Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A03
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: 105315579
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1369460 characters in sequence are not A, C, G, or T
File 169 of 325
Found at i:54763405 original size:15 final size:14
Alignment explanation
Indices: 54763385--54763421 Score: 58
Period size: 15 Copynumber: 2.6 Consensus size: 14
54763375 AAATGATGAT
54763385 GAAAAAAAGAAAAGA
1 GAAAAAAAGAAAA-A
54763400 GAAAAAAAGAAAAA
1 GAAAAAAAGAAAAA
54763414 -AAAAAAAG
1 GAAAAAAAG
54763422 GCTCTCATGT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 8 0.36
14 1 0.05
15 13 0.59
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (14 bp):
GAAAAAAAGAAAAA
Found at i:54764729 original size:40 final size:40
Alignment explanation
Indices: 54764674--54764811 Score: 181
Period size: 40 Copynumber: 3.5 Consensus size: 40
54764664 TGGATGATAA
*
54764674 CCGGGCTAAATCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAATCCCGAAGGCATTCGTGCGAGTTACTATAT
* *
54764714 CCGGGCTAAGTCCCGAAGGCATTGGTGCGAGTTACTATAT
1 CCGGGCTAAATCCCGAAGGCATTCGTGCGAGTTACTATAT
* ** *
54764754 CCGGGATATGTCCCGAAGGCATTCGAGCGAG-TAGCTATAT
1 CCGGGCTAAATCCCGAAGGCATTCGTGCGAGTTA-CTATAT
*
54764794 CC-GGTTAAATCCCGAAGG
1 CCGGGCTAAATCCCGAAGG
54764812 TACTTGGCTT
Statistics
Matches: 88, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
39 15 0.17
40 73 0.83
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.24
Consensus pattern (40 bp):
CCGGGCTAAATCCCGAAGGCATTCGTGCGAGTTACTATAT
Found at i:54769396 original size:40 final size:41
Alignment explanation
Indices: 54769335--54769580 Score: 249
Period size: 40 Copynumber: 6.2 Consensus size: 41
54769325 CTAACGGGGT
* * * * *
54769335 TAAGTCCTGAAGACATGTGTGCTAGTGATTAAT-TCCGGGC
1 TAAGTCCCGAAGGCATTTGTGCGAGTGACTAATATCCGGGC
* * *
54769375 TAAGTCCCGAAGGCATTTGTGCGAGTTACAAAT-TCCGAGC
1 TAAGTCCCGAAGGCATTTGTGCGAGTGACTAATATCCGGGC
* *
54769415 TAAGTCCCGAAGGCATTGGTGCGAGTTACTAAT-TCCGGGC
1 TAAGTCCCGAAGGCATTTGTGCGAGTGACTAATATCCGGGC
*
54769455 TAAGTCCCGAAGGCATCTGTGCGAGTTG-CT-ATATCCGGGC
1 TAAGTCCCGAAGGCATTTGTGCGAG-TGACTAATATCCGGGC
* * * *
54769495 TAAGACCCGAAGGCATTTATGCTAGTGAC-CATATCCGGGC
1 TAAGTCCCGAAGGCATTTGTGCGAGTGACTAATATCCGGGC
* * * *
54769535 TAAGACCCGAAGGC-CTTGTGCGAGTG-GTTATATCC-GGC
1 TAAGTCCCGAAGGCATTTGTGCGAGTGACTAATATCCGGGC
54769573 TAAGTCCC
1 TAAGTCCC
54769581 AAAGATACTT
Statistics
Matches: 177, Mismatches: 24, Indels: 12
0.83 0.11 0.06
Matches are distributed among these distances:
38 10 0.06
39 19 0.11
40 147 0.83
41 1 0.01
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (41 bp):
TAAGTCCCGAAGGCATTTGTGCGAGTGACTAATATCCGGGC
Found at i:54776891 original size:49 final size:49
Alignment explanation
Indices: 54776832--54776964 Score: 162
Period size: 49 Copynumber: 2.7 Consensus size: 49
54776822 CTTGTTGTGT
*
54776832 GTCAGTGTAAGACCTGTCTGGGACATGGCATCGACAC-CGATAGATGAGA
1 GTCAGTGTAAGACCTGTCTGGGACATGGCATCGAC-CTCGATAGATGAAA
* * * * *
54776881 G-CTAGTGTAAGACTTGTTTGGGACACGGCATCGGCCTCGATATATGAAA
1 GTC-AGTGTAAGACCTGTCTGGGACATGGCATCGACCTCGATAGATGAAA
* *
54776930 GTCAGTGTAAGACCTATCTGGAACATGGCATCGAC
1 GTCAGTGTAAGACCTGTCTGGGACATGGCATCGAC
54776965 TTTGATGTGT
Statistics
Matches: 69, Mismatches: 12, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
48 2 0.03
49 66 0.96
50 1 0.01
ACGTcount: A:0.28, C:0.20, G:0.29, T:0.23
Consensus pattern (49 bp):
GTCAGTGTAAGACCTGTCTGGGACATGGCATCGACCTCGATAGATGAAA
Found at i:54780999 original size:15 final size:15
Alignment explanation
Indices: 54780978--54781033 Score: 67
Period size: 15 Copynumber: 3.6 Consensus size: 15
54780968 TATAGTATTG
*
54780978 TATCTTGGATTTCTG
1 TATCTTGGATTTCTC
* *
54780993 AATCTTGGGAGTTTCTT
1 TATCTT-GGA-TTTCTC
54781010 TATCTTGGATTTCTC
1 TATCTTGGATTTCTC
54781025 TATCTTGGA
1 TATCTTGGA
54781034 CCTTTTTATT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
15 19 0.54
16 6 0.17
17 10 0.29
ACGTcount: A:0.16, C:0.14, G:0.20, T:0.50
Consensus pattern (15 bp):
TATCTTGGATTTCTC
Found at i:54788350 original size:48 final size:48
Alignment explanation
Indices: 54788230--54788361 Score: 183
Period size: 48 Copynumber: 2.8 Consensus size: 48
54788220 TCATTAGGGA
* *
54788230 ATACATTGAGTTGCCTTCGGGCCATGATATTGGCACTTCGGGTGCGAG
1 ATACATTGAGTTGGCTTCGGGCCATGATATTGGCACTTCGGGTACGAG
* * * *
54788278 TTACATTGATTTGGTTTTGGGCCATGATATTGGCACTTCGGGTACGAG
1 ATACATTGAGTTGGCTTCGGGCCATGATATTGGCACTTCGGGTACGAG
** *
54788326 ATACATTGAGTTGGCTTCAAGCCATGACATTGGCAC
1 ATACATTGAGTTGGCTTCGGGCCATGATATTGGCAC
54788362 CTAGGGTGGA
Statistics
Matches: 71, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
48 71 1.00
ACGTcount: A:0.21, C:0.19, G:0.28, T:0.32
Consensus pattern (48 bp):
ATACATTGAGTTGGCTTCGGGCCATGATATTGGCACTTCGGGTACGAG
Found at i:54790015 original size:37 final size:37
Alignment explanation
Indices: 54789965--54790038 Score: 148
Period size: 37 Copynumber: 2.0 Consensus size: 37
54789955 GTTTTAGGGA
54789965 AACTTAGAAAAATTTTCCTAAAAGAAGGTCACACGCC
1 AACTTAGAAAAATTTTCCTAAAAGAAGGTCACACGCC
54790002 AACTTAGAAAAATTTTCCTAAAAGAAGGTCACACGCC
1 AACTTAGAAAAATTTTCCTAAAAGAAGGTCACACGCC
54790039 CGTGTCCTCA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.43, C:0.22, G:0.14, T:0.22
Consensus pattern (37 bp):
AACTTAGAAAAATTTTCCTAAAAGAAGGTCACACGCC
Found at i:54791564 original size:16 final size:15
Alignment explanation
Indices: 54791540--54791569 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
54791530 AACTGTTTTA
54791540 TTACAAATTTCACTC
1 TTACAAATTTCACTC
54791555 TTACATAATTTCACT
1 TTACA-AATTTCACT
54791570 TACTCCATTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.33, C:0.23, G:0.00, T:0.43
Consensus pattern (15 bp):
TTACAAATTTCACTC
Found at i:54791890 original size:50 final size:50
Alignment explanation
Indices: 54791781--54792058 Score: 227
Period size: 50 Copynumber: 5.5 Consensus size: 50
54791771 CTGGTATGCA
* * * * * * *
54791781 TAGTAGCATGCACTTAGTACTACACATGCGACC-AACAACCCGATACAGG
1 TAGTAGCCTGCACTTAGTACTACACACGTGACCTAACCATCTGATACACG
* *
54791830 TAGTAGCCTGCACTTAGTACTACACAAGTGACCTAACCATCTGATACATG
1 TAGTAGCCTGCACTTAGTACTACACACGTGACCTAACCATCTGATACACG
* *** * * * *
54791880 TAGTAGCCTGCACTTAGTACTACACACGTGA-TTGAAGTTGTCGGGTACGCA
1 TAGTAGCCTGCACTTAGTACTACACACGTGACCT-AA-CCATCTGATACACG
* * * ** * * *
54791931 TAGTAGCCTACACTTGGTACTACACATGCAACCTAACTAGCTGGTACACG
1 TAGTAGCCTGCACTTAGTACTACACACGTGACCTAACCATCTGATACACG
* * * *
54791981 TACTAGCCTGCACTTAGTACTACACACGTGACCTAAAACCATCTTAAACACA
1 TAGTAGCCTGCACTTAGTACTACACACGTGACCT--AACCATCTGATACACG
* *
54792033 TAGTAGCCTGCACATACTACTACACA
1 TAGTAGCCTGCACTTAGTACTACACA
54792059 TGTGTTCTCA
Statistics
Matches: 179, Mismatches: 44, Indels: 9
0.77 0.19 0.04
Matches are distributed among these distances:
49 31 0.17
50 80 0.45
51 34 0.19
52 34 0.19
ACGTcount: A:0.32, C:0.27, G:0.17, T:0.24
Consensus pattern (50 bp):
TAGTAGCCTGCACTTAGTACTACACACGTGACCTAACCATCTGATACACG
Found at i:54791966 original size:101 final size:101
Alignment explanation
Indices: 54791830--54792011 Score: 274
Period size: 101 Copynumber: 1.8 Consensus size: 101
54791820 CCGATACAGG
* ** * * *
54791830 TAGTAGCCTGCACTTAGTACTACACAAGTGACCTAACCATCTGATACATGTAGTAGCCTGCACTT
1 TAGTAGCCTACACTTAGTACTACACAAGCAACCTAACCAGCTGATACACGTACTAGCCTGCACTT
54791895 AGTACTACACACGTGATTGAAGTTGTCGGGTACGCA
66 AGTACTACACACGTGATTGAAGTTGTCGGGTACGCA
* * * *
54791931 TAGTAGCCTACACTTGGTACTACACATGCAACCTAACTAGCTGGTACACGTACTAGCCTGCACTT
1 TAGTAGCCTACACTTAGTACTACACAAGCAACCTAACCAGCTGATACACGTACTAGCCTGCACTT
54791996 AGTACTACACACGTGA
66 AGTACTACACACGTGA
54792012 CCTAAAACCA
Statistics
Matches: 71, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
101 71 1.00
ACGTcount: A:0.29, C:0.26, G:0.19, T:0.26
Consensus pattern (101 bp):
TAGTAGCCTACACTTAGTACTACACAAGCAACCTAACCAGCTGATACACGTACTAGCCTGCACTT
AGTACTACACACGTGATTGAAGTTGTCGGGTACGCA
Found at i:54795206 original size:46 final size:46
Alignment explanation
Indices: 54795106--54795322 Score: 169
Period size: 46 Copynumber: 4.7 Consensus size: 46
54795096 GGGTGCAGGT
* *
54795106 GCCGATGCCATGTCCCAGACATGGTCTTACACTGAC--ACATCTCATA-
1 GCCGATG-CATGTCCCAGACAT-GTCTTACACTGGCTTAAATCTCA-AG
* *
54795152 GCCAATGCATATCCCAGACATGTCTTACACTGGCTTAAATCTCAAG
1 GCCGATGCATGTCCCAGACATGTCTTACACTGGCTTAAATCTCAAG
* * * ** *
54795198 GCCGATGCATGTCTCAGACATGTCATACACTAGCATT-CGTCTCAAT
1 GCCGATGCATGTCCCAGACATGTCTTACACTGGC-TTAAATCTCAAG
* * * * *
54795244 GTCGATGCCATATCCCTGACATCGTCTTACGCTGGCTCTCATAATGT---G
1 GCCGATG-CATGTCCCAGACAT-GTCTTACACTGGCT-T-A-AATCTCAAG
54795292 GCCGATGCATGTCCCAGACATGTCTTACACT
1 GCCGATGCATGTCCCAGACATGTCTTACACT
54795323 AGCTAACTCA
Statistics
Matches: 134, Mismatches: 27, Indels: 20
0.74 0.15 0.11
Matches are distributed among these distances:
44 12 0.09
45 14 0.10
46 63 0.47
47 26 0.19
48 17 0.13
51 2 0.01
ACGTcount: A:0.25, C:0.30, G:0.18, T:0.27
Consensus pattern (46 bp):
GCCGATGCATGTCCCAGACATGTCTTACACTGGCTTAAATCTCAAG
Found at i:54797421 original size:23 final size:24
Alignment explanation
Indices: 54797373--54797421 Score: 57
Period size: 22 Copynumber: 2.1 Consensus size: 24
54797363 GCTAAAACTC
**
54797373 AACTTTGTTCCCAAAACCTCTTGT
1 AACTTTGTTCCCAAAACCTCAGGT
54797397 AACTTT-TT-CCAAAACCTCGAGGT
1 AACTTTGTTCCCAAAACCTC-AGGT
54797420 AA
1 AA
54797422 ATCTTGGGTC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
22 10 0.45
23 6 0.27
24 6 0.27
ACGTcount: A:0.31, C:0.27, G:0.10, T:0.33
Consensus pattern (24 bp):
AACTTTGTTCCCAAAACCTCAGGT
Found at i:54801542 original size:20 final size:21
Alignment explanation
Indices: 54801517--54801556 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
54801507 GCTCTGGAAC
54801517 AGGGC-ACACGCCCGTGTAGA
1 AGGGCAACACGCCCGTGTAGA
*
54801537 AGGGCAACACGCTCGTGTAG
1 AGGGCAACACGCCCGTGTAG
54801557 CCATTAACTC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.25, C:0.28, G:0.35, T:0.12
Consensus pattern (21 bp):
AGGGCAACACGCCCGTGTAGA
Found at i:54802745 original size:46 final size:47
Alignment explanation
Indices: 54802657--54802826 Score: 147
Period size: 46 Copynumber: 3.7 Consensus size: 47
54802647 GCATATCTGT
* * *
54802657 GCTGATGCCATGTCCCAGACATGGTCTTACACTGAC--ATATCTCATA-
1 GCTGATGCCATATCCCAGACAT-GTCTTACACTGGCTTAAATCTCA-AG
54802703 GCTGATG-CATATCCCAGACATGTCTTACACTGGCTTAAATCTCAAG
1 GCTGATGCCATATCCCAGACATGTCTTACACTGGCTTAAATCTCAAG
* * * * * ** *
54802749 GCCGATG-CATGTCTCAGACATGTCATACACTAGCATT-CGTCTCAAT
1 GCTGATGCCATATCCCAGACATGTCTTACACTGGC-TTAAATCTCAAG
*
54802795 G-TCGATGCCATATCCTAGACATGTCTTACACT
1 GCT-GATGCCATATCCCAGACATGTCTTACACT
54802827 AGCTCACACA
Statistics
Matches: 102, Mismatches: 16, Indels: 11
0.79 0.12 0.09
Matches are distributed among these distances:
44 12 0.12
45 14 0.14
46 54 0.53
47 22 0.22
ACGTcount: A:0.26, C:0.28, G:0.17, T:0.29
Consensus pattern (47 bp):
GCTGATGCCATATCCCAGACATGTCTTACACTGGCTTAAATCTCAAG
Found at i:54804951 original size:15 final size:15
Alignment explanation
Indices: 54804917--54804976 Score: 75
Period size: 15 Copynumber: 4.0 Consensus size: 15
54804907 TATAGATAAC
* * *
54804917 AAGAAAACCAGGATT
1 AAGAAATCCAAGATA
*
54804932 AAGAAGTCCAAGATA
1 AAGAAATCCAAGATA
*
54804947 GAGAAATCCAAGATA
1 AAGAAATCCAAGATA
