Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr01 113035596
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: 113035596
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Warning! 271 characters in sequence are not A, C, G, or T
File 141 of 378
Found at i:40216554 original size:48 final size:46
Alignment explanation
Indices: 40216488--40216702 Score: 186
Period size: 46 Copynumber: 4.6 Consensus size: 46
40216478 AAGCTGACGC
* *
40216488 CATGTCCCAGACAGGTCTTACACTAGCTTGTTCATCATGAGGCTGATG
1 CATGTCCCAGACATGTCTTACACTAGCTT-CTCATCAT-AGGCTGATG
* * *
40216536 CATGTCCCAGTCATGTCTTACACTAGCTCTCCTC-TCA-ATGCCGATG
1 CATGTCCCAGACATGTCTTACACTAGCT-T-CTCATCATAGGCTGATG
* * * *
40216582 CATGTCCCAAACATGTCTTACACTGGCTTAAAT-ATCAAGAGGCTGATG
1 CATGTCCCAGACATGTCTTACACTAGCTT--CTCATC-ATAGGCTGATG
* * * * * * *
40216630 CATGTTCCTGACATGTCTTGCACTGGC-TCTCATAATATGGTTGGTG
1 CATGTCCCAGACATGTCTTACACTAGCTTCTCATCATA-GGCTGATG
40216676 CATGTCCCAGACATGTCTTACACTAGC
1 CATGTCCCAGACATGTCTTACACTAGC
40216703 ACACATACCA
Statistics
Matches: 134, Mismatches: 26, Indels: 16
0.76 0.15 0.09
Matches are distributed among these distances:
45 4 0.03
46 66 0.49
47 2 0.01
48 59 0.44
49 3 0.02
ACGTcount: A:0.23, C:0.27, G:0.20, T:0.30
Consensus pattern (46 bp):
CATGTCCCAGACATGTCTTACACTAGCTTCTCATCATAGGCTGATG
Found at i:40216624 original size:94 final size:94
Alignment explanation
Indices: 40216488--40216660 Score: 231
Period size: 94 Copynumber: 1.8 Consensus size: 94
40216478 AAGCTGACGC
* ** * *
40216488 CATGTCCCAGACAGGTCTTACACTAGCTTGTTCATCATGAGGCTGATGCATGTCCCAGTCATGTC
1 CATGTCCCAAACAGGTCTTACACTAGCTTAATCATCAAGAGGCTGATGCATGTCCCAGACATGTC
40216553 TTACACTAGCTCTCCTCTCAATGCCGATG
66 TTACACTAGCTCTCCTCTCAATGCCGATG
* * * *
40216582 CATGTCCCAAACATGTCTTACACTGGCTTAAAT-ATCAAGAGGCTGATGCATGTTCCTGACATGT
1 CATGTCCCAAACAGGTCTTACACTAGCTT-AATCATCAAGAGGCTGATGCATGTCCCAGACATGT
* *
40216646 CTTGCACTGGCTCTC
65 CTTACACTAGCTCTC
40216661 ATAATATGGT
Statistics
Matches: 67, Mismatches: 11, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
94 66 0.99
95 1 0.01
ACGTcount: A:0.23, C:0.28, G:0.19, T:0.30
Consensus pattern (94 bp):
CATGTCCCAAACAGGTCTTACACTAGCTTAATCATCAAGAGGCTGATGCATGTCCCAGACATGTC
TTACACTAGCTCTCCTCTCAATGCCGATG
Found at i:40221355 original size:46 final size:47
Alignment explanation
Indices: 40221288--40221462 Score: 173
Period size: 46 Copynumber: 3.8 Consensus size: 47
40221278 TGTAACCCGC
* *
40221288 CCATAAGTGAACTCGGACTCAACTCAAAGAGCTCGAG-CGTTCGCAT
1 CCATAAATGAACTCGGACTCAACTCAACGAGCTCGAGACGTTCGCAT
* * **
40221334 CCATAAATGAACTCGGACTCAACTCAACGAGCTTAGATGCCTAGTT-ATAT
1 CCATAAATGAACTCGGACTCAACTCAACGAGC-TCGA-GAC--GTTCGCAT
* * *
40221384 -C-T-CACGAACTCGGACTCAACTCAACGAGTTC-AGACGTTCGCAT
1 CCATAAATGAACTCGGACTCAACTCAACGAGCTCGAGACGTTCGCAT
* *
40221427 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGA
1 CCATAAATGAACTCGGACTCAACTCAACGAGCTCGA
40221463 ATGCCCAAAT
Statistics
Matches: 104, Mismatches: 15, Indels: 19
0.75 0.11 0.14
Matches are distributed among these distances:
42 3 0.03
43 2 0.02
44 3 0.03
45 2 0.02
46 57 0.55
47 28 0.27
48 2 0.02
49 2 0.02
50 2 0.02
51 3 0.03
ACGTcount: A:0.31, C:0.28, G:0.19, T:0.22
Consensus pattern (47 bp):
CCATAAATGAACTCGGACTCAACTCAACGAGCTCGAGACGTTCGCAT
Found at i:40241040 original size:5 final size:5
Alignment explanation
Indices: 40241030--40241061 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
40241020 CAATTTGTGA
40241030 AAAAT AAAAT AAAAT AAAAT -AAAT AAAAT AAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAA
40241062 GAACACACAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.15
5 22 0.85
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:40241055 original size:9 final size:9
Alignment explanation
Indices: 40241031--40241061 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
40241021 AATTTGTGAA
40241031 AAATAAAAT
1 AAATAAAAT
40241040 AAAATAAAAT
1 -AAATAAAAT
40241050 AAATAAAAT
1 AAATAAAAT
40241059 AAA
1 AAA
40241062 GAACACACAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 12 0.57
10 9 0.43
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (9 bp):
AAATAAAAT
Found at i:40245938 original size:31 final size:31
Alignment explanation
Indices: 40245898--40245983 Score: 156
Period size: 31 Copynumber: 2.8 Consensus size: 31
40245888 TCAAGCTCAG
40245898 CATAT-ACTGGGCCGAAGCCTTTACATTATT
1 CATATCACTGGGCCGAAGCCTTTACATTATT
*
40245928 CATATCACTGGGCCGAAGCCTTTTCATTATT
1 CATATCACTGGGCCGAAGCCTTTACATTATT
40245959 CATATCACTGGGCCGAAGCCTTTAC
1 CATATCACTGGGCCGAAGCCTTTAC
40245984 TGTAACAATA
Statistics
Matches: 53, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
30 5 0.09
31 48 0.91
ACGTcount: A:0.24, C:0.27, G:0.17, T:0.31
Consensus pattern (31 bp):
CATATCACTGGGCCGAAGCCTTTACATTATT
Found at i:40246246 original size:26 final size:25
Alignment explanation
Indices: 40246201--40246271 Score: 97
Period size: 26 Copynumber: 2.8 Consensus size: 25
40246191 CTCTTTTAAT
*
40246201 AACTGGGGCAAAGCCCTTTTTGATA
1 AACTGGGGCAAAGCCCTTTTCGATA
*
40246226 AACTGGGGCAAAAGCCCTTTTCGGTA
1 AACTGGGGC-AAAGCCCTTTTCGATA
* *
40246252 AACTAGGGTAAAGCCCTTTT
1 AACTGGGGCAAAGCCCTTTT
40246272 GCACTTCCTC
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
25 20 0.49
26 21 0.51
ACGTcount: A:0.28, C:0.21, G:0.24, T:0.27
Consensus pattern (25 bp):
AACTGGGGCAAAGCCCTTTTCGATA
Found at i:40246430 original size:25 final size:25
Alignment explanation
Indices: 40246402--40246449 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
40246392 ATAATTAAAC
* *
40246402 CCTAGGGGTAAAATGGTCATTTTTA
1 CCTAGGGGCAAAATAGTCATTTTTA
40246427 CCTAGGGGCAAAATAGTCATTTT
1 CCTAGGGGCAAAATAGTCATTTT
40246450 CACATTATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.29, C:0.15, G:0.23, T:0.33
Consensus pattern (25 bp):
CCTAGGGGCAAAATAGTCATTTTTA
Found at i:40247591 original size:14 final size:16
Alignment explanation
Indices: 40247572--40247604 Score: 52
Period size: 14 Copynumber: 2.2 Consensus size: 16
40247562 TCGGCTAGAG
40247572 AAGAAG-AAAGAA-AA
1 AAGAAGAAAAGAATAA
40247586 AAGAAGAAAAGAATAA
1 AAGAAGAAAAGAATAA
40247602 AAG
1 AAG
40247605 TATGGTTTAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 6 0.35
15 6 0.35
16 5 0.29
ACGTcount: A:0.76, C:0.00, G:0.21, T:0.03
Consensus pattern (16 bp):
AAGAAGAAAAGAATAA
Found at i:40253945 original size:31 final size:31
Alignment explanation
Indices: 40253897--40253982 Score: 147
Period size: 31 Copynumber: 2.8 Consensus size: 31
40253887 TCAAGCTCAG
40253897 CATAT-ACTGGGCCGAAGCCTTTACATTATT
1 CATATCACTGGGCCGAAGCCTTTACATTATT
* *
40253927 CATATCACTGGGCTGAAGCCTTTTCATTATT
1 CATATCACTGGGCCGAAGCCTTTACATTATT
40253958 CATATCACTGGGCCGAAGCCTTTAC
1 CATATCACTGGGCCGAAGCCTTTAC
40253983 TGTAACAATA
Statistics
Matches: 51, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
30 5 0.10
31 46 0.90
ACGTcount: A:0.24, C:0.26, G:0.17, T:0.33
Consensus pattern (31 bp):
CATATCACTGGGCCGAAGCCTTTACATTATT
Found at i:40254245 original size:26 final size:25
Alignment explanation
Indices: 40254200--40254270 Score: 106
Period size: 26 Copynumber: 2.8 Consensus size: 25
40254190 CTCTTTTAAT
*
40254200 AACTGGGGCAAAGCCCTTTTTGATA
1 AACTGGGGCAAAGCCCTTTTCGATA
*
40254225 AACTGGGGCAAAAGCCCTTTTCGGTA
1 AACTGGGGC-AAAGCCCTTTTCGATA
*
40254251 AACTGGAGCAAAGCCCTTTT
1 AACTGGGGCAAAGCCCTTTT
40254271 GCACTTCCTC
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
25 20 0.48
26 22 0.52
ACGTcount: A:0.28, C:0.23, G:0.24, T:0.25
Consensus pattern (25 bp):
AACTGGGGCAAAGCCCTTTTCGATA
Found at i:40254429 original size:25 final size:25
Alignment explanation
Indices: 40254401--40254448 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
40254391 ATAATTAAAC
* *
40254401 CCTAGGGGTAAAATGGTCATTTTTA
1 CCTAGGGGCAAAATAGTCATTTTTA
*
40254426 CCTAGGGGCAAAGTAGTCATTTT
1 CCTAGGGGCAAAATAGTCATTTT
40254449 CACATTATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.27, C:0.15, G:0.25, T:0.33
Consensus pattern (25 bp):
CCTAGGGGCAAAATAGTCATTTTTA
Found at i:40255583 original size:13 final size:13
Alignment explanation
Indices: 40255565--40255589 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
40255555 GTTCAGCTAG
40255565 AGAAGAAGAAAAA
1 AGAAGAAGAAAAA
40255578 AGAAGAAGAAAA
1 AGAAGAAGAAAA
40255590 GAATAAAACT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (13 bp):
AGAAGAAGAAAAA
Found at i:40256832 original size:46 final size:46
Alignment explanation
Indices: 40256725--40256943 Score: 180
Period size: 46 Copynumber: 4.7 Consensus size: 46
40256715 ATAGGATGCC
* * *
40256725 GATGCCATGTCCCGGACATGGTCTTACACTAGCT-T-AACTCGTA-GCG
1 GATG-CATGTCCCAGACAT-GTCTTACACTAGCTCTCATCTCG-AGGCA
* * *
40256771 GATGCATGTCTCAGACATGTCTTACACTGGCT-TACATCTCGAGGCT
1 GATGCATGTCCCAGACATGTCTTACACTAGCTCT-CATCTCGAGGCA
* * **
40256817 GATGCATGTCCCAGACATGTTTTACACTAGCTCTCGTCTC-ACTACA
1 GATGCATGTCCCAGACATGTCTTACACTAGCTCTCATCTCGA-GGCA
* * * * * *
40256863 GATGCCATGTCCCAAACATGGTCTTACACTGGCTCTCGTAAT-GTGGCC
1 GATG-CATGTCCCAGACAT-GTCTTACACTAGCTCTCAT-CTCGAGGCA
40256911 GATGCATGTCCCAGACATGTCTTACACTAGCTC
1 GATGCATGTCCCAGACATGTCTTACACTAGCTC
40256944 ACAATAGTCC
Statistics
Matches: 142, Mismatches: 22, Indels: 18
0.78 0.12 0.10
Matches are distributed among these distances:
44 14 0.10
45 14 0.10
46 64 0.45
47 27 0.19
48 22 0.15
49 1 0.01
ACGTcount: A:0.22, C:0.29, G:0.21, T:0.28
Consensus pattern (46 bp):
GATGCATGTCCCAGACATGTCTTACACTAGCTCTCATCTCGAGGCA
Found at i:40256896 original size:94 final size:92
Alignment explanation
Indices: 40256722--40256943 Score: 238
Period size: 94 Copynumber: 2.4 Consensus size: 92
40256712 GGGATAGGAT
* ** * * *
40256722 GCCGATGCCATGTCCCGGACATGGTCTTACACTAGCT-T-AACTC-GTAGCGGATGCATGTCTCA
1 GCCGATG-CATGTCCCAGACAT-GTCTTACACTAGCTCTCGTCTCACTA-CAGATGCATGTCCCA
* *
40256784 GACATGTCTTACACTGGCT-TACAT-CTCGAG
63 AACATGTCTTACACTGGCTCT-CATAAT-GAG
* *
40256814 GCTGATGCATGTCCCAGACATGTTTTACACTAGCTCTCGTCTCACTACAGATGCCATGTCCCAAA
1 GCCGATGCATGTCCCAGACATGTCTTACACTAGCTCTCGTCTCACTACAGATG-CATGTCCCAAA
* *
40256879 CATGGTCTTACACTGGCTCTCGTAATGTG
65 CAT-GTCTTACACTGGCTCTCATAATGAG
40256908 GCCGATGCATGTCCCAGACATGTCTTACACTAGCTC
1 GCCGATGCATGTCCCAGACATGTCTTACACTAGCTC
40256944 ACAATAGTCC
Statistics
Matches: 109, Mismatches: 14, Indels: 12
0.81 0.10 0.09
Matches are distributed among these distances:
90 13 0.12
91 14 0.13
92 14 0.13
93 14 0.13
94 52 0.48
95 2 0.02
ACGTcount: A:0.22, C:0.29, G:0.21, T:0.28
Consensus pattern (92 bp):
GCCGATGCATGTCCCAGACATGTCTTACACTAGCTCTCGTCTCACTACAGATGCATGTCCCAAAC
ATGTCTTACACTGGCTCTCATAATGAG
Found at i:40262043 original size:21 final size:21
Alignment explanation
Indices: 40262019--40262059 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 21
40262009 CACTAGACAC
