Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr14
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: 244914714
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.31
Warning! 4503000 characters in sequence are not A, C, G, or T
File 183 of 770
Found at i:54801502 original size:15 final size:15
Alignment explanation
Indices: 54801482--54801511 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
54801472 GGTAAATTTC
54801482 TAAACATGAACCCTA
1 TAAACATGAACCCTA
54801497 TAAACATGAACCCTA
1 TAAACATGAACCCTA
54801512 GCATGAAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.47, C:0.27, G:0.07, T:0.20
Consensus pattern (15 bp):
TAAACATGAACCCTA
Found at i:54803734 original size:46 final size:46
Alignment explanation
Indices: 54803684--54803771 Score: 167
Period size: 46 Copynumber: 1.9 Consensus size: 46
54803674 AGCTCAGGCG
*
54803684 TTTGCATCCATGAGTGAACTCGGACTCAACTCAACGAGTTCGCACA
1 TTTGCATCCATAAGTGAACTCGGACTCAACTCAACGAGTTCGCACA
54803730 TTTGCATCCATAAGTGAACTCGGACTCAACTCAACGAGTTCG
1 TTTGCATCCATAAGTGAACTCGGACTCAACTCAACGAGTTCG
54803772 GATGCCCAAA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 41 1.00
ACGTcount: A:0.28, C:0.27, G:0.19, T:0.25
Consensus pattern (46 bp):
TTTGCATCCATAAGTGAACTCGGACTCAACTCAACGAGTTCGCACA
Found at i:54810342 original size:27 final size:28
Alignment explanation
Indices: 54810286--54810355 Score: 124
Period size: 27 Copynumber: 2.5 Consensus size: 28
54810276 AAATTTGTAC
*
54810286 AGCACTAAGTGTACGAGTTTGATTATAT
1 AGCACTAAGTGTGCGAGTTTGATTATAT
54810314 AGCACTAAGTGTGCGAG-TTGATTATAT
1 AGCACTAAGTGTGCGAGTTTGATTATAT
54810341 AGCACTAAGTGTGCG
1 AGCACTAAGTGTGCG
54810356 GACTCACTAT
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
27 25 0.61
28 16 0.39
ACGTcount: A:0.30, C:0.13, G:0.26, T:0.31
Consensus pattern (28 bp):
AGCACTAAGTGTGCGAGTTTGATTATAT
Found at i:54810366 original size:27 final size:27
Alignment explanation
Indices: 54810286--54810367 Score: 76
Period size: 27 Copynumber: 3.0 Consensus size: 27
54810276 AAATTTGTAC
* * * *
54810286 AGCACTAAGTGTACGAGTTTGATTATAT
1 AGCACTAAGTGTGCGAG-CTCACTATAT
* * *
54810314 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGAGCTCACTATAT
54810341 AGCACTAAGTGTGCG-GACTCACTATAT
1 AGCACTAAGTGTGCGAG-CTCACTATAT
54810368 GTTTTTGAAT
Statistics
Matches: 49, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
26 1 0.02
27 32 0.65
28 16 0.33
ACGTcount: A:0.30, C:0.15, G:0.23, T:0.32
Consensus pattern (27 bp):
AGCACTAAGTGTGCGAGCTCACTATAT
Found at i:54813485 original size:28 final size:28
Alignment explanation
Indices: 54813447--54813520 Score: 114
Period size: 28 Copynumber: 2.6 Consensus size: 28
54813437 GTTCAAATTG
* *
54813447 TATAGCACTAAGTGTGCGAGTTTGATTA
1 TATAGCACTAAGTGTGCGAGTTCGACTA
54813475 TATAGCACTAAGTGTGCGAGTTCGACTA
1 TATAGCACTAAGTGTGCGAGTTCGACTA
54813503 T-TAAGCACTAAGTGTGCG
1 TAT-AGCACTAAGTGTGCG
54813521 GGCTTATTAT
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
27 1 0.02
28 42 0.98
ACGTcount: A:0.28, C:0.15, G:0.26, T:0.31
Consensus pattern (28 bp):
TATAGCACTAAGTGTGCGAGTTCGACTA
Found at i:54818210 original size:30 final size:30
Alignment explanation
Indices: 54818176--54818236 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
54818166 TCCTTAACTC
*
54818176 AAACTTTGGCAAAATTATAATTTTGCCCCT
1 AAACTTTGGCAAAATTACAATTTTGCCCCT
* * * *
54818206 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTGGCAAAATTACAATTTTGCCCCT
54818236 A
1 A
54818237 GGCTCGGGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.30, C:0.23, G:0.08, T:0.39
Consensus pattern (30 bp):
AAACTTTGGCAAAATTACAATTTTGCCCCT
Found at i:54833722 original size:47 final size:49
Alignment explanation
Indices: 54833608--54833784 Score: 198
Period size: 47 Copynumber: 3.8 Consensus size: 49
54833598 TGTAACCCGC
* *
54833608 CCATAAGCGAACTC-GACTCAACTCAACGAGCTCGG--G-C-TTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGCCATTCACAT
*
54833652 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGCC-A-TTCACAT
* *
54833702 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGA---CATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGCCATTCACAT
*
54833745 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGC
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGC
54833785 TCAACCATCC
Statistics
Matches: 111, Mismatches: 8, Indels: 23
0.78 0.06 0.16
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 15 0.14
45 22 0.20
46 29 0.26
47 30 0.27
48 3 0.03
49 1 0.01
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.30, G:0.20, T:0.21
Consensus pattern (49 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGCCATTCACAT
Found at i:54833780 original size:93 final size:91
Alignment explanation
Indices: 54833615--54833784 Score: 304
Period size: 93 Copynumber: 1.8 Consensus size: 91
54833605 CGCCCATAAG
*
54833615 CGAACTCGACTCAACTCAACGAGCTCGGGCTTCGCATCCATAAGTGAACTCGGACTCAACTCAAC
1 CGAACTCGACTCAACTCAACGAGCTCGGACTTCGCATCCATAAGTGAACTCGGACTCAACTCAAC
54833680 GAGTTCGGATGCCTAGTTACATCTCA
66 GAGTTCGGATGCCTAGTTACATCTCA
*
54833706 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTC-GACTCAACTCAACGAGCTCGGAC-TTCGCATCCATAAGTGAACTCGGACTCAACTCA
54833771 ACGAGTTCGGATGC
64 ACGAGTTCGGATGC
54833785 TCAACCATCC
Statistics
Matches: 75, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
91 7 0.09
92 21 0.28
93 47 0.63
ACGTcount: A:0.28, C:0.30, G:0.21, T:0.21
Consensus pattern (91 bp):
CGAACTCGACTCAACTCAACGAGCTCGGACTTCGCATCCATAAGTGAACTCGGACTCAACTCAAC
GAGTTCGGATGCCTAGTTACATCTCA
Found at i:54833800 original size:46 final size:46
Alignment explanation
Indices: 54833611--54833793 Score: 148
Period size: 46 Copynumber: 4.0 Consensus size: 46
54833601 AACCCGCCCA
* * * * * *
54833611 TAAGCGAACTC-GACTCAACTCAACGAGCTCGGGCTTCGCATCCA--
1 TAAGTGAACTCGGACTCAACTCAACGAGTTC-GGATGCTCAACCATC
54833655 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGC-CTAGTTA-CATC
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTC-A---ACCATC
* * * * *
54833703 TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA--
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGG--ATGCTCAACCATC
54833748 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATC
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATC
54833794 CTAGTGACAT
Statistics
Matches: 111, Mismatches: 14, Indels: 26
0.74 0.09 0.17
Matches are distributed among these distances:
43 1 0.01
44 23 0.21
45 20 0.18
46 30 0.27
47 30 0.27
48 2 0.02
49 4 0.04
50 1 0.01
ACGTcount: A:0.29, C:0.30, G:0.20, T:0.21
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATC
Found at i:54837273 original size:12 final size:12
Alignment explanation
Indices: 54837256--54837281 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
54837246 TTTTACTAAA
54837256 CTTAGCATACAG
1 CTTAGCATACAG
54837268 CTTAGCATACAG
1 CTTAGCATACAG
54837280 CT
1 CT
54837282 GCTTATCTCT
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:0.31, C:0.27, G:0.15, T:0.27
Consensus pattern (12 bp):
CTTAGCATACAG
Found at i:54841247 original size:47 final size:49
Alignment explanation
Indices: 54841127--54841304 Score: 198
Period size: 45 Copynumber: 3.8 Consensus size: 49
54841117 TGTAACCCGC
* * *
54841127 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGG--G-C-GTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGCCATTCACAT
*
54841172 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGCC-A-TTCACAT
* *
54841222 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGA---CATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGCCATTCACAT
*
54841265 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGC
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGC
54841305 TCAACCATCC
Statistics
Matches: 111, Mismatches: 9, Indels: 22
0.78 0.06 0.15
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 36 0.32
46 29 0.26
47 30 0.27
48 3 0.03
49 1 0.01
50 3 0.03
51 1 0.01
ACGTcount: A:0.29, C:0.30, G:0.21, T:0.20
Consensus pattern (49 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGCCATTCACAT
Found at i:54841292 original size:93 final size:92
Alignment explanation
Indices: 54841134--54841304 Score: 306
Period size: 93 Copynumber: 1.8 Consensus size: 92
54841124 CGCCCATAAG
*
54841134 CGAACTCGGACTCAACTCAACGAGCTCGGGCGTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACGTCGCATCCATAAGTGAACTCGGACTCAACTCAA
54841199 CGAGTTCGGATGCCTAGTTACATCTCA
66 CGAGTTCGGATGCCTAGTTACATCTCA
* *
54841226 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGAC-GTCGCATCCATAAGTGAACTCGGACTCAACTCA
54841291 ACGAGTTCGGATGC
65 ACGAGTTCGGATGC
54841305 TCAACCATCC
Statistics
Matches: 75, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
92 29 0.39
93 46 0.61
ACGTcount: A:0.28, C:0.30, G:0.22, T:0.20
Consensus pattern (92 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGACGTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCA
Found at i:54841758 original size:30 final size:30
Alignment explanation
Indices: 54841723--54841779 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
54841713 TAACTCAAAT
54841723 TTTTGCAAAATTACAATTTTACCCCTAAAC
1 TTTTGCAAAATTACAATTTTACCCCTAAAC
* * * *
54841753 TTTTGCATATTTACATTTTTGCCCCTA
1 TTTTGCAAAATTACAATTTTACCCCTA
54841780 GGCTCGGGAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.28, C:0.23, G:0.05, T:0.44
Consensus pattern (30 bp):
TTTTGCAAAATTACAATTTTACCCCTAAAC
Found at i:54850544 original size:31 final size:28
Alignment explanation
Indices: 54850486--54850545 Score: 75
Period size: 31 Copynumber: 2.0 Consensus size: 28
54850476 TTTCGTTTTC
54850486 TTTGATTATTCATCTAAATACATTCAAA
1 TTTGATTATTCATCTAAATACATTCAAA
* *
54850514 TTTGACTTATTCAATCATACATTCATTCAAA
1 TTTGA-TTATTC-ATC-TAAATACATTCAAA
54850545 T
1 T
54850546 CAATCCATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
28 5 0.19
29 6 0.22
30 3 0.11
31 13 0.48
ACGTcount: A:0.37, C:0.17, G:0.03, T:0.43
Consensus pattern (28 bp):
TTTGATTATTCATCTAAATACATTCAAA
Found at i:54850638 original size:9 final size:9
Alignment explanation
Indices: 54850624--54850649 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
54850614 GTCCCTAATT
54850624 CACAAAATA
1 CACAAAATA
54850633 CACAAAATA
1 CACAAAATA
54850642 CACAAAAT
1 CACAAAAT
54850650 TTCCAATTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.65, C:0.23, G:0.00, T:0.12
Consensus pattern (9 bp):
CACAAAATA
Found at i:54853919 original size:46 final size:49
Alignment explanation
Indices: 54853726--54854039 Score: 250
Period size: 46 Copynumber: 6.7 Consensus size: 49
54853716 AGGGTATAAT
* * *
54853726 GCCGATGCCATGTCCCAGATATGGTCTTACACTAGCTCATCCA--TC-AA
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTC-TACATCTCGAG
* * * *
54853773 GTCGATGTCATGTCCCAGACATGGTCTTACACTAGCTCTCACATATCCG-T
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCT-ACATCT-CGAG