54804962 AAGAAATCCAAGATA
1 AAGAAATCCAAGATA
54804977 CAATATCATA
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
15 38 1.00
ACGTcount: A:0.55, C:0.13, G:0.18, T:0.13
Consensus pattern (15 bp):
AAGAAATCCAAGATA
Found at i:54808443 original size:16 final size:15
Alignment explanation
Indices: 54808419--54808448 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
54808409 AACTGTTTTA
54808419 TTACAAATTTCACTC
1 TTACAAATTTCACTC
54808434 TTACATAATTTCACT
1 TTACA-AATTTCACT
54808449 TACTCCATTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.33, C:0.23, G:0.00, T:0.43
Consensus pattern (15 bp):
TTACAAATTTCACTC
Found at i:54808715 original size:49 final size:49
Alignment explanation
Indices: 54808659--54808834 Score: 174
Period size: 50 Copynumber: 3.5 Consensus size: 49
54808649 CTGGTACGCA
54808659 TAGTAGCCTGCACTTAGTACTACACATGCGACCAACAATCCGGGACACG
1 TAGTAGCCTGCACTTAGTACTACACATGCGACCAACAATCCGGGACACG
* * * ** ** *
54808708 TAGTAGCCTGCACTTAGTACTACACACGTGATCGAA-GTTCTCGGGTATGCA
1 TAGTAGCCTGCACTTAGTACTACACATGCGA-CCAACAATC-CGGG-ACACG
* * * * *
54808759 TAGTAGCCAGCACTTAGTACTACACATGCAACCTAACTATCTGGTACACG
1 TAGTAGCCTGCACTTAGTACTACACATGCGACC-AACAATCCGGGACACG
* *
54808809 TAGTCGCCTGAACTTAGTACTACACA
1 TAGTAGCCTGCACTTAGTACTACACA
54808835 CGTGACCTAA
Statistics
Matches: 99, Mismatches: 23, Indels: 9
0.76 0.18 0.07
Matches are distributed among these distances:
49 31 0.31
50 33 0.33
51 33 0.33
52 2 0.02
ACGTcount: A:0.30, C:0.27, G:0.19, T:0.24
Consensus pattern (49 bp):
TAGTAGCCTGCACTTAGTACTACACATGCGACCAACAATCCGGGACACG
Found at i:54811521 original size:55 final size:53
Alignment explanation
Indices: 54811395--54811580 Score: 216
Period size: 55 Copynumber: 3.5 Consensus size: 53
54811385 TTACCATTGT
* *
54811395 CATGTCTTGACATGGTCTTACGTGGTATCCTTGCCTTAT-GAACTCA-CTAATGC
1 CATGCCTTGACATGGTCTTACATGGTA-CCTTGCCTTATAGAACTCATC-AATGC
* *
54811448 CATGCCTTGGA-ATGGTCTTACATGGGACCTTTGCCTTATAGAAACACATCAATGC
1 CATGCCTT-GACATGGTCTTACATGGTACC-TTGCCTTATAG-AACTCATCAATGC
* * * *
54811503 CATGTCTTGACATGGTCTTACATGATTTCCTTGCCTTATAGAACTTATCAATGC
1 CATGCCTTGACATGGTCTTACATG-GTACCTTGCCTTATAGAACTCATCAATGC
*
54811557 CATGCCTTGGCATGGTCTTACATG
1 CATGCCTTGACATGGTCTTACATG
54811581 ATATCCTTAT
Statistics
Matches: 114, Mismatches: 12, Indels: 13
0.82 0.09 0.09
Matches are distributed among these distances:
52 2 0.02
53 30 0.26
54 38 0.33
55 41 0.36
56 3 0.03
ACGTcount: A:0.23, C:0.24, G:0.19, T:0.34
Consensus pattern (53 bp):
CATGCCTTGACATGGTCTTACATGGTACCTTGCCTTATAGAACTCATCAATGC
Found at i:54811577 original size:54 final size:54
Alignment explanation
Indices: 54811395--54811588 Score: 234
Period size: 54 Copynumber: 3.6 Consensus size: 54
54811385 TTACCATTGT
* * *
54811395 CATGTCTTGACATGGTCTTACGTGGTATCCTTGCCTTAT-GAACTCA-CTAATGC
1 CATGCCTTGACATGGTCTTACATGATATCCTTGCCTTATAGAACTCATC-AATGC
** *
54811448 CATGCCTTGGA-ATGGTCTTACATGGGA-CCTTTGCCTTATAGAAACACATCAATGC
1 CATGCCTT-GACATGGTCTTACATGATATCC-TTGCCTTATAG-AACTCATCAATGC
* * *
54811503 CATGTCTTGACATGGTCTTACATGATTTCCTTGCCTTATAGAACTTATCAATGC
1 CATGCCTTGACATGGTCTTACATGATATCCTTGCCTTATAGAACTCATCAATGC
*
54811557 CATGCCTTGGCATGGTCTTACATGATATCCTT
1 CATGCCTTGACATGGTCTTACATGATATCCTT
54811589 ATCTTACCAA
Statistics
Matches: 121, Mismatches: 13, Indels: 13
0.82 0.09 0.09
Matches are distributed among these distances:
52 2 0.02
53 30 0.25
54 45 0.37
55 41 0.34
56 3 0.02
ACGTcount: A:0.23, C:0.24, G:0.18, T:0.35
Consensus pattern (54 bp):
CATGCCTTGACATGGTCTTACATGATATCCTTGCCTTATAGAACTCATCAATGC
Found at i:54811620 original size:47 final size:47
Alignment explanation
Indices: 54811567--54811688 Score: 201
Period size: 47 Copynumber: 2.6 Consensus size: 47
54811557 CATGCCTTGG
* *
54811567 CATGGTCTTACATGATATCCTTATCTTACCAAATGT-CATGTTCCAAA
1 CATGGTCTTACATGGTATCCTTGTCTTACCAAAT-TCCATGTTCCAAA
*
54811614 CATGGTCTTACATGGTATCCTTGTCTTACCAAATTCCCTGTTCCAAA
1 CATGGTCTTACATGGTATCCTTGTCTTACCAAATTCCATGTTCCAAA
54811661 CATGGTCTTACATGGTATCCTTGTCTTA
1 CATGGTCTTACATGGTATCCTTGTCTTA
54811689 GTGCAATGCC
Statistics
Matches: 71, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
46 1 0.01
47 70 0.99
ACGTcount: A:0.25, C:0.25, G:0.13, T:0.38
Consensus pattern (47 bp):
CATGGTCTTACATGGTATCCTTGTCTTACCAAATTCCATGTTCCAAA
Found at i:54818581 original size:49 final size:49
Alignment explanation
Indices: 54818361--54818868 Score: 813
Period size: 49 Copynumber: 10.6 Consensus size: 49
54818351 CCCTTCGGGA
* * * *
54818361 CTTATCACAT-T-TATACACTTTCACATCCATCACGTTGGCCACT-CGC
1 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTAGGC
* * *
54818407 CCTGTCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTAGGC
*
54818454 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTAGGC
*
54818501 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTAGGC
*
54818548 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTAGGC
*
54818597 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTAGGC
*
54818646 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTAGGC
*
54818695 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTAGGC
*
54818742 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTAGGC
54818791 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTAGGC
54818840 CTTATCACATATATATACACTTTCACATT
1 CTTATCACATATATATACACTTTCACATT
54818869 TATTCAAATA
Statistics
Matches: 439, Mismatches: 16, Indels: 11
0.94 0.03 0.02
Matches are distributed among these distances:
45 1 0.00
46 34 0.08
47 147 0.33
49 257 0.59
ACGTcount: A:0.29, C:0.29, G:0.08, T:0.34
Consensus pattern (49 bp):
CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTAGGC
Found at i:54818655 original size:145 final size:144
Alignment explanation
Indices: 54818361--54818868 Score: 810
Period size: 145 Copynumber: 3.5 Consensus size: 144
54818351 CCCTTCGGGA
* * * * * * *
54818361 CTTATCAC-ATTTATACACTTTCACATCCATCACGTTGGCCACT-CGCCCTGTCACATATATACA
1 CTTATCACAATATATACACTTTCACATTCATCACATTGGCCATTAGGCCTTATCACATATATACA
54818424 CTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC--ATATATACACTTTCACATTCATCAC
66 CTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCAC
* *
54818487 ATCGGCCATTAGGC
131 ATTGGCCATTCGGC
*
54818501 CTTATCAC-ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATA
1 CTTATCACAATATATACACTTTCACATTCATCACATTGGCCATTAGGCCTTATCAC--ATATATA
* *
54818565 CACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATATACACTTTCACATTCATC
64 CACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATC
54818630 ACATTGGCCATTCGGC
129 ACATTGGCCATTCGGC
*
54818646 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATAC
1 CTTATCACA-ATATATACACTTTCACATTCATCACATTGGCCATTAGGCCTTATCACATATATAC
54818711 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCA
65 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCA
54818776 CATTGGCCATTCGGC
130 CATTGGCCATTCGGC
54818791 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTAGGCCTTATCACATATATAT
1 CTTATCACA-ATATATACACTTTCACATTCATCACATTGGCCATTAGGCCTTATCAC--ATATAT
54818856 ACACTTTCACATT
63 ACACTTTCACATT
54818869 TATTCAAATA
Statistics
Matches: 342, Mismatches: 17, Indels: 11
0.92 0.05 0.03
Matches are distributed among these distances:
140 38 0.11
141 8 0.02
143 45 0.13
145 187 0.55
147 64 0.19
ACGTcount: A:0.29, C:0.29, G:0.08, T:0.34
Consensus pattern (144 bp):
CTTATCACAATATATACACTTTCACATTCATCACATTGGCCATTAGGCCTTATCACATATATACA
CTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCAC
ATTGGCCATTCGGC
Found at i:54818709 original size:194 final size:194
Alignment explanation
Indices: 54818361--54818868 Score: 886
Period size: 194 Copynumber: 2.7 Consensus size: 194
54818351 CCCTTCGGGA
* * * * *
54818361 CTTATCACAT-T-TATACACTTTCACATCCATCACGTTGGCCACTC-GCCCTGTCAC--ATATAT
1 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATAT
*
54818421 ACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC--ATATATACACTTTCACATTCAT
66 ACACTTTCACATTCATCACATTGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCAT
54818484 CACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
131 CACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
54818548 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATAT
1 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATAT
*
54818613 ACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATATACACTTTCACATTCAT
66 ACACTTTCACATTCATCACATTGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCAT
* *
54818678 CACATTGGCCATTCGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
131 CACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
54818742 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATAT
1 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATAT
54818807 ACACTTTCACATTCATCACATTGGCCATTAGGCCTTATCACATATATATACACTTTCACATT
66 ACACTTTCACATTCATCACATTGGCCATTAGGCCTTATCACATATATATACACTTTCACATT
54818869 TATTCAAATA
Statistics
Matches: 304, Mismatches: 10, Indels: 7
0.95 0.03 0.02
Matches are distributed among these distances:
187 10 0.03
188 1 0.00
189 30 0.10
190 8 0.03
192 45 0.15
194 210 0.69
ACGTcount: A:0.29, C:0.29, G:0.08, T:0.34
Consensus pattern (194 bp):
CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATAT
ACACTTTCACATTCATCACATTGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCAT
CACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:54822337 original size:39 final size:40
Alignment explanation
Indices: 54822162--54822337 Score: 243
Period size: 40 Copynumber: 4.5 Consensus size: 40
54822152 CGGATGATAA
* *
54822162 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTA-AT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
54822201 TCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
54822240 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
54822280 CCGGGCTAAGTCCCGAAGGCATTTGAGCAAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT
* *
54822320 CC-GGCTAAATTCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
54822338 TACTTGGTTT
Statistics
Matches: 124, Mismatches: 10, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
38 24 0.19
39 36 0.29
40 64 0.52
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.24
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:54830318 original size:79 final size:80
Alignment explanation
Indices: 54830187--54830334 Score: 237
Period size: 79 Copynumber: 1.9 Consensus size: 80
54830177 TATTCGGATG
* * *
54830187 ATAACCGGGCTAAGTCCTGAAGGCATTTGTGCTAGTGACTAATTCCGGGCTAAG-CCCGAAGGCA
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTAATACCGGGCTAAGTCCCGAAGGCA
54830251 TTTGTGCGAGTTACT
66 TTTGTGCGAGTTACT
*
54830266 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTAAGTCCCGAAGGC
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTAAT-ACCGGGCTAAGTCCCGAAGGC
54830330 ATTTG
65 ATTTG
54830335 AGCAAGTAGC
Statistics
Matches: 63, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
78 2 0.03
79 47 0.75
80 14 0.22
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (80 bp):
ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTAATACCGGGCTAAGTCCCGAAGGCA
TTTGTGCGAGTTACT
Found at i:54830356 original size:79 final size:79
Alignment explanation
Indices: 54830187--54830367 Score: 233