40262019 AGGGGCACACA-CCCGTGTGGA
1 AGGGGCA-ACAGCCCGTGTGGA
40262040 AGGGGCAACAGGCCCGTGTG
1 AGGGGCAACA-GCCCGTGTG
40262060 ACCAATTATA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 3 0.17
21 7 0.39
22 8 0.44
ACGTcount: A:0.22, C:0.27, G:0.41, T:0.10
Consensus pattern (21 bp):
AGGGGCAACAGCCCGTGTGGA
Found at i:40264380 original size:47 final size:49
Alignment explanation
Indices: 40264263--40264437 Score: 183
Period size: 46 Copynumber: 3.8 Consensus size: 49
40264253 AACCCGCCCC
* * *
40264263 TAAGTGAACTCGGACTCAACTCAACGAGCTCGG--G-C-GTTCGCATCCA
1 TAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGCCAGTT-ACATCCA
*
40264309 TAA-TGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACAT-C-
1 TAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGCC-AGTTACATCCA
* * *
40264356 TCA-CGAACTCGGACTCAACTCAACGAGTTCGGA---CATTTGCATCCA
1 TAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGCCAGTTACATCCA
*
40264401 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGC
1 TAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGC
40264438 TCAACCATCC
Statistics
Matches: 110, Mismatches: 8, Indels: 19
0.80 0.06 0.14
Matches are distributed among these distances:
43 6 0.05
44 2 0.02
45 30 0.27
46 32 0.29
47 32 0.29
48 2 0.02
49 3 0.03
50 3 0.03
ACGTcount: A:0.29, C:0.28, G:0.21, T:0.22
Consensus pattern (49 bp):
TAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGCCAGTTACATCCA
Found at i:40264437 original size:93 final size:92
Alignment explanation
Indices: 40264268--40264437 Score: 295
Period size: 92 Copynumber: 1.8 Consensus size: 92
40264258 GCCCCTAAGT
* *
40264268 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAATGAACTCGGACTCAACTCAAC
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAATGAACTCGGACTCAACTCAAC
40264333 GAGTTCGGATGCCTAGTTACATCTCAC
66 GAGTTCGGATGCCTAGTTACATCTCAC
* *
40264360 GAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAA-TGAACTCGGACTCAACTCAA
40264425 CGAGTTCGGATGC
65 CGAGTTCGGATGC
40264438 TCAACCATCC
Statistics
Matches: 73, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
92 40 0.55
93 33 0.45
ACGTcount: A:0.28, C:0.29, G:0.21, T:0.22
Consensus pattern (92 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAATGAACTCGGACTCAACTCAAC
GAGTTCGGATGCCTAGTTACATCTCAC
Found at i:40264890 original size:30 final size:30
Alignment explanation
Indices: 40264856--40264915 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
40264846 ATTTAATACG
40264856 AACTTTGGAAAAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
* * *
40264886 AACTTTTGCATAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
40264916 GGCTCGGGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.30, C:0.25, G:0.08, T:0.37
Consensus pattern (30 bp):
AACTTTGGAAAAATTACACTTTTGCCCCTA
Found at i:40271953 original size:93 final size:93
Alignment explanation
Indices: 40271846--40272016 Score: 306
Period size: 93 Copynumber: 1.8 Consensus size: 93
40271836 GCCCCTAAGT
* *
40271846 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
40271911 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
* *
40271939 GAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
40272004 CGAGTTCGGATGC
66 CGAGTTCGGATGC
40272017 TCAACCATCC
Statistics
Matches: 74, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 74 1.00
ACGTcount: A:0.28, C:0.29, G:0.22, T:0.22
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:40272013 original size:46 final size:46
Alignment explanation
Indices: 40271841--40272013 Score: 217
Period size: 46 Copynumber: 3.7 Consensus size: 46
40271831 AACCCGCCCC
* * * *
40271841 TAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCA
* *
40271887 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACAT-C-
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-ATTTGCATCCA
* *
40271935 TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCA
40271980 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
40272014 TGCTCAACCA
Statistics
Matches: 108, Mismatches: 12, Indels: 14
0.81 0.09 0.10
Matches are distributed among these distances:
43 6 0.06
44 2 0.02
45 2 0.02
46 61 0.56
47 29 0.27
48 2 0.02
49 2 0.02
50 4 0.04
ACGTcount: A:0.29, C:0.28, G:0.21, T:0.22
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCA
Found at i:40272470 original size:30 final size:30
Alignment explanation
Indices: 40272436--40272495 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
40272426 ATTTAATACG
40272436 AACTTTGGAAAAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
* * *
40272466 AACTTTTGCATAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
40272496 GGCTCGGGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.30, C:0.25, G:0.08, T:0.37
Consensus pattern (30 bp):
AACTTTGGAAAAATTACACTTTTGCCCCTA
Found at i:40278479 original size:24 final size:24
Alignment explanation
Indices: 40278447--40278492 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
40278437 CGGCACCACT
40278447 CTCTTCCACCTACGACCCCAGCCG
1 CTCTTCCACCTACGACCCCAGCCG
40278471 CTCTTCCACCTACGACCCCAGC
1 CTCTTCCACCTACGACCCCAGC
40278493 TCGAAGGCCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.17, C:0.54, G:0.11, T:0.17
Consensus pattern (24 bp):
CTCTTCCACCTACGACCCCAGCCG
Found at i:40279170 original size:12 final size:11
Alignment explanation
Indices: 40279155--40279236 Score: 83
Period size: 12 Copynumber: 6.9 Consensus size: 11
40279145 ACTCCTCTTT
40279155 TTTTTATTCTTA
1 TTTTTATT-TTA
40279167 TTTTTATTTTA
1 TTTTTATTTTA
40279178 TTTTTATTTTTA
1 TTTTTA-TTTTA
*
40279190 TTTTTCTTTTGA
1 TTTTTATTTT-A
40279202 TTTTTATTTTCA
1 TTTTTATTTT-A
**
40279214 TTTCAATTTTA
1 TTTTTATTTTA
40279225 TTATTTTATTTT
1 -T-TTTTATTTT
40279237 GAAAGACATA
Statistics
Matches: 59, Mismatches: 7, Indels: 7
0.81 0.10 0.10
Matches are distributed among these distances:
11 14 0.24
12 38 0.64
13 7 0.12
ACGTcount: A:0.17, C:0.05, G:0.01, T:0.77
Consensus pattern (11 bp):
TTTTTATTTTA
Found at i:40279173 original size:6 final size:6
Alignment explanation
Indices: 40279155--40279216 Score: 81
Period size: 6 Copynumber: 10.5 Consensus size: 6
40279145 ACTCCTCTTT
* * *
40279155 TTTTTA TTCTTA TTTTTA -TTTTA TTTTTA TTTTTA TTTTTC TTTTGA
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA
*
40279202 TTTTTA TTTTCA TTT
1 TTTTTA TTTTTA TTT
40279217 CAATTTTATT
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
5 5 0.10
6 43 0.90
ACGTcount: A:0.15, C:0.05, G:0.02, T:0.79
Consensus pattern (6 bp):
TTTTTA
Found at i:40279178 original size:17 final size:17
Alignment explanation
Indices: 40279152--40279236 Score: 84
Period size: 17 Copynumber: 4.8 Consensus size: 17
40279142 TTGACTCCTC
*
40279152 TTTT-TTTTATTCTTAT
1 TTTTATTTTATTTTTAT
40279168 TTTTATTTTATTTTTAT
1 TTTTATTTTATTTTTAT
40279185 TTTTATTTT-TCTTTTGAT
1 TTTTATTTTAT-TTTT-AT
**
40279203 TTTTATTTTCATTTCAATT
1 TTTTATTTT-ATTTTTA-T
40279222 TTATTATTTTATTTT
1 TT-TTATTTTATTTT
40279237 GAAAGACATA
Statistics
Matches: 58, Mismatches: 4, Indels: 11
0.79 0.05 0.15
Matches are distributed among these distances:
16 5 0.09
17 24 0.41
18 12 0.21
19 9 0.16
20 8 0.14
ACGTcount: A:0.16, C:0.05, G:0.01, T:0.78
Consensus pattern (17 bp):
TTTTATTTTATTTTTAT
Found at i:40282989 original size:46 final size:46
Alignment explanation
Indices: 40282856--40283077 Score: 161
Period size: 46 Copynumber: 4.8 Consensus size: 46
40282846 GGGATAGGAT
* * *
40282856 GCCGATGCCATGTCCCGGACATGGTCTTACACTAGCT-T-AACTCGTA-
1 GCCGATG-CATGTCCCAGACAT-GTCTTACACTAGCTCTCATCTAG-AG
* * *
40282902 GCCGATGCTTGTCCTAGACATGTCTTACACTGGCT-TACATCTAGAG
1 GCCGATGCATGTCCCAGACATGTCTTACACTAGCTCT-CATCTAGAG
* **
40282948 GCTGATGCATGTCCCAGACATGTCTTACACTAGCTCTCATCTCA-CT
1 GCCGATGCATGTCCCAGACATGTCTTACACTAGCTCTCATCT-AGAG
* * * * * *
40282994 GCCGATACCATGT-CCTGAACATGGTCTTACACTGGCTCTCGT-AATGTG
1 GCCGAT-GCATGTCCCAG-ACAT-GTCTTACACTAGCTCTCATCTA-GAG
* *
40283042 GCCGATGCATGTTCCAGACATGTCTTACATTAGCTC
1 GCCGATGCATGTCCCAGACATGTCTTACACTAGCTC
40283078 ACAATAGTCC
Statistics
Matches: 141, Mismatches: 24, Indels: 22
0.75 0.13 0.12
Matches are distributed among these distances:
44 14 0.10
45 12 0.09
46 69 0.49
47 20 0.14
48 26 0.18
ACGTcount: A:0.22, C:0.29, G:0.20, T:0.29
Consensus pattern (46 bp):
GCCGATGCATGTCCCAGACATGTCTTACACTAGCTCTCATCTAGAG
Found at i:40283030 original size:94 final size:91
Alignment explanation
Indices: 40282856--40283077 Score: 231
Period size: 94 Copynumber: 2.4 Consensus size: 91
40282846 GGGATAGGAT
* * * *
40282856 GCCGATGCCATGTCCCGGACATGGTCTTACACTAGCT-TAACTCGTAGCCGATGCTTGTCCTAGA
1 GCCGATG-CATGTCCCAGACAT-GTCTTACACTAGCTCTAACTCCTAGCCGATCCATGTCCTAGA
40282920 CATGTCTTACACTGGCTTACATC-T-A-GAG
64 CATGTCTTACACTGGC-T-C-TCGTAATGAG
* *
40282948 GCTGATGCATGTCCCAGACATGTCTTACACTAGCTCTCATCTCACT-GCCGATACCATGTCCT-G
1 GCCGATGCATGTCCCAGACATGTCTTACACTAGCTCT-AACTC-CTAGCCGAT-CCATGTCCTAG
*
40283011 AACATGGTCTTACACTGGCTCTCGTAATGTG
63 -ACAT-GTCTTACACTGGCTCTCGTAATGAG
* *
40283042 GCCGATGCATGTTCCAGACATGTCTTACATTAGCTC
1 GCCGATGCATGTCCCAGACATGTCTTACACTAGCTC
40283078 ACAATAGTCC
Statistics
Matches: 111, Mismatches: 10, Indels: 16
0.81 0.07 0.12
Matches are distributed among these distances:
90 14 0.13
91 16 0.14
92 19 0.17
93 14 0.13
94 48 0.43
ACGTcount: A:0.22, C:0.29, G:0.20, T:0.29
Consensus pattern (91 bp):
GCCGATGCATGTCCCAGACATGTCTTACACTAGCTCTAACTCCTAGCCGATCCATGTCCTAGACA
TGTCTTACACTGGCTCTCGTAATGAG
Found at i:40284721 original size:28 final size:30
Alignment explanation
Indices: 40284675--40284731 Score: 73
Period size: 28 Copynumber: 2.0 Consensus size: 30
40284665 ATATGTCTTT
40284675 AGAATTTAGTTAATGTACT-TT-ATATTTA
1 AGAATTTAGTTAATGTACTCTTCATATTTA
** *
40284703 AGAATTTAGTTCCTTTACTCTTCATATTT
1 AGAATTTAGTTAATGTACTCTTCATATTT
40284732 CAAAATTCAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 16 0.67
29 2 0.08
30 6 0.25
ACGTcount: A:0.30, C:0.11, G:0.09, T:0.51
Consensus pattern (30 bp):
AGAATTTAGTTAATGTACTCTTCATATTTA
Found at i:40292936 original size:2 final size:2
Alignment explanation
Indices: 40292929--40292961 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
40292919 GTACAGATAC
40292929 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
40292962 GAAGAAAACA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:40301182 original size:213 final size:213
Alignment explanation
Indices: 40300815--40301243 Score: 795
Period size: 213 Copynumber: 2.0 Consensus size: 213
40300805 CTTCAACCCC
40300815 TTGTCAAAATCACTATTGGAGACCTAGGAAGCTTCAGTTTCAACTTCCTTGTGCATGTGAGCTCA
1 TTGTCAAAATCACTATTGGAGACCTAGGAAGCTTCAGTTTCAACTTCCTTGTGCATGTGAGCTCA
* * *
40300880 ATTCTCACCTGATTTTTGTAATTTTTATATTTTTTTAGATCGTTGAAACTAGGTCCAACTAGTAT
66 ATTCTCACCTAATTTTTGTAATTTTTATATTTTTTTAGATCGTTGAAACTAGGTCCAACTAGCAC