* * * *
54853823 GCCAATGCCATGTCCTAAACATGGTCTTACACT-G-AC-ACATCTCGTA-
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTACATCTCG-AG
* *
54853869 GCCGATG-CATGTCTCAGACAT-GTCTTACACTGGCT-TACATCTCGAG
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTACATCTCGAG
** * *
54853915 GCCGATG-CATGTCCCAGACAT-GTCTTACACTAGCTCT-TGTCTCAAT
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTACATCTCGAG
* * * * *
54853961 GTCGATGCCACGTCCTAGACATGGTCTTACACTAGCTCT-CATGAT-GTG
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTACAT-CTCGAG
*
54854009 GCTGATG-CATGTCCCAGACAT-GTCTTACACT
1 GCCGATGCCATGTCCCAGACATGGTCTTACACT
54854040 GGCACACAAA
Statistics
Matches: 216, Mismatches: 36, Indels: 31
0.76 0.13 0.11
Matches are distributed among these distances:
44 10 0.05
45 15 0.07
46 74 0.34
47 62 0.29
48 23 0.11
49 3 0.01
50 29 0.13
ACGTcount: A:0.23, C:0.30, G:0.19, T:0.28
Consensus pattern (49 bp):
GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTACATCTCGAG
Found at i:54853988 original size:94 final size:93
Alignment explanation
Indices: 54853726--54854039 Score: 283
Period size: 94 Copynumber: 3.4 Consensus size: 93
54853716 AGGGTATAAT
* * *
54853726 GCCGATGCCATGTCCCAGATATGGTCTTACACTAGCTCATCCATCAA-GTCGATGTCATGTCCCA
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTC-TTC-TCAATGTCGATG-CATGTCCTA
*
54853790 GACATGGTCTTACACTAGCTCTCACATATCCGT
63 GACATGGTCTTACACTAGCTCT-ACATAT-CGG
* * * * * * *
54853823 GCCAATGCCATGTCCTAAACATGGTCTTACACT-GACACATCTC-GTAGCCGATGCATGT-CTCA
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAG-CTCTTCTCAAT-GTCGATGCATGTCCT-A
* *
54853885 GACAT-GTCTTACACTGGCT-TACATCTCGAG
63 GACATGGTCTTACACTAGCTCTACATATCG-G
*
54853915 GCCGATG-CATGTCCCAGACAT-GTCTTACACTAGCTCTTGTCTCAATGTCGATGCCACGTCCTA
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTC-T-TCTCAATGTCGATG-CATGTCCTA
54853978 GACATGGTCTTACACTAGCTCT-CATGAT-GTG
63 GACATGGTCTTACACTAGCTCTACAT-ATCG-G
*
54854009 GCTGATG-CATGTCCCAGACAT-GTCTTACACT
1 GCCGATGCCATGTCCCAGACATGGTCTTACACT
54854040 GGCACACAAA
Statistics
Matches: 178, Mismatches: 25, Indels: 31
0.76 0.11 0.13
Matches are distributed among these distances:
90 12 0.07
91 15 0.08
92 21 0.12
93 12 0.07
94 64 0.36
95 15 0.08
96 8 0.04
97 31 0.17
ACGTcount: A:0.23, C:0.30, G:0.19, T:0.28
Consensus pattern (93 bp):
GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTTCTCAATGTCGATGCATGTCCTAGAC
ATGGTCTTACACTAGCTCTACATATCGG
Found at i:54854027 original size:140 final size:141
Alignment explanation
Indices: 54853726--54854042 Score: 342
Period size: 140 Copynumber: 2.2 Consensus size: 141
54853716 AGGGTATAAT
* * * *
54853726 GCCGATGCCATGTCCCAGATATGGTCTTACACTAGC-T-CATCCATC-AAGTCGATGTCATGTCC
1 GCCGATG-CATGTCCCAGACAT-GTCTTACACTGGCTTACAT-C-TCGAGGCCGATGTCATGTCC
** *
54853788 CAGACATGGTCTTACACTAGCTCTCACATATCCGTGCCAATGCCATGTCCTAAACATGGTCTTAC
62 CAGACATGGTCTTACACTAGCTCT-ACATATCAATGCCAATGCCACGTCCTAAACATGGTCTTAC
*
54853853 ACTGACACATCTCGTA
126 ACTGACACATATCGTA
*
54853869 GCCGATGCATGTCTCAGACATGTCTTACACTGGCTTACATCTCGAGGCCGATG-CATGTCCCAGA
1 GCCGATGCATGTCCCAGACATGTCTTACACTGGCTTACATCTCGAGGCCGATGTCATGTCCCAGA
** * * * *
54853933 CAT-GTCTTACACTAGCTCT-TGTCTCAATGTCGATGCCACGTCCTAGACATGGTCTTACACTAG
66 CATGGTCTTACACTAGCTCTACATATCAATGCCAATGCCACGTCCTAAACATGGTCTTACACT-G
* * *
54853996 CTCTCATGAT-GTG
130 -ACACAT-ATCGTA
*
54854009 GCTGATGCATGTCCCAGACATGTCTTACACTGGC
1 GCCGATGCATGTCCCAGACATGTCTTACACTGGC
54854043 ACACAAATAA
Statistics
Matches: 148, Mismatches: 20, Indels: 15
0.81 0.11 0.08
Matches are distributed among these distances:
138 33 0.22
139 1 0.01
140 54 0.36
141 29 0.20
142 21 0.14
143 10 0.07
ACGTcount: A:0.23, C:0.30, G:0.19, T:0.28
Consensus pattern (141 bp):
GCCGATGCATGTCCCAGACATGTCTTACACTGGCTTACATCTCGAGGCCGATGTCATGTCCCAGA
CATGGTCTTACACTAGCTCTACATATCAATGCCAATGCCACGTCCTAAACATGGTCTTACACTGA
CACATATCGTA
Found at i:54863476 original size:40 final size:40
Alignment explanation
Indices: 54863432--54863602 Score: 175
Period size: 40 Copynumber: 4.2 Consensus size: 40
54863422 CTTTGGGACA
* * *
54863432 TAGCCCGG-TTATAGTGATTCGCACAATTGCCTTCGGGAAT
1 TAGCCCGGATT-TAGTAACTCGCACAAATGCCTTCGGGAAT
* *
54863472 TAGCCCGGATTTAGTAACTCGCACAATTGCCTTCGGGACT
1 TAGCCCGGATTTAGTAACTCGCACAAATGCCTTCGGGAAT
* * * * *
54863512 TAACCTGGTTTTGGTAACTCGCACAAATGCCTTCGAGAAT
1 TAGCCCGGATTTAGTAACTCGCACAAATGCCTTCGGGAAT
* * * *
54863552 T-GACCCGGATTTAGTCACTTAGCACAAAAGCCTTCGGGACT
1 TAG-CCCGGATTTAGTAAC-TCGCACAAATGCCTTCGGGAAT
54863593 TAGCCCGGAT
1 TAGCCCGGAT
54863603 ACCATTCGAA
Statistics
Matches: 108, Mismatches: 19, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
40 79 0.73
41 28 0.26
42 1 0.01
ACGTcount: A:0.25, C:0.25, G:0.23, T:0.27
Consensus pattern (40 bp):
TAGCCCGGATTTAGTAACTCGCACAAATGCCTTCGGGAAT
Found at i:54887115 original size:13 final size:13
Alignment explanation
Indices: 54887082--54887115 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
54887072 ACATAATCGG
*
54887082 TAAAATTTTCTTA
1 TAAAATTTTCATA
54887095 TCAAAATTTTCATA
1 T-AAAATTTTCATA
54887109 TAAAATT
1 TAAAATT
54887116 CCTATCATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
13 7 0.37
14 12 0.63
ACGTcount: A:0.44, C:0.09, G:0.00, T:0.47
Consensus pattern (13 bp):
TAAAATTTTCATA
Found at i:54889354 original size:48 final size:48
Alignment explanation
Indices: 54889271--54889461 Score: 247
Period size: 48 Copynumber: 4.0 Consensus size: 48
54889261 ACTCGGGAGT
**
54889271 CTCGCACCTTAAGTGCCAATATCATGGCCCAAAGCCAAATCAATGAAG
1 CTCGCACCCGAAGTGCCAATATCATGGCCCAAAGCCAAATCAATGAAG
* * ** *
54889319 CTTGCACCCGAAGTGCCAATATCATAGCCTGAAGCCAAATCAATAAAG
1 CTCGCACCCGAAGTGCCAATATCATGGCCCAAAGCCAAATCAATGAAG
* * * * *
54889367 CACGCACCCGAAGTGTCGATATCATGTCCCAAAGCCAAATCAATGAAA
1 CTCGCACCCGAAGTGCCAATATCATGGCCCAAAGCCAAATCAATGAAG
* * *
54889415 CTCGAACCCGAAGTGCCGATATCATGGCCCGAAGCCAAATCAATGAA
1 CTCGCACCCGAAGTGCCAATATCATGGCCCAAAGCCAAATCAATGAA
54889462 TTCCCTAATG
Statistics
Matches: 121, Mismatches: 22, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
48 121 1.00
ACGTcount: A:0.36, C:0.29, G:0.18, T:0.17
Consensus pattern (48 bp):
CTCGCACCCGAAGTGCCAATATCATGGCCCAAAGCCAAATCAATGAAG
Found at i:54891656 original size:26 final size:26
Alignment explanation
Indices: 54891627--54891734 Score: 180
Period size: 26 Copynumber: 4.2 Consensus size: 26
54891617 TGGTACAAAT
*
54891627 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
54891653 TGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
54891679 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
54891705 TGATAATGGTTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
54891731 TGAT
1 TGAT
54891735 GGGCATTTCA
Statistics
Matches: 76, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 76 1.00
ACGTcount: A:0.32, C:0.06, G:0.24, T:0.37
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:54897765 original size:43 final size:43
Alignment explanation
Indices: 54897714--54897874 Score: 191
Period size: 43 Copynumber: 3.7 Consensus size: 43
54897704 TAGGATCCCA
54897714 ATATGTGATTTCGTGTAAGACCACATCTGGGACATTGGCATTG
1 ATATGTGATTTCGTGTAAGACCACATCTGGGACATTGGCATTG
* ** * *
54897757 ATTTGTGATTTGCGTGTAAGACCATGTCCGGGACATTGGCATCG
1 ATATGTGATTT-CGTGTAAGACCACATCTGGGACATTGGCATTG
* * * *
54897801 -TATATGAGTTCGTGTAAGACC-CTGTCTGGGACAGTGGCATTG
1 ATATGTGATTTCGTGTAAGACCAC-ATCTGGGACATTGGCATTG
* *
54897843 ATATGTGATTACATGTAAGACCACATCTGGGA
1 ATATGTGATTTCGTGTAAGACCACATCTGGGA
54897875 TGTTGGCGTT
Statistics
Matches: 97, Mismatches: 17, Indels: 8
0.80 0.14 0.07
Matches are distributed among these distances:
42 27 0.28
43 41 0.42
44 29 0.30
ACGTcount: A:0.25, C:0.17, G:0.27, T:0.31
Consensus pattern (43 bp):
ATATGTGATTTCGTGTAAGACCACATCTGGGACATTGGCATTG
Found at i:54898782 original size:34 final size:34
Alignment explanation
Indices: 54898739--54898805 Score: 125
Period size: 34 Copynumber: 2.0 Consensus size: 34
54898729 AATTGGTTTT
*
54898739 AGCATTGCTTATAAGGTATTTATGTATTCAATTG
1 AGCATTGCTTATAACGTATTTATGTATTCAATTG
54898773 AGCATTGCTTATAACGTATTTATGTATTCAATT
1 AGCATTGCTTATAACGTATTTATGTATTCAATT
54898806 ATGAAATGAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.30, C:0.10, G:0.15, T:0.45
Consensus pattern (34 bp):
AGCATTGCTTATAACGTATTTATGTATTCAATTG
Found at i:54898832 original size:37 final size:34
Alignment explanation
Indices: 54898747--54898837 Score: 103
Period size: 34 Copynumber: 2.6 Consensus size: 34
54898737 TTAGCATTGC
* * *
54898747 TTATAAGGTATTTATGTATTCAATTGAGCATTGC
1 TTATAAGGTATTTATGTATTCAATTGAGAAATGA
*
54898781 TTATAACGTATTTATGTATTCAATT-ATGAAATGAAA
1 TTATAAGGTATTTATGTATTCAATTGA-GAAATG--A
54898817 TATATAAGGTATTTATGTATT
1 T-TATAAGGTATTTATGTATT
54898838 TATGTATTTA
Statistics
Matches: 48, Mismatches: 5, Indels: 5
0.83 0.09 0.09
Matches are distributed among these distances:
33 1 0.02
34 28 0.58
36 1 0.02
37 18 0.38
ACGTcount: A:0.35, C:0.05, G:0.14, T:0.45
Consensus pattern (34 bp):
TTATAAGGTATTTATGTATTCAATTGAGAAATGA
Found at i:54904922 original size:10 final size:10
Alignment explanation
Indices: 54904907--54904931 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
54904897 GGCTCACACG
54904907 GCCCAGTTCA
1 GCCCAGTTCA
54904917 GCCCAGTTCA
1 GCCCAGTTCA
54904927 GCCCA
1 GCCCA
54904932 AAACGGCCTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.20, C:0.44, G:0.20, T:0.16
Consensus pattern (10 bp):
GCCCAGTTCA
Found at i:54914588 original size:21 final size:21
Alignment explanation
Indices: 54914562--54914617 Score: 112
Period size: 21 Copynumber: 2.7 Consensus size: 21
54914552 TAAAGTAGGC
54914562 TATATATTATTTTTCTAATAT
1 TATATATTATTTTTCTAATAT
54914583 TATATATTATTTTTCTAATAT
1 TATATATTATTTTTCTAATAT
54914604 TATATATTATTTTT
1 TATATATTATTTTT
54914618 ATTAATTCAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.32, C:0.04, G:0.00, T:0.64
Consensus pattern (21 bp):
TATATATTATTTTTCTAATAT
Found at i:54914629 original size:21 final size:20
Alignment explanation
Indices: 54914562--54914687 Score: 96
Period size: 21 Copynumber: 6.2 Consensus size: 20
54914552 TAAAGTAGGC
* *
54914562 TATATATTATTTTTCTAATAT
1 TATATATTATTTTTATTA-AT
* *
54914583 TATATATTATTTTTCTAATAT
1 TATATATTATTTTTATTA-AT
54914604 TATATATTATTTTTATTAAT
1 TATATATTATTTTTATTAAT
* **
54914624 T-CATATT-TTAATATTAAT
1 TATATATTATTTTTATTAAT
* * *
54914642 TATATTAATAATGTTATTAAAT
1 TATA-TATTATTTTTATT-AAT
*
54914664 TATATATTATTTTTA-AAAT
1 TATATATTATTTTTATTAAT
54914683 TATAT
1 TATAT
54914688 TTAATAATAA
Statistics
Matches: 87, Mismatches: 14, Indels: 10
0.78 0.13 0.09
Matches are distributed among these distances:
18 10 0.11
19 14 0.16
20 6 0.07
21 50 0.57
22 7 0.08
ACGTcount: A:0.38, C:0.02, G:0.01, T:0.59
Consensus pattern (20 bp):
TATATATTATTTTTATTAAT
Found at i:54914679 original size:45 final size:45
Alignment explanation
Indices: 54914629--54914717 Score: 119