Period size: 79 Copynumber: 2.3 Consensus size: 79
54830177 TATTCGGATG
* * *
54830187 ATAACCGGGCTAAGTCCTGAAGGCATTTGTGCTAGTGACTAATTCCGGGCTAAGCCCGAAGGCAT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTAATACCGGGCTAAGCCCGAAGGCAT
* *
54830252 TTGTGCGAGTTACT
66 TTGAGCAAGTTACT
*
54830266 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTAAGTCCCGAAGGC
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTAAT-ACCGGGCTAAG-CCCGAAGGC
54830330 ATTTGAGCAAG-TAGCT
64 ATTTGAGCAAGTTA-CT
* * *
54830346 ATATCC-GGCTAAATTCCGAAGG
1 ATAACCGGGCTAAGTCCCGAAGG
54830368 TACTTGGTTT
Statistics
Matches: 90, Mismatches: 9, Indels: 6
0.86 0.09 0.06
Matches are distributed among these distances:
78 2 0.02
79 63 0.70
80 25 0.28
ACGTcount: A:0.27, C:0.22, G:0.27, T:0.24
Consensus pattern (79 bp):
ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTAATACCGGGCTAAGCCCGAAGGCAT
TTGAGCAAGTTACT
Found at i:54830367 original size:39 final size:40
Alignment explanation
Indices: 54830187--54830334 Score: 237
Period size: 40 Copynumber: 3.7 Consensus size: 40
54830177 TATTCGGATG
* * *
54830187 ATAACCGGGCTAAGTCCTGAAGGCATTTGTGCTAGTGACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
*
54830227 A-ATTCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACT
1 ATA-ACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
54830266 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
54830306 ATAACCGGGCTAAGTCCCGAAGGCATTTG
1 ATAACCGGGCTAAGTCCCGAAGGCATTTG
54830335 AGCAAGTAGC
Statistics
Matches: 100, Mismatches: 5, Indels: 6
0.90 0.05 0.05
Matches are distributed among these distances:
39 34 0.34
40 66 0.66
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
Found at i:54831879 original size:27 final size:27
Alignment explanation
Indices: 54831822--54831881 Score: 68
Period size: 27 Copynumber: 2.2 Consensus size: 27
54831812 ATAAATCTTA
*
54831822 TAGGGGCATATCAATCATTTCACCATG
1 TAGGGGCATATCAATCATTTCACAATG
* * *
54831849 TAGGGGCATTTCATTCATTTTATCAAT-
1 TAGGGGCATATCAATCATTTCA-CAATG
54831876 TAGGGG
1 TAGGGG
54831882 ATCTAGGTAC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
27 25 0.89
28 3 0.11
ACGTcount: A:0.27, C:0.17, G:0.22, T:0.35
Consensus pattern (27 bp):
TAGGGGCATATCAATCATTTCACAATG
Found at i:54842204 original size:27 final size:27
Alignment explanation
Indices: 54842162--54842296 Score: 135
Period size: 27 Copynumber: 5.0 Consensus size: 27
54842152 AAATGGTGAT
* *
54842162 CGAAATACCCCCATAGGGTGAAATAAC
1 CGAAATACCCCCATAGGGTAAAATGAC
* *
54842189 CGAAATACCCCTATAGGGTAAAATGAT
1 CGAAATACCCCCATAGGGTAAAATGAC
* *
54842216 CGAAATACCCCCATAGGGCAAAATGGC
1 CGAAATACCCCCATAGGGTAAAATGAC
** *
54842243 CGAAATACCCATATAGGATAAAATGAC
1 CGAAATACCCCCATAGGGTAAAATGAC
* * * ** *
54842270 TGTATTACCCCTGTAAGGTAAAATGAC
1 CGAAATACCCCCATAGGGTAAAATGAC
54842297 TGTTTTACCC
Statistics
Matches: 88, Mismatches: 20, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 88 1.00
ACGTcount: A:0.40, C:0.22, G:0.19, T:0.19
Consensus pattern (27 bp):
CGAAATACCCCCATAGGGTAAAATGAC
Found at i:54842280 original size:54 final size:54
Alignment explanation
Indices: 54842158--54842268 Score: 168
Period size: 54 Copynumber: 2.1 Consensus size: 54
54842148 GCCAAAATGG
** * *
54842158 TGATCGAAATACCCCCATAGGGTGAAATAACCGAAATACCCCTATAGGGTAAAA
1 TGATCGAAATACCCCCATAGGGCAAAATAACCGAAATACCCATATAGGATAAAA
**
54842212 TGATCGAAATACCCCCATAGGGCAAAATGGCCGAAATACCCATATAGGATAAAA
1 TGATCGAAATACCCCCATAGGGCAAAATAACCGAAATACCCATATAGGATAAAA
54842266 TGA
1 TGA
54842269 CTGTATTACC
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
54 51 1.00
ACGTcount: A:0.41, C:0.22, G:0.19, T:0.18
Consensus pattern (54 bp):
TGATCGAAATACCCCCATAGGGCAAAATAACCGAAATACCCATATAGGATAAAA
Found at i:54842297 original size:27 final size:27
Alignment explanation
Indices: 54842261--54842325 Score: 112
Period size: 27 Copynumber: 2.4 Consensus size: 27
54842251 CCATATAGGA
54842261 TAAAATGACTGTATTACCCCTGTAAGG
1 TAAAATGACTGTATTACCCCTGTAAGG
* *
54842288 TAAAATGACTGTTTTACCCTTGTAAGG
1 TAAAATGACTGTATTACCCCTGTAAGG
54842315 TAAAATGACTG
1 TAAAATGACTG
54842326 ATTTGCCCTA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.32
Consensus pattern (27 bp):
TAAAATGACTGTATTACCCCTGTAAGG
Found at i:54842334 original size:27 final size:26
Alignment explanation
Indices: 54842261--54842334 Score: 103
Period size: 27 Copynumber: 2.7 Consensus size: 26
54842251 CCATATAGGA
*
54842261 TAAAATGACTGTATTACCCCTGTAAGG
1 TAAAATGACTGT-TTACCCTTGTAAGG
54842288 TAAAATGACTGTTTTACCCTTGTAAGG
1 TAAAATGACTG-TTTACCCTTGTAAGG
*
54842315 TAAAATGACTGATTTGCCCT
1 TAAAATGACTG-TTTACCCT
54842335 ACGATGTGTA
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
27 42 0.98
28 1 0.02
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.34
Consensus pattern (26 bp):
TAAAATGACTGTTTACCCTTGTAAGG
Found at i:54846284 original size:46 final size:46
Alignment explanation
Indices: 54846213--54846383 Score: 166
Period size: 46 Copynumber: 3.7 Consensus size: 46
54846203 TCATTTGTGT
54846213 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCACAATATGAGA
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCACAATATGAGA
* * * * *
54846259 GCTAGTGTAAGACATGTCTGAGACATGCTTCAGCCTCGAGATATTTA-A
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCAC-A-ATA-TGAGA
* * * * ** * *
54846307 GCCAATGTAAGACATGTTTGGGGCATGCATCGG-CATTGAGACGAGA
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCA-CAATATGAGA
*
54846353 GCTAGTGTAAGACATCTCTGGGACATGCATC
1 GCTAGTGTAAGACATGTCTGGGACATGCATC
54846384 AGCCTCGCTA
Statistics
Matches: 97, Mismatches: 23, Indels: 10
0.75 0.18 0.08
Matches are distributed among these distances:
45 1 0.01
46 62 0.64
47 2 0.02
48 30 0.31
49 2 0.02
ACGTcount: A:0.29, C:0.19, G:0.27, T:0.25
Consensus pattern (46 bp):
GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCACAATATGAGA
Found at i:54846410 original size:94 final size:94
Alignment explanation
Indices: 54846213--54846413 Score: 251
Period size: 94 Copynumber: 2.1 Consensus size: 94
54846203 TCATTTGTGT
* * *
54846213 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCACAATATGAGAGCTAGTGTAAGACATGTCT
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCACAAGACGAGAGCTAGTGTAAGACATCTCT
* **
54846278 GAGACATGCTTCAGCCTCGAGATATTTAA
66 GAGACATGCATCAGCCTCGAGATATACAA
* * * * **
54846307 GCCAATGTAAGACATGTTTGGGGCATGCATCGG-CATTGAGACGAGAGCTAGTGTAAGACATCTC
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCA-CAAGACGAGAGCTAGTGTAAGACATCTC
* **
54846371 TGGGACATGCATCAGCCTCGCTATATACAA
65 TGAGACATGCATCAGCCTCGAGATATACAA
54846401 GCTAGTGTAAGAC
1 GCTAGTGTAAGAC
54846414 CTATCTGTGA
Statistics
Matches: 89, Mismatches: 17, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
93 2 0.02
94 87 0.98
ACGTcount: A:0.29, C:0.20, G:0.26, T:0.24
Consensus pattern (94 bp):
GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCACAAGACGAGAGCTAGTGTAAGACATCTCT
GAGACATGCATCAGCCTCGAGATATACAA
Found at i:54848185 original size:18 final size:18
Alignment explanation
Indices: 54848162--54848270 Score: 200
Period size: 18 Copynumber: 6.1 Consensus size: 18
54848152 GCCGTGTGAG
54848162 CCAGACACGCCCGTGTCA
1 CCAGACACGCCCGTGTCA
54848180 CCAGACACGCCCGTGTCA
1 CCAGACACGCCCGTGTCA
54848198 CCAGACACGCCCGTGTCA
1 CCAGACACGCCCGTGTCA
54848216 CCAGACACGCCCGTGTCA
1 CCAGACACGCCCGTGTCA
54848234 CCAGACACGCCCGTGTCA
1 CCAGACACGCCCGTGTCA
* *
54848252 CCAGACATGCCTGTGTCA
1 CCAGACACGCCCGTGTCA
54848270 C
1 C
54848271 AGGACGTGTG
Statistics
Matches: 89, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
18 89 1.00
ACGTcount: A:0.22, C:0.43, G:0.22, T:0.13
Consensus pattern (18 bp):
CCAGACACGCCCGTGTCA
Found at i:54849552 original size:43 final size:43
Alignment explanation
Indices: 54849504--54849615 Score: 136
Period size: 43 Copynumber: 2.6 Consensus size: 43
54849494 TCTTAGATAT
* *
54849504 GGTCTTACATGTTATCACATATCGATGCCACTGTCCCAGACAA
1 GGTCTTACATGTAATCACATATCGATGCCAATGTCCCAGACAA
* * * *
54849547 GGTCTTACACGAAATCACA-ATACAATGCCAATGTCCCAGACAT
1 GGTCTTACATGTAATCACATAT-CGATGCCAATGTCCCAGACAA
* *
54849590 GGTCTTACATGTAATTACATCTCGAT
1 GGTCTTACATGTAATCACATATCGAT
54849616 AGTCCTAATG
Statistics
Matches: 56, Mismatches: 11, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
42 2 0.04
43 53 0.95
44 1 0.02
ACGTcount: A:0.31, C:0.26, G:0.15, T:0.28
Consensus pattern (43 bp):
GGTCTTACATGTAATCACATATCGATGCCAATGTCCCAGACAA
Found at i:54857664 original size:52 final size:52
Alignment explanation
Indices: 54857605--54857714 Score: 220
Period size: 52 Copynumber: 2.1 Consensus size: 52
54857595 TTTTGTGACT
54857605 AACATGTTTGATTGAATGCATATGTTTAGGCAATTTTGCCAAGTTGATGGAA
1 AACATGTTTGATTGAATGCATATGTTTAGGCAATTTTGCCAAGTTGATGGAA
54857657 AACATGTTTGATTGAATGCATATGTTTAGGCAATTTTGCCAAGTTGATGGAA
1 AACATGTTTGATTGAATGCATATGTTTAGGCAATTTTGCCAAGTTGATGGAA
54857709 AACATG
1 AACATG
54857715 ACTTTGTATG
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 58 1.00
ACGTcount: A:0.32, C:0.10, G:0.23, T:0.35
Consensus pattern (52 bp):
AACATGTTTGATTGAATGCATATGTTTAGGCAATTTTGCCAAGTTGATGGAA
Found at i:54863697 original size:29 final size:29
Alignment explanation
Indices: 54863655--54863710 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
54863645 TACAAGTATC
*
54863655 TATAGTTTTCAGAATCTAGAGTTTCACAA
1 TATAGTTTTCAGAATCTAAAGTTTCACAA
*
54863684 TATAGTTTTCAGAATTTAAAGTTTCAC
1 TATAGTTTTCAGAATCTAAAGTTTCAC
54863711 GGTGTATAGA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.34, C:0.12, G:0.12, T:0.41
Consensus pattern (29 bp):
TATAGTTTTCAGAATCTAAAGTTTCACAA
Found at i:54864114 original size:40 final size:40
Alignment explanation
Indices: 54864070--54864151 Score: 164
Period size: 40 Copynumber: 2.0 Consensus size: 40
54864060 TATATTTAGA
54864070 AAACTCAAGTTCTGATATTTTTCAGAAAACACCCTACTTC
1 AAACTCAAGTTCTGATATTTTTCAGAAAACACCCTACTTC
54864110 AAACTCAAGTTCTGATATTTTTCAGAAAACACCCTACTTC
1 AAACTCAAGTTCTGATATTTTTCAGAAAACACCCTACTTC
54864150 AA
1 AA
54864152 TTAAAACATT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.37, C:0.24, G:0.07, T:0.32
Consensus pattern (40 bp):
AAACTCAAGTTCTGATATTTTTCAGAAAACACCCTACTTC
Found at i:54865073 original size:35 final size:36
Alignment explanation
Indices: 54864996--54865080 Score: 102
Period size: 36 Copynumber: 2.4 Consensus size: 36
54864986 TGATGGCTGG
* * *
54864996 GCATGCCTAACATGGGAATCAGAATGAGAAATAATG
1 GCATGCTTAACATGGGAATCAAAATGAGAAATAATA
* *
54865032 GCATGCTTAACATGTGAGTCAAAAT-A-AAATTAATA
1 GCATGCTTAACATGGGAATCAAAATGAGAAA-TAATA
54865067 GCATGCTTAACATG
1 GCATGCTTAACATG
54865081 CAAACCAAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
34 3 0.07
35 19 0.44
36 21 0.49
ACGTcount: A:0.41, C:0.14, G:0.20, T:0.25
Consensus pattern (36 bp):
GCATGCTTAACATGGGAATCAAAATGAGAAATAATA
Found at i:54871829 original size:43 final size:43
Alignment explanation
Indices: 54871672--54871830 Score: 148
Period size: 43 Copynumber: 3.7 Consensus size: 43
54871662 TATGTGTTTT
* * *
54871672 CGTGTAAGACCACATCTGAGACGTTGGCATTGA-ATTATGATTGA
1 CGTGTAAGACCACGTCTGGGACGTTGGCATCGATATT-TGATT-A
* * * *
54871716 CGTGTAAGACCATGTCTGGGACGTTCGTATC-ATATTTGATTT
1 CGTGTAAGACCACGTCTGGGACGTTGGCATCGATATTTGATTA
*
54871758 CGTGTAAGACGCTA--TCTAGGACAG-TGGCATCGATATTTGATTA