*
40300945 ATACCTTTGTTTTTGAATTTGTTAAAAATTTTAGAAGTTTCAATTGATGAATCTTGAATGTTTTT
131 ATACCTTCGTTTTTGAATTTGTTAAAAATTTTAGAAGTTTCAATTGATGAATCTTGAATGTTTTT
40301010 TTTATGATAATTATGTGT
196 TTTATGATAATTATGTGT
*
40301028 TTGTCAAAATCACTATTGGAGACCTAGGAAGCTTCGGTTTCAACTTCCTTGTGCATGTGAGCTCA
1 TTGTCAAAATCACTATTGGAGACCTAGGAAGCTTCAGTTTCAACTTCCTTGTGCATGTGAGCTCA
* *
40301093 ATTCTCACCTAATTTTTGTAATTTTTATGTTTTTTTAGATCGTTGAAACTAGGTCCAACTAGCCC
66 ATTCTCACCTAATTTTTGTAATTTTTATATTTTTTTAGATCGTTGAAACTAGGTCCAACTAGCAC
40301158 ATACCTTCGTTTTTGAATTTGTTAAAAATTTTAGAAGTTTCAATTGATGAATCTTGAATGTTTTT
131 ATACCTTCGTTTTTGAATTTGTTAAAAATTTTAGAAGTTTCAATTGATGAATCTTGAATGTTTTT
40301223 TTTATGATAATTATGTGT
196 TTTATGATAATTATGTGT
40301241 TTG
1 TTG
40301244 AAGCTTTGAT
Statistics
Matches: 209, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
213 209 1.00
ACGTcount: A:0.27, C:0.14, G:0.16, T:0.44
Consensus pattern (213 bp):
TTGTCAAAATCACTATTGGAGACCTAGGAAGCTTCAGTTTCAACTTCCTTGTGCATGTGAGCTCA
ATTCTCACCTAATTTTTGTAATTTTTATATTTTTTTAGATCGTTGAAACTAGGTCCAACTAGCAC
ATACCTTCGTTTTTGAATTTGTTAAAAATTTTAGAAGTTTCAATTGATGAATCTTGAATGTTTTT
TTTATGATAATTATGTGT
Found at i:40306462 original size:29 final size:29
Alignment explanation
Indices: 40306422--40306498 Score: 118
Period size: 29 Copynumber: 2.7 Consensus size: 29
40306412 CACGATAACG
40306422 TAAGTGACTAAAACGTAACATTTCAAATA
1 TAAGTGACTAAAACGTAACATTTCAAATA
* *
40306451 TAAGTGATTAAAACATAACATTTCAAATA
1 TAAGTGACTAAAACGTAACATTTCAAATA
* *
40306480 TAAGTTACTAAAATGTAAC
1 TAAGTGACTAAAACGTAAC
40306499 TTGAGACAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 42 1.00
ACGTcount: A:0.49, C:0.12, G:0.09, T:0.30
Consensus pattern (29 bp):
TAAGTGACTAAAACGTAACATTTCAAATA
Found at i:40307133 original size:23 final size:22
Alignment explanation
Indices: 40307099--40307141 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 22
40307089 ATCAACATTT
40307099 TAAATATATAAATACCACATTTGA
1 TAAATATATAAA-ACC-CATTTGA
40307123 TAAA-ATATAAAACCCATTT
1 TAAATATATAAAACCCATTT
40307142 ATACCATTCT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 5 0.26
22 3 0.16
23 7 0.37
24 4 0.21
ACGTcount: A:0.51, C:0.14, G:0.02, T:0.33
Consensus pattern (22 bp):
TAAATATATAAAACCCATTTGA
Found at i:40307711 original size:10 final size:10
Alignment explanation
Indices: 40307696--40307725 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
40307686 TATATATAAA
*
40307696 ATTTAATTGT
1 ATTTAATTAT
40307706 ATTTAATTAT
1 ATTTAATTAT
40307716 ATTTAATTAT
1 ATTTAATTAT
40307726 TGCATATTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (10 bp):
ATTTAATTAT
Found at i:40307712 original size:29 final size:29
Alignment explanation
Indices: 40307650--40307713 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 29
40307640 GTTTTAATGC
* * * *
40307650 GTAAATTTATACATAAATTTTAATTTTGT
1 GTAATTTTATACATAAAATTTAATTGTAT
*
40307679 GTAATTTTATATATAAAATTTAATTGTAT
1 GTAATTTTATACATAAAATTTAATTGTAT
*
40307708 TTAATT
1 GTAATT
40307714 ATATTTAATT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.39, C:0.02, G:0.06, T:0.53
Consensus pattern (29 bp):
GTAATTTTATACATAAAATTTAATTGTAT
Found at i:40307957 original size:29 final size:27
Alignment explanation
Indices: 40307889--40307957 Score: 66
Period size: 31 Copynumber: 2.4 Consensus size: 27
40307879 TAAAGTTTTA
* * *
40307889 CATATATAATTACACTAAATTAAAGTT
1 CATATATAATTACACTAAATCAAAATC
*
40307916 CATATATCAAATTACAAATTAAATCAAAATC
1 CATATAT--AATTAC--ACTAAATCAAAATC
40307947 CATATATAATT
1 CATATATAATT
40307958 TTGAGATTTA
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
27 7 0.21
29 10 0.29
31 17 0.50
ACGTcount: A:0.51, C:0.13, G:0.01, T:0.35
Consensus pattern (27 bp):
CATATATAATTACACTAAATCAAAATC
Found at i:40308837 original size:16 final size:16
Alignment explanation
Indices: 40308793--40308839 Score: 51
Period size: 16 Copynumber: 3.0 Consensus size: 16
40308783 ACAATTGAAA
40308793 TTAAATTTTT-AAAAT
1 TTAAATTTTTAAAAAT
** **
40308808 TTAAAAGTAAAAAAAT
1 TTAAATTTTTAAAAAT
40308824 TTAAATTTTTAAAAAT
1 TTAAATTTTTAAAAAT
40308840 AAAAATACAA
Statistics
Matches: 23, Mismatches: 8, Indels: 1
0.72 0.25 0.03
Matches are distributed among these distances:
15 6 0.26
16 17 0.74
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (16 bp):
TTAAATTTTTAAAAAT
Found at i:40311391 original size:5 final size:5
Alignment explanation
Indices: 40311381--40311413 Score: 66
Period size: 5 Copynumber: 6.6 Consensus size: 5
40311371 GTCTTTCTCC
40311381 TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTT
1 TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTT
40311414 TCCATATGAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTCT
Found at i:40318960 original size:26 final size:26
Alignment explanation
Indices: 40318931--40318983 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
40318921 TAATCTAAAA
* *
40318931 ATTTTAATTAATTACGTAAATGATCT
1 ATTTTAATAAAATACGTAAATGATCT
*
40318957 ATTTTTATAAAATACGTAAATGATCT
1 ATTTTAATAAAATACGTAAATGATCT
40318983 A
1 A
40318984 AAATTTATAG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.42, C:0.08, G:0.08, T:0.43
Consensus pattern (26 bp):
ATTTTAATAAAATACGTAAATGATCT
Found at i:40319250 original size:11 final size:11
Alignment explanation
Indices: 40319232--40319261 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
40319222 TATTTTTCTG
40319232 TTTA-TTATTA
1 TTTATTTATTA
40319242 TTTATTTATTA
1 TTTATTTATTA
40319253 TTTATTTAT
1 TTTATTTAT
40319262 AATATTTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 4 0.21
11 15 0.79
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (11 bp):
TTTATTTATTA
Found at i:40319323 original size:11 final size:11
Alignment explanation
Indices: 40319298--40319336 Score: 53
Period size: 10 Copynumber: 3.5 Consensus size: 11
40319288 ATTTAAATCT
40319298 TTTTTTATTTA
1 TTTTTTATTTA
40319309 -TTTTTATTTA
1 TTTTTTATTTA
*
40319319 TTTTTTATATAA
1 TTTTTTAT-TTA
40319331 TTTTTT
1 TTTTTT
40319337 GGTGGAGTCA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
10 10 0.40
11 7 0.28
12 8 0.32
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (11 bp):
TTTTTTATTTA
Found at i:40322016 original size:39 final size:39
Alignment explanation
Indices: 40321962--40322168 Score: 287
Period size: 39 Copynumber: 5.3 Consensus size: 39
40321952 CAGGACTTTA
*
40321962 AGCCCGGATATAATACCAGCAC-AAAGCCTGT-GGGACTTT
1 AGCCCGGATATAACACCAGCACGAAAGCCT-TCGGGAC-TT
* *
40322001 AGCCCGGATATAATACCAGCAC-AAAGCCTGCGGGACTTT
1 AGCCCGGATATAACACCAGCACGAAAGCCTTCGGGAC-TT
* *
40322040 AGCCCGGATATAACACCAGCACGAATGCCTTCAGGACTT
1 AGCCCGGATATAACACCAGCACGAAAGCCTTCGGGACTT
*
40322079 AGCCCGGATAT-ACACCAGCACGAATGCCTTCGGGACTT
1 AGCCCGGATATAACACCAGCACGAAAGCCTTCGGGACTT
*
40322117 AGCCCGGATATAACACCAGCACGAATGCCTTCGGGACTT
1 AGCCCGGATATAACACCAGCACGAAAGCCTTCGGGACTT
*
40322156 GGCCCGGATATAA
1 AGCCCGGATATAA
40322169 TTCTCCATTA
Statistics
Matches: 158, Mismatches: 7, Indels: 6
0.92 0.04 0.04
Matches are distributed among these distances:
38 37 0.23
39 110 0.70
40 11 0.07
ACGTcount: A:0.29, C:0.29, G:0.23, T:0.18
Consensus pattern (39 bp):
AGCCCGGATATAACACCAGCACGAAAGCCTTCGGGACTT
Found at i:40322136 original size:77 final size:77
Alignment explanation
Indices: 40321935--40322167 Score: 310
Period size: 77 Copynumber: 3.0 Consensus size: 77
40321925 CAAATCCAAT
* * * * *
40321935 CACCACCACAAAGCATGCAGGACTTTAAGCCCGGATATAATACCAGCAC-AAAGCCTGT-GGGAC
1 CACCAGCACAAAGCCTGCGGGACTTT-AGCCCGGATATAACACCAGCACGAATGCCT-TCGGGAC
40321998 TTTAGCCCGGATATAA
64 -TTAGCCCGGATAT-A
* *
40322014 TACCAGCACAAAGCCTGCGGGACTTTAGCCCGGATATAACACCAGCACGAATGCCTTCAGGACTT
1 CACCAGCACAAAGCCTGCGGGACTTTAGCCCGGATATAACACCAGCACGAATGCCTTCGGGACTT
40322079 AGCCCGGATATA
66 AGCCCGGATATA
* *
40322091 CACCAGCACGAATGCCTTCGGGAC-TTAGCCCGGATATAACACCAGCACGAATGCCTTCGGGACT
1 CACCAGCAC-AAAGCCTGCGGGACTTTAGCCCGGATATAACACCAGCACGAATGCCTTCGGGACT
*
40322155 TGGCCCGGATATA
65 TAGCCCGGATATA
40322168 ATTCTCCATT
Statistics
Matches: 139, Mismatches: 12, Indels: 8
0.87 0.08 0.05
Matches are distributed among these distances:
77 60 0.43
78 47 0.34
79 32 0.23
ACGTcount: A:0.30, C:0.30, G:0.22, T:0.18
Consensus pattern (77 bp):
CACCAGCACAAAGCCTGCGGGACTTTAGCCCGGATATAACACCAGCACGAATGCCTTCGGGACTT
AGCCCGGATATA
Found at i:40322194 original size:2 final size:2
Alignment explanation
Indices: 40322187--40322212 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
40322177 TATCATGCAC
40322187 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
40322213 CATAACACAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:40328392 original size:39 final size:40
Alignment explanation
Indices: 40328324--40328618 Score: 383
Period size: 39 Copynumber: 7.5 Consensus size: 40
40328314 ACAAAGCATG
* * * *
40328324 CGGGACTTGAAGCCCGGATATAATACCAGCAC-AAAGCCTG
1 CGGGACTT-TAGCCCGGATATAACACCAGCACGAATGCCTT
* * * *
40328364 CGGGACTTTAGCTCGGATATAATACCAGCAC-AAAGCCTG
1 CGGGACTTTAGCCCGGATATAACACCAGCACGAATGCCTT
40328403 CGGGACTTTAGCCCGGATATAACACCAGCACGAATGCCTT
1 CGGGACTTTAGCCCGGATATAACACCAGCACGAATGCCTT
*
40328443 CGGGAC-TTAGCTCGGATAT-ACACCAGCACGAATGCCTT
1 CGGGACTTTAGCCCGGATATAACACCAGCACGAATGCCTT
* *
40328481 CGGGA-GTTAGCCCAGATATAACACCAGCACGAATGCCTT
1 CGGGACTTTAGCCCGGATATAACACCAGCACGAATGCCTT
* *
40328520 CAGGAC-TTAGCCCGGACATAACACCAGCACGAATGCCTT
1 CGGGACTTTAGCCCGGATATAACACCAGCACGAATGCCTT
*
40328559 CGGGAC-TTAGCCTGGATATAACACCAGCACGAATGCCTT
1 CGGGACTTTAGCCCGGATATAACACCAGCACGAATGCCTT
40328598 CGGGAC-TT-GTCCCGGATATAA
1 CGGGACTTTAG-CCCGGATATAA
40328619 TTCTCCATTA
Statistics
Matches: 234, Mismatches: 16, Indels: 11
0.90 0.06 0.04
Matches are distributed among these distances:
38 36 0.15
39 178 0.76
40 20 0.09
ACGTcount: A:0.29, C:0.28, G:0.23, T:0.19
Consensus pattern (40 bp):
CGGGACTTTAGCCCGGATATAACACCAGCACGAATGCCTT
Found at i:40328616 original size:155 final size:155
Alignment explanation
Indices: 40328334--40328617 Score: 412
Period size: 155 Copynumber: 1.8 Consensus size: 155
40328324 CGGGACTTGA
* * * * * *
40328334 AGCCCGGATATAATACCAGCACAAAGCCTGCGGGACTTTAGCTCGGATATAATACCAGCACAAAG
1 AGCCCAGATATAACACCAGCACAAAGCCTGCAGGACTTTAGCCCGGACATAACACCAGCACAAAG
*
40328399 CCTGCGGGACTTTAGCCCGGATATAACACCAGCACGAATGCCTTCGGGACTTAGCTCGGATATAC
66 CCTGCGGGACTTTAGCCCGGATATAACACCAGCACGAATGCCTTCGGGACTTAGCCCGGATATAC
40328464 ACCAGCACGAATGCCTTCGGGAGTT
131 ACCAGCACGAATGCCTTCGGGAGTT
* *
40328489 AGCCCAGATATAACACCAGCACGAATGCCTTCAGGAC-TTAGCCCGGACATAACACCAGCACGAA
1 AGCCCAGATATAACACCAGCAC-AAAGCCTGCAGGACTTTAGCCCGGACATAACACCAGCAC-AA
* * *
40328553 TGCCTTCGGGAC-TTAGCCTGGATATAACACCAGCACGAATGCCTTCGGGACTT-GTCCCGGATA
64 AGCCTGCGGGACTTTAGCCCGGATATAACACCAGCACGAATGCCTTCGGGACTTAG-CCCGGATA
40328616 TA
128 TA
40328618 ATTCTCCATT