Period size: 45 Copynumber: 2.0 Consensus size: 45
54914619 TTAATTCATA
* *
54914629 TTTTAATATTA-ATTATATTAATAATGTTATTAAATTATAT-ATTAT
1 TTTTAAAATTATATT-TAATAATAATGTTATTAAA-TATATGATTAT
*
54914674 TTTTAAAATTATATTTAATAATAATTTTATTAAATATATGATTA
1 TTTTAAAATTATATTTAATAATAATGTTATTAAATATATGATTA
54914718 AATTATTTAT
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
44 5 0.13
45 31 0.79
46 3 0.08
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (45 bp):
TTTTAAAATTATATTTAATAATAATGTTATTAAATATATGATTAT
Found at i:54914699 original size:57 final size:55
Alignment explanation
Indices: 54914602--54914762 Score: 184
Period size: 57 Copynumber: 2.8 Consensus size: 55
54914592 TTTTTCTAAT
* *
54914602 ATTATATATTATTTTTATTAATTCATATTTTAATATTAATTATATTAATA-ATGTTATTAA
1 ATTATATATTATTTTTA-AAATT-ATA-TTTAATAATAATT-TATTAATATATG--ATTAA
54914662 ATTATATATTATTTTTAAAATTATATTTAATAATAATTTTATTAAATATATGATTAA
1 ATTATATATTATTTTTAAAATTATATTTAATAATAA-TTTATT-AATATATGATTAA
*
54914719 ATTATTTATT-TTTATT-AAATTATATTTAATAATAATCTTATTAA
1 ATTATATATTATTT-TTAAAATTATATTTAATAATAAT-TTATTAA
54914763 AATTTAATAA
Statistics
Matches: 93, Mismatches: 3, Indels: 15
0.84 0.03 0.14
Matches are distributed among these distances:
55 3 0.03
56 27 0.29
57 30 0.32
58 9 0.10
59 7 0.08
60 17 0.18
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.55
Consensus pattern (55 bp):
ATTATATATTATTTTTAAAATTATATTTAATAATAATTTATTAATATATGATTAA
Found at i:54915302 original size:22 final size:22
Alignment explanation
Indices: 54915260--54915303 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
54915250 AGGAATTTTC
* *
54915260 TATTAAATTTAAATTTTAAAAT
1 TATTAAATTAAAATTTAAAAAT
54915282 TATTAAA-TAAAATTATAAAAAT
1 TATTAAATTAAAATT-TAAAAAT
54915304 AGGTTTAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (22 bp):
TATTAAATTAAAATTTAAAAAT
Found at i:54918902 original size:53 final size:53
Alignment explanation
Indices: 54918817--54919023 Score: 200
Period size: 53 Copynumber: 3.8 Consensus size: 53
54918807 TTTCTTTTTA
* * * *
54918817 AACTTACCATTTCCATGTCTTGACATGGTCTTACGTGGTATCCTTGCCTTATG
1 AACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATG
* * * *
54918870 AACTCACCATTGCCATGCCTTGGCATGGTCTTACATGGGAT-CTTAGCCTTATTG
1 AACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTT-GCCTTA-TG
** * * * * * *
54918924 TAGTTTATCAATGCCATGTCTTGACATGGTCTTACATGATTTCCTTGCCTTGTAA
1 -AACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTAT-G
* * *
54918979 AACTTATCAATGCCATGCCTTGGCATGGTCTTACTTGGTATCCTT
1 AACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTT
54919024 AAACCCTAAT
Statistics
Matches: 124, Mismatches: 25, Indels: 9
0.78 0.16 0.06
Matches are distributed among these distances:
52 3 0.02
53 41 0.33
54 41 0.33
55 36 0.29
56 3 0.02
ACGTcount: A:0.20, C:0.24, G:0.18, T:0.38
Consensus pattern (53 bp):
AACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATG
Found at i:54920699 original size:17 final size:18
Alignment explanation
Indices: 54920677--54920711 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
54920667 GATATGATAC
*
54920677 TAAAAT-TATTAAAAAAT
1 TAAAATATATAAAAAAAT
54920694 TAAAATATATAAAAAAAT
1 TAAAATATATAAAAAAAT
54920712 CAGGGAAACA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (18 bp):
TAAAATATATAAAAAAAT
Found at i:54921029 original size:19 final size:19
Alignment explanation
Indices: 54921001--54921091 Score: 134
Period size: 19 Copynumber: 4.9 Consensus size: 19
54920991 AACCATATCT
54921001 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
* *
54921020 TCTAATATTGTA-ATCATA
1 TCTAAGATTGCATATCATA
54921038 TCTAAGATTG--TATCATA
1 TCTAAGATTGCATATCATA
54921055 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
*
54921074 TCTAAGATTACATATCAT
1 TCTAAGATTGCATATCAT
54921092 TGAAGATTAT
Statistics
Matches: 65, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
17 16 0.25
18 15 0.23
19 34 0.52
ACGTcount: A:0.37, C:0.14, G:0.09, T:0.40
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:54921070 original size:14 final size:15
Alignment explanation
Indices: 54921033--54921070 Score: 51
Period size: 17 Copynumber: 2.5 Consensus size: 15
54921023 AATATTGTAA
54921033 TCATATCTAAGATTG
1 TCATATCTAAGATTG
54921048 TATCATATCTAAGATTG
1 --TCATATCTAAGATTG
54921065 -CATATC
1 TCATATC
54921071 ATATCTAAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 6 0.29
17 15 0.71
ACGTcount: A:0.34, C:0.16, G:0.11, T:0.39
Consensus pattern (15 bp):
TCATATCTAAGATTG
Found at i:54924011 original size:29 final size:31
Alignment explanation
Indices: 54923979--54924036 Score: 93
Period size: 29 Copynumber: 1.9 Consensus size: 31
54923969 AAAAAGTTAT
54923979 TTTTAATTTTT-AATTT-AATTATTTATCTC
1 TTTTAATTTTTAAATTTGAATTATTTATCTC
*
54924008 TTTTAATTTTTAAATTTGTATTATTTATC
1 TTTTAATTTTTAAATTTGAATTATTTATC
54924037 AAATCATCTT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 11 0.42
30 5 0.19
31 10 0.38
ACGTcount: A:0.28, C:0.05, G:0.02, T:0.66
Consensus pattern (31 bp):
TTTTAATTTTTAAATTTGAATTATTTATCTC
Found at i:54924193 original size:19 final size:18
Alignment explanation
Indices: 54924159--54924222 Score: 67
Period size: 18 Copynumber: 3.4 Consensus size: 18
54924149 AATATTAAAA
*
54924159 ATATTTTATTATGATTTTT
1 ATATTTT-TAATGATTTTT
*
54924178 ATACTTTTTAATGATTTTA
1 ATA-TTTTTAATGATTTTT
*
54924197 ATATTTTAAAT-ATTTTTT
1 ATATTTTTAATGA-TTTTT
54924215 ATATTTTT
1 ATATTTTT
54924223 TAAATTTTTA
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
17 1 0.03
18 18 0.47
19 15 0.39
20 4 0.11
ACGTcount: A:0.30, C:0.02, G:0.03, T:0.66
Consensus pattern (18 bp):
ATATTTTTAATGATTTTT
Found at i:54924218 original size:9 final size:9
Alignment explanation
Indices: 54924159--54924231 Score: 51
Period size: 9 Copynumber: 7.9 Consensus size: 9
54924149 AATATTAAAA
54924159 ATATTTTATT
1 ATATTTT-TT
54924169 ATGA-TTTTT
1 AT-ATTTTTT
*
54924178 ATACTTTTT
1 ATATTTTTT
*
54924187 A-ATGATTTTA
1 ATAT--TTTTT
**
54924197 ATATTTTAA
1 ATATTTTTT
54924206 ATATTTTTT
1 ATATTTTTT
54924215 ATATTTTTT
1 ATATTTTTT
*
54924224 AAATTTTT
1 ATATTTTT
54924232 AAAATTAAAA
Statistics
Matches: 52, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
8 2 0.04
9 37 0.71
10 10 0.19
11 3 0.06
ACGTcount: A:0.30, C:0.01, G:0.03, T:0.66
Consensus pattern (9 bp):
ATATTTTTT
Found at i:54929496 original size:24 final size:25
Alignment explanation
Indices: 54929469--54929529 Score: 70
Period size: 25 Copynumber: 2.5 Consensus size: 25
54929459 TTAATTTAGC
*
54929469 TATTTTTATTTT-ATTTTATTTTAA
1 TATTTTTATTTTAATTTAATTTTAA
* *
54929493 TATTTTTGTTTTAATTTAATTTTTA
1 TATTTTTATTTTAATTTAATTTTAA
* *
54929518 CATTTTAATTTT
1 TATTTTTATTTT
54929530 TCTTTTGTTT
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
24 11 0.37
25 19 0.63
ACGTcount: A:0.25, C:0.02, G:0.02, T:0.72
Consensus pattern (25 bp):
TATTTTTATTTTAATTTAATTTTAA
Found at i:54929499 original size:19 final size:18
Alignment explanation
Indices: 54929477--54929528 Score: 59
Period size: 19 Copynumber: 2.8 Consensus size: 18
54929467 GCTATTTTTA
*
54929477 TTTTATTTTATTTTAATAT
1 TTTTATTTTAATTTAAT-T
*
54929496 TTTTGTTTTAATTTAATT
1 TTTTATTTTAATTTAATT
*
54929514 TTTACATTTTAATTT
1 TTT-TATTTTAATTT
54929529 TTCTTTTGTT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
18 4 0.14
19 24 0.86
ACGTcount: A:0.25, C:0.02, G:0.02, T:0.71
Consensus pattern (18 bp):
TTTTATTTTAATTTAATT
Found at i:54933130 original size:29 final size:29
Alignment explanation
Indices: 54933098--54933175 Score: 102
Period size: 29 Copynumber: 2.7 Consensus size: 29
54933088 ATACCCTCCG
** *
54933098 AGCTCGCACACCCAGTGCCGTATTTTTCC
1 AGCTCGCACACTTAGTGCCGTATATTTCC
* *
54933127 AGCTTGCACACTTAGTGCCATATATTTCC
1 AGCTCGCACACTTAGTGCCGTATATTTCC
*
54933156 AGCACGCACACTTAGTGCCG
1 AGCTCGCACACTTAGTGCCG
54933176 ATCTCGTCAC
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 41 1.00
ACGTcount: A:0.22, C:0.33, G:0.18, T:0.27
Consensus pattern (29 bp):
AGCTCGCACACTTAGTGCCGTATATTTCC
Found at i:54940987 original size:29 final size:29
Alignment explanation
Indices: 54940949--54941027 Score: 86
Period size: 29 Copynumber: 2.7 Consensus size: 29
54940939 CATACCCTCG
* *
54940949 AGCTCGCACACCCAGTGCCGTATTTTTCC
1 AGCTCGCACACCCAGTGCCATATATTTCC
* **
54940978 AGCTTGCACACTTAGTGCCATATATTTCC
1 AGCTCGCACACCCAGTGCCATATATTTCC
* **
54941007 AGCACGCACACTTAGTGCCAT
1 AGCTCGCACACCCAGTGCCAT
54941028 CTCGTCACCG
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 43 1.00
ACGTcount: A:0.23, C:0.33, G:0.16, T:0.28
Consensus pattern (29 bp):
AGCTCGCACACCCAGTGCCATATATTTCC
Found at i:54946712 original size:13 final size:11
Alignment explanation
Indices: 54946685--54946709 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
54946675 TTTATTTTCC
54946685 TTTAATATTAG
1 TTTAATATTAG
54946696 TTTAATATTAG
1 TTTAATATTAG
54946707 TTT
1 TTT
54946710 TTATGATTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.32, C:0.00, G:0.08, T:0.60
Consensus pattern (11 bp):
TTTAATATTAG
Found at i:54950617 original size:23 final size:23
Alignment explanation
Indices: 54950585--54950628 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
54950575 ACTTTATCCA
54950585 TTTTTACTTTTA-TTGTAATTTAC
1 TTTTTACTTTTAGTT-TAATTTAC
*
54950608 TTTTTGCTTTTAGTTTAATTT
1 TTTTTACTTTTAGTTTAATTT
54950629 TTCTTTTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 17 0.89
24 2 0.11
ACGTcount: A:0.18, C:0.07, G:0.07, T:0.68
Consensus pattern (23 bp):
TTTTTACTTTTAGTTTAATTTAC
Found at i:54952190 original size:22 final size:22
Alignment explanation
Indices: 54952162--54952205 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
54952152 AAAGAAGATG
54952162 AGGAGGCAAAACCCGAAATCAA
1 AGGAGGCAAAACCCGAAATCAA
54952184 AGGAGGCAAAACCCGAAATCAA
1 AGGAGGCAAAACCCGAAATCAA
54952206 TAAAAAACCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.50, C:0.23, G:0.23, T:0.05
Consensus pattern (22 bp):
AGGAGGCAAAACCCGAAATCAA
Found at i:54957139 original size:19 final size:20
Alignment explanation
Indices: 54957112--54957149 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
54957102 TCCCTTCCCT
**
54957112 TTCTCTTTCTTTTTTCCCCC
1 TTCTCTTTCCCTTTTCCCCC
54957132 TTCT-TTTCCCTTTTCCCC
1 TTCTCTTTCCCTTTTCCCC
54957150 TCCCTTCTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 12 0.75
20 4 0.25
ACGTcount: A:0.00, C:0.42, G:0.00, T:0.58
Consensus pattern (20 bp):
TTCTCTTTCCCTTTTCCCCC
Found at i:54967661 original size:73 final size:74
Alignment explanation
Indices: 54967572--54967721 Score: 225
Period size: 73 Copynumber: 2.0 Consensus size: 74
54967562 GCCATAGTCA
* *
54967572 GGAAGCTCCTGATAGCTTATTATAAGGAAGTTCAAGCGAGCCAATAAT-GGGAAACTC-CGAATA
1 GGAAGCTCCTGATAGCTTATTATAAGGAAGTTCAAGCGAGCC-AT-ATCGGGAAACTCACAAAGA
54967635 GCCAT-TAACG
64 GCCATATAACG
* *
54967645 GGAAGCTCCTGATAGCTTATTATCAGGAAGTTCAAGCGAGCCATATCGGGAAGCTCACAAAGAGC