1 CGTGTAAGAC-C-ACGTCTGGGAC-GTTGGCATCGATATTTGATTA
* *
54871801 CATGTAAGACCACGTCTGGGTCGTTGGCAT
1 CGTGTAAGACCACGTCTGGGACGTTGGCAT
54871831 TGTATAAGCT
Statistics
Matches: 93, Mismatches: 14, Indels: 17
0.75 0.11 0.14
Matches are distributed among these distances:
41 1 0.01
42 24 0.26
43 39 0.42
44 29 0.31
ACGTcount: A:0.25, C:0.18, G:0.26, T:0.31
Consensus pattern (43 bp):
CGTGTAAGACCACGTCTGGGACGTTGGCATCGATATTTGATTA
Found at i:54881759 original size:25 final size:25
Alignment explanation
Indices: 54881698--54881758 Score: 79
Period size: 25 Copynumber: 2.4 Consensus size: 25
54881688 ATAAAACCTA
*
54881698 AAAATGAAATAGTATTAAATGAAGAT
1 AAAAT-AAAAAGTATTAAATGAAGAT
54881724 AAAATAAAAAGTACTTAAA-GAAGAT
1 AAAATAAAAAGTA-TTAAATGAAGAT
54881749 AAATATAAAA
1 AAA-ATAAAA
54881759 GGAAAAATAA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
25 16 0.50
26 16 0.50
ACGTcount: A:0.64, C:0.02, G:0.11, T:0.23
Consensus pattern (25 bp):
AAAATAAAAAGTATTAAATGAAGAT
Found at i:54887064 original size:51 final size:51
Alignment explanation
Indices: 54887008--54887108 Score: 202
Period size: 51 Copynumber: 2.0 Consensus size: 51
54886998 AAACTGATTG
54887008 ATTAAGACAATACCCAAGGAAAAATTCACCTTGACTTCACTTTTTATTTGA
1 ATTAAGACAATACCCAAGGAAAAATTCACCTTGACTTCACTTTTTATTTGA
54887059 ATTAAGACAATACCCAAGGAAAAATTCACCTTGACTTCACTTTTTATTTG
1 ATTAAGACAATACCCAAGGAAAAATTCACCTTGACTTCACTTTTTATTTG
54887109 GCTCTGAATC
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 50 1.00
ACGTcount: A:0.37, C:0.20, G:0.10, T:0.34
Consensus pattern (51 bp):
ATTAAGACAATACCCAAGGAAAAATTCACCTTGACTTCACTTTTTATTTGA
Found at i:54889196 original size:49 final size:49
Alignment explanation
Indices: 54889137--54889328 Score: 206
Period size: 49 Copynumber: 3.9 Consensus size: 49
54889127 TAGCCAAAGC
*
54889137 TATCTAGTACACATAGTAGCCTGCACTTAGTACTACACATGCAACCAAT
1 TATCTGGTACACATAGTAGCCTGCACTTAGTACTACACATGCAACCAAT
* * ** *
54889186 TATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCTAAC
1 TATCTGGTACACATAGTAGCCTGCACTTAGTACTACACATGCAACC-AAT
* * * * ***
54889236 CATCTGATACACGTAGTAGCCTACACTTAGTACTACACACGTG-ATTGAAGT
1 TATCTGGTACACATAGTAGCCTGCACTTAGTACTACACA--TGCAACCAA-T
* *
54889287 TATCGGGTACGCATAGTAGCCTGCACTTAGTACTACACATGC
1 TATCTGGTACACATAGTAGCCTGCACTTAGTACTACACATGC
54889329 GACCTTACAA
Statistics
Matches: 117, Mismatches: 21, Indels: 9
0.80 0.14 0.06
Matches are distributed among these distances:
49 43 0.37
50 40 0.34
51 33 0.28
52 1 0.01
ACGTcount: A:0.30, C:0.26, G:0.17, T:0.27
Consensus pattern (49 bp):
TATCTGGTACACATAGTAGCCTGCACTTAGTACTACACATGCAACCAAT
Found at i:54889263 original size:50 final size:49
Alignment explanation
Indices: 54889144--54889325 Score: 193
Period size: 50 Copynumber: 3.7 Consensus size: 49
54889134 AGCTATCTAG
* * ** ** *
54889144 TACACATAGTAGCCTGCACTTAGTACTACACATGCAACCAATTATCTGG
1 TACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCAACCATCTGA
54889193 TACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCTAACCATCTGA
1 TACACGTAGTAGCCTGCACTTAGTACTACACACGTGACC-AACCATCTGA
* ** ** * *
54889243 TACACGTAGTAGCCTACACTTAGTACTACACACGTGATTGAAGTTATCGGG
1 TACACGTAGTAGCCTGCACTTAGTACTACACACGTGA-CCAA-CCATCTGA
* *
54889294 TACGCATAGTAGCCTGCACTTAGTACTACACA
1 TACACGTAGTAGCCTGCACTTAGTACTACACA
54889326 TGCGACCTTA
Statistics
Matches: 113, Mismatches: 17, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
49 35 0.31
50 45 0.40
51 33 0.29
ACGTcount: A:0.31, C:0.26, G:0.17, T:0.26
Consensus pattern (49 bp):
TACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCAACCATCTGA
Found at i:54889319 original size:101 final size:99
Alignment explanation
Indices: 54889144--54889325 Score: 258
Period size: 101 Copynumber: 1.8 Consensus size: 99
54889134 AGCTATCTAG
* * *
54889144 TACACATAGTAGCCTGCACTTAGTACTACACATGCAACCAATTATCTGGTACACGTAGTAGCCTG
1 TACACATAGTAGCCTACACTTAGTACTACACATGCAACCAATTATCGGGTACACATAGTAGCCTG
54889209 CACTTAGTACTACACACGTGACCTAACCATCTGA
66 CACTTAGTACTACACACGTGACCTAACCATCTGA
* *** *
54889243 TACACGTAGTAGCCTACACTTAGTACTACACACGTG-ATTGAAGTTATCGGGTACGCATAGTAGC
1 TACACATAGTAGCCTACACTTAGTACTACACA--TGCAACCAA-TTATCGGGTACACATAGTAGC
54889307 CTGCACTTAGTACTACACA
63 CTGCACTTAGTACTACACA
54889326 TGCGACCTTA
Statistics
Matches: 72, Mismatches: 8, Indels: 4
0.86 0.10 0.05
Matches are distributed among these distances:
99 30 0.42
100 3 0.04
101 39 0.54
ACGTcount: A:0.31, C:0.26, G:0.17, T:0.26
Consensus pattern (99 bp):
TACACATAGTAGCCTACACTTAGTACTACACATGCAACCAATTATCGGGTACACATAGTAGCCTG
CACTTAGTACTACACACGTGACCTAACCATCTGA
Found at i:54890791 original size:32 final size:32
Alignment explanation
Indices: 54890754--54890819 Score: 123
Period size: 32 Copynumber: 2.1 Consensus size: 32
54890744 TCGAATTCAC
54890754 AAATCTAAGGATAATTCTTCCAAAAATATGCT
1 AAATCTAAGGATAATTCTTCCAAAAATATGCT
*
54890786 AAATCTAAGGATAATTCTTCCAACAATATGCT
1 AAATCTAAGGATAATTCTTCCAAAAATATGCT
54890818 AA
1 AA
54890820 GCATGAGGTA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.44, C:0.17, G:0.09, T:0.30
Consensus pattern (32 bp):
AAATCTAAGGATAATTCTTCCAAAAATATGCT
Found at i:54892603 original size:28 final size:29
Alignment explanation
Indices: 54892538--54892636 Score: 125
Period size: 28 Copynumber: 3.5 Consensus size: 29
54892528 CATGAGATTG
* *
54892538 GCACTAAGTGTGCG-GGTTCAAATTGTATA
1 GCACTAAGTGTGCGAGGTTC-GATTATATA
54892567 GCACTAAGTGTGCGAGGTT-GATTATATA
1 GCACTAAGTGTGCGAGGTTCGATTATATA
*
54892595 GCACTAAGTGTGCGA-GTTCGACTAT-TAA
1 GCACTAAGTGTGCGAGGTTCGATTATAT-A
54892623 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
54892637 GGCTTATTAT
Statistics
Matches: 64, Mismatches: 3, Indels: 7
0.86 0.04 0.09
Matches are distributed among these distances:
27 4 0.06
28 42 0.66
29 14 0.22
30 4 0.06
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (29 bp):
GCACTAAGTGTGCGAGGTTCGATTATATA
Found at i:54896383 original size:8 final size:8
Alignment explanation
Indices: 54896370--54896394 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
54896360 CTTAATATGG
54896370 AGCTTGAA
1 AGCTTGAA
54896378 AGCTTGAA
1 AGCTTGAA
54896386 AGCTTGAA
1 AGCTTGAA
54896394 A
1 A
54896395 CAAACCCTAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.40, C:0.12, G:0.24, T:0.24
Consensus pattern (8 bp):
AGCTTGAA
Found at i:54903899 original size:30 final size:30
Alignment explanation
Indices: 54903865--54903925 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
54903855 TCCTTAACTC
54903865 AAACTTTGGAAAAATTACAATTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
* * * * *
54903895 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
54903925 A
1 A
54903926 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:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (30 bp):
AAACTTTGGAAAAATTACAATTTTGCCCCT
Found at i:54906292 original size:46 final size:46
Alignment explanation
Indices: 54906157--54906332 Score: 169
Period size: 46 Copynumber: 3.8 Consensus size: 46
54906147 TCAATTGTGT
* ** ** *
54906157 GAGCTAGTGTAAGACATGTCTAGGG-CATGCATCGGCCACATCATGA
1 GAGCCAGTGTAAGACATGTCT-GGGACATGCATCGGCCTTAAGACGA
* *
54906203 GAGCCAGTGTAAGACCATGTCT-AGACCATGGCATCGGCATTAAGACGA
1 GAGCCAGTGTAAGA-CATGTCTGGGA-CAT-GCATCGGCCTTAAGACGA
* * *
54906251 GTGCTAGTGTAAGACATGTCTGGGACATGCATCAGCCTTAAGACGTA
1 GAGCCAGTGTAAGACATGTCTGGGACATGCATCGGCCTTAAGACG-A
* *
54906298 -AGCCAGTGGAAGACATGTTTGGGACATGCATCGGC
1 GAGCCAGTGTAAGACATGTCTGGGACATGCATCGGC
54906333 ACCTGACCCC
Statistics
Matches: 106, Mismatches: 18, Indels: 12
0.78 0.13 0.09
Matches are distributed among these distances:
45 1 0.01
46 58 0.55
47 21 0.20
48 26 0.25
ACGTcount: A:0.28, C:0.21, G:0.29, T:0.22
Consensus pattern (46 bp):
GAGCCAGTGTAAGACATGTCTGGGACATGCATCGGCCTTAAGACGA
Found at i:54911696 original size:35 final size:36
Alignment explanation
Indices: 54911610--54911711 Score: 125
Period size: 35 Copynumber: 2.9 Consensus size: 36
54911600 TCGATTTAAC
* * * *
54911610 ATAATTGCATGCCTAACATGCGAATCAGAATGAGAA
1 ATAATAGCATGCTTAACATGCGAATCAAAATCAGAA
* *
54911646 ATAATGGCATGCTTAACATGCGAGTCAAAATCA-AA
1 ATAATAGCATGCTTAACATGCGAATCAAAATCAGAA
* *
54911681 TTAATAGCATGCTTAACATGCGAACCAAAAT
1 ATAATAGCATGCTTAACATGCGAATCAAAAT
54911712 ATTATAATAT
Statistics
Matches: 57, Mismatches: 9, Indels: 1
0.85 0.13 0.01
Matches are distributed among these distances:
35 29 0.51
36 28 0.49
ACGTcount: A:0.42, C:0.18, G:0.17, T:0.24
Consensus pattern (36 bp):
ATAATAGCATGCTTAACATGCGAATCAAAATCAGAA
Found at i:54920346 original size:28 final size:29
Alignment explanation
Indices: 54920314--54920412 Score: 107
Period size: 28 Copynumber: 3.5 Consensus size: 29
54920304 ATAATAAGCC
*
54920314 CGCACACTTAGTGCTTA-ATAGTCGAACT
1 CGCACACTTAGTGCTTACATAATCGAACT
*
54920342 CGCACACTTAGTGC-TATATAATC-AACCT
1 CGCACACTTAGTGCTTACATAATCGAA-CT
* * *
54920370 CGCACACTTAGTGCTATACA-ATTTGAACC
1 CGCACACTTAGTGCT-TACATAATCGAACT
54920399 CGCACACTTAGTGC
1 CGCACACTTAGTGC
54920413 CAATCTCATG
Statistics
Matches: 61, Mismatches: 5, Indels: 9
0.81 0.07 0.12
Matches are distributed among these distances:
27 4 0.07
28 35 0.57
29 17 0.28
30 5 0.08
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (29 bp):
CGCACACTTAGTGCTTACATAATCGAACT
Found at i:54923277 original size:17 final size:19
Alignment explanation
Indices: 54923235--54923280 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
54923225 ATGAAATTTT
*
54923235 AATTAGTATTATGAGATAA
1 AATTATTATTATGAGATAA
*
54923254 AATTATTATTATTAGA-AA
1 AATTATTATTATGAGATAA
54923272 AA-TATTATT
1 AATTATTATT
54923281 GTATGTATGT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 7 0.28
18 4 0.16
19 14 0.56
ACGTcount: A:0.48, C:0.00, G:0.09, T:0.43
Consensus pattern (19 bp):
AATTATTATTATGAGATAA
Found at i:54923390 original size:15 final size:15
Alignment explanation
Indices: 54923372--54923400 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
54923362 ATATTTATAA
54923372 AATTATTATTATTAT
1 AATTATTATTATTAT
54923387 AATTATTATTATTA
1 AATTATTATTATTA
54923401 GATAGGAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
AATTATTATTATTAT
Found at i:54924355 original size:5 final size:5
Alignment explanation
Indices: 54924337--54924395 Score: 73
Period size: 5 Copynumber: 11.0 Consensus size: 5
54924327 GATGCAATTT
*
54924337 TTTTC TTCTTC TTTTC TTTTC TTTTC TTTTC TTTTC ATTTAC TTTCTC
1 TTTTC TT-TTC TTTTC TTTTC TTTTC TTTTC TTTTC -TTTTC TTT-TC
54924385 TTCTTC TTTTC
1 TT-TTC TTTTC
54924396 CCCCATAGCC
Statistics
Matches: 48, Mismatches: 2, Indels: 8
0.83 0.03 0.14
Matches are distributed among these distances:
5 31 0.65
6 16 0.33
7 1 0.02
ACGTcount: A:0.03, C:0.24, G:0.00, T:0.73
Consensus pattern (5 bp):
TTTTC
Found at i:54924365 original size:15 final size:15
Alignment explanation
Indices: 54924337--54924395 Score: 73
Period size: 16 Copynumber: 3.7 Consensus size: 15
54924327 GATGCAATTT
54924337 TTTTCTTCTTCTTTTC
1 TTTTCTT-TTCTTTTC
54924353 TTTTCTTTTCTTTTC
1 TTTTCTTTTCTTTTC
*
54924368 TTTTCATTTACTTTCTC
1 TTTTC-TTTTCTTT-TC
54924385 TTCTTCTTTTC
1 TT-TTCTTTTC
54924396 CCCCATAGCC
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
15 13 0.34
16 14 0.37
17 8 0.21
18 3 0.08
ACGTcount: A:0.03, C:0.24, G:0.00, T:0.73