Statistics
Matches: 114, Mismatches: 12, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
154 1 0.01
155 90 0.79
156 23 0.20
ACGTcount: A:0.29, C:0.29, G:0.23, T:0.19
Consensus pattern (155 bp):
AGCCCAGATATAACACCAGCACAAAGCCTGCAGGACTTTAGCCCGGACATAACACCAGCACAAAG
CCTGCGGGACTTTAGCCCGGATATAACACCAGCACGAATGCCTTCGGGACTTAGCCCGGATATAC
ACCAGCACGAATGCCTTCGGGAGTT
Found at i:40333450 original size:241 final size:241
Alignment explanation
Indices: 40333018--40333508 Score: 822
Period size: 241 Copynumber: 2.0 Consensus size: 241
40333008 AATGAGAAAA
* * *
40333018 TATGATAAAAATTGATTTTCGGACCTAGAGGTAAAATGGTCATTTTGTCAAAGTCTAGGGGCAAA
1 TATG-TAAAAATTGATTTTCGAACCTAGAGGTAAAATGGCCAATTTGTCAAAGTCTAGGGGCAAA
* *
40333083 ATGGTCAATTTGCCCAATTATGAATTTTTGAGTGTTTAGGTTAATATGCTGATGAAATGAATAAA
65 ATGGTCAATTTACCCAATTATGAATTTTTGAGTGTCTAGGTTAATATGCTGATGAAATGAATAAA
* * * *
40333148 CTTCTATCATTTTAGATCAAGAATTACAAAATTCGGGTTTAGACCGAGGAAAAGAAAAACAAGTG
130 CTTCTATCATTTTAGATCAAGAATTACAAAATCCAGGCTTAGACCGAGGAAAAGAAAAACAAGTA
40333213 GACAAAGTCGAACTAGTCGTCTACATTTTGTATACCA-AGGTAAGTTC
195 GACAAAGTCGAACTAGTCGTCTACATTTTGTATA-CAGAGGTAAGTTC
*
40333260 TATGTAAAAATTGATTTTCGAACCTAGAGGTAAAATGGCCAATTTGTGAAAGTCTAGGGGCAAAA
1 TATGTAAAAATTGATTTTCGAACCTAGAGGTAAAATGGCCAATTTGTCAAAGTCTAGGGGCAAAA
* *
40333325 TGGTCAATTTATCCAATTATGAATTTTTGAGTGTCTAGGTTAATATGCTGATGAAATGAATAAAT
66 TGGTCAATTTACCCAATTATGAATTTTTGAGTGTCTAGGTTAATATGCTGATGAAATGAATAAAC
* *
40333390 TTCTATCATTTTAGATCAAGAATTACAAAATCCAGGCTTAGACCGGGGAAAAGCAAAACAAGTAG
131 TTCTATCATTTTAGATCAAGAATTACAAAATCCAGGCTTAGACCGAGGAAAAGAAAAACAAGTAG
*
40333455 ACTAAGTCGAACTAGTCGTCTACATTTTGTATACAGAGGTAAGTTC
196 ACAAAGTCGAACTAGTCGTCTACATTTTGTATACAGAGGTAAGTTC
40333501 TATGTAAA
1 TATGTAAA
40333509 TAATACAACT
Statistics
Matches: 233, Mismatches: 15, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
240 2 0.01
241 227 0.97
242 4 0.02
ACGTcount: A:0.36, C:0.12, G:0.20, T:0.31
Consensus pattern (241 bp):
TATGTAAAAATTGATTTTCGAACCTAGAGGTAAAATGGCCAATTTGTCAAAGTCTAGGGGCAAAA
TGGTCAATTTACCCAATTATGAATTTTTGAGTGTCTAGGTTAATATGCTGATGAAATGAATAAAC
TTCTATCATTTTAGATCAAGAATTACAAAATCCAGGCTTAGACCGAGGAAAAGAAAAACAAGTAG
ACAAAGTCGAACTAGTCGTCTACATTTTGTATACAGAGGTAAGTTC
Found at i:40333766 original size:48 final size:48
Alignment explanation
Indices: 40333711--40334088 Score: 228
Period size: 48 Copynumber: 7.9 Consensus size: 48
40333701 CGGCCACATT
*
40333711 ATGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCGTCGGCATTGAG
1 ATGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGAG
* *
40333759 ATGAGAGCCAGTGTAAGA-CATGTCTGGGACAT-GCATCTGC-TACGAG
1 ATGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCAT-TGAG
* ** * * * * *
40333805 AT--GTGTTAGTGTAAGACTATATCAGGGACATAGCATCAGCACGTAT-AG
1 ATGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCA--T-TGAG
* * * * *
40333853 A-G-GTGTCAGTGTAAAACCATGTCTAGGACATGGCATCGACACGTAT-AG
1 ATGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCA--T-TGAG
* ** * * * ** *
40333901 A-G-GTGTAAATGCAAGACCATGTTTGGGACATGGCATCGGCACGGAT
1 ATGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGAG
* * * *
40333947 ATGTGAGAGCTC-GTGTAAGACCATGTCTGGGACATGGCGTCAGCCTTGAT
1 A--TGAGAGC-CAGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGAG
* * * * *
40333997 TTCAATAGTCAGTGTAAGACCATGTCTGGGACATGGCATCGAC-TT--G
1 AT-GAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGAG
40334043 ATGAATGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCAT
1 ATG-A-GAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCAT
40334089 CATACCCTAT
Statistics
Matches: 258, Mismatches: 54, Indels: 36
0.74 0.16 0.10
Matches are distributed among these distances:
44 11 0.04
45 12 0.05
46 22 0.09
47 49 0.19
48 97 0.38
49 35 0.14
50 32 0.12
ACGTcount: A:0.28, C:0.19, G:0.30, T:0.24
Consensus pattern (48 bp):
ATGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGAG
Found at i:40334022 original size:49 final size:47
Alignment explanation
Indices: 40333959--40334084 Score: 182
Period size: 47 Copynumber: 2.6 Consensus size: 47
40333949 GTGAGAGCTC
* * *
40333959 GTGTAAGACCATGTCTGGGACATGGCGTCAGCCTTGATTTCAAT-AGTCA
1 GTGTAAGACCATGTCTGGGACATGGCATC-GACTTGA--TCAATGAGCCA
*
40334008 GTGTAAGACCATGTCTGGGACATGGCATCGACTTGATGAATGAGCCA
1 GTGTAAGACCATGTCTGGGACATGGCATCGACTTGATCAATGAGCCA
40334055 GTGTAAGACCATGTCTGGGACATGGCATCG
1 GTGTAAGACCATGTCTGGGACATGGCATCG
40334085 GCATCATACC
Statistics
Matches: 72, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
46 4 0.06
47 34 0.47
48 6 0.08
49 28 0.39
ACGTcount: A:0.25, C:0.20, G:0.29, T:0.25
Consensus pattern (47 bp):
GTGTAAGACCATGTCTGGGACATGGCATCGACTTGATCAATGAGCCA
Found at i:40334074 original size:146 final size:140
Alignment explanation
Indices: 40333719--40334087 Score: 329
Period size: 146 Copynumber: 2.6 Consensus size: 140
40333709 TTATGAGAGC
* *
40333719 CAGTGTAAGACCATGTCTGGGACATGGCGTCGGCATTGA-G-ATGAGAGCCAGTGTAAGA-CATG
1 CAGTGTAAGACCATGTCTGGGACATGGCATCGAC-TTGATGAAT--GAGCCAGTGTAAGACCATG
* * *
40333781 TCTGGGACAT-GCATCTGCTACGAGATGTGTTAGTGTAAGACTATATCAGGGACATAGCATCAGC
63 TCTGGGACATGGCATCGGC-ACGAGATGTGCTAGTGTAAGACCATATCAGGGACATAGCATCAGC
* *
40333845 ACGTATAGAGGTGT
127 ACGTATACAGATGT
* * ** * * ** * *
40333859 CAGTGTAAAACCATGTCTAGGACATGGCATCGACACGTAT-AGAGGTGTAAATGCAAGACCATGT
1 CAGTGTAAGACCATGTCTGGGACATGGCATCGACTTG-ATGA-ATGAGCCAGTGTAAGACCATGT
* * * * * * *
40333923 TTGGGACATGGCATCGGCACGGATATGTGAGAGCTCGTGTAAGACCATGTCTGGGACATGGCGTC
64 CTGGGACATGGCATCGGCAC-GAGATGT----GCTAGTGTAAGACCATATCAGGGACATAGCATC
* *
40333988 AGC-CTTGATTTCA-ATAGT
124 AGCACGT-A-TACAGAT-GT
40334006 CAGTGTAAGACCATGTCTGGGACATGGCATCGACTTGATGAATGAGCCAGTGTAAGACCATGTCT
1 CAGTGTAAGACCATGTCTGGGACATGGCATCGACTTGATGAATGAGCCAGTGTAAGACCATGTCT
40334071 GGGACATGGCATCGGCA
66 GGGACATGGCATCGGCA
40334088 TCATACCCTA
Statistics
Matches: 177, Mismatches: 37, Indels: 24
0.74 0.16 0.10
Matches are distributed among these distances:
139 1 0.01
140 40 0.23
141 15 0.08
142 14 0.08
145 2 0.01
146 67 0.38
147 38 0.21
ACGTcount: A:0.28, C:0.19, G:0.30, T:0.24
Consensus pattern (140 bp):
CAGTGTAAGACCATGTCTGGGACATGGCATCGACTTGATGAATGAGCCAGTGTAAGACCATGTCT
GGGACATGGCATCGGCACGAGATGTGCTAGTGTAAGACCATATCAGGGACATAGCATCAGCACGT
ATACAGATGT
Found at i:40335110 original size:28 final size:28
Alignment explanation
Indices: 40335079--40335160 Score: 110
Period size: 28 Copynumber: 2.9 Consensus size: 28
40335069 AAGACATGGG
*
40335079 CGTGTCATGGCCGTATGAGAGACACGAA
1 CGTGTCATGGCCGTGTGAGAGACACGAA
* *
40335107 CGTGTCATGGCCGTGTGAGAGACATGAG
1 CGTGTCATGGCCGTGTGAGAGACACGAA
* * *
40335135 CATGTCATGGTCATGTGAGAGACACG
1 CGTGTCATGGCCGTGTGAGAGACACG
40335161 GGCAATGAAC
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 47 1.00
ACGTcount: A:0.26, C:0.20, G:0.34, T:0.21
Consensus pattern (28 bp):
CGTGTCATGGCCGTGTGAGAGACACGAA
Found at i:40339399 original size:15 final size:15
Alignment explanation
Indices: 40339381--40339414 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
40339371 CACATTACAT
40339381 AAATTAT-TTTCATGA
1 AAATTATATTTCAT-A
40339396 AAATTATATTTCATA
1 AAATTATATTTCATA
40339411 AAAT
1 AAAT
40339415 AACTATCAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 12 0.67
16 6 0.33
ACGTcount: A:0.47, C:0.06, G:0.03, T:0.44
Consensus pattern (15 bp):
AAATTATATTTCATA
Found at i:40340938 original size:16 final size:18
Alignment explanation
Indices: 40340912--40340944 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
40340902 TAATATGCTC
40340912 AATTCCACAAA-CATACA
1 AATTCCACAAATCATACA
40340929 AATT-CACAAATCATAC
1 AATTCCACAAATCATAC
40340945 CATATTGACA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.52, C:0.27, G:0.00, T:0.21
Consensus pattern (18 bp):
AATTCCACAAATCATACA
Found at i:40344930 original size:22 final size:22
Alignment explanation
Indices: 40344900--40344941 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
40344890 GTGTAGCAAT
* *
40344900 CATCAAAAACTTTTTTACATAA
1 CATCAAAAACTCTTTCACATAA
*
40344922 CATCGAAAACTCTTTCACAT
1 CATCAAAAACTCTTTCACAT
40344942 CTTTCTGTAG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.40, C:0.24, G:0.02, T:0.33
Consensus pattern (22 bp):
CATCAAAAACTCTTTCACATAA
Found at i:40348555 original size:16 final size:18
Alignment explanation
Indices: 40348529--40348561 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
40348519 TAATATGCTC
40348529 AATTCCACAAA-CATACA
1 AATTCCACAAATCATACA
40348546 AATT-CACAAATCATAC
1 AATTCCACAAATCATAC
40348562 CATATTGACA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.52, C:0.27, G:0.00, T:0.21
Consensus pattern (18 bp):
AATTCCACAAATCATACA
Found at i:40348652 original size:2 final size:2
Alignment explanation
Indices: 40348645--40348672 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
40348635 AAGTATAGTC
40348645 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
40348673 GATTCAACTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:40349018 original size:27 final size:27
Alignment explanation
Indices: 40348980--40349035 Score: 103
Period size: 27 Copynumber: 2.1 Consensus size: 27
40348970 TAGCATCTAA
40348980 AATCAACTTACTAAATGTGTACAATTT
1 AATCAACTTACTAAATGTGTACAATTT
*
40349007 AATCAACTTACTAAATGTGTACATTTT
1 AATCAACTTACTAAATGTGTACAATTT
40349034 AA
1 AA
40349036 CCGTAAAGTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.41, C:0.14, G:0.07, T:0.38
Consensus pattern (27 bp):
AATCAACTTACTAAATGTGTACAATTT
Found at i:40359735 original size:15 final size:15
Alignment explanation
Indices: 40359715--40359756 Score: 57
Period size: 15 Copynumber: 2.8 Consensus size: 15
40359705 GCTGTAAATG
40359715 GGATTTCATTATCAT
1 GGATTTCATTATCAT
* *
40359730 GGATTTCTTTATCTT
1 GGATTTCATTATCAT
*
40359745 GGATTTCCTTAT
1 GGATTTCATTAT
40359757 TCTGGGCTCC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.19, C:0.14, G:0.14, T:0.52
Consensus pattern (15 bp):
GGATTTCATTATCAT
Found at i:40364556 original size:2 final size:2
Alignment explanation
Indices: 40364549--40364579 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
40364539 TCATGACATG
40364549 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
40364580 GACCAGCCTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:40368219 original size:151 final size:152
Alignment explanation
Indices: 40367940--40368235 Score: 465
Period size: 151 Copynumber: 1.9 Consensus size: 152
40367930 TAAACTTTAA
* *
40367940 GATATTTTTCAGTATTTTGAATTGTTTAGAAGTTTTATGTTTCTTAAGCAGCAAGAGAATTCAGT
1 GATATTTTTCAATATTTTGAATTGTTTAGAAGTTTTATGTTTCTTAAGCAACAAGAG-ATTCAGT
40368005 TTCATAAAACTACTTCTTATTTAGATTAATTAGAGTTTTATTATACTTAGGAGTTTTACTTTGAT
65 TTCATAAAACTACTTCTTATTTAGATTAATTAGAGTTTTATTATACTTAGGAGTTTTACTTTGAT
40368070 ATAATTAACTAGTCTTGATAGAG