1 GGAAGCTCCTGATAGCTTATTATAAGGAAGTTCAAGCGAGCCATATCGGGAAACTCACAAAGAGC
54967710 CATATAACG
66 CATATAACG
54967719 GGA
1 GGA
54967722 CATTCATAAG
Statistics
Matches: 70, Mismatches: 4, Indels: 5
0.89 0.05 0.06
Matches are distributed among these distances:
71 2 0.03
72 10 0.14
73 50 0.71
74 8 0.11
ACGTcount: A:0.35, C:0.20, G:0.25, T:0.21
Consensus pattern (74 bp):
GGAAGCTCCTGATAGCTTATTATAAGGAAGTTCAAGCGAGCCATATCGGGAAACTCACAAAGAGC
CATATAACG
Found at i:54970797 original size:29 final size:29
Alignment explanation
Indices: 54970761--54970816 Score: 112
Period size: 29 Copynumber: 1.9 Consensus size: 29
54970751 TTAGATTTAA
54970761 ATCTTTCCGCGACATCAAATAATTTAAAT
1 ATCTTTCCGCGACATCAAATAATTTAAAT
54970790 ATCTTTCCGCGACATCAAATAATTTAA
1 ATCTTTCCGCGACATCAAATAATTTAA
54970817 GTTTTTATGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.38, C:0.21, G:0.07, T:0.34
Consensus pattern (29 bp):
ATCTTTCCGCGACATCAAATAATTTAAAT
Found at i:54971672 original size:86 final size:86
Alignment explanation
Indices: 54971527--54971698 Score: 299
Period size: 86 Copynumber: 2.0 Consensus size: 86
54971517 AATACTGCAG
* *
54971527 GTGCATTAGTCAAGCCAAACAATATCACAAGGAATTCATAATGCCCGTACTTGGTTCTGAAGGCT
1 GTGCATTAGTCAAGCCAAACAATATCACAAGGAATTCATAATGCCCATACCTGGTTCTGAAGGCT
54971592 ATTTTCGGTACATCCGAGTCT
66 ATTTTCGGTACATCCGAGTCT
* *
54971613 GTGCATTAGTCAAGCCAAACGATATCACAAGGAATTCATAATGCCCATTCCTGGTTCTGAAGGCT
1 GTGCATTAGTCAAGCCAAACAATATCACAAGGAATTCATAATGCCCATACCTGGTTCTGAAGGCT
*
54971678 ATTTTCGGTACATTCGAGTCT
66 ATTTTCGGTACATCCGAGTCT
54971699 TTCACTCGTA
Statistics
Matches: 81, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
86 81 1.00
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.30
Consensus pattern (86 bp):
GTGCATTAGTCAAGCCAAACAATATCACAAGGAATTCATAATGCCCATACCTGGTTCTGAAGGCT
ATTTTCGGTACATCCGAGTCT
Found at i:54973322 original size:71 final size:71
Alignment explanation
Indices: 54973238--54973401 Score: 310
Period size: 71 Copynumber: 2.3 Consensus size: 71
54973228 CGATTTGTCT
54973238 CGTAGCTCTCTTGTCTACATGGTGTCCGTCACTTGGAATCACGCATGCGACCCAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTCCGTCACTTGGAATCACGCATGCGACCCAGCTACATTTAT
54973303 CTTTCA
66 CTTTCA
* *
54973309 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTCCGTCACTTGGAATCACGCATGCGACCCAGCTACATTTAT
54973374 CTTTCA
66 CTTTCA
54973380 CGTAGCTCTCTTGTCTACATGG
1 CGTAGCTCTCTTGTCTACATGG
54973402 GATACATCTC
Statistics
Matches: 91, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
71 91 1.00
ACGTcount: A:0.19, C:0.29, G:0.18, T:0.34
Consensus pattern (71 bp):
CGTAGCTCTCTTGTCTACATGGTGTCCGTCACTTGGAATCACGCATGCGACCCAGCTACATTTAT
CTTTCA
Found at i:54973439 original size:71 final size:70
Alignment explanation
Indices: 54973238--54973435 Score: 249
Period size: 71 Copynumber: 2.8 Consensus size: 70
54973228 CGATTTGTCT
* * * * *
54973238 CGTAGCTCTCTTGTCTACATGGTGTCCGTCACTTGGAATCACGCATGCGACCCAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTACAT-ACTTCGAATCACACATGCGACCTAGCTACATTTAT
54973303 CTTTCA
65 CTTTCA
* * * *
54973309 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTACAT-ACTTCGAATCACACATGCGACCTAGCTACATTTAT
54973374 CTTTCA
65 CTTTCA
* *
54973380 CGTAGCTCTCTTGTCTACATGG-GATACAT-C-TCGTATCACACATGTGACCTAGCTAC
1 CGTAGCTCTCTTGTCTACATGGTG-TACATACTTCGAATCACACATGCGACCTAGCTAC
54973436 TACAGGGTGT
Statistics
Matches: 118, Mismatches: 8, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
68 22 0.19
69 1 0.01
70 1 0.01
71 94 0.80
ACGTcount: A:0.21, C:0.29, G:0.18, T:0.33
Consensus pattern (70 bp):
CGTAGCTCTCTTGTCTACATGGTGTACATACTTCGAATCACACATGCGACCTAGCTACATTTATC
TTTCA
Found at i:54980820 original size:65 final size:68
Alignment explanation
Indices: 54980751--54980935 Score: 254
Period size: 70 Copynumber: 2.7 Consensus size: 68
54980741 TAGTACCACT
*
54980751 CATGCGACCTAGC-CGATTTGTC-T-CGTAGCTCTC-TGTCTACATGGTGTCCGTCACTTGGAAT
1 CATGCGACCTAGCAC-ATTTATCTTACGTAGCTCTCTTGTCTACATGGTGTCCGTCACTTGGAAT
54980812 CACG
65 CACG
*
54980816 CATGCGACC-AGCTACATTTATCTTTCACGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGA
1 CATGCGACCTAGC-ACATTTATC-TT-ACGTAGCTCTCTTGTCTACATGGTGTCCGTCACTTGGA
54980880 ATCACG
63 ATCACG
54980886 CATGCGACCTAGCTACATTTATCTTTCACGTAGCTCTCTTGTCTACATGG
1 CATGCGACCTAGC-ACATTTATC-TT-ACGTAGCTCTCTTGTCTACATGG
54980936 GATACATCTC
Statistics
Matches: 110, Mismatches: 2, Indels: 10
0.90 0.02 0.08
Matches are distributed among these distances:
64 3 0.03
65 15 0.14
66 1 0.01
67 1 0.01
69 10 0.09
70 40 0.36
71 40 0.36
ACGTcount: A:0.19, C:0.29, G:0.19, T:0.34
Consensus pattern (68 bp):
CATGCGACCTAGCACATTTATCTTACGTAGCTCTCTTGTCTACATGGTGTCCGTCACTTGGAATC
ACG
Found at i:54980867 original size:70 final size:71
Alignment explanation
Indices: 54980774--54980935 Score: 301
Period size: 70 Copynumber: 2.3 Consensus size: 71
54980764 CGATTTGTCT
54980774 CGTAGCTCTC-TGTCTACATGGTGTCCGTCACTTGGAATCACGCATGCGACC-AGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTCCGTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
54980837 CTTTCA
66 CTTTCA
*
54980843 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTCCGTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
54980908 CTTTCA
66 CTTTCA
54980914 CGTAGCTCTCTTGTCTACATGG
1 CGTAGCTCTCTTGTCTACATGG
54980936 GATACATCTC
Statistics
Matches: 90, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
69 10 0.11
70 40 0.44
71 40 0.44
ACGTcount: A:0.19, C:0.28, G:0.19, T:0.34
Consensus pattern (71 bp):
CGTAGCTCTCTTGTCTACATGGTGTCCGTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
CTTTCA
Found at i:54980973 original size:71 final size:70
Alignment explanation
Indices: 54980774--54980969 Score: 240
Period size: 71 Copynumber: 2.8 Consensus size: 70
54980764 CGATTTGTCT
* * * *
54980774 CGTAGCTCTC-TGTCTACATGGTGTCCGTCACTTGGAATCACGCATGCGACC-AGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTACAT-ACTTCGAATCACACATGCGACCTAGCTACATTTAT
54980837 CTTTCA
65 CTTTCA
* * * *
54980843 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTACAT-ACTTCGAATCACACATGCGACCTAGCTACATTTAT
54980908 CTTTCA
65 CTTTCA
* *
54980914 CGTAGCTCTCTTGTCTACATGG-GATACAT-C-TCGTATCACACATGTGACCTAGCTAC
1 CGTAGCTCTCTTGTCTACATGGTG-TACATACTTCGAATCACACATGCGACCTAGCTAC
54980970 TACAGGGTGT
Statistics
Matches: 117, Mismatches: 7, Indels: 7
0.89 0.05 0.05
Matches are distributed among these distances:
68 22 0.19
69 11 0.09
70 41 0.35
71 43 0.37
ACGTcount: A:0.21, C:0.29, G:0.18, T:0.33
Consensus pattern (70 bp):
CGTAGCTCTCTTGTCTACATGGTGTACATACTTCGAATCACACATGCGACCTAGCTACATTTATC
TTTCA
Found at i:54986843 original size:80 final size:80
Alignment explanation
Indices: 54986759--54986907 Score: 183
Period size: 80 Copynumber: 1.9 Consensus size: 80
54986749 TATGGTAACC
* * * *
54986759 CGCACCAAGGCCTACGGGACTTAACCCGGATATCA-CGATTTGCACAAATGCCTTCGGGTCTTAG
1 CGCACCAAGGCCTACGGGACTTAACCCGGATAT-AGCCACTAGCACAAATGCCTTCGGGTCTTAA
54986823 CCCGGATAGAATGACT
65 CCCGGATAGAATGACT
* * * * * * *
54986839 CGCACGAATGCCTTCGGGTCTTAGCCCGGATGTAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CGCACCAAGGCCTACGGGACTTAACCCGGATATAGCCACTAGCACAAATGCCTTCGGGTCTTAAC
54986904 CCGG
66 CCGG
54986908 TTATAATTTC
Statistics
Matches: 57, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
79 1 0.02
80 56 0.98
ACGTcount: A:0.23, C:0.30, G:0.25, T:0.22
Consensus pattern (80 bp):
CGCACCAAGGCCTACGGGACTTAACCCGGATATAGCCACTAGCACAAATGCCTTCGGGTCTTAAC
CCGGATAGAATGACT
Found at i:54986849 original size:40 final size:38
Alignment explanation
Indices: 54986800--54986907 Score: 128
Period size: 40 Copynumber: 2.7 Consensus size: 38
54986790 ATCACGATTT
*
54986800 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATG-ACTC
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGAT-GAA-GCACTA
*
54986840 GCACGAATGCCTTCGGGTCTTAGCCCGGATGTAGCCACTA
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGATGAAG-CACTA
*
54986880 GCACAATTGCCTTCGGGTCTTAACCCGG
1 GCACAA-TGCCTTCGGGTCTTAGCCCGG
54986908 TTATAATTTC
Statistics
Matches: 61, Mismatches: 4, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
38 1 0.02
39 4 0.07
40 56 0.92
ACGTcount: A:0.21, C:0.30, G:0.26, T:0.23
Consensus pattern (38 bp):
GCACAATGCCTTCGGGTCTTAGCCCGGATGAAGCACTA
Found at i:54991256 original size:11 final size:11
Alignment explanation
Indices: 54991242--54991312 Score: 63
Period size: 11 Copynumber: 6.5 Consensus size: 11
54991232 GGTGCAAGGA
54991242 TGGTGATATGG
1 TGGTGATATGG
*
54991253 TGGTGCTATGG
1 TGGTGATATGG
* * *
54991264 TGATGGTGTGG
1 TGGTGATATGG
*
54991275 TGGTGCTATGG
1 TGGTGATATGG
*
54991286 TGGTTG-TATTG
1 TGG-TGATATGG
*
54991297 TGGTGATATAG
1 TGGTGATATGG
54991308 TGGTG
1 TGGTG
54991313 TTTTGGTTGT
Statistics
Matches: 49, Mismatches: 9, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
10 2 0.04
11 45 0.92
12 2 0.04
ACGTcount: A:0.13, C:0.03, G:0.45, T:0.39
Consensus pattern (11 bp):
TGGTGATATGG
Found at i:54991299 original size:22 final size:22
Alignment explanation
Indices: 54991229--54991312 Score: 80
Period size: 22 Copynumber: 3.8 Consensus size: 22
54991219 TGGTTTTGGA
* *
54991229 GGTGGTGC-AAGGATGGTGATAT
1 GGTGGTGCTATGG-TGGTGGTAT
* *
54991251 GGTGGTGCTATGGTGATGGTGT
1 GGTGGTGCTATGGTGGTGGTAT
*
54991273 GGTGGTGCTATGGTGGTTGTAT
1 GGTGGTGCTATGGTGGTGGTAT
* * *
54991295 TGTGGTGATATAGTGGTG
1 GGTGGTGCTATGGTGGTG
54991313 TTTTGGTTGT
Statistics
Matches: 50, Mismatches: 11, Indels: 2
0.79 0.17 0.03
Matches are distributed among these distances:
22 47 0.94
23 3 0.06
ACGTcount: A:0.14, C:0.04, G:0.46, T:0.36
Consensus pattern (22 bp):
GGTGGTGCTATGGTGGTGGTAT
Found at i:54994466 original size:40 final size:40
Alignment explanation
Indices: 54994421--54994588 Score: 185
Period size: 40 Copynumber: 4.2 Consensus size: 40
54994411 CGGAATATAA
54994421 CCGGATATAATCACGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCAC-TAGCACAAATGCCTTCGGGTCTTAGC
* * * *
54994461 CCGGATAGAATAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * *
54994501 CCGGATATAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * * * * *
54994541 CCGGATATAATTTCCAGCATAATTGTCTTCGGGGCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
54994581 CCGGATAT
1 CCGGATAT
54994589 CATTCAATTT
Statistics
Matches: 107, Mismatches: 20, Indels: 2
0.83 0.16 0.02
Matches are distributed among these distances:
39 1 0.01
40 106 0.99
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.26
Consensus pattern (40 bp):
CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:54998887 original size:6 final size:6
Alignment explanation
Indices: 54998857--54998993 Score: 93
Period size: 6 Copynumber: 22.3 Consensus size: 6
54998847 AAGAAACATT
* * *
54998857 ATCAGA A-CTAGA ATCAAA ATGAGA ATCAGA ATCAGA ATCAG- GTGACAGA
1 ATCAGA ATC-AGA ATCAGA ATCAGA ATCAGA ATCAGA ATCAGA AT--CAGA
* * * * *
54998906 ATCAGA ATCAGA ATCAGA ATCAGG ATCAGA ATTAG- GTGACAAA ATTAGA