Consensus pattern (15 bp):
TTTTCTTTTCTTTTC
Found at i:54929184 original size:5 final size:5
Alignment explanation
Indices: 54929176--54929236 Score: 54
Period size: 5 Copynumber: 12.0 Consensus size: 5
54929166 GGATTTAGTT
* * *
54929176 TTTTT TTTTC -TT-C TTTTC TTTTC TTTTC TTTTC TCTTC ATTTAC TTTCTC
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC -TTTTC TTT-TC
54929226 TTCTTC TTTTC
1 TT-TTC TTTTC
54929237 CACCATAGCC
Statistics
Matches: 46, Mismatches: 5, Indels: 10
0.75 0.08 0.16
Matches are distributed among these distances:
3 1 0.02
4 4 0.09
5 30 0.65
6 10 0.22
7 1 0.02
ACGTcount: A:0.03, C:0.23, G:0.00, T:0.74
Consensus pattern (5 bp):
TTTTC
Found at i:54937930 original size:42 final size:42
Alignment explanation
Indices: 54937812--54937922 Score: 123
Period size: 43 Copynumber: 2.6 Consensus size: 42
54937802 ACCATACTAT
**
54937812 TGCCATATCCCAGATATGGTCTTACATGGGATCTTAAATCGA
1 TGCCATATCCCAGATATGGTCTTACATGAAATCTTAAATCGA
* * * * * * *
54937854 TGCTAATAGCCTAGCTCTGGTCTTACATAAAATCTTATATCGA
1 TGC-CATATCCCAGATATGGTCTTACATGAAATCTTAAATCGA
*
54937897 TGCCATATCCCAAATATGGTCTTACA
1 TGCCATATCCCAGATATGGTCTTACA
54937923 CGTAATCTCA
Statistics
Matches: 53, Mismatches: 15, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
42 20 0.38
43 33 0.62
ACGTcount: A:0.30, C:0.23, G:0.15, T:0.32
Consensus pattern (42 bp):
TGCCATATCCCAGATATGGTCTTACATGAAATCTTAAATCGA
Found at i:54951831 original size:46 final size:45
Alignment explanation
Indices: 54951654--54951860 Score: 176
Period size: 46 Copynumber: 4.5 Consensus size: 45
54951644 ATTGTAAGCT
* * * *
54951654 AGTGTAAGACATGTCTAGGACATGCATCGGCCACATAATGA-G-AGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCTAC--GA-GACGTAGTC
*
54951700 AGTGTAAGACCATGT-TAGGGACATGGCATCGGC-ATTGAGACG-AGTAC
1 AGTGTAAGA-CATGTCT-GGGACAT-GCATCGGCTA-CGAGACGTAGT-C
*
54951747 TAGTGTAAGACATGTCTGGGATATGCATCGGCCT-CGAGACGTAAGTC
1 -AGTGTAAGACATGTCTGGGACATGCATCGG-CTACGAGACGT-AGTC
* * *
54951794 AGTGTAAGACATGTATGGGACATGCATCGGCTACGAGATGT-GTT
1 AGTGTAAGACATGTCTGGGACATGCATCGGCTACGAGACGTAGTC
54951838 AGTGTAAGACCATGTCTGGGACA
1 AGTGTAAGA-CATGTCTGGGACA
54951861 CGGATCGGTA
Statistics
Matches: 136, Mismatches: 11, Indels: 29
0.77 0.06 0.16
Matches are distributed among these distances:
44 11 0.08
45 16 0.12
46 62 0.46
47 26 0.19
48 21 0.15
ACGTcount: A:0.29, C:0.18, G:0.30, T:0.23
Consensus pattern (45 bp):
AGTGTAAGACATGTCTGGGACATGCATCGGCTACGAGACGTAGTC
Found at i:54958186 original size:42 final size:43
Alignment explanation
Indices: 54958076--54958187 Score: 138
Period size: 43 Copynumber: 2.6 Consensus size: 43
54958066 AGGTCGTACA
* *
54958076 ATGCCAATGTCCCAGACGTAGTCTTACATATAATCAAATATCG
1 ATGCCAATGTCCCAGACGTGGTCTTACAGATAATCAAATATCG
* * **
54958119 ATGTCATTGTCCCAGACAAGGTCTTACACGA-AATCAAATAT-G
1 ATGCCAATGTCCCAGACGTGGTCTTACA-GATAATCAAATATCG
*
54958161 ATGCCAACGTCCCAGACGTGGTCTTAC
1 ATGCCAATGTCCCAGACGTGGTCTTAC
54958188 CCGCGTACTT
Statistics
Matches: 57, Mismatches: 11, Indels: 3
0.80 0.15 0.04
Matches are distributed among these distances:
42 23 0.40
43 33 0.58
44 1 0.02
ACGTcount: A:0.32, C:0.25, G:0.17, T:0.26
Consensus pattern (43 bp):
ATGCCAATGTCCCAGACGTGGTCTTACAGATAATCAAATATCG
Found at i:54961309 original size:47 final size:48
Alignment explanation
Indices: 54961112--54961620 Score: 704
Period size: 48 Copynumber: 10.9 Consensus size: 48
54961102 GCCCTTCGGA
* * * * * *
54961112 CTTATCACATTTA-TACACTTTCACATCCA-CACGT-TGCCACTCGGC
1 CTTATCACATATATTACACTTTCACATTCATCACATCGGCCATTAGGC
54961157 C-T-TCACATATA-TACAC-TTCACA-TCATCACATCGGCCATTAGGC
1 CTTATCACATATATTACACTTTCACATTCATCACATCGGCCATTAGGC
54961200 C--ATCACA-ATA-TACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATTACACTTTCACATTCATCACATCGGCCATTAGGC
* *
54961244 CTTATCACA-ATTAATACACTTTCACATTCATCACA-CAGCCATTAGGC
1 CTTATCACATA-TATTACACTTTCACATTCATCACATCGGCCATTAGGC
54961291 CTTATCACATATATTACACTTTCACATTCATCACATCGG-CATTAGGC
1 CTTATCACATATATTACACTTTCACATTCATCACATCGGCCATTAGGC
54961338 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATAT-TACACTTTCACATTCATCACATCGGCCATTAGGC
54961387 CTTATCACATATATATACACTTTCACATTCATTCACATCGGCCATTA-GC
1 CTTATCACATATAT-TACACTTTCACATTCA-TCACATCGGCCATTAGGC
54961436 CTTATCACATATATATACACTTTCACATTCATCACATC-GCCATTA-GC
1 CTTATCACATATAT-TACACTTTCACATTCATCACATCGGCCATTAGGC
54961483 C-TATCACATATA-TACACTTTCACA-TCATCACATC-GCCATTAGGC
1 CTTATCACATATATTACACTTTCACATTCATCACATCGGCCATTAGGC
*
54961527 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAAGC
1 CTTATCACATATAT-TACACTTTCACATTCATCACATCGGCCATTAGGC
*
54961576 CTTATCACATA-ATATACACTTTCACATTCATCACATCAGCCATTA
1 CTTATCACATATAT-TACACTTTCACATTCATCACATCGGCCATTA
54961621 CGCCATACTA
Statistics
Matches: 433, Mismatches: 11, Indels: 37
0.90 0.02 0.08
Matches are distributed among these distances:
41 2 0.00
42 18 0.04
43 50 0.12
44 38 0.09
45 12 0.03
46 18 0.04
47 89 0.21
48 99 0.23
49 92 0.21
50 15 0.03
ACGTcount: A:0.31, C:0.30, G:0.07, T:0.32
Consensus pattern (48 bp):
CTTATCACATATATTACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:54961548 original size:237 final size:231
Alignment explanation
Indices: 54961112--54961620 Score: 722
Period size: 237 Copynumber: 2.2 Consensus size: 231
54961102 GCCCTTCGGA
* * * * *
54961112 CTTATCACAT-T-TATACACTTTCACATCCA-CACGT-TGCCACTCGGCCTTCACATATATACAC
1 CTTATCACATATATATACACTTTCACATTCATCACATCAGCCATTAGGCCTTCACATATATACAC
54961173 TTCACATCATCACATCGGCCATTAGGCCATCACAATATACACTTTCACATTCATCACATCGGCCA
66 TTCACATCATCACATCGGCCATTAGGCCATCACAATATACACTTTCACATTCATCACATCGGCCA
54961238 TTAGGCCTTATCACAATTAATACACTTTCACATTCATCACACAGCCATTAGGCCTTATCACATAT
131 TTAGGCCTTATCACAATTAATACACTTTCACATTCATCACACAGCCATTAGGCCTTATCACATAT
*
54961303 ATTACACTTTCACATTCATCACATCGG-CATTAGGC
196 ATTACACTTTCACATTCATCACATCGGCCATTAAGC
*
54961338 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAT
1 CTTATCACATATATATACACTTTCACATTCATCACATCAGCCATTAGGCC-T-TCAC--ATATAT
54961403 ACACTTTCACATTCATTCACATCGGCCATTA-GCCTTATCACATATATATACACTTTCACATTCA
62 ACAC-TTCACA-TCA-TCACATCGGCCATTAGGCC--ATCAC--A-ATATACACTTTCACATTCA
54961467 TCACATC-GCCATTA-GCC-TATCAC-A-TATATACACTTTCACA-TCATCACATC-GCCATTAG
119 TCACATCGGCCATTAGGCCTTATCACAATTA-ATACACTTTCACATTCATCACA-CAGCCATTAG
54961525 GCCTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAAGC
182 GCCTTATCACATATAT-TACACTTTCACATTCATCACATCGGCCATTAAGC
54961576 CTTATCACATA-ATATACACTTTCACATTCATCACATCAGCCATTA
1 CTTATCACATATATATACACTTTCACATTCATCACATCAGCCATTA
54961621 CGCCATACTA
Statistics
Matches: 256, Mismatches: 7, Indels: 29
0.88 0.02 0.10
Matches are distributed among these distances:
226 10 0.04
227 1 0.00
228 17 0.07
229 4 0.02
230 9 0.04
231 1 0.00
232 4 0.02
234 10 0.04
235 6 0.02
236 40 0.16
237 88 0.34
238 29 0.11
239 3 0.01
240 8 0.03
241 26 0.10
ACGTcount: A:0.31, C:0.30, G:0.07, T:0.32
Consensus pattern (231 bp):
CTTATCACATATATATACACTTTCACATTCATCACATCAGCCATTAGGCCTTCACATATATACAC
TTCACATCATCACATCGGCCATTAGGCCATCACAATATACACTTTCACATTCATCACATCGGCCA
TTAGGCCTTATCACAATTAATACACTTTCACATTCATCACACAGCCATTAGGCCTTATCACATAT
ATTACACTTTCACATTCATCACATCGGCCATTAAGC
Found at i:54961553 original size:189 final size:189
Alignment explanation
Indices: 54961112--54961620 Score: 762
Period size: 189 Copynumber: 2.7 Consensus size: 189
54961102 GCCCTTCGGA
* * * * *
54961112 CTTATCACATTTATACACTTTCACATCCA-CACGTTGCCACTCGGCC-T-TCAC--ATATATACA
1 CTTATCACATATATACACTTTCACAT-CATCACATCGCCATTAGGCCTTATCACATATATATACA
54961172 C-TTCACA-TCATCACATCGGCCATTAGGCC--ATCAC--AATATACACTTTCACATTCATCACA
65 CTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATAATATACACTTTCACATTCATCACA
54961231 TCGGCCATTAGGCCTTATCACAATTAATACACTTTCACATTCATCACACAGCCATTAGGC
130 TCGGCCATTAGGCCTTATCACAATTAATACACTTTCACATTCATCACACAGCCATTAGGC
*
54961291 CTTATCACATATATTACACTTTCACATTCATCACATCGGCATTAGGCCTTATCACATATATATAC
1 CTTATCACATATA-TACACTTTCACA-TCATCACATCGCCATTAGGCCTTATCACATATATATAC
54961356 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATTC
64 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATA-ATATACACTTTCACATTCA-TC
54961421 ACATCGGCCATTA-GCCTTATCAC-ATATATATACACTTTCACATTCATCACATC-GCCATTA-G
127 ACATCGGCCATTAGGCCTTATCACAAT-TA-ATACACTTTCACATTCATCACA-CAGCCATTAGG
54961482 C
189 C
54961483 C-TATCACATATATACACTTTCACATCATCACATCGCCATTAGGCCTTATCACATATATATACAC
1 CTTATCACATATATACACTTTCACATCATCACATCGCCATTAGGCCTTATCACATATATATACAC
*
54961547 TTTCACATTCATCACATCGGCCATTAAGCCTTATCACATAATATACACTTTCACATTCATCACAT
66 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATAATATACACTTTCACATTCATCACAT
*
54961612 CAGCCATTA
131 CGGCCATTA
54961621 CGCCATACTA
Statistics
Matches: 303, Mismatches: 9, Indels: 28
0.89 0.03 0.08
Matches are distributed among these distances:
179 12 0.04
180 14 0.05
181 13 0.04
182 1 0.00
183 4 0.01
185 10 0.03
186 6 0.02
187 36 0.12
188 19 0.06
189 83 0.27
190 12 0.04
191 14 0.05
192 34 0.11
193 44 0.15
194 1 0.00
ACGTcount: A:0.31, C:0.30, G:0.07, T:0.32
Consensus pattern (189 bp):
CTTATCACATATATACACTTTCACATCATCACATCGCCATTAGGCCTTATCACATATATATACAC
TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATAATATACACTTTCACATTCATCACAT
CGGCCATTAGGCCTTATCACAATTAATACACTTTCACATTCATCACACAGCCATTAGGC
Found at i:54973128 original size:49 final size:49
Alignment explanation
Indices: 54972954--54973477 Score: 883
Period size: 47 Copynumber: 10.9 Consensus size: 49
54972944 CCCTTCGGGA
* * * * *
54972954 CTTATCACAT-T-TATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
54973001 CCTGTCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
54973048 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
54973095 CTTATCACATATATATACACTTTCACATTCATCACATCAGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
54973144 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
54973191 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
54973240 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
54973289 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
54973336 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
54973383 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
54973432 CTTATCACATATATATACACTTTCACATTCATCACATCAGCCATTA
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTA
54973478 CGCCATACTA
Statistics
Matches: 457, Mismatches: 12, Indels: 14
0.95 0.02 0.03
Matches are distributed among these distances:
46 1 0.00
47 230 0.50
49 226 0.49
ACGTcount: A:0.30, C:0.30, G:0.08, T:0.32
Consensus pattern (49 bp):
CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:54973151 original size:96 final size:96
Alignment explanation
Indices: 54972954--54973477 Score: 894
Period size: 96 Copynumber: 5.5 Consensus size: 96
54972944 CCCTTCGGGA
* * * * * * * *
54972954 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGCCCTGTCAC--ATATATAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
54973017 ACTTTCACATTCATCACATCGGCCATTAGGC
66 ACTTTCACATTCATCACATCGGCCATTAGGC
54973048 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
*
54973113 ACTTTCACATTCATCACATCAGCCATTAGGC
66 ACTTTCACATTCATCACATCGGCCATTAGGC
54973144 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
54973209 ACTTTCACATTCATCACATCGGCCATTAGGC
66 ACTTTCACATTCATCACATCGGCCATTAGGC
