Copynumber: 5.2 Consensus size: 16
27555614 AAAAAATATA
27555624 AAAAATTTTAAAACAC
1 AAAAATTTTAAAACAC
*
27555640 AAAAATTTGTGAAACAC
1 AAAAATTT-TAAAACAC
* *
27555657 GAGAATTATTGAAAACAC
1 AAAAATT-TT-AAAACAC
* *
27555675 GAAAAATTTGAAAATAC
1 -AAAAATTTTAAAACAC
* *
27555692 GAAAATTTAAAAACAC
1 AAAAATTTTAAAACAC
27555708 AAA
1 AAA
27555711 TTTTTTTTTT
Statistics
Matches: 55, Mismatches: 12, Indels: 8
0.73 0.16 0.11
Matches are distributed among these distances:
16 23 0.42
17 19 0.35
18 8 0.15
19 5 0.09
ACGTcount: A:0.59, C:0.10, G:0.09, T:0.22
Consensus pattern (16 bp):
AAAAATTTTAAAACAC
Done.