1 ATCAGA ATCAGA ATCAGA ATCAGA ATCAGA ATCAGA AT--CAGA ATCAGA
* *
54998955 ATCAGA ATCAGT ATCAGGTA A-CAGA ATCAAA ATCAGA AT
1 ATCAGA ATCAGA ATCA-G-A ATCAGA ATCAGA ATCAGA AT
54998994 TTGAATGCAA
Statistics
Matches: 100, Mismatches: 20, Indels: 22
0.70 0.14 0.15
Matches are distributed among these distances:
5 5 0.05
6 84 0.84
7 8 0.08
8 3 0.03
ACGTcount: A:0.48, C:0.14, G:0.19, T:0.19
Consensus pattern (6 bp):
ATCAGA
Found at i:54998919 original size:37 final size:37
Alignment explanation
Indices: 54998866--54998993 Score: 136
Period size: 37 Copynumber: 3.5 Consensus size: 37
54998856 TATCAGAACT
* *
54998866 AGAATCAAAATGAGAATCAGAATCAGAATCAGGTGAC
1 AGAATCAAAATCAGAATCAGAATCAGAATCAGGTAAC
* * *
54998903 AGAATCAGAATCAGAATCAGAATCAGGATCA-G-AATT
1 AGAATCAAAATCAGAATCAGAATCAGAATCAGGTAA-C
* * *
54998939 AG-GTGACAAAATTAGAATCAGAATCAGTATCAGGTAAC
1 AGAAT--CAAAATCAGAATCAGAATCAGAATCAGGTAAC
54998977 AGAATCAAAATCAGAAT
1 AGAATCAAAATCAGAAT
54998994 TTGAATGCAA
Statistics
Matches: 73, Mismatches: 12, Indels: 12
0.75 0.12 0.12
Matches are distributed among these distances:
35 2 0.03
36 3 0.04
37 62 0.85
38 3 0.04
39 3 0.04
ACGTcount: A:0.48, C:0.13, G:0.20, T:0.19
Consensus pattern (37 bp):
AGAATCAAAATCAGAATCAGAATCAGAATCAGGTAAC
Found at i:54998972 original size:43 final size:43
Alignment explanation
Indices: 54998865--54998983 Score: 157
Period size: 43 Copynumber: 2.7 Consensus size: 43
54998855 TTATCAGAAC
* * * *
54998865 TAGAATCAAAATGAGAATCAGAATCAGAATCAGGTGACAGAAT
1 TAGAATCAGAATCAGAATCAGGATCAGAATCAGGTGACAAAAT
* *
54998908 CAGAATCAGAATCAGAATCAGGATCAGAATTAGGTGACAAAAT
1 TAGAATCAGAATCAGAATCAGGATCAGAATCAGGTGACAAAAT
* *
54998951 TAGAATCAGAATCAGTATCAGGTAACAGAATCA
1 TAGAATCAGAATCAGAATCAGG-ATCAGAATCA
54998984 AAATCAGAAT
Statistics
Matches: 65, Mismatches: 10, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
43 57 0.88
44 8 0.12
ACGTcount: A:0.47, C:0.13, G:0.20, T:0.19
Consensus pattern (43 bp):
TAGAATCAGAATCAGAATCAGGATCAGAATCAGGTGACAAAAT
Found at i:54998989 original size:31 final size:31
Alignment explanation
Indices: 54998883--54998993 Score: 102
Period size: 31 Copynumber: 3.6 Consensus size: 31
54998873 AAATGAGAAT
*
54998883 CAGAATCAGAATCAG-GTGACAGAATCA-G-AA
1 CAGAATCAGAATCAGAAT--CAGAATCAGGTAA
* * *
54998913 TCAGAATCAGAATCAGGATCAGAATTAGGTGA
1 -CAGAATCAGAATCAGAATCAGAATCAGGTAA
* * *
54998945 CAAAATTAGAATCAGAATCAGTATCAGGTAA
1 CAGAATCAGAATCAGAATCAGAATCAGGTAA
*
54998976 CAGAATCAAAATCAGAAT
1 CAGAATCAGAATCAGAAT
54998994 TTGAATGCAA
Statistics
Matches: 65, Mismatches: 12, Indels: 6
0.78 0.14 0.07
Matches are distributed among these distances:
30 7 0.11
31 56 0.86
32 2 0.03
ACGTcount: A:0.47, C:0.14, G:0.20, T:0.19
Consensus pattern (31 bp):
CAGAATCAGAATCAGAATCAGAATCAGGTAA
Found at i:54999535 original size:27 final size:27
Alignment explanation
Indices: 54999505--54999617 Score: 174
Period size: 27 Copynumber: 4.2 Consensus size: 27
54999495 AACACCCTAG
* *
54999505 GGGTAAAACAGTAATTTTTTAAATCGA
1 GGGTAAAACAGTAATTCTGTAAATCGA
*
54999532 GGGTAAAACGGTAATTCTGTAAATCGA
1 GGGTAAAACAGTAATTCTGTAAATCGA
*
54999559 GGGTAAAATAGTAATTCTGTAAATCGA
1 GGGTAAAACAGTAATTCTGTAAATCGA
54999586 GGGTAAAAC-GATAATTCTGTAAATCGA
1 GGGTAAAACAG-TAATTCTGTAAATCGA
54999613 GGGTA
1 GGGTA
54999618 CTTTGGTAAT
Statistics
Matches: 79, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
26 1 0.01
27 78 0.99
ACGTcount: A:0.39, C:0.09, G:0.24, T:0.28
Consensus pattern (27 bp):
GGGTAAAACAGTAATTCTGTAAATCGA
Found at i:54999627 original size:54 final size:52
Alignment explanation
Indices: 54999505--54999644 Score: 172
Period size: 54 Copynumber: 2.6 Consensus size: 52
54999495 AACACCCTAG
* *
54999505 GGGTAAAACAGTAATTTTTTAAATCGAGGGTAAAACGGTAATTCTGTAAATCGA
1 GGGTAAAATAGTAA--TTTTAAATCGAGGGTAAAACGATAATTCTGTAAATCGA
54999559 GGGTAAAATAGTAATTCTGTAAATCGAGGGTAAAACGATAATTCTGTAAATCGA
1 GGGTAAAATAGTAATT-T-TAAATCGAGGGTAAAACGATAATTCTGTAAATCGA
*** *
54999613 GGGTACTTTGGTAATTTTACAAGTCGAGGGTA
1 GGGTAAAATAGTAATTTTA-AA-TCGAGGGTA
54999645 TTTCAGTAAT
Statistics
Matches: 76, Mismatches: 6, Indels: 8
0.84 0.07 0.09
Matches are distributed among these distances:
52 4 0.05
53 4 0.05
54 68 0.89
ACGTcount: A:0.36, C:0.09, G:0.24, T:0.30
Consensus pattern (52 bp):
GGGTAAAATAGTAATTTTAAATCGAGGGTAAAACGATAATTCTGTAAATCGA
Found at i:55001407 original size:27 final size:27
Alignment explanation
Indices: 55001377--55001462 Score: 77
Period size: 27 Copynumber: 3.2 Consensus size: 27
55001367 AGGATACCAA
*
55001377 GTAAGACCATGCCAAGGCATGAGATTG
1 GTAAGACCATGCCAAGGCATGAAATTG
** * * *
55001404 GTAAGTTC-T-ACAAGGCAAGGAAATTAT
1 GTAAGACCATGCCAAGGC-ATGAAATT-G
*
55001431 GTAAGACCATGCCAAGGCATGACATTG
1 GTAAGACCATGCCAAGGCATGAAATTG
55001458 GTAAG
1 GTAAG
55001463 TTCTACAAGG
Statistics
Matches: 43, Mismatches: 12, Indels: 8
0.68 0.19 0.13
Matches are distributed among these distances:
25 6 0.14
26 7 0.16
27 17 0.40
28 7 0.16
29 6 0.14
ACGTcount: A:0.36, C:0.16, G:0.27, T:0.21
Consensus pattern (27 bp):
GTAAGACCATGCCAAGGCATGAAATTG
Found at i:55001418 original size:25 final size:25
Alignment explanation
Indices: 55001389--55001474 Score: 73
Period size: 25 Copynumber: 3.3 Consensus size: 25
55001379 AAGACCATGC
*
55001389 CAAGGCATGAGATTGGTAAGTTCTA
1 CAAGGCATGAAATTGGTAAGTTCTA
* * ** *
55001414 CAAGGCAAGGAAATTATGTAAGACCATGC
1 CAAGGC-ATGAAATT-GGTAAGTTC-T-A
*
55001443 CAAGGCATGACATTGGTAAGTTCTA
1 CAAGGCATGAAATTGGTAAGTTCTA
55001468 CAAGGCA
1 CAAGGCA
55001475 AGGAAATTAT
Statistics
Matches: 45, Mismatches: 12, Indels: 8
0.69 0.18 0.12
Matches are distributed among these distances:
25 13 0.29
26 7 0.16
27 12 0.27
28 7 0.16
29 6 0.13
ACGTcount: A:0.36, C:0.16, G:0.26, T:0.22
Consensus pattern (25 bp):
CAAGGCATGAAATTGGTAAGTTCTA
Found at i:55001447 original size:29 final size:29
Alignment explanation
Indices: 55001413--55001500 Score: 85
Period size: 27 Copynumber: 3.2 Consensus size: 29
55001403 GGTAAGTTCT
55001413 ACAAGGCAAGGAAATTATGTAAGACCATG
1 ACAAGGCAAGGAAATTATGTAAGACCATG
* * * * **
55001442 CCAAGGC-ATGACATT-GGTAAGTTC-T-
1 ACAAGGCAAGGAAATTATGTAAGACCATG
55001467 ACAAGGCAAGGAAATTATGTAAGACCATG
1 ACAAGGCAAGGAAATTATGTAAGACCATG
*
55001496 TCAAG
1 ACAAG
55001501 ACATGGCATT
Statistics
Matches: 42, Mismatches: 13, Indels: 8
0.67 0.21 0.13
Matches are distributed among these distances:
25 6 0.14
26 7 0.17
27 12 0.29
28 7 0.17
29 10 0.24
ACGTcount: A:0.40, C:0.16, G:0.24, T:0.20
Consensus pattern (29 bp):
ACAAGGCAAGGAAATTATGTAAGACCATG
Found at i:55001448 original size:54 final size:54
Alignment explanation
Indices: 55001377--55001511 Score: 234
Period size: 54 Copynumber: 2.5 Consensus size: 54
55001367 AGGATACCAA
*
55001377 GTAAGACCATGCCAAGGCATGAGATTGGTAAGTTCTACAAGGCAAGGAAATTAT
1 GTAAGACCATGCCAAGGCATGACATTGGTAAGTTCTACAAGGCAAGGAAATTAT
55001431 GTAAGACCATGCCAAGGCATGACATTGGTAAGTTCTACAAGGCAAGGAAATTAT
1 GTAAGACCATGCCAAGGCATGACATTGGTAAGTTCTACAAGGCAAGGAAATTAT
* * *
55001485 GTAAGACCATGTCAAGACATGGCATTG
1 GTAAGACCATGCCAAGGCATGACATTG
55001512 ATAAACTACT
Statistics
Matches: 77, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
54 77 1.00
ACGTcount: A:0.36, C:0.16, G:0.25, T:0.22
Consensus pattern (54 bp):
GTAAGACCATGCCAAGGCATGACATTGGTAAGTTCTACAAGGCAAGGAAATTAT
Found at i:55001488 original size:27 final size:27
Alignment explanation
Indices: 55001404--55001489 Score: 86
Period size: 27 Copynumber: 3.2 Consensus size: 27
55001394 CATGAGATTG
55001404 GTAAGTTCTACAAGGCAAGGAAATTAT
1 GTAAGTTCTACAAGGCAAGGAAATTAT
** * * * *
55001431 GTAAGACCATGCCAAGGC-ATGACATT-G
1 GTAAGTTC-T-ACAAGGCAAGGAAATTAT
55001458 GTAAGTTCTACAAGGCAAGGAAATTAT
1 GTAAGTTCTACAAGGCAAGGAAATTAT
55001485 GTAAG
1 GTAAG
55001490 ACCATGTCAA
Statistics
Matches: 43, Mismatches: 12, Indels: 8
0.68 0.19 0.13
Matches are distributed among these distances:
25 6 0.14
26 7 0.16
27 17 0.40
28 7 0.16
29 6 0.14
ACGTcount: A:0.38, C:0.14, G:0.24, T:0.23
Consensus pattern (27 bp):
GTAAGTTCTACAAGGCAAGGAAATTAT
Found at i:55003971 original size:29 final size:28
Alignment explanation
Indices: 55003938--55004126 Score: 121
Period size: 29 Copynumber: 6.6 Consensus size: 28
55003928 CACGAAGGTG
* * **
55003938 TCCTTTTAACAAAGTTTTCCACAAGACA
1 TCCTTTTAACAGAGATAACCACAAGACA
* *
55003966 TTCC-TTTAATAGAGATGACCACAAGGACA
1 -TCCTTTTAACAGAGATAACCACAA-GACA
*
55003995 TCCTTTTAACAGAGATAGCCACAAAGACA
1 TCCTTTTAACAGAGATAACCAC-AAGACA
* * *
55004024 TCCTTTTAATATAGATAACCATAAAGACA
1 TCCTTTTAACAGAGATAACCA-CAAGACA
** * *
55004053 TCCTTTTAATTGAGATAGCCACAAAGGCA
1 TCCTTTTAACAGAGATAACCAC-AAGACA
* * * *
55004082 TTCATTTAACA-ATGATAGCCACAAAGGCA
1 TCCTTTTAACAGA-GATAACCAC-AAGACA
**
55004111 TAATTTTAACAGAGAT
1 TCCTTTTAACAGAGAT
55004127 TGCCACATAG
Statistics
Matches: 129, Mismatches: 24, Indels: 14
0.77 0.14 0.08
Matches are distributed among these distances:
28 19 0.15
29 107 0.83
30 3 0.02
ACGTcount: A:0.40, C:0.20, G:0.13, T:0.28
Consensus pattern (28 bp):
TCCTTTTAACAGAGATAACCACAAGACA
Found at i:55004053 original size:58 final size:56
Alignment explanation
Indices: 55003938--55004133 Score: 178
Period size: 58 Copynumber: 3.4 Consensus size: 56
55003928 CACGAAGGTG
* * ** * *
55003938 TCCTTTTAACAAAGTTTTCCAC-AAGACATTCCTTTAATAGAGATGACCACAAGGACA
1 TCCTTTTAACAGAGATAGCCACAAAGACA-TCCTTTAATA-AGATAACCACAAAGACA
*
55003995 TCCTTTTAACAGAGATAGCCACAAAGACATCCTTTTAATATAGATAACCATAAAGACA
1 TCCTTTTAACAGAGATAGCCACAAAGACATCC-TTTAATA-AGATAACCACAAAGACA
** * * * * *
55004053 TCCTTTTAATTGAGATAGCCACAAAGGCATTCATTTAACAATGATAGCCACAAAGGCA
1 TCCTTTTAACAGAGATAGCCACAAAGACA-TCCTTTAATAA-GATAACCACAAAGACA
** *
55004111 TAATTTTAACAGAGATTGCCACA
1 TCCTTTTAACAGAGATAGCCACA
55004134 TAGGCGTTCA
Statistics
Matches: 114, Mismatches: 21, Indels: 7
0.80 0.15 0.05
Matches are distributed among these distances:
57 22 0.19
58 90 0.79
59 2 0.02
ACGTcount: A:0.39, C:0.21, G:0.13, T:0.27
Consensus pattern (56 bp):
TCCTTTTAACAGAGATAGCCACAAAGACATCCTTTAATAAGATAACCACAAAGACA
Found at i:55004118 original size:87 final size:87
Alignment explanation
Indices: 55003960--55004119 Score: 202
Period size: 87 Copynumber: 1.8 Consensus size: 87
55003950 AGTTTTCCAC
*
55003960 AAGACATTCCTTTAATAGAGATGACCACAAGGACATCCTTTTAACAGAGATAGCCACAAAGACAT
1 AAGACATTCCTTTAATAGAGATGACCACAAGGACATCCATTTAACAGAGATAGCCACAAAGACAT
**
55004025 CCTTTTAATATAGATAACCATA
66 AATTTTAATATAGATAACCATA
* *
55004047 AAGACA-TCCTTTTAATTGAGAT-AGCCACAAAGG-CATTCATTTAACA-ATGATAGCCACAAAG
1 AAGACATTCC-TTTAATAGAGATGA-CCAC-AAGGACATCCATTTAACAGA-GATAGCCACAAAG
*
55004108 GCATAATTTTAA
62 ACATAATTTTAA
55004120 CAGAGATTGC
Statistics
Matches: 63, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
86 5 0.08
87 54 0.86
88 4 0.06
ACGTcount: A:0.41, C:0.19, G:0.13, T:0.26
Consensus pattern (87 bp):
AAGACATTCCTTTAATAGAGATGACCACAAGGACATCCATTTAACAGAGATAGCCACAAAGACAT
AATTTTAATATAGATAACCATA