54973240 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC--ATATAT
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAT
54973303 ACACTTTCACATTCATCACATCGGCCATTAGGC
64 ACACTTTCACATTCATCACATCGGCCATTAGGC
54973336 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
54973401 ACTTTCACATTCATCACATCGGCCATTAGGC
66 ACTTTCACATTCATCACATCGGCCATTAGGC
*
54973432 CTTATCACATATATATACACTTTCACATTCATCACATCAGCCATTA
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTA
54973478 CGCCATACTA
Statistics
Matches: 411, Mismatches: 11, Indels: 12
0.95 0.03 0.03
Matches are distributed among these distances:
94 94 0.23
96 235 0.57
98 82 0.20
ACGTcount: A:0.30, C:0.30, G:0.08, T:0.32
Consensus pattern (96 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
ACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:54978589 original size:24 final size:24
Alignment explanation
Indices: 54978557--54978603 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
54978547 CTGTCAGGAG
**
54978557 AGGATTTAGGAGTTGATAAGGGAT
1 AGGATTTAGGAGCAGATAAGGGAT
54978581 AGGATTTAGGAGCAGATAAGGGA
1 AGGATTTAGGAGCAGATAAGGGA
54978604 GGAAATCTAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.36, C:0.02, G:0.38, T:0.23
Consensus pattern (24 bp):
AGGATTTAGGAGCAGATAAGGGAT
Found at i:54980050 original size:27 final size:28
Alignment explanation
Indices: 54980018--54980102 Score: 79
Period size: 27 Copynumber: 3.1 Consensus size: 28
54980008 AGGAAGCGTC
* *
54980018 CTGGTGGTTATGCCAC-ATATTTCTGT-T
1 CTGGTGGCTATGCCACGAT-TATCTGTAT
*
54980045 CTGGTGGCTCTGCCACGATTATCTGTAT
1 CTGGTGGCTATGCCACGATTATCTGTAT
* * *
54980073 CTGGTGACTCTGTCAC-ATTATCTGT-T
1 CTGGTGGCTATGCCACGATTATCTGTAT
54980099 CTGG
1 CTGG
54980103 CAGCCATGCT
Statistics
Matches: 51, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
26 5 0.10
27 29 0.57
28 17 0.33
ACGTcount: A:0.14, C:0.22, G:0.24, T:0.40
Consensus pattern (28 bp):
CTGGTGGCTATGCCACGATTATCTGTAT
Found at i:54980083 original size:28 final size:26
Alignment explanation
Indices: 54980028--54980102 Score: 96
Period size: 27 Copynumber: 2.8 Consensus size: 26
54980018 CTGGTGGTTA
* *
54980028 TGCCACATATTTCTGTTCTGGTGGCTC
1 TGCCACAT-TATCTGTTCTGGTGACTC
54980055 TGCCACGATTATCTGTATCTGGTGACTC
1 TGCCAC-ATTATCTGT-TCTGGTGACTC
*
54980083 TGTCACATTATCTGTTCTGG
1 TGCCACATTATCTGTTCTGG
54980103 CAGCCATGCT
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
26 5 0.12
27 21 0.49
28 17 0.40
ACGTcount: A:0.15, C:0.24, G:0.21, T:0.40
Consensus pattern (26 bp):
TGCCACATTATCTGTTCTGGTGACTC
Found at i:54985419 original size:28 final size:28
Alignment explanation
Indices: 54985373--54985426 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
54985363 TCTTTATGGA
* *
54985373 GAAGCCTTTGTGGGGATCTACTAAAAAT
1 GAAGCCTTTATGGGGATCTACGAAAAAT
**
54985401 GAAGCCTTTATGGTTATCTACGAAAA
1 GAAGCCTTTATGGGGATCTACGAAAA
54985427 CAAAACCTTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 22 1.00
ACGTcount: A:0.33, C:0.15, G:0.22, T:0.30
Consensus pattern (28 bp):
GAAGCCTTTATGGGGATCTACGAAAAAT
Found at i:54989722 original size:21 final size:21
Alignment explanation
Indices: 54989655--54989722 Score: 57
Period size: 21 Copynumber: 3.1 Consensus size: 21
54989645 ATCTGAACTT
54989655 ATTGAGTTGTGGTCTGAGTTC
1 ATTGAGTTGTGGTCTGAGTTC
* * **
54989676 A-TGATATTTGTGACATCTGAACTC
1 ATTG--AGTTGTG--GTCTGAGTTC
54989700 ATTGAGTTGTGGTCTGAGTTC
1 ATTGAGTTGTGGTCTGAGTTC
54989721 AT
1 AT
54989723 GATGCATGTG
Statistics
Matches: 34, Mismatches: 8, Indels: 10
0.65 0.15 0.19
Matches are distributed among these distances:
20 2 0.06
21 10 0.29
22 6 0.18
23 6 0.18
24 8 0.24
25 2 0.06
ACGTcount: A:0.21, C:0.12, G:0.26, T:0.41
Consensus pattern (21 bp):
ATTGAGTTGTGGTCTGAGTTC
Found at i:54989733 original size:45 final size:45
Alignment explanation
Indices: 54989645--54989735 Score: 146
Period size: 45 Copynumber: 2.0 Consensus size: 45
54989635 GAACTATGTG
* **
54989645 ATCTGAACTTATTGAGTTGTGGTCTGAGTTCATGATATTTGTGAC
1 ATCTGAACTCATTGAGTTGTGGTCTGAGTTCATGATACATGTGAC
*
54989690 ATCTGAACTCATTGAGTTGTGGTCTGAGTTCATGATGCATGTGAC
1 ATCTGAACTCATTGAGTTGTGGTCTGAGTTCATGATACATGTGAC
54989735 A
1 A
54989736 CATGTTTTGG
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.23, C:0.13, G:0.25, T:0.38
Consensus pattern (45 bp):
ATCTGAACTCATTGAGTTGTGGTCTGAGTTCATGATACATGTGAC
Found at i:54993408 original size:18 final size:18
Alignment explanation
Indices: 54993385--54993422 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
54993375 CTTGTCCCAT
*
54993385 TACAGTAACAGTAAATAG
1 TACAGTAACAGTAAACAG
*
54993403 TACAGTAATAGTAAACAG
1 TACAGTAACAGTAAACAG
54993421 TA
1 TA
54993423 TGCAAGTCCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.50, C:0.11, G:0.16, T:0.24
Consensus pattern (18 bp):
TACAGTAACAGTAAACAG
Found at i:54993884 original size:27 final size:27
Alignment explanation
Indices: 54993787--54993875 Score: 133
Period size: 27 Copynumber: 3.3 Consensus size: 27
54993777 GGCATTTCAG
* *
54993787 TCATTTTACCATATAAGGGAAAAATAA
1 TCATTTTACCACATAAGGGAAAAACAA
*
54993814 TCATTTTACCACATAAGGGCAAAACAA
1 TCATTTTACCACATAAGGGAAAAACAA
* *
54993841 TCATTTTACCAGATAAGGGAAAAACAC
1 TCATTTTACCACATAAGGGAAAAACAA
54993868 TCATTTTA
1 TCATTTTA
54993876 TCAATTAAGA
Statistics
Matches: 56, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 56 1.00
ACGTcount: A:0.44, C:0.17, G:0.11, T:0.28
Consensus pattern (27 bp):
TCATTTTACCACATAAGGGAAAAACAA
Found at i:54993995 original size:20 final size:20
Alignment explanation
Indices: 54993970--54994016 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
54993960 CAGAGAAAAT
54993970 GGGCCCAAGGCCCATATTGC
1 GGGCCCAAGGCCCATATTGC
*
54993990 GGGCCCAAGTCCCATATTGC
1 GGGCCCAAGGCCCATATTGC
*
54994010 AGGCCCA
1 GGGCCCA
54994017 TGTGGGTCTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.21, C:0.36, G:0.28, T:0.15
Consensus pattern (20 bp):
GGGCCCAAGGCCCATATTGC
Found at i:54997259 original size:18 final size:18
Alignment explanation
Indices: 54997206--54997260 Score: 74
Period size: 18 Copynumber: 3.1 Consensus size: 18
54997196 CTTGGCCCAT
* * *
54997206 TGCAGTAATAGTAAATAA
1 TGCAGCAATAGTAAACAG
*
54997224 TGCAGCAATAGTGAACAG
1 TGCAGCAATAGTAAACAG
54997242 TGCAGCAATAGTAAACAG
1 TGCAGCAATAGTAAACAG
54997260 T
1 T
54997261 ATGCAAGTCC
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.44, C:0.13, G:0.22, T:0.22
Consensus pattern (18 bp):
TGCAGCAATAGTAAACAG
Found at i:54997618 original size:54 final size:53
Alignment explanation
Indices: 54997552--54997724 Score: 183
Period size: 54 Copynumber: 3.2 Consensus size: 53
54997542 GGGGCAACAC
* * * * *
54997552 AGTCAATTTACCATGTAGGGGAATTTCAGTCATTTTACCACATGAGGGAAAAAT
1 AGTCATTTTACCAAGTAGGGCAA-ATCAGTCATTTTACCACATAAGGGAAAAAT
*
54997606 AGTCATTTTACCACAGAAGGGCAAAAT-AGTCATTTTACCACATAAGGGAAAAAT
1 AGTCATTTTACCA-AGTAGGGC-AAATCAGTCATTTTACCACATAAGGGAAAAAT
* * *
54997660 AGTCA-TTTACCACA-TAAGGGCAAAACAGTCA-TTTACCACATAAGGGCAAAAC
1 AGTCATTTTACCA-AGT-AGGGCAAATCAGTCATTTTACCACATAAGGGAAAAAT
*
54997712 AGTTATTTTACCA
1 AGTCATTTTACCA
54997725 CATAAGGGAA
Statistics
Matches: 103, Mismatches: 11, Indels: 11
0.82 0.09 0.09
Matches are distributed among these distances:
52 26 0.25
53 26 0.25
54 43 0.42
55 6 0.06
56 2 0.02
ACGTcount: A:0.39, C:0.18, G:0.17, T:0.26
Consensus pattern (53 bp):
AGTCATTTTACCAAGTAGGGCAAATCAGTCATTTTACCACATAAGGGAAAAAT
Found at i:54997668 original size:26 final size:27
Alignment explanation
Indices: 54997579--54997748 Score: 254
Period size: 27 Copynumber: 6.4 Consensus size: 27
54997569 GGGGAATTTC
*
54997579 AGTCATTTTACCACATGAGGGAAAAAT
1 AGTCATTTTACCACATAAGGGAAAAAT
* *
54997606 AGTCATTTTACCACAGAAGGGCAAAAT
1 AGTCATTTTACCACATAAGGGAAAAAT
54997633 AGTCATTTTACCACATAAGGGAAAAAT
1 AGTCATTTTACCACATAAGGGAAAAAT
* *
54997660 AGTCA-TTTACCACATAAGGGCAAAAC
1 AGTCATTTTACCACATAAGGGAAAAAT
* *
54997686 AGTCA-TTTACCACATAAGGGCAAAAC
1 AGTCATTTTACCACATAAGGGAAAAAT
*
54997712 AGTTATTTTACCACATAAGGGAAAAAT
1 AGTCATTTTACCACATAAGGGAAAAAT
54997739 AGTCATTTTA
1 AGTCATTTTA
54997749 TCGATTAAAG
Statistics
Matches: 131, Mismatches: 11, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
26 49 0.37
27 82 0.63
ACGTcount: A:0.42, C:0.17, G:0.16, T:0.25
Consensus pattern (27 bp):
AGTCATTTTACCACATAAGGGAAAAAT
Found at i:54997692 original size:53 final size:54
Alignment explanation
Indices: 54997578--54997748 Score: 256
Period size: 53 Copynumber: 3.2 Consensus size: 54
54997568 AGGGGAATTT
* *
54997578 CAGTCATTTTACCACATGAGGGAAAAATAGTCATTTTACCACAGAAGGGCAAAA
1 CAGTCATTTTACCACATAAGGGAAAAATAGTCATTTTACCACATAAGGGCAAAA
*
54997632 TAGTCATTTTACCACATAAGGGAAAAATAGTCA-TTTACCACATAAGGGCAAAA
1 CAGTCATTTTACCACATAAGGGAAAAATAGTCATTTTACCACATAAGGGCAAAA
* * * *
54997685 CAGTCA-TTTACCACATAAGGGCAAAACAGTTATTTTACCACATAAGGGAAAAA
1 CAGTCATTTTACCACATAAGGGAAAAATAGTCATTTTACCACATAAGGGCAAAA
*
54997738 TAGTCATTTTA
1 CAGTCATTTTA
54997749 TCGATTAAAG
Statistics
Matches: 106, Mismatches: 9, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
52 23 0.22
53 48 0.45
54 35 0.33
ACGTcount: A:0.42, C:0.18, G:0.16, T:0.25
Consensus pattern (54 bp):
CAGTCATTTTACCACATAAGGGAAAAATAGTCATTTTACCACATAAGGGCAAAA
Found at i:55000657 original size:163 final size:163
Alignment explanation
Indices: 55000387--55000719 Score: 605
Period size: 163 Copynumber: 2.0 Consensus size: 163
55000377 TGTTTATGTG
*
55000387 GCACTTGTGTGCAATTTTCTGTGTATCCAATAGTATTTCGAGTGTTCAACGAGTATTATATGAAT
1 GCACTTGTGTGCAATTTTCCGTGTATCCAATAGTATTTCGAGTGTTCAACGAGTATTATATGAAT
* * *
55000452 GATGAGATGAAAGTCCTAAGCTGGGCATGGCAATGAAGGTAAAGTTATTTGATATGCTACGGATA
66 GATGAGATGAAAGTCCTAAGATGGGCATGGCAATAAAGGTAAAGTTATTTAATATGCTACGGATA
55000517 TGTACAGGTACGTACGTTATACTCATGGGTGGT
131 TGTACAGGTACGTACGTTATACTCATGGGTGGT
*
55000550 GCACTTGTGTGCAATTTTCCGTGTATCCAATAGTATTTCGAGTGTTCAACGGGTATTATATGAAT
1 GCACTTGTGTGCAATTTTCCGTGTATCCAATAGTATTTCGAGTGTTCAACGAGTATTATATGAAT
55000615 GATGAGATGAAAGTCCTAAGATGGGCATGGCAATAAAGGTAAAGTTATTTAATATGCTACGGATA
66 GATGAGATGAAAGTCCTAAGATGGGCATGGCAATAAAGGTAAAGTTATTTAATATGCTACGGATA
*
55000680 TGTACAGGTACGTATGTTATACTCATGGGTGGT
131 TGTACAGGTACGTACGTTATACTCATGGGTGGT
55000713 GC-CTTGT
1 GCACTTGT
55000720 TAAAGGATGA
Statistics
Matches: 164, Mismatches: 6, Indels: 1
0.96 0.04 0.01
Matches are distributed among these distances:
162 5 0.03
163 159 0.97
ACGTcount: A:0.28, C:0.13, G:0.26, T:0.33
Consensus pattern (163 bp):
GCACTTGTGTGCAATTTTCCGTGTATCCAATAGTATTTCGAGTGTTCAACGAGTATTATATGAAT
GATGAGATGAAAGTCCTAAGATGGGCATGGCAATAAAGGTAAAGTTATTTAATATGCTACGGATA
TGTACAGGTACGTACGTTATACTCATGGGTGGT
Found at i:55004002 original size:15 final size:15
Alignment explanation
Indices: 55003970--55003998 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
55003960 ATTTTCTGTG
55003970 TTTATTATGTGTGAA
1 TTTATTATGTGTGAA
55003985 TTTA-TATGTGTGAA
1 TTTATTATGTGTGAA
55003999 ATTTTCGTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.28, C:0.00, G:0.21, T:0.52
Consensus pattern (15 bp):
TTTATTATGTGTGAA
Found at i:55005239 original size:41 final size:43
Alignment explanation
Indices: 55005139--55005295 Score: 201
Period size: 43 Copynumber: 3.7 Consensus size: 43
55005129 TATGTGTTCT
* *
55005139 CGTGTAAGACCAAGTTTGGGACATTGGCATCAATATGTAATTA