130 ATAATTAACTAGTCTTGATAGAG
*
40368093 GATATTTTTTCAATATTTTGAATTG-TTAGAAG-TTTATGTTTCTTAAGCAACAACGAG-TTTAG
1 GATA-TTTTTCAATATTTTGAATTGTTTAGAAGTTTTATGTTTCTTAAGCAACAA-GAGATTCAG
* * *
40368155 TTTCACTAAAACTA-TTCTTATTTAGATTAATTAGAGTTTTATTGTATTTAGGAGTTTTATTTTG
64 TTTCA-TAAAACTACTTCTTATTTAGATTAATTAGAGTTTTATTATACTTAGGAGTTTTACTTTG
*
40368219 ATATAATTAGCTAGTCT
128 ATATAATTAACTAGTCT
40368236 ATATAAAAAA
Statistics
Matches: 133, Mismatches: 7, Indels: 8
0.90 0.05 0.05
Matches are distributed among these distances:
151 72 0.54
152 28 0.21
153 14 0.11
154 19 0.14
ACGTcount: A:0.31, C:0.08, G:0.15, T:0.47
Consensus pattern (152 bp):
GATATTTTTCAATATTTTGAATTGTTTAGAAGTTTTATGTTTCTTAAGCAACAAGAGATTCAGTT
TCATAAAACTACTTCTTATTTAGATTAATTAGAGTTTTATTATACTTAGGAGTTTTACTTTGATA
TAATTAACTAGTCTTGATAGAG
Found at i:40370026 original size:78 final size:77
Alignment explanation
Indices: 40369890--40370047 Score: 226
Period size: 78 Copynumber: 2.0 Consensus size: 77
40369880 AGTTTGACTT
40369890 AAAATTATTGGATATATATAGAATTACTAAGTGTCTATCTATAGACTTAACAAATGTCTTACAAG
1 AAAATTATTGGATATATATAGAATTACTAAGTGTCTATCTATAGACTTAACAAATGTCTTACAAG
40369955 TATCCTATTAAA
66 TATCCTATTAAA
* * * * * * *
40369967 AAAATGTATTGGATATCTATGGACTTACTAAGTGTCTATTTATAGGCTTACCAAGTGTCTTACAA
1 AAAAT-TATTGGATATATATAGAATTACTAAGTGTCTATCTATAGACTTAACAAATGTCTTACAA
* *
40370032 GTGTCCTATTTAA
65 GTATCCTATTAAA
40370045 AAA
1 AAA
40370048 TAAAATAAAG
Statistics
Matches: 71, Mismatches: 9, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
77 5 0.07
78 66 0.93
ACGTcount: A:0.37, C:0.13, G:0.13, T:0.37
Consensus pattern (77 bp):
AAAATTATTGGATATATATAGAATTACTAAGTGTCTATCTATAGACTTAACAAATGTCTTACAAG
TATCCTATTAAA
Found at i:40370355 original size:84 final size:84
Alignment explanation
Indices: 40370260--40370413 Score: 220
Period size: 84 Copynumber: 1.8 Consensus size: 84
40370250 TATTATTTGC
* * ** * **
40370260 CTTACTTAAATGTATATTCATTTTGCTTATGTTCATTGTCA-AGTATCAAATGGGGTTGGTAATT
1 CTTACTCAAATGTATATTCATTTTGCATATGTTCATCAT-AGAGTACCAAATGGGGTTGACAATT
40370324 AAATATGCATTATTGCTTTT
65 AAATATGCATTATTGCTTTT
*
40370344 CTTACTCAAATGTATATTCATTTTGCATCTGTTCATCATAGAGTACCAAATGGGGTTGACAATTA
1 CTTACTCAAATGTATATTCATTTTGCATATGTTCATCATAGAGTACCAAATGGGGTTGACAATTA
40370409 AATAT
66 AATAT
40370414 TAGGACATTG
Statistics
Matches: 61, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
83 1 0.02
84 60 0.98
ACGTcount: A:0.30, C:0.13, G:0.15, T:0.42
Consensus pattern (84 bp):
CTTACTCAAATGTATATTCATTTTGCATATGTTCATCATAGAGTACCAAATGGGGTTGACAATTA
AATATGCATTATTGCTTTT
Found at i:40371699 original size:42 final size:42
Alignment explanation
Indices: 40371650--40371734 Score: 170
Period size: 42 Copynumber: 2.0 Consensus size: 42
40371640 TGATATGCCG
40371650 TTAGGGAGAGCTTAGTCATGATACTATAGTGGAATGACTTCA
1 TTAGGGAGAGCTTAGTCATGATACTATAGTGGAATGACTTCA
40371692 TTAGGGAGAGCTTAGTCATGATACTATAGTGGAATGACTTCA
1 TTAGGGAGAGCTTAGTCATGATACTATAGTGGAATGACTTCA
40371734 T
1 T
40371735 GACTAAATGA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.31, C:0.12, G:0.26, T:0.32
Consensus pattern (42 bp):
TTAGGGAGAGCTTAGTCATGATACTATAGTGGAATGACTTCA
Found at i:40375574 original size:40 final size:40
Alignment explanation
Indices: 40375495--40375652 Score: 151
Period size: 40 Copynumber: 4.0 Consensus size: 40
40375485 TTCGAATGAT
* * * *
40375495 ATCCGGGCTAAG-TCCCGAAGGC-TTTGTGCTAAGTGACTAA
1 ATCCGGACTAAGAT-CCGAAGGCATTCGTGC-GAGTTACTAA
* *
40375535 ATCCGGACTAAGATCCGACGGCATACGTGCGAGTTACTAA
1 ATCCGGACTAAGATCCGAAGGCATTCGTGCGAGTTACTAA
* * * *
40375575 ATCCGGACTAAGATCCGAAGGCTTTCGAGCAAGCTACTAA
1 ATCCGGACTAAGATCCGAAGGCATTCGTGCGAGTTACTAA
** *
40375615 ATCCGGGTTGAG-TCCCGAAGGCATTCGTGCGAGTTACT
1 ATCCGGACTAAGAT-CCGAAGGCATTCGTGCGAGTTACT
40375653 GTAACCGGGC
Statistics
Matches: 96, Mismatches: 19, Indels: 6
0.79 0.16 0.05
Matches are distributed among these distances:
39 1 0.01
40 89 0.93
41 6 0.06
ACGTcount: A:0.27, C:0.24, G:0.27, T:0.23
Consensus pattern (40 bp):
ATCCGGACTAAGATCCGAAGGCATTCGTGCGAGTTACTAA
Found at i:40375673 original size:80 final size:80
Alignment explanation
Indices: 40375495--40375682 Score: 206
Period size: 80 Copynumber: 2.3 Consensus size: 80
40375485 TTCGAATGAT
* *
40375495 ATCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACTAAATCCGGACTAAGATCCGACGGCATA
1 ATCCGGGCTAAGTCCCGAAGGCTTTGAGCTAAGTGACTAAATCCGGACTAAGATCCGAAGGCATA
40375560 CGTGCGAGTTACTAA
66 CGTGCGAGTTACTAA
* ** *
40375575 ATCCGGACTAAGAT-CCGAAGGCTTTCGAGC-AAGCT-ACTAAATCCGGGTTGAG-TCCCGAAGG
1 ATCCGGGCTAAG-TCCCGAAGGCTTT-GAGCTAAG-TGACTAAATCCGGACTAAGAT-CCGAAGG
* *
40375636 CATTCGTGCGAGTTACTGTA
62 CATACGTGCGAGTTACT-AA
*
40375656 A-CCGGGCTATGTCCCGAAGGCATTTGA
1 ATCCGGGCTAAGTCCCGAAGGC-TTTGA
40375683 ATGTGTAGCC
Statistics
Matches: 91, Mismatches: 10, Indels: 14
0.79 0.09 0.12
Matches are distributed among these distances:
79 2 0.02
80 79 0.87
81 10 0.11
ACGTcount: A:0.26, C:0.24, G:0.27, T:0.23
Consensus pattern (80 bp):
ATCCGGGCTAAGTCCCGAAGGCTTTGAGCTAAGTGACTAAATCCGGACTAAGATCCGAAGGCATA
CGTGCGAGTTACTAA
Found at i:40383633 original size:40 final size:40
Alignment explanation
Indices: 40383554--40383711 Score: 151
Period size: 40 Copynumber: 4.0 Consensus size: 40
40383544 TTCGAATGAT
* * * *
40383554 ATCCGGGCTAAG-TCCCGAAGGC-TTTGTGCTAAGTGACTAA
1 ATCCGGACTAAGAT-CCGAAGGCATTCGTGC-GAGTTACTAA
* *
40383594 ATCCGGACTAAGATCCGACGGCATACGTGCGAGTTACTAA
1 ATCCGGACTAAGATCCGAAGGCATTCGTGCGAGTTACTAA
* * * *
40383634 ATCCGGACTAAGATCCGAAGGCTTTCGAGCAAGCTACTAA
1 ATCCGGACTAAGATCCGAAGGCATTCGTGCGAGTTACTAA
** *
40383674 ATCCGGGTTGAG-TCCCGAAGGCATTCGTGCGAGTTACT
1 ATCCGGACTAAGAT-CCGAAGGCATTCGTGCGAGTTACT
40383712 GTAACCGGGC
Statistics
Matches: 96, Mismatches: 19, Indels: 6
0.79 0.16 0.05
Matches are distributed among these distances:
39 1 0.01
40 89 0.93
41 6 0.06
ACGTcount: A:0.27, C:0.24, G:0.27, T:0.23
Consensus pattern (40 bp):
ATCCGGACTAAGATCCGAAGGCATTCGTGCGAGTTACTAA
Found at i:40383732 original size:80 final size:80
Alignment explanation
Indices: 40383554--40383741 Score: 206
Period size: 80 Copynumber: 2.3 Consensus size: 80
40383544 TTCGAATGAT
* *
40383554 ATCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACTAAATCCGGACTAAGATCCGACGGCATA
1 ATCCGGGCTAAGTCCCGAAGGCTTTGAGCTAAGTGACTAAATCCGGACTAAGATCCGAAGGCATA
40383619 CGTGCGAGTTACTAA
66 CGTGCGAGTTACTAA
* ** *
40383634 ATCCGGACTAAGAT-CCGAAGGCTTTCGAGC-AAGCT-ACTAAATCCGGGTTGAG-TCCCGAAGG
1 ATCCGGGCTAAG-TCCCGAAGGCTTT-GAGCTAAG-TGACTAAATCCGGACTAAGAT-CCGAAGG
* *
40383695 CATTCGTGCGAGTTACTGTA
62 CATACGTGCGAGTTACT-AA
*
40383715 A-CCGGGCTATGTCCCGAAGGCATTTGA
1 ATCCGGGCTAAGTCCCGAAGGC-TTTGA
40383742 ATGTGTAGCC
Statistics
Matches: 91, Mismatches: 10, Indels: 14
0.79 0.09 0.12
Matches are distributed among these distances:
79 2 0.02
80 79 0.87
81 10 0.11
ACGTcount: A:0.26, C:0.24, G:0.27, T:0.23
Consensus pattern (80 bp):
ATCCGGGCTAAGTCCCGAAGGCTTTGAGCTAAGTGACTAAATCCGGACTAAGATCCGAAGGCATA
CGTGCGAGTTACTAA
Found at i:40386813 original size:47 final size:47
Alignment explanation
Indices: 40386744--40386928 Score: 316
Period size: 47 Copynumber: 3.9 Consensus size: 47
40386734 GATGAAGTGA
*
40386744 TGTTAAATTTGTTCTTACTATTTCCAGATAAGTTACTTAGTTAAGCT
1 TGTTAAATTTGTTCTTAATATTTCCAGATAAGTTACTTAGTTAAGCT
*
40386791 TGTTAAATTTGTTCTTAATATTTCCGGATAAGTTACTTAGTTAAGCT
1 TGTTAAATTTGTTCTTAATATTTCCAGATAAGTTACTTAGTTAAGCT
** *
40386838 TGTTAAATTTGTTCTTCCTATTTCCGGATAAGTTACTTAGTTAAGCT
1 TGTTAAATTTGTTCTTAATATTTCCAGATAAGTTACTTAGTTAAGCT
*
40386885 TGTTAAATTTGTTCTTAATATTTCTAGATAAGTTACTTAGTTAA
1 TGTTAAATTTGTTCTTAATATTTCCAGATAAGTTACTTAGTTAA
40386929 AGAAAATAAT
Statistics
Matches: 130, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
47 130 1.00
ACGTcount: A:0.28, C:0.11, G:0.14, T:0.48
Consensus pattern (47 bp):
TGTTAAATTTGTTCTTAATATTTCCAGATAAGTTACTTAGTTAAGCT
Found at i:40388229 original size:31 final size:31
Alignment explanation
Indices: 40388187--40388272 Score: 138
Period size: 31 Copynumber: 2.8 Consensus size: 31
40388177 TCAAGCTCAG
40388187 CATA-TACTGGGCCGAAGCCTTTACATTATT
1 CATATTACTGGGCCGAAGCCTTTACATTATT
* *
40388217 CATATTACTGGGCCAAAGCCTTTTCATTATT
1 CATATTACTGGGCCGAAGCCTTTACATTATT
*
40388248 CATATCACTGGGCCGAAGCCTTTAC
1 CATATTACTGGGCCGAAGCCTTTAC
40388273 TGTAACAATA
Statistics
Matches: 50, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
30 4 0.08
31 46 0.92
ACGTcount: A:0.26, C:0.26, G:0.16, T:0.33
Consensus pattern (31 bp):
CATATTACTGGGCCGAAGCCTTTACATTATT
Found at i:40388535 original size:26 final size:25
Alignment explanation
Indices: 40388490--40388560 Score: 115
Period size: 26 Copynumber: 2.8 Consensus size: 25
40388480 CTCTTTTAAT
*
40388490 AACTGGGGCAAAGCCCTTTTTGATA
1 AACTGGGGCAAAGCCCTTTTCGATA
*
40388515 AACTGGGGCAAAAGCCCTTTTCGGTA
1 AACTGGGGC-AAAGCCCTTTTCGATA
40388541 AACTGGGGCAAAGCCCTTTT
1 AACTGGGGCAAAGCCCTTTT
40388561 GCACTTCCTC
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
25 20 0.47
26 23 0.53
ACGTcount: A:0.27, C:0.23, G:0.25, T:0.25
Consensus pattern (25 bp):
AACTGGGGCAAAGCCCTTTTCGATA
Found at i:40388645 original size:5 final size:5
Alignment explanation
Indices: 40388615--40388660 Score: 51
Period size: 5 Copynumber: 9.4 Consensus size: 5
40388605 ACATCATGTG
* *
40388615 CATAT CATA- CATAT CATGT GCATAT CATAT CAAAT CATAT -ATAT CA
1 CATAT CATAT CATAT CATAT -CATAT CATAT CATAT CATAT CATAT CA
40388661 AACTCTCATG
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
4 8 0.24
5 22 0.65
6 4 0.12
ACGTcount: A:0.41, C:0.20, G:0.04, T:0.35
Consensus pattern (5 bp):
CATAT
Found at i:40390507 original size:45 final size:45
Alignment explanation
Indices: 40390443--40390624 Score: 262
Period size: 45 Copynumber: 4.1 Consensus size: 45
40390433 GAATATTACA
** **
40390443 AGGCTATAATGTCGGTGATATACTATTCGGGCCTTTAAGCCTAGC
1 AGGCTATAATACCGGTGATATACTATTCGGGCCTTCGAGCCTAGC
40390488 AGGCTATAATACCGGTGATATACTATTCGGGCCTTCGAGCCTAGC
1 AGGCTATAATACCGGTGATATACTATTCGGGCCTTCGAGCCTAGC
*
40390533 AGGCTATAATACCGGTGATATACTATTCGAGCCTTCGAGCCTAGC
1 AGGCTATAATACCGGTGATATACTATTCGGGCCTTCGAGCCTAGC
* * *
40390578 AGGCTATAATGCCAGTGAAATGA-TA-TC-GGCCTTCGAGCCTAGC
1 AGGCTATAATACCGGTGATAT-ACTATTCGGGCCTTCGAGCCTAGC
40390621 AGGC
1 AGGC
40390625 GAAATGCCGA
Statistics
Matches: 127, Mismatches: 9, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
43 19 0.15
44 2 0.02
45 105 0.83
46 1 0.01
ACGTcount: A:0.26, C:0.23, G:0.25, T:0.26
Consensus pattern (45 bp):
AGGCTATAATACCGGTGATATACTATTCGGGCCTTCGAGCCTAGC
Found at i:40397043 original size:10 final size:10
Alignment explanation
Indices: 40397028--40397086 Score: 64
Period size: 10 Copynumber: 5.7 Consensus size: 10
40397018 ACACCTATTA
*
40397028 TTTTTACCTT
1 TTTTTATCTT
*
40397038 TTTTTATTTT
1 TTTTTATCTT
40397048 ATTTTTATCTT