Found at i:55004131 original size:29 final size:29
Alignment explanation
Indices: 55003970--55004167 Score: 145
Period size: 29 Copynumber: 6.8 Consensus size: 29
55003960 AAGACATTCC
* *
55003970 TTTAATAGAGAT-GACCAC-AAGGACATCCT
1 TTTAACAGAGATAG-CCACAAAGG-CATCAT
* *
55003999 TTTAACAGAGATAGCCACAAAGACATCCT
1 TTTAACAGAGATAGCCACAAAGGCATCAT
* * * * * *
55004028 TTTAATATAGATAACCATAAAGACATCCT
1 TTTAACAGAGATAGCCACAAAGGCATCAT
**
55004057 TTTAATTGAGATAGCCACAAAGGCATTCA-
1 TTTAACAGAGATAGCCACAAAGGCA-TCAT
*
55004086 TTTAACA-ATGATAGCCACAAAGGCATAAT
1 TTTAACAGA-GATAGCCACAAAGGCATCAT
* * *
55004115 TTTAACAGAGATTGCCACATAGGCGTTCA-
1 TTTAACAGAGATAGCCACAAAGGC-ATCAT
** *
55004144 TTTAATTGAGACAGCCACAAAGGC
1 TTTAACAGAGATAGCCACAAAGGC
55004168 TTCCTTATAA
Statistics
Matches: 138, Mismatches: 24, Indels: 14
0.78 0.14 0.08
Matches are distributed among these distances:
28 3 0.02
29 126 0.91
30 9 0.07
ACGTcount: A:0.39, C:0.20, G:0.16, T:0.25
Consensus pattern (29 bp):
TTTAACAGAGATAGCCACAAAGGCATCAT
Found at i:55004178 original size:29 final size:28
Alignment explanation
Indices: 55003966--55004219 Score: 80
Period size: 29 Copynumber: 8.9 Consensus size: 28
55003956 CCACAAGACA
*
55003966 TTCCTTTAATAGAGATGA-CCAC-AAGGAC
1 TTCCTTTAAT-GAGATCAGCCACAAAGG-C
* * *
55003994 ATCCTTTTAACAGAGAT-AGCCACAAAGAC
1 TTCC-TTTAA-TGAGATCAGCCACAAAGGC
* * * * *
55004023 ATCCTTTTAATATAGAT-AACCATAAAGAC
1 TTCC-TTTAAT-GAGATCAGCCACAAAGGC
*
55004052 ATCCTTTTAATTGAGAT-AGCCACAAAGGC
1 TTCC-TTTAA-TGAGATCAGCCACAAAGGC
* **
55004081 ATTCATTTAACAATGAT-AGCCACAAAGGC
1 -TTCCTTTAATGA-GATCAGCCACAAAGGC
*** * * *
55004110 ATAATTTTAACAGAGAT-TGCCACATAGGC
1 -TTCCTTTAA-TGAGATCAGCCACAAAGGC
*
55004139 GTTCATTTAATTGAGA-CAGCCACAAAGGC
1 -TTCCTTTAA-TGAGATCAGCCACAAAGGC
* *
55004168 TTCCTTATAATGAGATCA-CCATAAAGAC
1 TTCCTT-TAATGAGATCAGCCACAAAGGC
* *
55004196 TTCCATTCA-GAGAT-AGCCACAAAG
1 TTCCTTTAATGAGATCAGCCACAAAG
55004220 ATGTCTATTC
Statistics
Matches: 177, Mismatches: 36, Indels: 28
0.73 0.15 0.12
Matches are distributed among these distances:
25 1 0.01
26 12 0.07
27 2 0.01
28 28 0.16
29 127 0.72
30 7 0.04
ACGTcount: A:0.39, C:0.21, G:0.15, T:0.26
Consensus pattern (28 bp):
TTCCTTTAATGAGATCAGCCACAAAGGC
Found at i:55007506 original size:64 final size:64
Alignment explanation
Indices: 55007401--55007560 Score: 257
Period size: 64 Copynumber: 2.5 Consensus size: 64
55007391 ATAGCTATGT
* * *
55007401 CCTGGACACATGCCGGTGTCCTTGGCCCATATGATCGTTATCTTGTAATCAGTGAGTTACACGG
1 CCTGGACACATGCCCGTGTCCTTGGCCCATGTGATCCTTATCTTGTAATCAGTGAGTTACACGG
* * *
55007465 CCTGGACACACGCCCTTATCCTTGGCCCATGTGATCCTTATCTTGTAATCAGTGAGTTACACGG
1 CCTGGACACATGCCCGTGTCCTTGGCCCATGTGATCCTTATCTTGTAATCAGTGAGTTACACGG
*
55007529 CCTGGACACATGCCCGTGTCCTTGGCCTATGT
1 CCTGGACACATGCCCGTGTCCTTGGCCCATGT
55007561 AAACCCCGCA
Statistics
Matches: 86, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
64 86 1.00
ACGTcount: A:0.19, C:0.29, G:0.23, T:0.29
Consensus pattern (64 bp):
CCTGGACACATGCCCGTGTCCTTGGCCCATGTGATCCTTATCTTGTAATCAGTGAGTTACACGG
Found at i:55009751 original size:29 final size:29
Alignment explanation
Indices: 55009718--55009907 Score: 227
Period size: 29 Copynumber: 6.6 Consensus size: 29
55009708 GTGACGAGAT
55009718 TGGCACTAAGTGTGCGTGCTGGAAATATA
1 TGGCACTAAGTGTGCGTGCTGGAAATATA
55009747 TGGCACTAAGTGTGCGTGCTGGAAATATA
1 TGGCACTAAGTGTGCGTGCTGGAAATATA
55009776 TGGCACTAAGTGTGCGTGCTGGAAATATA
1 TGGCACTAAGTGTGCGTGCTGGAAATATA
* * *
55009805 AGGCACTAAGTGTGCATGCTGGAAAAATA
1 TGGCACTAAGTGTGCGTGCTGGAAATATA
* * ** *
55009834 TGACACTATGTGTGCAAGCTGGAAAAATA
1 TGGCACTAAGTGTGCGTGCTGGAAATATA
* ** * * ***
55009863 CGGCACTGGGTGTGCGAGCTCGAAGGGTA
1 TGGCACTAAGTGTGCGTGCTGGAAATATA
*
55009892 TGGCACTATGTGTGCG
1 TGGCACTAAGTGTGCG
55009908 GGCTTAAATT
Statistics
Matches: 142, Mismatches: 19, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 142 1.00
ACGTcount: A:0.28, C:0.15, G:0.32, T:0.25
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGTGCTGGAAATATA
Found at i:55017887 original size:29 final size:29
Alignment explanation
Indices: 55017854--55017985 Score: 165
Period size: 29 Copynumber: 4.6 Consensus size: 29
55017844 GTGACGAGAT
*
55017854 TGGCACTAAGTGTGCGTGCTGGAAATATA
1 TGGCACTAAGTGTGCGTGCTGGAAAAATA
*
55017883 TGGCACTAAGTGTGCGTGCTGGAAATATA
1 TGGCACTAAGTGTGCGTGCTGGAAAAATA
* *
55017912 AGGCACTAAGTGTGCATGCTGGAAAAATA
1 TGGCACTAAGTGTGCGTGCTGGAAAAATA
* * **
55017941 TGACACTATGTGTGCAAGCTGGAAAAATA
1 TGGCACTAAGTGTGCGTGCTGGAAAAATA
* **
55017970 CGGCACTGGGTGTGCG
1 TGGCACTAAGTGTGCG
55017986 AGCTCGAAGG
Statistics
Matches: 91, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 91 1.00
ACGTcount: A:0.30, C:0.15, G:0.31, T:0.24
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGTGCTGGAAAAATA
Found at i:55019624 original size:32 final size:31
Alignment explanation
Indices: 55019588--55019663 Score: 91
Period size: 32 Copynumber: 2.4 Consensus size: 31
55019578 CAACGAAAAG
*
55019588 AAAAGAAAGGAAGAGAAGAAGAAT-AAAAATGA
1 AAAAGAAAGGAAGA-AA-AAGAATGAAAAAGGA
*
55019620 AAAAGAAAAGAAGAAAAAGAATGAAAAAGGA
1 AAAAGAAAGGAAGAAAAAGAATGAAAAAGGA
*
55019651 AAAGAGACAGGAA
1 AAA-AGAAAGGAA
55019664 ATAAGACGTT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
30 6 0.16
31 12 0.32
32 20 0.53
ACGTcount: A:0.70, C:0.01, G:0.25, T:0.04
Consensus pattern (31 bp):
AAAAGAAAGGAAGAAAAAGAATGAAAAAGGA
Found at i:55019625 original size:24 final size:24
Alignment explanation
Indices: 55019598--55019655 Score: 77
Period size: 24 Copynumber: 2.5 Consensus size: 24
55019588 AAAAGAAAGG
55019598 AAGAGAAGAAGAATAAA-AATGAAA
1 AAGAGAAGAAGAA-AAAGAATGAAA
*
55019622 AAGAAAAGAAGAAAAAGAATGAAA
1 AAGAGAAGAAGAAAAAGAATGAAA
55019646 AAG-GAA-AAGA
1 AAGAGAAGAAGA
55019656 GACAGGAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
22 4 0.13
23 5 0.16
24 22 0.71
ACGTcount: A:0.72, C:0.00, G:0.22, T:0.05
Consensus pattern (24 bp):
AAGAGAAGAAGAAAAAGAATGAAA
Found at i:55019654 original size:30 final size:31
Alignment explanation
Indices: 55019583--55019655 Score: 89
Period size: 30 Copynumber: 2.4 Consensus size: 31
55019573 GCCCGCAACG
*
55019583 AAAA-GAAAAGAAAGGAAGAGAAGAAGAATA
1 AAAAGGAAAAGAAAAGAAGAGAAGAAGAATA
*
55019613 AAAATGAAAAAGAAAAGAAGA-AA-AAGAATGA
1 AAAA-GGAAAAGAAAAGAAGAGAAGAAGAAT-A
55019644 AAAAGGAAAAGA
1 AAAAGGAAAAGA
55019656 GACAGGAAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
30 17 0.46
31 7 0.19
32 13 0.35
ACGTcount: A:0.73, C:0.00, G:0.23, T:0.04
Consensus pattern (31 bp):
AAAAGGAAAAGAAAAGAAGAGAAGAAGAATA
Found at i:55021518 original size:27 final size:28
Alignment explanation
Indices: 55021461--55021530 Score: 115
Period size: 27 Copynumber: 2.5 Consensus size: 28
55021451 AAACTTGTAC
*
55021461 AGCACTAAGTGTGCGAGTTTGATCATGT
1 AGCACTAAGTGTGCGAGTTTGATCATAT
*
55021489 AGCACTAAGTGTGCGAG-TTGATTATAT
1 AGCACTAAGTGTGCGAGTTTGATCATAT
55021516 AGCACTAAGTGTGCG
1 AGCACTAAGTGTGCG
55021531 GACTCACTAT
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:0.27, C:0.14, G:0.29, T:0.30
Consensus pattern (28 bp):
AGCACTAAGTGTGCGAGTTTGATCATAT
Found at i:55021541 original size:27 final size:27
Alignment explanation
Indices: 55021461--55021542 Score: 69
Period size: 27 Copynumber: 3.0 Consensus size: 27
55021451 AAACTTGTAC
* * *
55021461 AGCACTAAGTGTGCGAGTTTGA-TCATGT
1 AGCACTAAGTGTGCGAG-CTCACT-ATAT
* * *
55021489 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGAGCTCACTATAT
55021516 AGCACTAAGTGTGCG-GACTCACTATAT
1 AGCACTAAGTGTGCGAG-CTCACTATAT
55021543 GCTTTTGAAT
Statistics
Matches: 48, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
26 1 0.02
27 29 0.60
28 18 0.38
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGAGCTCACTATAT
Found at i:55026566 original size:41 final size:40
Alignment explanation
Indices: 55026519--55026638 Score: 152
Period size: 41 Copynumber: 2.9 Consensus size: 40
55026509 ATTTTATTAA
55026519 AAACGCCGTAAAAAACTGAGCAATAGCGGCGTTTTTGGTCC
1 AAACGCCGT-AAAAACTGAGCAATAGCGGCGTTTTTGGTCC
* * *
55026560 AAACGCCACTAAAAACTAAGCAATAGCGGCGTCTTTGGTCC
1 AAACGCC-GTAAAAACTGAGCAATAGCGGCGTTTTTGGTCC
* *
55026601 AAACGCCGCTAAAAA-TGGAGCAATAGCGACGCTTTTGG
1 AAACGCCG-TAAAAACT-GAGCAATAGCGGCGTTTTTGG
55026639 AAAAACGCCG
Statistics
Matches: 68, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
40 1 0.01
41 66 0.97
42 1 0.01
ACGTcount: A:0.33, C:0.23, G:0.23, T:0.20
Consensus pattern (40 bp):
AAACGCCGTAAAAACTGAGCAATAGCGGCGTTTTTGGTCC
Found at i:55026787 original size:40 final size:41
Alignment explanation
Indices: 55026624--55026855 Score: 229
Period size: 41 Copynumber: 5.7 Consensus size: 41
55026614 AATGGAGCAA
* *
55026624 TAGCGACGCTTTTGGAAAAACGCCGTTATTGCTC-AGTTTTT
1 TAGCGGCGCTTTTGGAAAAACGCCGCTATTGCTCGAG-TTTT
** * * * * *
55026665 TAGAAGCGCTTTTGGAAAAATGTCGCTATAGATCGAGGTTT
1 TAGCGGCGCTTTTGGAAAAACGCCGCTATTGCTCGAGTTTT
* * * * * *
55026706 TAGCGGCACTTTTGG-AAAACACCACTATAGATCGAGGTTT
1 TAGCGGCGCTTTTGGAAAAACGCCGCTATTGCTCGAGTTTT
* * *
55026746 TAGCGGCGATTTTGGAAAAATGCCACTATTGCTC-AGTTTT
1 TAGCGGCGCTTTTGGAAAAACGCCGCTATTGCTCGAGTTTT
* * *
55026786 TAGCGGCG-TTTCTGAAAAAACGCCGCTATTGCTCAATTTTT
1 TAGCGGCGCTTT-TGGAAAAACGCCGCTATTGCTCGAGTTTT
55026827 TAGCGGCGCTTTTGGAAAAACGCCGCTAT
1 TAGCGGCGCTTTTGGAAAAACGCCGCTAT
55026856 AGATTGAAGT
Statistics
Matches: 158, Mismatches: 28, Indels: 10
0.81 0.14 0.05
Matches are distributed among these distances:
39 3 0.02
40 66 0.42
41 84 0.53
42 5 0.03
ACGTcount: A:0.26, C:0.19, G:0.23, T:0.32
Consensus pattern (41 bp):
TAGCGGCGCTTTTGGAAAAACGCCGCTATTGCTCGAGTTTT
Found at i:55026869 original size:81 final size:81
Alignment explanation
Indices: 55026632--55026867 Score: 217
Period size: 81 Copynumber: 2.9 Consensus size: 81
55026622 AATAGCGACG
* * ** *
55026632 CTTTTGGAAAAACGCCGTTATTGCTCAGTTTTTTAGAAGCGCTTTTGGAAAAATGTCGCTATAGA
1 CTTTT-GAAAAACGCCGCTATTGCTCAATTTTTTAGCGGCGCTTTTGGAAAAATGCCGCTATAGA
* *
55026697 TCGAGGTTTTAGCGGCA
65 TTGAAGTTTTAGCGGCA
* * * * * * ** * * * *
55026714 CTTTTGGAAAACACCACTATAGATCGAGGTTTTAGCGGCGATTTTGGAAAAATGCCACTATTG-C
1 CTTTTGAAAAACGCCGCTATTGCTCAATTTTTTAGCGGCGCTTTTGGAAAAATGCCGCTATAGAT
*
55026778 T-CAGTTTTTAGCGGC-
66 TGAAG-TTTTAGCGGCA
* *
55026793 GTTTCTGAAAAAACGCCGCTATTGCTCAATTTTTTAGCGGCGCTTTTGGAAAAACGCCGCTATAG
1 CTTT-TG-AAAAACGCCGCTATTGCTCAATTTTTTAGCGGCGCTTTTGGAAAAATGCCGCTATAG
55026858 ATTGAAGTTT
64 ATTGAAGTTT
55026868 AGGGTTTAGA
Statistics
Matches: 114, Mismatches: 35, Indels: 10
0.72 0.22 0.06
Matches are distributed among these distances:
79 4 0.04
80 12 0.11
81 87 0.76
82 9 0.08
83 2 0.02
ACGTcount: A:0.26, C:0.18, G:0.23, T:0.33
Consensus pattern (81 bp):
CTTTTGAAAAACGCCGCTATTGCTCAATTTTTTAGCGGCGCTTTTGGAAAAATGCCGCTATAGAT
TGAAGTTTTAGCGGCA
Found at i:55027536 original size:28 final size:30
Alignment explanation
Indices: 55027477--55027537 Score: 81
Period size: 28 Copynumber: 2.1 Consensus size: 30
55027467 CCTGAAAACT