1 CGTGTAAGACCATGTCTGGGACATTGGCATCAATATGTAATTA
* *
55005182 CGTGTAAGACCATGTCTGGGACATTGGCATC-GTATTTAATT-
1 CGTGTAAGACCATGTCTGGGACATTGGCATCAATATGTAATTA
* * * *
55005223 CGTGTAAGACCCTGTCTGGGACAGTGGCATCAATATGTGATTG
1 CGTGTAAGACCATGTCTGGGACATTGGCATCAATATGTAATTA
* * *
55005266 CATGTAAGACCACGTCTGGGACGTTGGCAT
1 CGTGTAAGACCATGTCTGGGACATTGGCAT
55005296 TGTATGATAT
Statistics
Matches: 98, Mismatches: 14, Indels: 4
0.84 0.12 0.03
Matches are distributed among these distances:
41 29 0.30
42 15 0.15
43 54 0.55
ACGTcount: A:0.26, C:0.18, G:0.27, T:0.29
Consensus pattern (43 bp):
CGTGTAAGACCATGTCTGGGACATTGGCATCAATATGTAATTA
Found at i:55005283 original size:84 final size:84
Alignment explanation
Indices: 55005138--55005300 Score: 236
Period size: 84 Copynumber: 1.9 Consensus size: 84
55005128 ATATGTGTTC
* * * *
55005138 TCGTGTAAGACCAAGTTTGGGACATTGGCATCAATATGTAATTACGTGTAAGACCATGTCTGGGA
1 TCGTGTAAGACCAAGTCTGGGACAGTGGCATCAATATGTAATTACATGTAAGACCACGTCTGGGA
55005203 CATTGGCATCGTATTTAAT
66 CATTGGCATCGTATTTAAT
** * *
55005222 TCGTGTAAGACCCTGTCTGGGACAGTGGCATCAATATGTGATTGCATGTAAGACCACGTCTGGGA
1 TCGTGTAAGACCAAGTCTGGGACAGTGGCATCAATATGTAATTACATGTAAGACCACGTCTGGGA
* *
55005287 CGTTGGCATTGTAT
66 CATTGGCATCGTAT
55005301 GATATGCGTG
Statistics
Matches: 69, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
84 69 1.00
ACGTcount: A:0.26, C:0.17, G:0.26, T:0.31
Consensus pattern (84 bp):
TCGTGTAAGACCAAGTCTGGGACAGTGGCATCAATATGTAATTACATGTAAGACCACGTCTGGGA
CATTGGCATCGTATTTAAT
Found at i:55007600 original size:40 final size:40
Alignment explanation
Indices: 55007554--55007702 Score: 235
Period size: 40 Copynumber: 3.7 Consensus size: 40
55007544 GCAACTCACG
*
55007554 CAAATGCCTTCGGGTCTTAGCCCAGATATAGTCACTAGCA
1 CAAATGCCTTCGGGACTTAGCCCAGATATAGTCACTAGCA
** *
55007594 TGAATGCCTTCGGGACTTAGCCCGGATATAGTCACTAGCA
1 CAAATGCCTTCGGGACTTAGCCCAGATATAGTCACTAGCA
* *
55007634 CAAATGCCTTCGGGACTTAGCCCAGATATAGTAACTTGCA
1 CAAATGCCTTCGGGACTTAGCCCAGATATAGTCACTAGCA
*
55007674 CAAATGCCTTCGGGACTTAGCCCGGATAT
1 CAAATGCCTTCGGGACTTAGCCCAGATAT
55007703 CATCCGAATA
Statistics
Matches: 99, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
40 99 1.00
ACGTcount: A:0.27, C:0.26, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCAGATATAGTCACTAGCA
Found at i:55007654 original size:80 final size:80
Alignment explanation
Indices: 55007522--55007702 Score: 260
Period size: 80 Copynumber: 2.3 Consensus size: 80
55007512 ACCCAAGTAT
* * *
55007522 CTTCGGGATTTAG-CCGGATATAGCAACTCACGCAAATGCCTTCGGGTCTTAGCCCAGATATAGT
1 CTTCGGGACTTAGCCCGGATATAGCAACTCACACAAATGCCTTCGGGACTTAGCCCAGATATAGT
* **
55007586 CACTAGCATGAATGC
66 AACTAGCACAAATGC
55007601 CTTCGGGACTTAGCCCGGATATAGTC-ACT-AGCACAAATGCCTTCGGGACTTAGCCCAGATATA
1 CTTCGGGACTTAGCCCGGATATAG-CAACTCA-CACAAATGCCTTCGGGACTTAGCCCAGATATA
*
55007664 GTAACTTGCACAAATGC
64 GTAACTAGCACAAATGC
55007681 CTTCGGGACTTAGCCCGGATAT
1 CTTCGGGACTTAGCCCGGATAT
55007703 CATCCGAATA
Statistics
Matches: 92, Mismatches: 7, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
79 13 0.14
80 78 0.85
81 1 0.01
ACGTcount: A:0.27, C:0.26, G:0.23, T:0.25
Consensus pattern (80 bp):
CTTCGGGACTTAGCCCGGATATAGCAACTCACACAAATGCCTTCGGGACTTAGCCCAGATATAGT
AACTAGCACAAATGC
Found at i:55014799 original size:40 final size:40
Alignment explanation
Indices: 55014718--55014936 Score: 279
Period size: 40 Copynumber: 5.5 Consensus size: 40
55014708 ACCCAAGTAT
* *
55014718 CTTCGGGATTTAG-CCGGATATAG-CAACT--CGCAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTC-ACTAGCACAAATGC
* **
55014755 CTTCGGGTCTTAGCCCGGATATAGTCACTAGCATGAATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
55014795 CTTC-GGACTTAGCCCGGATATAGTCACTAGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
* *
55014834 CTTCGGGACTTAGCCCGG-TATAGAACTACTCGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAG-TC-ACTAGCACAAATGC
* *
55014875 CTTCGGGACTTAGCCCGGATATAGTAACTTGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
*
55014915 CTTCGGGACTTAGCCCGAATAT
1 CTTCGGGACTTAGCCCGGATAT
55014937 CATCCGAATA
Statistics
Matches: 160, Mismatches: 14, Indels: 13
0.86 0.07 0.07
Matches are distributed among these distances:
37 11 0.07
38 13 0.08
39 42 0.26
40 58 0.36
41 31 0.19
42 5 0.03
ACGTcount: A:0.26, C:0.26, G:0.23, T:0.25
Consensus pattern (40 bp):
CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
Found at i:55014909 original size:81 final size:80
Alignment explanation
Indices: 55014718--55014936 Score: 286
Period size: 81 Copynumber: 2.8 Consensus size: 80
55014708 ACCCAAGTAT
* * * * *
55014718 CTTCGGGATTTAG-CCGGATATAGCAAC-T-CGCAAATGCCTTCGGGTCTTAGCCCGGATATAGT
1 CTTCGGGACTTAGCCCGGATATAGTAACTTGCACAAATGCCTTCGGGACTTAGCCCGGATATAGA
**
55014780 CACTAGCATGAATGC
66 CACTAGCACAAATGC
* *
55014795 CTTC-GGACTTAGCCCGGATATAGTCACTAGCACAAATGCCTTCGGGACTTAGCCCGG-TATAGA
1 CTTCGGGACTTAGCCCGGATATAGTAACTTGCACAAATGCCTTCGGGACTTAGCCCGGATATAG-
*
55014858 ACTACTCGCACAAATGC
65 AC-ACTAGCACAAATGC
*
55014875 CTTCGGGACTTAGCCCGGATATAGTAACTTGCACAAATGCCTTCGGGACTTAGCCCGAATAT
1 CTTCGGGACTTAGCCCGGATATAGTAACTTGCACAAATGCCTTCGGGACTTAGCCCGGATAT
55014937 CATCCGAATA
Statistics
Matches: 122, Mismatches: 13, Indels: 9
0.85 0.09 0.06
Matches are distributed among these distances:
76 7 0.06
77 16 0.13
78 5 0.04
79 26 0.21
80 15 0.12
81 50 0.41
82 3 0.02
ACGTcount: A:0.26, C:0.26, G:0.23, T:0.25
Consensus pattern (80 bp):
CTTCGGGACTTAGCCCGGATATAGTAACTTGCACAAATGCCTTCGGGACTTAGCCCGGATATAGA
CACTAGCACAAATGC
Found at i:55018404 original size:21 final size:22
Alignment explanation
Indices: 55018364--55018404 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
55018354 GCCTAAACAG
*
55018364 TCACACAGGCGTATTGCCCCTC
1 TCACACAGGCGTAGTGCCCCTC
*
55018386 TCACACGGGCGT-GTGCCCC
1 TCACACAGGCGTAGTGCCCC
55018405 AATGTTAAGT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 6 0.35
22 11 0.65
ACGTcount: A:0.15, C:0.41, G:0.24, T:0.20
Consensus pattern (22 bp):
TCACACAGGCGTAGTGCCCCTC
Found at i:55021056 original size:18 final size:18
Alignment explanation
Indices: 55021023--55021058 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
55021013 TTTGAGCCTT
*
55021023 GGCCCATTGCAGTAACAG
1 GGCCCATTGCAATAACAG
*
55021041 GGCCCATTGTAATAACAG
1 GGCCCATTGCAATAACAG
55021059 TAAACAGTGC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.25, G:0.25, T:0.19
Consensus pattern (18 bp):
GGCCCATTGCAATAACAG
Found at i:55021439 original size:27 final size:27
Alignment explanation
Indices: 55021406--55021587 Score: 103
Period size: 27 Copynumber: 7.0 Consensus size: 27
55021396 ATAAACATAC
*
55021406 ATCACATAGGGGTAAAATAGTCATTTT
1 ATCACATAAGGGTAAAATAGTCATTTT
* *
55021433 ATCACATAAGGGCAAAATCGTCATTTT
1 ATCACATAAGGGTAAAATAGTCATTTT
*
55021460 AACACATAA-GG-------GTCATTTT
1 ATCACATAAGGGTAAAATAGTCATTTT
* * * * **
55021479 AACATATAAGGGCAAAACAACCATTTT
1 ATCACATAAGGGTAAAATAGTCATTTT
** * * * *
55021506 AAAAAATAAGGGCAATACAGTCATTTT
1 ATCACATAAGGGTAAAATAGTCATTTT
** * *
55021533 GCCATATAAGGGCAAAACT-GTCATTTT
1 ATCACATAAGGGTAAAA-TAGTCATTTT
*
55021560 ATCACATAAGGGAAAAATAGTCATTTT
1 ATCACATAAGGGTAAAATAGTCATTTT
55021587 A
1 A
55021588 CCCTATATGG
Statistics
Matches: 123, Mismatches: 22, Indels: 20
0.75 0.13 0.12
Matches are distributed among these distances:
19 16 0.13
20 2 0.02
26 3 0.02
27 102 0.83
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.29
Consensus pattern (27 bp):
ATCACATAAGGGTAAAATAGTCATTTT
Found at i:55021476 original size:19 final size:19
Alignment explanation
Indices: 55021452--55021490 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
55021442 GGGCAAAATC
55021452 GTCATTTTAACACATAAGG
1 GTCATTTTAACACATAAGG
*
55021471 GTCATTTTAACATATAAGG
1 GTCATTTTAACACATAAGG
55021490 G
1 G
55021491 CAAAACAACC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.36, C:0.13, G:0.18, T:0.33
Consensus pattern (19 bp):
GTCATTTTAACACATAAGG
Found at i:55021504 original size:46 final size:46
Alignment explanation
Indices: 55021425--55021517 Score: 116
Period size: 46 Copynumber: 2.0 Consensus size: 46
55021415 GGGTAAAATA
* ** * *
55021425 GTCATTTTATCACATAAGGGCAAAATCGTCATTTTAACACATAAGG
1 GTCATTTTAACACATAAGGGCAAAATCACCATTTTAAAAAATAAGG
*
55021471 GTCATTTTAACATATAAGGGCAAAA-CAACCATTTTAAAAAATAAGG
1 GTCATTTTAACACATAAGGGCAAAATC-ACCATTTTAAAAAATAAGG
55021517 G
1 G
55021518 CAATACAGTC
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
45 1 0.03
46 39 0.98
ACGTcount: A:0.42, C:0.15, G:0.15, T:0.28
Consensus pattern (46 bp):
GTCATTTTAACACATAAGGGCAAAATCACCATTTTAAAAAATAAGG
Found at i:55021569 original size:54 final size:54
Alignment explanation
Indices: 55021471--55021587 Score: 135
Period size: 54 Copynumber: 2.2 Consensus size: 54
55021461 ACACATAAGG
* *
55021471 GTCATTTTAACATATAAGGGCAAAACAACCATTTTAAAAAATAAGGGCAATACA
1 GTCATTTTAACATATAAGGGCAAAACAACCATTTTAAAAAATAAGGGAAAAACA
** *** ** * *
55021525 GTCATTTTGCCATATAAGGGCAAAACTGTCATTTTATCACATAAGGGAAAAATA
1 GTCATTTTAACATATAAGGGCAAAACAACCATTTTAAAAAATAAGGGAAAAACA
55021579 GTCATTTTA
1 GTCATTTTA
55021588 CCCTATATGG
Statistics
Matches: 51, Mismatches: 12, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
54 51 1.00
ACGTcount: A:0.42, C:0.15, G:0.15, T:0.29
Consensus pattern (54 bp):
GTCATTTTAACATATAAGGGCAAAACAACCATTTTAAAAAATAAGGGAAAAACA
Found at i:55021608 original size:27 final size:27
Alignment explanation
Indices: 55021579--55021907 Score: 428
Period size: 27 Copynumber: 12.2 Consensus size: 27
55021569 GGGAAAAATA
* ** *
55021579 GTCATTTTACCCTATATGGGTATTTCA
1 GTCATCTTACCCTATGGGGGTATTTCG
*
55021606 GTCATCTTACCCTATGGGGGTATTTTG
1 GTCATCTTACCCTATGGGGGTATTTCG
*
55021633 GTCATCTTACCCTATGGGGGTATTTCA
1 GTCATCTTACCCTATGGGGGTATTTCG
* * * *
55021660 GTCACCTTACCTTATTGGGGTATTTCA
1 GTCATCTTACCCTATGGGGGTATTTCG
55021687 GTCATCTTACCCTATGGGGGTATTTCG
1 GTCATCTTACCCTATGGGGGTATTTCG
* * * *
55021714 GTCATATTACCTTGTGGGGGTA-TTCA
1 GTCATCTTACCCTATGGGGGTATTTCG
* *
55021740 GTCAT-TTGACCTTATGGGGGTATTTTG
1 GTCATCTT-ACCCTATGGGGGTATTTCG
* * *
55021767 ATCATTTTACCCTATGGGGGTATTTTG
1 GTCATCTTACCCTATGGGGGTATTTCG
* *
55021794 ATCATCTTACCCTATAGGGGTATTTCG
1 GTCATCTTACCCTATGGGGGTATTTCG
*
55021821 GTCATCTTACCCTATGAGGGTATTTCG
1 GTCATCTTACCCTATGGGGGTATTTCG
*
55021848 GTCATCTTACCCTATGAGGGTATTTCG
1 GTCATCTTACCCTATGGGGGTATTTCG
55021875 GTCATCTTACCCTATGGGGGTATTTCG
1 GTCATCTTACCCTATGGGGGTATTTCG
55021902 GTCATC
1 GTCATC
55021908 ATTTCGGCCC
Statistics
Matches: 269, Mismatches: 30, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
25 2 0.01
26 21 0.08
27 244 0.91
28 2 0.01
ACGTcount: A:0.18, C:0.20, G:0.23, T:0.40
Consensus pattern (27 bp):
GTCATCTTACCCTATGGGGGTATTTCG
Found at i:55024747 original size:43 final size:42
Alignment explanation
Indices: 55024651--55024767 Score: 144
Period size: 43 Copynumber: 2.8 Consensus size: 42
55024641 GAAGTCCAAA
* * ** * *
55024651 CTCGTTGAGTGGTCCAAGTTCATGATATATGTGGCATCCGAG
1 CTCGTTGAGTGGTCCGAGTTCATAATGGATGCGGCATCCGAC
* *
55024693 CTCGTTGAGTGGTCCGAGTTCATTATGGATGCGAGCATCTGAC
1 CTCGTTGAGTGGTCCGAGTTCATAATGGATGCG-GCATCCGAC
*
55024736 CTCGTTCAGTGGTCCGAGTTCATAATGGATGC
1 CTCGTTGAGTGGTCCGAGTTCATAATGGATGC
55024768 AATATATGTG
Statistics
Matches: 65, Mismatches: 9, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