1 -TTTTTATCTT
*
40397059 TTTTTATTTT
1 TTTTTATCTT
40397069 ATTTTTATCTT
1 -TTTTTATCTT
*
40397080 TATTTAT
1 TTTTTAT
40397087 ATGTTGAAAT
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
10 23 0.56
11 18 0.44
ACGTcount: A:0.15, C:0.07, G:0.00, T:0.78
Consensus pattern (10 bp):
TTTTTATCTT
Found at i:40397049 original size:21 final size:21
Alignment explanation
Indices: 40397025--40397086 Score: 106
Period size: 21 Copynumber: 3.0 Consensus size: 21
40397015 TAAACACCTA
*
40397025 TTATTTTTACCTTTTTTTATT
1 TTATTTTTATCTTTTTTTATT
40397046 TTATTTTTATCTTTTTTTATT
1 TTATTTTTATCTTTTTTTATT
*
40397067 TTATTTTTATCTTTATTTAT
1 TTATTTTTATCTTTTTTTAT
40397087 ATGTTGAAAT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.16, C:0.06, G:0.00, T:0.77
Consensus pattern (21 bp):
TTATTTTTATCTTTTTTTATT
Found at i:40404242 original size:16 final size:17
Alignment explanation
Indices: 40404212--40404258 Score: 55
Period size: 16 Copynumber: 2.9 Consensus size: 17
40404202 ATGATTCACA
*
40404212 ACATAT-CCGTACAATC
1 ACATATCCCGTGCAATC
40404228 A-ATTATCCC-TGCAATC
1 ACA-TATCCCGTGCAATC
40404244 ACATATCCCGTGCAA
1 ACATATCCCGTGCAA
40404259 ATTCGCATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
15 1 0.04
16 17 0.65
17 8 0.31
ACGTcount: A:0.34, C:0.32, G:0.09, T:0.26
Consensus pattern (17 bp):
ACATATCCCGTGCAATC
Found at i:40405176 original size:15 final size:16
Alignment explanation
Indices: 40405148--40405186 Score: 64
Period size: 15 Copynumber: 2.6 Consensus size: 16
40405138 ATCAACTTAA
40405148 TTAA-TAAACATTTAT
1 TTAATTAAACATTTAT
40405163 TTAATTAAAC-TTTAT
1 TTAATTAAACATTTAT
40405178 TTAATTAAA
1 TTAATTAAA
40405187 ACTCAATGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
15 18 0.78
16 5 0.22
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (16 bp):
TTAATTAAACATTTAT
Found at i:40406211 original size:43 final size:43
Alignment explanation
Indices: 40406150--40406237 Score: 176
Period size: 43 Copynumber: 2.0 Consensus size: 43
40406140 GGATTCATGT
40406150 AACTTATTCCAAAATCTGGAGGTAAATCTCAATCTCAATTTGA
1 AACTTATTCCAAAATCTGGAGGTAAATCTCAATCTCAATTTGA
40406193 AACTTATTCCAAAATCTGGAGGTAAATCTCAATCTCAATTTGA
1 AACTTATTCCAAAATCTGGAGGTAAATCTCAATCTCAATTTGA
40406236 AA
1 AA
40406238 TGACAGACAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 45 1.00
ACGTcount: A:0.39, C:0.18, G:0.11, T:0.32
Consensus pattern (43 bp):
AACTTATTCCAAAATCTGGAGGTAAATCTCAATCTCAATTTGA
Found at i:40425003 original size:28 final size:28
Alignment explanation
Indices: 40424971--40425040 Score: 99
Period size: 28 Copynumber: 2.5 Consensus size: 28
40424961 ATAGTAAGTC
40424971 CGCACACTTAGTGCT-TA-ATAGTCAAACT
1 CGCACACTTAGTGCTATACA-A-TCAAACT
*
40424999 CGCACACTTAGTGCTATACAATTAAACT
1 CGCACACTTAGTGCTATACAATCAAACT
40425027 CGCACACTTAGTGC
1 CGCACACTTAGTGC
40425041 CAATCTCATT
Statistics
Matches: 39, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
28 35 0.90
29 3 0.08
30 1 0.03
ACGTcount: A:0.31, C:0.27, G:0.14, T:0.27
Consensus pattern (28 bp):
CGCACACTTAGTGCTATACAATCAAACT
Found at i:40427575 original size:24 final size:24
Alignment explanation
Indices: 40427547--40427599 Score: 97
Period size: 24 Copynumber: 2.2 Consensus size: 24
40427537 AAATCACATT
40427547 ACATAGAAACACAACACTCAATTA
1 ACATAGAAACACAACACTCAATTA
*
40427571 ACATAGAAACACAACATTCAATTA
1 ACATAGAAACACAACACTCAATTA
40427595 ACATA
1 ACATA
40427600 ATTACATGCT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.55, C:0.23, G:0.04, T:0.19
Consensus pattern (24 bp):
ACATAGAAACACAACACTCAATTA
Found at i:40430645 original size:21 final size:21
Alignment explanation
Indices: 40430619--40430662 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
40430609 TAAGAACCCT
40430619 TAGCACGAGAATATTCTACCA
1 TAGCACGAGAATATTCTACCA
40430640 TAGCACGAGAATATTCTACCA
1 TAGCACGAGAATATTCTACCA
40430661 TA
1 TA
40430663 TTTAAAGTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.39, C:0.23, G:0.14, T:0.25
Consensus pattern (21 bp):
TAGCACGAGAATATTCTACCA
Found at i:40431141 original size:50 final size:50
Alignment explanation
Indices: 40431062--40431163 Score: 186
Period size: 50 Copynumber: 2.0 Consensus size: 50
40431052 TACTCCTCTC
*
40431062 TAATGTTGCGGCATTACTGCTCAATACTTATTAGCAAATCTGGACCTTTT
1 TAATGTTGCGGCATTACTGCTCAACACTTATTAGCAAATCTGGACCTTTT
*
40431112 TAATGTTGCGGCATTACTGCTCAGCACTTATTAGCAAATCTGGACCTTTT
1 TAATGTTGCGGCATTACTGCTCAACACTTATTAGCAAATCTGGACCTTTT
40431162 TA
1 TA
40431164 TTCTACTTCG
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.25, C:0.21, G:0.17, T:0.37
Consensus pattern (50 bp):
TAATGTTGCGGCATTACTGCTCAACACTTATTAGCAAATCTGGACCTTTT
Found at i:40433354 original size:40 final size:40
Alignment explanation
Indices: 40433247--40433410 Score: 150
Period size: 40 Copynumber: 4.1 Consensus size: 40
40433237 CGGGATTTAA
* * * * *
40433247 CCGGATACAACCACAAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
* ** * * * *
40433287 CCGGATTTGGTGATTTGCACAATTGCCTTCGGGTCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
* * * *
40433327 CTGGATATAA-CAACTCGCACGAATGCCTTTGGGTCTTAGC
1 CCGGATATAATC-ACTAGCACAAATGCCTTCGGGTCTTAGC
* *
40433367 CCGGATATAATCACTAGCATAAATGCCTTCGGGACTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
40433407 CCGG
1 CCGG
40433411 GTATCATTCA
Statistics
Matches: 96, Mismatches: 26, Indels: 4
0.76 0.21 0.03
Matches are distributed among these distances:
40 95 0.99
41 1 0.01
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.26
Consensus pattern (40 bp):
CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:40441282 original size:40 final size:40
Alignment explanation
Indices: 40441238--40441378 Score: 230
Period size: 40 Copynumber: 3.5 Consensus size: 40
40441228 TTTGCACAAT
40441238 TGCCTTCGGGTCTTAGCCCGGATATAACAACTCGCACGAA
1 TGCCTTCGGGTCTTAGCCCGGATATAACAACTCGCACGAA
40441278 TGCCTTCGGGTCTTAGCCCGGATATAACAACTCGCACGAA
1 TGCCTTCGGGTCTTAGCCCGGATATAACAACTCGCACGAA
* **
40441318 TGCCTTCGGGTCTTAGCCCGGATATAATC-ACTAGCATAAA
1 TGCCTTCGGGTCTTAGCCCGGATATAA-CAACTCGCACGAA
*
40441358 TGCCTTCGGGACTTAGCCCGG
1 TGCCTTCGGGTCTTAGCCCGG
40441379 GTATCATTCA
Statistics
Matches: 96, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
40 95 0.99
41 1 0.01
ACGTcount: A:0.23, C:0.29, G:0.23, T:0.24
Consensus pattern (40 bp):
TGCCTTCGGGTCTTAGCCCGGATATAACAACTCGCACGAA
Found at i:40445424 original size:43 final size:42
Alignment explanation
Indices: 40445371--40445532 Score: 168
Period size: 43 Copynumber: 3.8 Consensus size: 42
40445361 TGCCATATCT
* * *
40445371 CAGATATGGTCTTACATGTTATCTCATATCGATGCCAATGTCC
1 CAGACATGGTCTTACACG-AATCTCATATCGATGCCAATGTCC
*
40445414 CAGACATGGTCTTACACGAAATCATC-TAACGATGCCAATGTCC
1 CAGACATGGTCTTACACG-AATC-TCATATCGATGCCAATGTCC
* *
40445457 CAGACATGGTCTTACACGTAA--TCATAGTACAATACCAATGTCC
1 CAGACATGGTCTTACACG-AATCTCATA-T-CGATGCCAATGTCC
* *
40445500 CAGACTTGGTCTTACATGCAATCTCATATCGAT
1 CAGACATGGTCTTACACG-AATCTCATATCGAT
40445533 AATCCTAATG
Statistics
Matches: 100, Mismatches: 13, Indels: 12
0.80 0.10 0.10
Matches are distributed among these distances:
40 2 0.02
41 2 0.02
43 88 0.88
44 3 0.03
45 5 0.05
ACGTcount: A:0.30, C:0.25, G:0.15, T:0.29
Consensus pattern (42 bp):
CAGACATGGTCTTACACGAATCTCATATCGATGCCAATGTCC
Found at i:40448233 original size:47 final size:49
Alignment explanation
Indices: 40448161--40448385 Score: 172
Period size: 47 Copynumber: 4.8 Consensus size: 49
40448151 TCACTCGTAT
* *
40448161 GAGCTAGTGTAAG-TCATGTCTGGGACAT-GCATCGGCCACATTATG-A
1 GAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCCACATTATGAA
*
40448207 GAGCCAGTGTAAGACCATTTCTGGGACATGGCATC-G--ACATTGA-GACAA
1 GAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCCACATT-ATG--AA
* * * * ** *
40448255 GTGCTAGTGTAAGA-CATGTCTGGGGCAT-GCATCGGCCTCAAGATGTA
1 GAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCCACATTATGAA
* *
40448302 -AGCCAGTGTAAGACCATGTCTGGGACATGGCAT---CTACATGA-GATA
1 GAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCCACATTATGA-A
* **
40448347 TGAGCTAGTGTAAGACTGTGTCTGGGACATGGCATCGGC
1 -GAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGC
40448386 ACCTTAACCA
Statistics
Matches: 140, Mismatches: 21, Indels: 32
0.73 0.11 0.17
Matches are distributed among these distances:
44 1 0.01
45 12 0.09
46 29 0.21
47 71 0.51
48 23 0.16
49 3 0.02
50 1 0.01
ACGTcount: A:0.27, C:0.20, G:0.30, T:0.24
Consensus pattern (49 bp):
GAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCCACATTATGAA
Found at i:40448324 original size:94 final size:93
Alignment explanation
Indices: 40448161--40448385 Score: 308
Period size: 94 Copynumber: 2.4 Consensus size: 93
40448151 TCACTCGTAT
* ** *
40448161 GAGCTAGTGTAAGTCATGTCTGGGACATGCATCGGCCACATTATGAGAGCCAGTGTAAGACCATT
1 GAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCACAAGATGAGAGCCAGTGTAAGACCATG
40448226 TCTGGGACATGGCATCGACATTGAGACAA
66 TCTGGGACATGGCATCGACA-TGAGACAA
* * *
40448255 GTGCTAGTGTAAGACATGTCTGGGGCATGCATCGGCCTCAAGATGTA-AGCCAGTGTAAGACCAT
1 GAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCACAAGATG-AGAGCCAGTGTAAGACCAT
* * *
40448319 GTCTGGGACATGGCATCTACATGAGATAT
65 GTCTGGGACATGGCATCGACATGAGACAA
*
40448348 GAGCTAGTGTAAGACTGTGTCTGGGACATGGCATCGGC
1 GAGCTAGTGTAAGAC-ATGTCTGGGACAT-GCATCGGC
40448386 ACCTTAACCA
Statistics
Matches: 115, Mismatches: 13, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
93 20 0.17
94 86 0.75
95 9 0.08
ACGTcount: A:0.27, C:0.20, G:0.30, T:0.24
Consensus pattern (93 bp):
GAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCACAAGATGAGAGCCAGTGTAAGACCATG
TCTGGGACATGGCATCGACATGAGACAA
Found at i:40464602 original size:61 final size:63
Alignment explanation
Indices: 40464486--40464606 Score: 151
Period size: 61 Copynumber: 2.0 Consensus size: 63
40464476 GTTTTCTCCA
*** **
40464486 AAATGAAAATGAAAATGGAGAAAATTGAATCATTTGAAAATGAATGCGGTTTTCTCAAAATGG
1 AAATGAAAATGAAAATGGAGAAAATTGAATCATTTGAAAATGAACAAGGAATTCTCAAAATGG
40464549 AAATGAAAATGAAAAT-GAG-AAA-TGAATTCATTT-AGAAATGAACAAGGAATTCTCAAAA
1 AAATGAAAATGAAAATGGAGAAAATTGAA-TCATTTGA-AAATGAACAAGGAATTCTCAAAA
40464607 ATGATCGACA
Statistics
Matches: 51, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
60 5 0.10
61 27 0.53
62 3 0.06
63 16 0.31
ACGTcount: A:0.50, C:0.07, G:0.18, T:0.25
Consensus pattern (63 bp):
AAATGAAAATGAAAATGGAGAAAATTGAATCATTTGAAAATGAACAAGGAATTCTCAAAATGG
Found at i:40474951 original size:43 final size:42
Alignment explanation
Indices: 40474893--40475013 Score: 145
Period size: 43 Copynumber: 2.8 Consensus size: 42
40474883 CTGAGATGAT
* * *
40474893 ATTACATGTAAGACCATGTTTGGGACATTGGCAT-TGTATTGTG
1 ATTACGTGTAAGACCATGTCTGGGACATTGGCATCT-TA-TATG
* * *
40474936 ATTACGTTTAGGACCATATCTGGGACATTGGCATCCTTATATG
1 ATTACGTGTAAGACCATGTCTGGGACATTGGCAT-CTTATATG