***
55027477 AATCTCTAAACCCATAAACTATAAATTGTA
1 AATCTCTAAACCCATAAACTATAAACCATA
55027507 AATCTC-AAACCC-TAAACTATAAACCATA
1 AATCTCTAAACCCATAAACTATAAACCATA
55027535 AAT
1 AAT
55027538 AATAAGCTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
28 16 0.57
29 6 0.21
30 6 0.21
ACGTcount: A:0.49, C:0.23, G:0.02, T:0.26
Consensus pattern (30 bp):
AATCTCTAAACCCATAAACTATAAACCATA
Found at i:55027643 original size:21 final size:21
Alignment explanation
Indices: 55027613--55027655 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
55027603 ATATATGTTC
55027613 ATGGTCTAGGATTTAGGG-TTT
1 ATGGTCTAGGATTT-GGGATTT
*
55027634 ATGGTTTAGGATTTGGGATTT
1 ATGGTCTAGGATTTGGGATTT
55027655 A
1 A
55027656 ATTTTTAGTG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 3 0.15
21 17 0.85
ACGTcount: A:0.21, C:0.02, G:0.33, T:0.44
Consensus pattern (21 bp):
ATGGTCTAGGATTTGGGATTT
Found at i:55028040 original size:7 final size:7
Alignment explanation
Indices: 55028027--55028090 Score: 74
Period size: 8 Copynumber: 8.6 Consensus size: 7
55028017 AAATCTTCAA
55028027 AAAAATT
1 AAAAATT
*
55028034 GAAAATTT
1 -AAAAATT
55028042 AAAAATT
1 AAAAATT
55028049 AAAAATT
1 AAAAATT
*
55028056 AAAACTT
1 AAAAATT
55028063 AAAAACTT
1 AAAAA-TT
55028071 AAAAACTT
1 AAAAA-TT
55028079 AAAAACTT
1 AAAAA-TT
55028087 AAAA
1 AAAA
55028091 TTTTAATATT
Statistics
Matches: 51, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
7 23 0.45
8 28 0.55
ACGTcount: A:0.66, C:0.06, G:0.02, T:0.27
Consensus pattern (7 bp):
AAAAATT
Found at i:55028046 original size:8 final size:8
Alignment explanation
Indices: 55028001--55028096 Score: 63
Period size: 8 Copynumber: 11.9 Consensus size: 8
55027991 CTTATATGTT
55028001 AATTTAAA
1 AATTTAAA
*
55028009 AATAATAAA
1 AAT-TTAAA
55028018 AATCTTCAAAA
1 AAT-TT--AAA
* *
55028029 AAATTGAA
1 AATTTAAA
55028037 AATTTAAA
1 AATTTAAA
55028045 AA-TTAAA
1 AATTTAAA
55028052 AA-TT-AA
1 AATTTAAA
*
55028058 AACTTAAA
1 AATTTAAA
*
55028066 AACTTAAA
1 AATTTAAA
*
55028074 AACTTAAA
1 AATTTAAA
*
55028082 AACTTAAA
1 AATTTAAA
*
55028090 ATTTTAA
1 AATTTAA
55028097 TATTTAATAT
Statistics
Matches: 74, Mismatches: 9, Indels: 10
0.80 0.10 0.11
Matches are distributed among these distances:
6 4 0.05
7 11 0.15
8 44 0.59
9 8 0.11
10 2 0.03
11 5 0.07
ACGTcount: A:0.62, C:0.06, G:0.01, T:0.30
Consensus pattern (8 bp):
AATTTAAA
Found at i:55028047 original size:15 final size:15
Alignment explanation
Indices: 55028027--55028090 Score: 85
Period size: 15 Copynumber: 4.3 Consensus size: 15
55028017 AAATCTTCAA
* *
55028027 AAAAATTGAAAATTT
1 AAAAATTAAAAACTT
55028042 AAAAATTAAAAA-TT
1 AAAAATTAAAAACTT
*
55028056 AAAACTTAAAAACTT
1 AAAAATTAAAAACTT
55028071 AAAAACTTAAAAACTT
1 AAAAA-TTAAAAACTT
55028087 AAAA
1 AAAA
55028091 TTTTAATATT
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
14 13 0.30
15 17 0.39
16 14 0.32
ACGTcount: A:0.66, C:0.06, G:0.02, T:0.27
Consensus pattern (15 bp):
AAAAATTAAAAACTT
Found at i:55028077 original size:16 final size:16
Alignment explanation
Indices: 55028035--55028090 Score: 82
Period size: 16 Copynumber: 3.7 Consensus size: 16
55028025 AAAAAAATTG
*
55028035 AAAATTTAAAAA-TTA
1 AAAACTTAAAAACTTA
55028050 AAAA-TT-AAAACTTA
1 AAAACTTAAAAACTTA
55028064 AAAACTTAAAAACTTA
1 AAAACTTAAAAACTTA
55028080 AAAACTTAAAA
1 AAAACTTAAAA
55028091 TTTTAATATT
Statistics
Matches: 38, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
13 4 0.11
14 9 0.24
15 6 0.16
16 19 0.50
ACGTcount: A:0.66, C:0.07, G:0.00, T:0.27
Consensus pattern (16 bp):
AAAACTTAAAAACTTA
Found at i:55047542 original size:29 final size:29
Alignment explanation
Indices: 55047478--55047560 Score: 116
Period size: 28 Copynumber: 2.9 Consensus size: 29
55047468 AGCATGACTG
* *
55047478 TAAATGTGATTTGGGCCTAAT-AGCCATA
1 TAAATGTGATTTGGGCCTAATGGGCCACA
*
55047506 TGAATGTGATTTGGGCCTAATGGGCCACA
1 TAAATGTGATTTGGGCCTAATGGGCCACA
*
55047535 TAAATGTGA-TTGGACCTAATGGGCCA
1 TAAATGTGATTTGGGCCTAATGGGCCA
55047561 ATTGAAAGAG
Statistics
Matches: 49, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
28 36 0.73
29 13 0.27
ACGTcount: A:0.29, C:0.16, G:0.27, T:0.29
Consensus pattern (29 bp):
TAAATGTGATTTGGGCCTAATGGGCCACA
Found at i:55047573 original size:28 final size:28
Alignment explanation
Indices: 55047478--55047588 Score: 93
Period size: 28 Copynumber: 3.9 Consensus size: 28
55047468 AGCATGACTG
* * *
55047478 TAAATGTGATTTGGGCCTAAT-AGCCATA
1 TAAATGAGA-TTGGGCCTAATGGGCCACA
* *
55047506 TGAATGTGATTTGGGCCTAATGGGCCACA
1 TAAATGAGA-TTGGGCCTAATGGGCCACA
* *
55047535 TAAATGTGATTGGACCTAATGGGCCA-A
1 TAAATGAGATTGGGCCTAATGGGCCACA
*
55047562 TTGAAA-GAGATTGGGCCTAGTGGGCCA
1 -T-AAATGAGATTGGGCCTAATGGGCCA
55047589 TATACAGGTA
Statistics
Matches: 72, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
27 1 0.01
28 55 0.76
29 16 0.22
ACGTcount: A:0.29, C:0.15, G:0.29, T:0.27
Consensus pattern (28 bp):
TAAATGAGATTGGGCCTAATGGGCCACA
Found at i:55054683 original size:2 final size:2
Alignment explanation
Indices: 55054678--55054712 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
55054668 CCAAATTGAA
55054678 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
55054713 AAGAAAAAAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:55057119 original size:16 final size:16
Alignment explanation
Indices: 55057098--55057128 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
55057088 TTGTAACGAG
55057098 CCAAAAATCCCGAAAC
1 CCAAAAATCCCGAAAC
*
55057114 CCAAAAATCTCGAAA
1 CCAAAAATCCCGAAA
55057129 TCTTGAATTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.52, C:0.32, G:0.06, T:0.10
Consensus pattern (16 bp):
CCAAAAATCCCGAAAC
Found at i:55058371 original size:16 final size:16
Alignment explanation
Indices: 55058352--55058382 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
55058342 AAGCTGAAAT
*
55058352 GCCGAAAAGTCAAAAA
1 GCCGAAAAGCCAAAAA
55058368 GCCGAAAAGCCAAAA
1 GCCGAAAAGCCAAAA
55058383 GTTTGGCTAC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.23, G:0.19, T:0.03
Consensus pattern (16 bp):
GCCGAAAAGCCAAAAA
Found at i:55058374 original size:24 final size:23
Alignment explanation
Indices: 55058340--55058384 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
55058330 GTAGATAAGC
* *
55058340 AAAAGCTGAAATGCCGAAAAGTCA
1 AAAAGCCGAAAAGCC-AAAAGTCA
55058364 AAAAGCCGAAAAGCCAAAAGT
1 AAAAGCCGAAAAGCCAAAAGT
55058385 TTGGCTACGG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 6 0.32
24 13 0.68
ACGTcount: A:0.53, C:0.18, G:0.20, T:0.09
Consensus pattern (23 bp):
AAAAGCCGAAAAGCCAAAAGTCA
Found at i:55059972 original size:46 final size:46
Alignment explanation
Indices: 55059919--55060094 Score: 201
Period size: 46 Copynumber: 3.8 Consensus size: 46
55059909 TATTTGGGCA
*
55059919 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
* * *** * * * *
55059965 TCCGAACTCGTTGTGTTGAGTCTGAGTTCGAGAGATGTA-ACTAGGCG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATGGATGCGA-ACG
* *
55060012 TTCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
* *
55060058 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
55060095 GCGGGTTACA
Statistics
Matches: 104, Mismatches: 23, Indels: 6
0.78 0.17 0.05
Matches are distributed among these distances:
46 71 0.68
47 33 0.32
ACGTcount: A:0.20, C:0.20, G:0.30, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
Found at i:55061449 original size:19 final size:19
Alignment explanation
Indices: 55061425--55061462 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
55061415 AAATGTGCCA
55061425 CATAAATGTGATTGGGCCT
1 CATAAATGTGATTGGGCCT
55061444 CATAAATGTGATTGGGCCT
1 CATAAATGTGATTGGGCCT
55061463 AATGGGCCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.16, G:0.26, T:0.32
Consensus pattern (19 bp):
CATAAATGTGATTGGGCCT
Found at i:55061485 original size:47 final size:48
Alignment explanation
Indices: 55061400--55061490 Score: 123
Period size: 47 Copynumber: 1.9 Consensus size: 48
55061390 CGTTACAATG
* *
55061400 AATGTGATTTGGGCCAAATGTGCCACATAAATGTGATTGGGCCTCATA
1 AATGTGATTTGGGCCAAATGGGCCACATAAATGAGATTGGGCCTCATA
* *
55061448 AATGTGA-TTGGGCCTAATGGGCCATATGAAA-GAGATTGGGCCT
1 AATGTGATTTGGGCCAAATGGGCCACAT-AAATGAGATTGGGCCT
55061491 AGTGGGCCAT
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
47 28 0.74
48 10 0.26
ACGTcount: A:0.29, C:0.15, G:0.29, T:0.27
Consensus pattern (48 bp):
AATGTGATTTGGGCCAAATGGGCCACATAAATGAGATTGGGCCTCATA
Found at i:55064127 original size:21 final size:20
Alignment explanation
Indices: 55064079--55064128 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 20
55064069 AGCCCACAAC
*
55064079 GAAAAGAAAAGAAAGGAAGA
1 GAAAAGAAAAGAAAGGAAAA
55064099 GAAGAAGAATAA-AAAGGAAAAA
1 GAA-AAGAA-AAGAAAGG-AAAA
55064121 GAAAAGAA
1 GAAAAGAA
55064129 GAACAAAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
20 3 0.12
21 15 0.58
22 8 0.31
ACGTcount: A:0.72, C:0.00, G:0.26, T:0.02
Consensus pattern (20 bp):
GAAAAGAAAAGAAAGGAAAA
Found at i:55064145 original size:27 final size:28
Alignment explanation
Indices: 55064098--55064155 Score: 75
Period size: 27 Copynumber: 2.1 Consensus size: 28
55064088 AGAAAGGAAG
* *
55064098 AGAAGAAGAATAAAAAGGAAAAA-GAAA
1 AGAAGAACAATAAAAAAGAAAAATGAAA
55064125 AGAAGAACAA-AAATAAAGAAAAATGAAA
1 AGAAGAACAATAAA-AAAGAAAAATGAAA
55064153 AGA
1 AGA
55064156 GATAGGAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
26 3 0.11
27 17 0.63
28 7 0.26
ACGTcount: A:0.74, C:0.02, G:0.19, T:0.05
Consensus pattern (28 bp):
AGAAGAACAATAAAAAAGAAAAATGAAA
Found at i:55070333 original size:4 final size:4
Alignment explanation
Indices: 55070324--55070368 Score: 56
Period size: 4 Copynumber: 10.8 Consensus size: 4
55070314 GTTCTGATAT
55070324 TTTA TTTA -TTA TTCTA TTTTA TTTA TCTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TT-TA -TTTA TTTA T-TTA TTTA TTTA TTTA TTT
55070369 TGACTTGGAT
Statistics
Matches: 37, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
3 3 0.08
4 24 0.65
5 8 0.22
6 2 0.05
ACGTcount: A:0.22, C:0.04, G:0.00, T:0.73
Consensus pattern (4 bp):
TTTA
Found at i:55070338 original size:20 final size:17
Alignment explanation
Indices: 55070321--55070367 Score: 62
Period size: 17 Copynumber: 2.8 Consensus size: 17
55070311 ATTGTTCTGA
55070321 TATTTTATTTATTATTC
1 TATTTTATTTATTATTC
55070338 TATTTTATTTATCTTATT-
1 TATTTTATTTA--TTATTC
55070356 TA-TTTATTTATT
1 TATTTTATTTATT
55070368 TTGACTTGGA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
15 2 0.07
17 19 0.68
18 2 0.07
19 5 0.18
ACGTcount: A:0.23, C:0.04, G:0.00, T:0.72
Consensus pattern (17 bp):
TATTTTATTTATTATTC
Found at i:55070357 original size:13 final size:12
Alignment explanation
Indices: 55070324--55070368 Score: 56
Period size: 13 Copynumber: 3.6 Consensus size: 12
55070314 GTTCTGATAT
55070324 TTTATTTA-TTA
1 TTTATTTATTTA
55070335 TTCTATTTTATTTA
1 TT-TA-TTTATTTA
55070349 TCTTATTTATTTA
1 T-TTATTTATTTA