*
40474979 ATTTCGTGTAAGACCATGTCTGGGACATTGGCATC
1 ATTACGTGTAAGACCATGTCTGGGACATTGGCATC
40475014 AATATGAGAT
Statistics
Matches: 66, Mismatches: 10, Indels: 5
0.81 0.12 0.06
Matches are distributed among these distances:
42 1 0.02
43 62 0.94
44 2 0.03
45 1 0.02
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.35
Consensus pattern (42 bp):
ATTACGTGTAAGACCATGTCTGGGACATTGGCATCTTATATG
Found at i:40475032 original size:43 final size:43
Alignment explanation
Indices: 40474888--40475044 Score: 138
Period size: 43 Copynumber: 3.7 Consensus size: 43
40474878 GATTGCTGAG
* * * **
40474888 ATGATATTACATGTAAGACCATGTTTGGGACATTGGCAT-TGT
1 ATGAGATTACATGTAAGACCATATCTGGGACATTGGCATCAAT
* * * * **
40474930 ATTGTGATTACGTTTAGGACCATATCTGGGACATTGGCATCCTT
1 A-TGAGATTACATGTAAGACCATATCTGGGACATTGGCATCAAT
* * *
40474974 AT-ATGATTTCGTGTAAGACCATGTCTGGGACATTGGCATCAAT
1 ATGA-GATTACATGTAAGACCATATCTGGGACATTGGCATCAAT
* *
40475017 ATGAGATAACATGTAAAACCATATCTGG
1 ATGAGATTACATGTAAGACCATATCTGG
40475045 TATATGGCAT
Statistics
Matches: 90, Mismatches: 21, Indels: 7
0.76 0.18 0.06
Matches are distributed among these distances:
42 1 0.01
43 86 0.96
44 3 0.03
ACGTcount: A:0.29, C:0.15, G:0.22, T:0.33
Consensus pattern (43 bp):
ATGAGATTACATGTAAGACCATATCTGGGACATTGGCATCAAT
Found at i:40477793 original size:2 final size:2
Alignment explanation
Indices: 40477786--40477816 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
40477776 TGAAAACACT
40477786 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
40477817 TTCCATGCTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:40484770 original size:42 final size:42
Alignment explanation
Indices: 40484711--40484794 Score: 159
Period size: 42 Copynumber: 2.0 Consensus size: 42
40484701 CAAAAACTGG
40484711 TTATGAAAATTTGAATAAGAATTTCCAGTATTCTCTCTTTCT
1 TTATGAAAATTTGAATAAGAATTTCCAGTATTCTCTCTTTCT
*
40484753 TTATGAAAATTTGAATAATAATTTCCAGTATTCTCTCTTTCT
1 TTATGAAAATTTGAATAAGAATTTCCAGTATTCTCTCTTTCT
40484795 CTTTTCTCTC
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.31, C:0.14, G:0.08, T:0.46
Consensus pattern (42 bp):
TTATGAAAATTTGAATAAGAATTTCCAGTATTCTCTCTTTCT
Found at i:40497314 original size:16 final size:16
Alignment explanation
Indices: 40497295--40497328 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
40497285 CTAGCTTTAT
40497295 ACCTTTAGATATTTGG
1 ACCTTTAGATATTTGG
40497311 ACCTTTAGATATTTGG
1 ACCTTTAGATATTTGG
40497327 AC
1 AC
40497329 TACTGCTCCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.26, C:0.15, G:0.18, T:0.41
Consensus pattern (16 bp):
ACCTTTAGATATTTGG
Found at i:40501434 original size:28 final size:27
Alignment explanation
Indices: 40501384--40501436 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 27
40501374 TATATCTGAG
*
40501384 ACTATATCTGAATGGGCCAAGGCCCAA
1 ACTAAATCTGAATGGGCCAAGGCCCAA
40501411 ACTAAATCTGTAATGGGCTC-AGGCCC
1 ACTAAATCTG-AATGGGC-CAAGGCCC
40501437 CAGACTGCAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
27 9 0.39
28 13 0.57
29 1 0.04
ACGTcount: A:0.30, C:0.26, G:0.23, T:0.21
Consensus pattern (27 bp):
ACTAAATCTGAATGGGCCAAGGCCCAA
Found at i:40504999 original size:31 final size:31
Alignment explanation
Indices: 40504964--40505024 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
40504954 AGCTACTGAG
*
40504964 TTAAATAAAAAATTTTAAATAGTTCAATGAC
1 TTAAATAAAAAATTTCAAATAGTTCAATGAC
* *
40504995 TTAAATGAAAACTTTCAAATAGTTCAATGA
1 TTAAATAAAAAATTTCAAATAGTTCAATGA
40505025 TCAAATTGTA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.49, C:0.08, G:0.08, T:0.34
Consensus pattern (31 bp):
TTAAATAAAAAATTTCAAATAGTTCAATGAC
Found at i:40505498 original size:8 final size:8
Alignment explanation
Indices: 40505485--40505511 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
40505475 TAATCTTTAT
40505485 ATTTTAAA
1 ATTTTAAA
40505493 ATTTTAAA
1 ATTTTAAA
40505501 ATTTTAAA
1 ATTTTAAA
40505509 ATT
1 ATT
40505512 CAATTCATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (8 bp):
ATTTTAAA
Found at i:40506722 original size:29 final size:30
Alignment explanation
Indices: 40506676--40506733 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 30
40506666 TCAATAGATT
* *
40506676 AATATAGTTTTTTTGTTTATTATATTATTA
1 AATATAGTTATTTAGTTTATTATATTATTA
* *
40506706 AATAT-GTTATTTAGTTTTTTTTATTATT
1 AATATAGTTATTTAGTTTATTATATTATT
40506734 TATAAAATTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 19 0.79
30 5 0.21
ACGTcount: A:0.28, C:0.00, G:0.07, T:0.66
Consensus pattern (30 bp):
AATATAGTTATTTAGTTTATTATATTATTA
Found at i:40506884 original size:74 final size:74
Alignment explanation
Indices: 40506740--40506884 Score: 175
Period size: 74 Copynumber: 2.0 Consensus size: 74
40506730 TATTTATAAA
* * *
40506740 ATTTATCATATGTATAAATCAAAATTTTAATTTTAATAAAATAATTTGATGAAATTAATTTATTT
1 ATTTATCATATGTATAAATCAAAATTTTAATTTTAATAAAAGAATTTGATGAAATGAATTTATAT
*
40506805 GATAAAAAT
66 AATAAAAAT
* * * ** * *
40506814 ATTTATCATATTTATAAAT-AAGAATTTTGATTTTATTAAAAGGGTTTTATTAAATGAATTTATA
1 ATTTATCATATGTATAAATCAA-AATTTTAATTTTAATAAAAGAATTTGATGAAATGAATTTATA
40506878 TAATAAA
65 TAATAAA
40506885 TAAGAAGTTT
Statistics
Matches: 59, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
73 2 0.03
74 57 0.97
ACGTcount: A:0.46, C:0.02, G:0.07, T:0.46
Consensus pattern (74 bp):
ATTTATCATATGTATAAATCAAAATTTTAATTTTAATAAAAGAATTTGATGAAATGAATTTATAT
AATAAAAAT
Found at i:40507529 original size:16 final size:15
Alignment explanation
Indices: 40507501--40507553 Score: 72
Period size: 15 Copynumber: 3.5 Consensus size: 15
40507491 TTTATTAATT
*
40507501 TTAATTAAATTTAAG
1 TTAATTAAATTTAAA
40507516 TTAATTAAAGTTTAAA
1 TTAATTAAA-TTTAAA
*
40507532 TTAATT-AATTTAGA
1 TTAATTAAATTTAAA
40507546 TTAATTAA
1 TTAATTAA
40507554 GTTAATAAAG
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
14 11 0.32
15 12 0.35
16 11 0.32
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (15 bp):
TTAATTAAATTTAAA
Found at i:40516940 original size:28 final size:27
Alignment explanation
Indices: 40516840--40516940 Score: 78
Period size: 28 Copynumber: 3.4 Consensus size: 27
40516830 CAGAGTTAAC
* * *
40516840 TGGGCCTTAGCCCATATCAATATTAATC
1 TGGGCC-TAGCCCATATCAGTATCAATT
*
40516868 TGGGCCATAGCCCCT-TACAGTATCAGAGTAT
1 TGGGCC-TAGCCCATAT-CAGTATCA-A-T-T
40516899 ACTGGGCCTAGCCCATATCAGTATCAATT
1 --TGGGCCTAGCCCATATCAGTATCAATT
40516928 TGGGCCGTAGCCC
1 TGGGCC-TAGCCC
40516941 TATTACAAGT
Statistics
Matches: 59, Mismatches: 6, Indels: 16
0.73 0.07 0.20
Matches are distributed among these distances:
27 7 0.12
28 25 0.42
29 2 0.03
30 2 0.03
31 1 0.02
32 15 0.25
33 7 0.12
ACGTcount: A:0.25, C:0.28, G:0.21, T:0.27
Consensus pattern (27 bp):
TGGGCCTAGCCCATATCAGTATCAATT
Found at i:40516965 original size:60 final size:59
Alignment explanation
Indices: 40516828--40516976 Score: 160
Period size: 60 Copynumber: 2.5 Consensus size: 59
40516818 CTATTCAGAA
* *
40516828 ATCAGAGT-TAACTGGGCCTTAGCCCATATCAATATTAATCTGGGCCATAGCCCCTTACAG
1 ATCAGAGTAT-ACTGGGCC-TAGCCCATATCAATATCAATCTGGGCCATAGCCCATTACAG
* * *
40516888 TATCAGAGTATACTGGGCCTAGCCCATATCAGTATCAATTTGGGCCGTAGCCCTATTACA-
1 -ATCAGAGTATACTGGGCCTAGCCCATATCAATATCAATCTGGGCCATAGCCC-ATTACAG
* *
40516948 AGTC-GAGATATATTGGGCCTTGCCCATAT
1 A-TCAGAG-TATACTGGGCCTAGCCCATAT
40516977 TAACACAGTT
Statistics
Matches: 77, Mismatches: 7, Indels: 9
0.83 0.08 0.10
Matches are distributed among these distances:
59 4 0.05
60 51 0.66
61 21 0.27
62 1 0.01
ACGTcount: A:0.27, C:0.25, G:0.20, T:0.28
Consensus pattern (59 bp):
ATCAGAGTATACTGGGCCTAGCCCATATCAATATCAATCTGGGCCATAGCCCATTACAG
Found at i:40518662 original size:19 final size:19
Alignment explanation
Indices: 40518634--40518677 Score: 79
Period size: 19 Copynumber: 2.3 Consensus size: 19
40518624 AATAGAAGGT
*
40518634 ATATACGTAAAGATATAAA
1 ATATATGTAAAGATATAAA
40518653 ATATATGTAAAGATATAAA
1 ATATATGTAAAGATATAAA
40518672 ATATAT
1 ATATAT
40518678 TTTTTAATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.57, C:0.02, G:0.09, T:0.32
Consensus pattern (19 bp):
ATATATGTAAAGATATAAA
Found at i:40522831 original size:46 final size:46
Alignment explanation
Indices: 40522662--40522833 Score: 181
Period size: 46 Copynumber: 3.7 Consensus size: 46
40522652 GGTTGAGCAT
* * *
40522662 CCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAATGT
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
* * * *
40522708 TCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGGC
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAC---GC
*
40522753 AACCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
1 --CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
* *
40522801 CCGAGCTCGTTGAGTTGAGTCCTAGTTCACTTA
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
40522834 AGGGCGGGTT
Statistics
Matches: 102, Mismatches: 15, Indels: 18
0.76 0.11 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
45 2 0.02
46 57 0.56
47 26 0.25
48 4 0.04
50 4 0.04
51 3 0.03
ACGTcount: A:0.23, C:0.22, G:0.27, T:0.28
Consensus pattern (46 bp):
CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
Found at i:40534095 original size:45 final size:45
Alignment explanation
Indices: 40534038--40534215 Score: 187
Period size: 45 Copynumber: 3.8 Consensus size: 45
40534028 TCAAAACAAG
* * *
40534038 TCTTATCTCCTTGAAGTTGCAATGGAGCAGACTGAAGATATTGAA
1 TCTTATCTCCTTGAAGTTGCAGTGGAGCAGATTGAAGATATTAAA
* * *
40534083 TCTTGTCTCCTTGAAATTACAGTGGAGCAGATTGAAGATGGAATTTACAA
1 TCTTATCTCCTTGAAGTTGCAGTGGAGCAGATTGAAGAT---A-TTA-AA
* * **
40534133 GTCTTATCCCCCTGAAGTTGCAGTGGAGCA-AGTTGAAGATAGCAAA
1 -TCTTATCTCCTTGAAGTTGCAGTGGAGCAGA-TTGAAGATATTAAA
*
40534179 TCTTATCTCCTTGAAGTTGCAGTGGGGCAGATTGAAG
1 TCTTATCTCCTTGAAGTTGCAGTGGAGCAGATTGAAG
40534216 CTACGAATCC
Statistics
Matches: 109, Mismatches: 16, Indels: 16
0.77 0.11 0.11
Matches are distributed among these distances:
45 66 0.61
46 3 0.03
47 1 0.01
48 2 0.02
49 2 0.02
50 3 0.03
51 32 0.29
ACGTcount: A:0.29, C:0.16, G:0.25, T:0.30
Consensus pattern (45 bp):
TCTTATCTCCTTGAAGTTGCAGTGGAGCAGATTGAAGATATTAAA
Found at i:40534202 original size:96 final size:96
Alignment explanation
Indices: 40534033--40534215 Score: 251
Period size: 96 Copynumber: 1.9 Consensus size: 96
40534023 ATAGATCAAA
* * *** *
40534033 ACAAGTCTTATCTCCTTGAAGTTGCAATGGAGCAGACTGAAGATATTGAATCTTGTCTCCTTGAA
1 ACAAGTCTTATCCCCCTGAAGTTGCAATGGAGCAGACTGAAGATAGCAAATCTTATCTCCTTGAA
40534098 ATTACAGTGGAGCAGATTGAAGATGGAATTT
66 ATTACAGTGGAGCAGATTGAAGATGGAATTT
* *
40534129 ACAAGTCTTATCCCCCTGAAGTTGCAGTGGAGCA-AGTTGAAGATAGCAAATCTTATCTCCTTGA
1 ACAAGTCTTATCCCCCTGAAGTTGCAATGGAGCAGA-CTGAAGATAGCAAATCTTATCTCCTTGA
* * *
40534193 AGTTGCAGTGGGGCAGATTGAAG
65 AATTACAGTGGAGCAGATTGAAG
40534216 CTACGAATCC
Statistics