55070362 TTTATTT
1 TTTATTT
55070369 TGACTTGGAT
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
11 2 0.07
12 8 0.27
13 13 0.43
14 6 0.20
15 1 0.03
ACGTcount: A:0.22, C:0.04, G:0.00, T:0.73
Consensus pattern (12 bp):
TTTATTTATTTA
Found at i:55073539 original size:40 final size:39
Alignment explanation
Indices: 55073484--55073635 Score: 151
Period size: 40 Copynumber: 3.8 Consensus size: 39
55073474 TGAATGGTAT
55073484 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACCAAAA
1 CCGGGCT-AGTCCCGAAGGCATTTGTGCGAGTTACCAAAA
* * * *
55073524 CCGGGTTAATTCCCGAAGGCATTTGTGCGAGTTCCCAAAT
1 CCGGGCT-AGTCCCGAAGGCATTTGTGCGAGTTACCAAAA
* * * * ** *
55073564 CCGGGATTAGTCCCAAAGGCATTTATGCGAGCTATTATAA
1 CCGGG-CTAGTCCCGAAGGCATTTGTGCGAGTTACCAAAA
* *
55073604 CCGGGCTATGTCCCGAAGGCTTTTGAGCGAGT
1 CCGGGCTA-GTCCCGAAGGCATTTGTGCGAGT
55073636 CGCTATATCC
Statistics
Matches: 91, Mismatches: 19, Indels: 4
0.80 0.17 0.04
Matches are distributed among these distances:
39 2 0.02
40 87 0.96
41 2 0.02
ACGTcount: A:0.24, C:0.24, G:0.27, T:0.25
Consensus pattern (39 bp):
CCGGGCTAGTCCCGAAGGCATTTGTGCGAGTTACCAAAA
Found at i:55073618 original size:80 final size:80
Alignment explanation
Indices: 55073482--55073635 Score: 193
Period size: 80 Copynumber: 1.9 Consensus size: 80
55073472 TTTGAATGGT
* * * * *
55073482 ATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACCAAAACCGGGTTAATTCCCGAAGGCATT
1 ATCCGGGATAAGTCCCAAAGGCATTTATGCGAGCTACCAAAACCGGGCTAATTCCCGAAGGCATT
*
55073547 TGTGCGAGTTCCCAA
66 TGAGCGAGTTCCCAA
* ** * *
55073562 ATCCGGGATTAGTCCCAAAGGCATTTATGCGAGCTATTATAACCGGGCT-ATGTCCCGAAGGCTT
1 ATCCGGGATAAGTCCCAAAGGCATTTATGCGAGCTACCAAAACCGGGCTAAT-TCCCGAAGGCAT
55073626 TTGAGCGAGT
65 TTGAGCGAGT
55073636 CGCTATATCC
Statistics
Matches: 62, Mismatches: 11, Indels: 2
0.83 0.15 0.03
Matches are distributed among these distances:
79 2 0.03
80 60 0.97
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.25
Consensus pattern (80 bp):
ATCCGGGATAAGTCCCAAAGGCATTTATGCGAGCTACCAAAACCGGGCTAATTCCCGAAGGCATT
TGAGCGAGTTCCCAA
Found at i:55083853 original size:31 final size:31
Alignment explanation
Indices: 55083818--55083894 Score: 127
Period size: 31 Copynumber: 2.5 Consensus size: 31
55083808 AGCATATACT
55083818 GGCCGAAGCCTTTACATTATTCATACCACTA
1 GGCCGAAGCCTTTACATTATTCATACCACTA
* * *
55083849 GGCCGAAGCCTTTTCATTATTCATATCACTG
1 GGCCGAAGCCTTTACATTATTCATACCACTA
55083880 GGCCGAAGCCTTTAC
1 GGCCGAAGCCTTTAC
55083895 TGTAAACGGT
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 42 1.00
ACGTcount: A:0.25, C:0.29, G:0.17, T:0.30
Consensus pattern (31 bp):
GGCCGAAGCCTTTACATTATTCATACCACTA
Found at i:55084141 original size:25 final size:25
Alignment explanation
Indices: 55084113--55084181 Score: 111
Period size: 25 Copynumber: 2.8 Consensus size: 25
55084103 CTCTTTTAAT
*
55084113 AACTGGGGCAAAGCCCTTTTTGATA
1 AACTGGGGCAAAGCCCTTTTCGATA
*
55084138 AACTGGGGCAAAGCCCTTTTCGGTA
1 AACTGGGGCAAAGCCCTTTTCGATA
*
55084163 AACTGGGGCATAGCCCTTT
1 AACTGGGGCAAAGCCCTTT
55084182 AGCACTTCCT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 41 1.00
ACGTcount: A:0.25, C:0.23, G:0.26, T:0.26
Consensus pattern (25 bp):
AACTGGGGCAAAGCCCTTTTCGATA
Found at i:55086891 original size:20 final size:21
Alignment explanation
Indices: 55086859--55086897 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
55086849 ATGCACCATC
55086859 ATTTTATAAATTTA-ACATGA
1 ATTTTATAAATTTATACATGA
55086879 ATTTT-TAATATTTATACAT
1 ATTTTATAA-ATTTATACAT
55086898 ATTAATCCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 3 0.18
20 10 0.59
21 4 0.24
ACGTcount: A:0.41, C:0.05, G:0.03, T:0.51
Consensus pattern (21 bp):
ATTTTATAAATTTATACATGA
Found at i:55088069 original size:18 final size:18
Alignment explanation
Indices: 55088046--55088089 Score: 72
Period size: 18 Copynumber: 2.4 Consensus size: 18
55088036 TGGCCCAATA
55088046 CAGTAACAATACAT-AGTG
1 CAGTAACAATA-ATCAGTG
55088064 CAGTAACAATAATCAGTG
1 CAGTAACAATAATCAGTG
55088082 CAGTAACA
1 CAGTAACA
55088090 GAATACATGT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
17 2 0.08
18 23 0.92
ACGTcount: A:0.45, C:0.18, G:0.16, T:0.20
Consensus pattern (18 bp):
CAGTAACAATAATCAGTG
Found at i:55088617 original size:27 final size:27
Alignment explanation
Indices: 55088403--55088616 Score: 252
Period size: 27 Copynumber: 8.0 Consensus size: 27
55088393 ATATATACAT
* *
55088403 CACAT-AGGGCAAAACAGTCATATTAC
1 CACATAAGGGCAAAACAATCATTTTAC
*
55088429 CATATAAGGGCAAAACAATCATTTTAC
1 CACATAAGGGCAAAACAATCATTTTAC
* * * *
55088456 CACATAAGGGAAAAACATTTATCTTAC
1 CACATAAGGGCAAAACAATCATTTTAC
* *
55088483 CACCTAATGG-AAAAGCAATCATTTTAC
1 CACATAAGGGCAAAA-CAATCATTTTAC
* ** *
55088510 TACATAACAGCAAAACAATCATTTTAT
1 CACATAAGGGCAAAACAATCATTTTAC
*
55088537 CACATAAGGGAAAAACAATCATTTTAC
1 CACATAAGGGCAAAACAATCATTTTAC
* *
55088564 CACTTAAGGGCAAAACAATCATTTTAT
1 CACATAAGGGCAAAACAATCATTTTAC
*
55088591 CACATAAGGGCAAAACATTCATTTTA
1 CACATAAGGGCAAAACAATCATTTTA
55088617 TTAATTTAGG
Statistics
Matches: 157, Mismatches: 28, Indels: 5
0.83 0.15 0.03
Matches are distributed among these distances:
26 8 0.05
27 145 0.92
28 4 0.03
ACGTcount: A:0.44, C:0.20, G:0.11, T:0.26
Consensus pattern (27 bp):
CACATAAGGGCAAAACAATCATTTTAC
Found at i:55088766 original size:17 final size:19
Alignment explanation
Indices: 55088733--55088771 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
55088723 CATAATGCAG
55088733 GCCCATGTGGTCCTACA-C
1 GCCCATGTGGTCCTACATC
*
55088751 GCCCGTGTGG-CCTACATC
1 GCCCATGTGGTCCTACATC
55088769 GCC
1 GCC
55088772 TAGAAATGGC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 6 0.32
18 13 0.68
ACGTcount: A:0.13, C:0.41, G:0.26, T:0.21
Consensus pattern (19 bp):
GCCCATGTGGTCCTACATC
Found at i:55095852 original size:49 final size:49
Alignment explanation
Indices: 55095789--55095910 Score: 140
Period size: 49 Copynumber: 2.5 Consensus size: 49
55095779 AAGTCGATGC
* * *
55095789 CATGTCCCAAACAGGTCTTACATTGACTTTCATATATCGAG-G-CTAATGA
1 CATGTCCCAGACAGGTCTTACACTGACTCTCATATATC-AGTGTC-AATGA
* * * *
55095838 CGTGTCCCAGACAGGTCTTACACTGGCTCTCATCTATCAGTGTCAATGC
1 CATGTCCCAGACAGGTCTTACACTGACTCTCATATATCAGTGTCAATGA
*
55095887 CATGTCCCAGACAAGTCTTACACT
1 CATGTCCCAGACAGGTCTTACACT
55095911 AGCTTGTATA
Statistics
Matches: 62, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
48 2 0.03
49 59 0.95
50 1 0.02
ACGTcount: A:0.26, C:0.28, G:0.17, T:0.29
Consensus pattern (49 bp):
CATGTCCCAGACAGGTCTTACACTGACTCTCATATATCAGTGTCAATGA
Found at i:55095930 original size:98 final size:97
Alignment explanation
Indices: 55095741--55096053 Score: 275
Period size: 98 Copynumber: 3.3 Consensus size: 97
55095731 ATGCCGACAC
* ** * * *
55095741 CATGTCACAGACATGGTCTTACACTGGCTAGCA-CATCAAAGTCGATGCCATGTCCCAAACAGGT
1 CATGTCCCAGACA-GGTCTTACACTGGCTCTCATCATCAATGTCGATGCCATGTCCCAGACAAGT
* *
55095805 CTTACA-TTGACTTTCATATATCGAGGCTAATG
65 CTTACACTAGACTTTCATATATCAAGGCTAATG
* * *
55095837 ACGTGTCCCAGACAGGTCTTACACTGGCTCTCATCTATCAGTGTCAATGCCATGTCCCAGACAAG
1 -CATGTCCCAGACAGGTCTTACACTGGCTCTCATC-ATCAATGTCGATGCCATGTCCCAGACAAG
* * *
55095902 TCTTACACTAG-CTTGT-ATATCTTAAGGCTGATG
64 TCTTACACTAGACTT-TCATATATCAAGGCTAATG
* * * * * * *
55095935 CATGTCCTAGACATGTCTTACACTAGCTCTCGTC-TCAATGCCGATG-CATGCCCCAGACATGTC
1 CATGTCCCAGACAGGTCTTACACTGGCTCTCATCATCAATGTCGATGCCATGTCCCAGACAAGTC
* * ** **
55095998 TTACACT-GGCTCTCATA-AT-GTGGCCGATG
66 TTACACTAGACTTTCATATATCAAGGCTAATG
*
55096027 CATGTCCCAGACATGTCTTACACTGGC
1 CATGTCCCAGACAGGTCTTACACTGGC
55096054 ACACATATCA
Statistics
Matches: 179, Mismatches: 31, Indels: 17
0.79 0.14 0.07
Matches are distributed among these distances:
92 32 0.18
93 3 0.02
94 27 0.15
95 9 0.05
96 17 0.09
97 41 0.23
98 47 0.26
99 3 0.02
ACGTcount: A:0.25, C:0.28, G:0.19, T:0.28
Consensus pattern (97 bp):
CATGTCCCAGACAGGTCTTACACTGGCTCTCATCATCAATGTCGATGCCATGTCCCAGACAAGTC
TTACACTAGACTTTCATATATCAAGGCTAATG
Found at i:55095995 original size:46 final size:46
Alignment explanation
Indices: 55095840--55096050 Score: 194
Period size: 46 Copynumber: 4.5 Consensus size: 46
55095830 GCTAATGACG
* * * * *
55095840 TGTCCCAGACAGGTCTTACACTGGCTCTCATCTATCAGTGTCAATGCCA
1 TGTCCCAGACATGTCTTACACTAGCTCTCATC--TCAATGCCGATG-CA
* * * * * *
55095889 TGTCCCAGACAAGTCTTACACTAGCTTGTATATCTTAAGGCTGATGCA
1 TGTCCCAGACATGTCTTACACTAGC-TCT-CATCTCAATGCCGATGCA
* *
55095937 TGTCCTAGACATGTCTTACACTAGCTCTCGTCTCAATGCCGATGCA
1 TGTCCCAGACATGTCTTACACTAGCTCTCATCTCAATGCCGATGCA
* *
55095983 TGCCCCAGACATGTCTTACACTGGCTCTCA--T-AATGTGGCCGATGCA
1 TGTCCCAGACATGTCTTACACTAGCTCTCATCTCAA--T-GCCGATGCA
55096029 TGTCCCAGACATGTCTTACACT
1 TGTCCCAGACATGTCTTACACT
55096051 GGCACACATA
Statistics
Matches: 134, Mismatches: 23, Indels: 13
0.79 0.14 0.08
Matches are distributed among these distances:
43 2 0.01
44 1 0.01
45 1 0.01
46 69 0.51
47 2 0.01
48 25 0.19
49 29 0.22
50 2 0.01
51 3 0.02
ACGTcount: A:0.23, C:0.29, G:0.18, T:0.29
Consensus pattern (46 bp):
TGTCCCAGACATGTCTTACACTAGCTCTCATCTCAATGCCGATGCA
Found at i:55102910 original size:43 final size:43
Alignment explanation
Indices: 55102863--55103012 Score: 160
Period size: 43 Copynumber: 3.5 Consensus size: 43
55102853 TTGATACCAC
* * * *
55102863 TGTCCCAGACAGGGTCTTACACGAAATTGAATAACGAAGCCGA
1 TGTCCCAAACATGGTCTTACACGAAATCGAATAACGAAGCCAA
* * * *
55102906 TGTCCCATACATGGTCTTACACGTAATCGAATAATGATGCCAA
1 TGTCCCAAACATGGTCTTACACGAAATCGAATAACGAAGCCAA
* * * *
55102949 TGTCCCAAACATGGTCTTATATGTAATCACAAT-AC-AATGCCAA
1 TGTCCCAAACATGGTCTTACACGAAATC-GAATAACGAA-GCCAA
55102992 TGTCCCAAACATGGTCTTACA
1 TGTCCCAAACATGGTCTTACA
55103013 TGTGATCACA
Statistics
Matches: 91, Mismatches: 14, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
42 1 0.01
43 87 0.96
44 3 0.03
ACGTcount: A:0.34, C:0.24, G:0.17, T:0.25
Consensus pattern (43 bp):
TGTCCCAAACATGGTCTTACACGAAATCGAATAACGAAGCCAA
Found at i:55103069 original size:62 final size:62
Alignment explanation
Indices: 55102972--55103099 Score: 229
Period size: 62 Copynumber: 2.1 Consensus size: 62
55102962 GTCTTATATG
* *
55102972 TAATCACAATACAATGCCAATGTCCCAAACATGGTCTTACATGTGATCACATCTCGGTAACC
1 TAATCACAATACAATGCCAATGTCCCAAACATGGTCGTACATGTAATCACATCTCGGTAACC
*
55103034 TAATCACAATACAATGCCAATGTCCTAAACATGGTCGTACATGTAATCACATCTCGGTAACC
1 TAATCACAATACAATGCCAATGTCCCAAACATGGTCGTACATGTAATCACATCTCGGTAACC
55103096 TAAT
1 TAAT
55103100 GTCATGACAT
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
62 63 1.00
ACGTcount: A:0.35, C:0.26, G:0.12, T:0.27
Consensus pattern (62 bp):
TAATCACAATACAATGCCAATGTCCCAAACATGGTCGTACATGTAATCACATCTCGGTAACC
Found at i:55108800 original size:2 final size:2
Alignment explanation
Indices: 55108793--55108830 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
55108783 GAGACTAGTC
*
55108793 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
55108831 GTCATGATAC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Done.