Matches: 75, Mismatches: 11, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
95 1 0.01
96 74 0.99
ACGTcount: A:0.30, C:0.16, G:0.25, T:0.29
Consensus pattern (96 bp):
ACAAGTCTTATCCCCCTGAAGTTGCAATGGAGCAGACTGAAGATAGCAAATCTTATCTCCTTGAA
ATTACAGTGGAGCAGATTGAAGATGGAATTT
Found at i:40534234 original size:96 final size:96
Alignment explanation
Indices: 40534033--40534255 Score: 234
Period size: 96 Copynumber: 2.3 Consensus size: 96
40534023 ATAGATCAAA
* * * *** *
40534033 ACAAGTCTTATCTCCTTGAAGTTGCAATGGAGCAGACTGAAGATATTGAATCTTGTCTCCTTGAA
1 ACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAGCAAATCTTATCTCCTTGAA
* *
40534098 ATTACAGTGGAGCAGATTGAAGATGGAATTT
66 ATTACAGTGGAGCAGATTGAAGATCGAATTC
* * *
40534129 ACAAGTCTTATCCCCCTGAAGTTGCAGTGGAGCA-AGTTGAAGATAGCAAATCTTATCTCCTTGA
1 ACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-CTGAAGATAGCAAATCTTATCTCCTTGA
* * * *
40534193 AGTTGCAGTGGGGCAGATTGAAGCTACGAA-TC
65 AATTACAGTGGAGCAGATTGAAGAT-CGAATTC
* * * *
40534225 CCAAATCTTATTTCCCTAAAGTTACAGTGGA
1 ACAAATCTTATCTCCCTGAAGTTGCAGTGGA
40534256 ATAGATCAAA
Statistics
Matches: 105, Mismatches: 20, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
95 1 0.01
96 101 0.96
97 3 0.03
ACGTcount: A:0.30, C:0.18, G:0.22, T:0.29
Consensus pattern (96 bp):
ACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAGCAAATCTTATCTCCTTGAA
ATTACAGTGGAGCAGATTGAAGATCGAATTC
Found at i:40534998 original size:14 final size:14
Alignment explanation
Indices: 40534979--40535005 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
40534969 ACTATTTCTT
40534979 TTTTATTTTCTTTC
1 TTTTATTTTCTTTC
40534993 TTTTATTTTCTTT
1 TTTTATTTTCTTT
40535006 TTTAAATCAG
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:0.07, C:0.11, G:0.00, T:0.81
Consensus pattern (14 bp):
TTTTATTTTCTTTC
Found at i:40537896 original size:27 final size:26
Alignment explanation
Indices: 40537849--40537924 Score: 100
Period size: 27 Copynumber: 2.8 Consensus size: 26
40537839 CGAGGCTGCC
* *
40537849 AGATATTGTGAC-GAAGTCACCAGATAT
1 AGATATTGTGGCAG-AGCCACCAGA-AT
40537876 AGATATTGTGGCAGAGCCACCAGAAT
1 AGATATTGTGGCAGAGCCACCAGAAT
40537902 AGATATATGTGGCAGAGCCACCA
1 AGATAT-TGTGGCAGAGCCACCA
40537925 TGTAACGCCC
Statistics
Matches: 45, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
26 8 0.18
27 36 0.80
28 1 0.02
ACGTcount: A:0.36, C:0.18, G:0.25, T:0.21
Consensus pattern (26 bp):
AGATATTGTGGCAGAGCCACCAGAAT
Found at i:40539354 original size:93 final size:93
Alignment explanation
Indices: 40539247--40539417 Score: 306
Period size: 93 Copynumber: 1.8 Consensus size: 93
40539237 GCCCCTAAGT
* *
40539247 GAACTCGGACTCAACTCAACAAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACAAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
40539312 CGAGTTCGGATGCCTAGTTACATTTCAC
66 CGAGTTCGGATGCCTAGTTACATTTCAC
* *
40539340 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACAAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
40539405 CGAGTTCGGATGC
66 CGAGTTCGGATGC
40539418 TCAACCATCC
Statistics
Matches: 74, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 74 1.00
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.22
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACAAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATTTCAC
Found at i:40539414 original size:46 final size:46
Alignment explanation
Indices: 40539242--40539414 Score: 201
Period size: 46 Copynumber: 3.7 Consensus size: 46
40539232 AACCCGCCCC
* * * *
40539242 TAAGTGAACTCGGACTCAACTCAACAAGCTCGGGCGTTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
* *
40539288 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT--T
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCATCCA
* *
40539336 TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
40539381 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
40539415 TGCTCAACCA
Statistics
Matches: 106, Mismatches: 12, Indels: 18
0.78 0.09 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 1 0.01
45 2 0.02
46 60 0.57
47 29 0.27
48 2 0.02
49 1 0.01
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.28, G:0.21, T:0.22
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
Found at i:40540737 original size:27 final size:26
Alignment explanation
Indices: 40540707--40540793 Score: 129
Period size: 27 Copynumber: 3.2 Consensus size: 26
40540697 GGATATTACA
40540707 CACCAGATCAGATAATCGTGGCATAGC
1 CACCAGATCAGATAAT-GTGGCATAGC
* *
40540734 CACCAGAACAGATATATGTGGCAGAGC
1 CACCAGATCAGATA-ATGTGGCATAGC
40540761 CACCAGATCAGATAATTGTGGCATAGC
1 CACCAGATCAGATAA-TGTGGCATAGC
40540788 CACCAG
1 CACCAG
40540794 GACGCTTCCT
Statistics
Matches: 54, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
26 1 0.02
27 51 0.94
28 2 0.04
ACGTcount: A:0.34, C:0.25, G:0.23, T:0.17
Consensus pattern (26 bp):
CACCAGATCAGATAATGTGGCATAGC
Found at i:40540961 original size:28 final size:26
Alignment explanation
Indices: 40540899--40540972 Score: 76
Period size: 26 Copynumber: 2.8 Consensus size: 26
40540889 AAATTAACCC
** * *
40540899 TAGGGGTATAACGGTAATTTTGCACC
1 TAGGGGTATAAAAGTAATTTTCCACA
40540925 TAGGGGTATAAAAGTAATTTTCCATACA
1 TAGGGGTATAAAAGTAATTTTCC--ACA
* *
40540953 TAGGGGTATTATAGTAATTT
1 TAGGGGTATAAAAGTAATTT
40540973 AGCTACTTTT
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
26 20 0.50
28 20 0.50
ACGTcount: A:0.32, C:0.09, G:0.23, T:0.35
Consensus pattern (26 bp):
TAGGGGTATAAAAGTAATTTTCCACA
Found at i:40542449 original size:26 final size:26
Alignment explanation
Indices: 40542415--40542497 Score: 148
Period size: 26 Copynumber: 3.2 Consensus size: 26
40542405 TGAAATTCCC
*
40542415 ATCATGGAACATTTACCTAACCCATT
1 ATCAAGGAACATTTACCTAACCCATT
40542441 ATCAAGGAACATTTACCTAACCCATT
1 ATCAAGGAACATTTACCTAACCCATT
*
40542467 ATCATGGAACATTTACCTAACCCATT
1 ATCAAGGAACATTTACCTAACCCATT
40542493 ATCAA
1 ATCAA
40542498 TTTGTATCAA
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 54 1.00
ACGTcount: A:0.37, C:0.27, G:0.07, T:0.29
Consensus pattern (26 bp):
ATCAAGGAACATTTACCTAACCCATT
Found at i:40543919 original size:16 final size:17
Alignment explanation
Indices: 40543898--40543937 Score: 66
Period size: 16 Copynumber: 2.5 Consensus size: 17
40543888 TGAAATGCCG
40543898 GCTTTTCGGCATTT-TA
1 GCTTTTCGGCATTTCTA
40543914 GCTTTTCGGCATTTCTA
1 GCTTTTCGGCATTTCTA
40543931 -CTTTTCG
1 GCTTTTCG
40543938 TCTTTTGCCG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
16 21 0.91
17 2 0.09
ACGTcount: A:0.10, C:0.23, G:0.17, T:0.50
Consensus pattern (17 bp):
GCTTTTCGGCATTTCTA
Found at i:40545442 original size:19 final size:19
Alignment explanation
Indices: 40545396--40545446 Score: 52
Period size: 19 Copynumber: 2.7 Consensus size: 19
40545386 AAGTTAATTA
*
40545396 AAGTTTAAGCTTAATTAACT
1 AAGTTTAA-ATTAATTAACT
*
40545416 ATA-ATTAAATTAATTAACT
1 A-AGTTTAAATTAATTAACT
40545435 AAGTTT-AATTAA
1 AAGTTTAAATTAA
40545447 AATAAAATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 6
0.74 0.09 0.17
Matches are distributed among these distances:
18 7 0.27
19 13 0.50
20 5 0.19
21 1 0.04
ACGTcount: A:0.47, C:0.06, G:0.06, T:0.41
Consensus pattern (19 bp):
AAGTTTAAATTAATTAACT
Found at i:40548741 original size:19 final size:18
Alignment explanation
Indices: 40548695--40548742 Score: 51
Period size: 20 Copynumber: 2.5 Consensus size: 18
40548685 AAATCATTCG
*
40548695 ATAACAGTAACTCATCCGT
1 ATAACAGT-ACTCATCCAT
*
40548714 TTAAACAGTACGTCATCCAT
1 AT-AACAGTAC-TCATCCAT
40548734 ATAACAGTA
1 ATAACAGTA
40548743 ATTCAACTGT
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
19 10 0.42
20 14 0.58
ACGTcount: A:0.40, C:0.23, G:0.10, T:0.27
Consensus pattern (18 bp):
ATAACAGTACTCATCCAT
Found at i:40548982 original size:47 final size:51
Alignment explanation
Indices: 40548915--40549020 Score: 125
Period size: 50 Copynumber: 2.2 Consensus size: 51
40548905 AGCTCCTCCT
* *
40548915 GAGCTGATAGACAGTAAGCTC-TATTGAGC-TA-AAAT-AGTAAGCTCTA-AC
1 GAGCTGAGAGACAATAAGCTCATA-TGAGCTTATAAATCAGTAAGCT-TATAC
*
40548963 GAGCTGAGA-ACAATAAGCTCATATGAGCTTATATATCAGTAAGCTTATAC
1 GAGCTGAGAGACAATAAGCTCATATGAGCTTATAAATCAGTAAGCTTATAC
40549013 GAGCTGAG
1 GAGCTGAG
40549021 GTGAGTCCAC
Statistics
Matches: 50, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
47 15 0.30
48 12 0.24
49 5 0.10
50 18 0.36
ACGTcount: A:0.37, C:0.16, G:0.22, T:0.25
Consensus pattern (51 bp):
GAGCTGAGAGACAATAAGCTCATATGAGCTTATAAATCAGTAAGCTTATAC
Found at i:40556575 original size:19 final size:19
Alignment explanation
Indices: 40556515--40556577 Score: 63
Period size: 19 Copynumber: 3.3 Consensus size: 19
40556505 AAATTATTCA
*
40556515 ATAACAGTAACTCATCCGT
1 ATAACAGTAATTCATCCGT
* * * **
40556534 TTAAAAAGTACTTCATCTAT
1 AT-AACAGTAATTCATCCGT
40556554 ATAACAGTAATTCATCCGT
1 ATAACAGTAATTCATCCGT
40556573 ATAAC
1 ATAAC
40556578 TCATTCGTCA
Statistics
Matches: 32, Mismatches: 11, Indels: 2
0.71 0.24 0.04
Matches are distributed among these distances:
19 19 0.59
20 13 0.41
ACGTcount: A:0.40, C:0.21, G:0.08, T:0.32
Consensus pattern (19 bp):
ATAACAGTAATTCATCCGT
Found at i:40556700 original size:24 final size:23
Alignment explanation
Indices: 40556637--40556742 Score: 79
Period size: 24 Copynumber: 4.3 Consensus size: 23
40556627 AGCTCCTCCT
* * *
40556637 GAGCTGATGGACAATAAGCTCTATT
1 GAGCTGA-GAACAGTAAGCTCTA-C
*
40556662 GAGTTGA-AACAGTAAGCTCTGAC
1 GAGCTGAGAACAGTAAGCTCT-AC
*
40556685 GAGCTGAGAACAGTAAGCTCTTAT
1 GAGCTGAGAACAGTAAGCTC-TAC
* *
40556709 GAGCTGATATATCGGTAAGCTCATAC
1 GAGCTGAGA-A-CAGTAAGCTC-TAC
40556735 GAGCTGAG
1 GAGCTGAG
40556743 GTGAGTCTGA
Statistics
Matches: 65, Mismatches: 11, Indels: 9
0.76 0.13 0.11
Matches are distributed among these distances:
23 17 0.26
24 22 0.34
25 8 0.12
26 18 0.28
ACGTcount: A:0.32, C:0.17, G:0.26, T:0.25
Consensus pattern (23 bp):
GAGCTGAGAACAGTAAGCTCTAC
Found at i:40564554 original size:3 final size:3
Alignment explanation
Indices: 40564546--40564574 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
40564536 TGTTGGTAAT
40564546 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
40564575 TGGTCCCAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:40566299 original size:35 final size:35
Alignment explanation
Indices: 40566226--40566300 Score: 84
Period size: 35 Copynumber: 2.1 Consensus size: 35
40566216 TCAAAATTAT
* *
40566226 TATTTTATTTTTTTTAAAATTTAAACATTTTTATA
1 TATTTTATTTTTTTTAAAATTTAAACATTTTAAAA
40566261 TATTTT-TTCTTTTTTAAATATTGT-AA-ATTTTAAAA
1 TATTTTATT-TTTTTTAAA-ATT-TAAACATTTTAAAA
40566296 TATTT
1 TATTT
40566301 ATAAAAATTA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
34 2 0.06
35 27 0.77
36 5 0.14
37 1 0.03
ACGTcount: A:0.33, C:0.03, G:0.01, T:0.63
Consensus pattern (35 bp):
TATTTTATTTTTTTTAAAATTTAAACATTTTAAAA
Done.