42 28 0.43
43 37 0.57
ACGTcount: A:0.20, C:0.21, G:0.29, T:0.31
Consensus pattern (42 bp):
CTCGTTGAGTGGTCCGAGTTCATAATGGATGCGGCATCCGAC
Found at i:55025723 original size:32 final size:32
Alignment explanation
Indices: 55025682--55025745 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
55025672 TAAACAAGAA
55025682 AGAAAAAGAAAAAGAAGCTAGGGTTCAGCTTC
1 AGAAAAAGAAAAAGAAGCTAGGGTTCAGCTTC
55025714 AGAAAAAGAAAAAGAAGCTAGGGTTCAGCTTC
1 AGAAAAAGAAAAAGAAGCTAGGGTTCAGCTTC
55025746 TTTCAAGCTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.47, C:0.12, G:0.25, T:0.16
Consensus pattern (32 bp):
AGAAAAAGAAAAAGAAGCTAGGGTTCAGCTTC
Found at i:55034422 original size:24 final size:24
Alignment explanation
Indices: 55034385--55034451 Score: 66
Period size: 24 Copynumber: 2.8 Consensus size: 24
55034375 TACCGATATA
* *
55034385 TCAGCTCGTAAGAGCTTATTATTT
1 TCAGCTCATTAGAGCTTATTATTT
* **
55034409 TCAGCTCATTAGAGCCTACCATTT
1 TCAGCTCATTAGAGCTTATTATTT
55034433 T-AGCTCA-TACGAGCTTATT
1 TCAGCTCATTA-GAGCTTATT
55034452 GTTCAACTCG
Statistics
Matches: 34, Mismatches: 8, Indels: 3
0.76 0.18 0.07
Matches are distributed among these distances:
22 2 0.06
23 12 0.35
24 20 0.59
ACGTcount: A:0.25, C:0.22, G:0.15, T:0.37
Consensus pattern (24 bp):
TCAGCTCATTAGAGCTTATTATTT
Found at i:55034488 original size:23 final size:23
Alignment explanation
Indices: 55034407--55034495 Score: 83
Period size: 23 Copynumber: 3.9 Consensus size: 23
55034397 AGCTTATTAT
* * *
55034407 TTTCAGCTCATTAGAGCCTACCA
1 TTTCAGCTCAATAGAGCTTACCG
* **
55034430 TTTTAGCTC-ATACGAGCTTATTG
1 TTTCAGCTCAATA-GAGCTTACCG
* *
55034453 -TTCAACTCGATAGAGCTTACCG
1 TTTCAGCTCAATAGAGCTTACCG
55034475 TTTCAGCTCAATAGAGCTTAC
1 TTTCAGCTCAATAGAGCTTAC
55034496 TGTCCATCAG
Statistics
Matches: 51, Mismatches: 12, Indels: 6
0.74 0.17 0.09
Matches are distributed among these distances:
22 16 0.31
23 35 0.69
ACGTcount: A:0.26, C:0.25, G:0.16, T:0.34
Consensus pattern (23 bp):
TTTCAGCTCAATAGAGCTTACCG
Found at i:55035581 original size:41 final size:43
Alignment explanation
Indices: 55035501--55035582 Score: 105
Period size: 42 Copynumber: 2.0 Consensus size: 43
55035491 CCTACAAGTT
* *
55035501 TTACACGGCCTAGACACACGGGCGTGTCTGCTGGCCATGTGTG
1 TTACACGGCCTAGACACACGGGCGTGTCGGCCGGCCATGTGTG
* * *
55035544 TTACACGGGCT-GGCACATGGGCGTGT-GGCCGGCCATGTG
1 TTACACGGCCTAGACACACGGGCGTGTCGGCCGGCCATGTG
55035583 ACCTAATTCA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
41 11 0.32
42 13 0.38
43 10 0.29
ACGTcount: A:0.15, C:0.27, G:0.37, T:0.22
Consensus pattern (43 bp):
TTACACGGCCTAGACACACGGGCGTGTCGGCCGGCCATGTGTG
Found at i:55037153 original size:48 final size:48
Alignment explanation
Indices: 55037093--55037224 Score: 165
Period size: 48 Copynumber: 2.8 Consensus size: 48
55037083 GTGCAAATTA
* * * ** *
55037093 TACCTTGATTTGGCTTTGGGCCATGGTATAGGTATTTCGATTATGAGT
1 TACCTTGATTTGGCTTCGGGCCATGGTATAGGTACTCCGAGGATAAGT
** * * *
55037141 TACCTTGATTTGGCCACAGGCCATGGTATAGGCACTCCGGGGATAAGT
1 TACCTTGATTTGGCTTCGGGCCATGGTATAGGTACTCCGAGGATAAGT
55037189 TACCTTGATTTGGCTTCGGGCCATGGTATAGGTACT
1 TACCTTGATTTGGCTTCGGGCCATGGTATAGGTACT
55037225 TATTTATTGA
Statistics
Matches: 69, Mismatches: 15, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
48 69 1.00
ACGTcount: A:0.20, C:0.18, G:0.28, T:0.34
Consensus pattern (48 bp):
TACCTTGATTTGGCTTCGGGCCATGGTATAGGTACTCCGAGGATAAGT
Found at i:55039344 original size:27 final size:27
Alignment explanation
Indices: 55039303--55039399 Score: 149
Period size: 27 Copynumber: 3.6 Consensus size: 27
55039293 CTTTAATCGA
*
55039303 TAAAATGATTATTTTTCCCTCATGAGG
1 TAAAATGATTATTTTGCCCTCATGAGG
* *
55039330 TAAATTGATTTTTTTGCCCTCATGAGG
1 TAAAATGATTATTTTGCCCTCATGAGG
*
55039357 TAAAATGACTATTTTGCCCTCATGAGG
1 TAAAATGATTATTTTGCCCTCATGAGG
*
55039384 TAAAATGACTATTTTG
1 TAAAATGATTATTTTG
55039400 TACTTATGTG
Statistics
Matches: 64, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 64 1.00
ACGTcount: A:0.29, C:0.14, G:0.16, T:0.40
Consensus pattern (27 bp):
TAAAATGATTATTTTGCCCTCATGAGG
Found at i:55039412 original size:27 final size:27
Alignment explanation
Indices: 55039303--55039414 Score: 125
Period size: 27 Copynumber: 4.1 Consensus size: 27
55039293 CTTTAATCGA
* * *
55039303 TAAAATGATTATTTTTCCCTCATGAGG
1 TAAAATGACTATTTTGCACTCATGAGG
* * * *
55039330 TAAATTGATTTTTTTGCCCTCATGAGG
1 TAAAATGACTATTTTGCACTCATGAGG
*
55039357 TAAAATGACTATTTTGCCCTCATGAGG
1 TAAAATGACTATTTTGCACTCATGAGG
* * *
55039384 TAAAATGACTATTTTGTACTTATGTGG
1 TAAAATGACTATTTTGCACTCATGAGG
55039411 TAAA
1 TAAA
55039415 TGATTGAAAT
Statistics
Matches: 75, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 75 1.00
ACGTcount: A:0.29, C:0.13, G:0.17, T:0.40
Consensus pattern (27 bp):
TAAAATGACTATTTTGCACTCATGAGG
Found at i:55039413 original size:54 final size:54
Alignment explanation
Indices: 55039303--55039414 Score: 143
Period size: 54 Copynumber: 2.1 Consensus size: 54
55039293 CTTTAATCGA
* * * * * *
55039303 TAAAATGATTATTTTTCCCTCATGAGGTAAATTGATTTTTTTGCCCTCATGAGG
1 TAAAATGACTATTTTGCCCTCATGAGGTAAAATGACTATTTTGCACTCATGAGG
* * *
55039357 TAAAATGACTATTTTGCCCTCATGAGGTAAAATGACTATTTTGTACTTATGTGG
1 TAAAATGACTATTTTGCCCTCATGAGGTAAAATGACTATTTTGCACTCATGAGG
55039411 TAAA
1 TAAA
55039415 TGATTGAAAT
Statistics
Matches: 49, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
54 49 1.00
ACGTcount: A:0.29, C:0.13, G:0.17, T:0.40
Consensus pattern (54 bp):
TAAAATGACTATTTTGCCCTCATGAGGTAAAATGACTATTTTGCACTCATGAGG
Found at i:55044306 original size:80 final size:80
Alignment explanation
Indices: 55044173--55044334 Score: 324
Period size: 80 Copynumber: 2.0 Consensus size: 80
55044163 AGTTTTCAAC
55044173 ATTTTCAAGCTCAATAGTAAGTGTTCCCTAGCCTCGTTTTTAATGTTCTTCGTATTTTTGAAATC
1 ATTTTCAAGCTCAATAGTAAGTGTTCCCTAGCCTCGTTTTTAATGTTCTTCGTATTTTTGAAATC
55044238 CTCGTAACATGCTCT
66 CTCGTAACATGCTCT
55044253 ATTTTCAAGCTCAATAGTAAGTGTTCCCTAGCCTCGTTTTTAATGTTCTTCGTATTTTTGAAATC
1 ATTTTCAAGCTCAATAGTAAGTGTTCCCTAGCCTCGTTTTTAATGTTCTTCGTATTTTTGAAATC
55044318 CTCGTAACATGCTCT
66 CTCGTAACATGCTCT
55044333 AT
1 AT
55044335 CCATTTCTAC
Statistics
Matches: 82, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
80 82 1.00
ACGTcount: A:0.23, C:0.21, G:0.14, T:0.43
Consensus pattern (80 bp):
ATTTTCAAGCTCAATAGTAAGTGTTCCCTAGCCTCGTTTTTAATGTTCTTCGTATTTTTGAAATC
CTCGTAACATGCTCT
Found at i:55052137 original size:47 final size:47
Alignment explanation
Indices: 55052074--55052530 Score: 853
Period size: 47 Copynumber: 9.7 Consensus size: 47
55052064 ATGATAGTAT
55052074 GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAA
1 GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAA
55052121 GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAA
1 GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAA
55052168 GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAA
1 GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAA
55052215 GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAA
1 GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAA
*
55052262 TGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAA
1 GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAA
55052309 GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAA
1 GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAA
55052356 GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAA
1 GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAA
55052403 GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAA
1 GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAA
*
55052450 GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATAATATGTGATGAG
1 GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTAT-ATATGTGAT-AA
*
55052499 GGCC-AATGGCCAATGTGATGAATGTGATAAGT
1 GGCCTAATGGCCGATGTGATGAATGTGA-AAGT
55052531 CTCGAAGGGC
Statistics
Matches: 403, Mismatches: 4, Indels: 4
0.98 0.01 0.01
Matches are distributed among these distances:
47 363 0.90
48 31 0.08
49 9 0.02
ACGTcount: A:0.32, C:0.09, G:0.30, T:0.30
Consensus pattern (47 bp):
GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAA
Found at i:55052704 original size:37 final size:37
Alignment explanation
Indices: 55052648--55052726 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
55052638 CCGAGCTCTA
* * *
55052648 AAGACCCGATGACTACGTGTGGGGATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
*
55052685 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
55052722 AAGAC
1 AAGAC
55052727 TTCGTAATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.24, C:0.19, G:0.32, T:0.25
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:55054668 original size:29 final size:29
Alignment explanation
Indices: 55054633--55054706 Score: 105
Period size: 29 Copynumber: 2.6 Consensus size: 29
55054623 GTTGTGAGAT
* *
55054633 TGGCACTAAGTGTGCGGGCTTGAAA-TGCA
1 TGGCACTAAGTGTGCGAG-TTGAAAGTACA
*
55054662 TGGCACTAAGTGTGCGAGTTTAAAGTACA
1 TGGCACTAAGTGTGCGAGTTGAAAGTACA
55054691 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
55054707 TGGTTGATTA
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
28 5 0.12
29 36 0.88
ACGTcount: A:0.26, C:0.16, G:0.32, T:0.26
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGAGTTGAAAGTACA
Found at i:55055140 original size:40 final size:40
Alignment explanation
Indices: 55055096--55055372 Score: 374
Period size: 40 Copynumber: 6.9 Consensus size: 40
55055086 GAGTTACTAA
* *
55055096 ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGCGATGT
1 ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATAT
*
55055136 ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGT
1 ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATAT
*
55055176 ATCCGGGCTAAGTTCCGAAGAGCATTCATGCTAGTGATAT
1 ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATAT
* * *
55055216 ATCCGGGCTAAGTCCCGAGGAGCATTCGTGCTAGTGATGT
1 ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATAT
* *
55055256 ATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATAT
1 ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATAT
* ** * * * *
55055296 ATCCGTGCTAAACCCCAAAGAGCATTCGTGCTGGTGTTAT
1 ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATAT
* * * *
55055336 ATCCGGGCTAGGTCCCGAAGAGTAATCATGCTGGTGA
1 ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGA
55055373 CGTGTATTCG
Statistics
Matches: 211, Mismatches: 26, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 211 1.00
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATAT
Found at i:55055154 original size:80 final size:80
Alignment explanation
Indices: 55055017--55055372 Score: 371
Period size: 80 Copynumber: 4.5 Consensus size: 80
55055007 TCGAATGATG
* ** * * *
55055017 TCCGGGCTAAGTCCCAAAG-GC-TTTGTGCTAAGTGACCATATCCAGACTAAGAT-CCGAAG-GC
1 TCCGGGCTAAGTCCCGAAGAGCATTCATGCT-AGTGA-TATATCCGGGCTAAG-TCCCGAAGAGC
* * *
55055078 ATTGGTGCGAGTTACTAAA
63 ATTCGTGCGAGTGA-TATA
* *
55055097 TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGCGATGTATCCGGGCTAAGTCCCGAAGAGCATT
1 TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATATATCCGGGCTAAGTCCCGAAGAGCATT
* * *
55055162 CATGCTAGTGATGTA
66 CGTGCGAGTGATATA
* *
55055177 TCCGGGCTAAGTTCCGAAGAGCATTCATGCTAGTGATATATCCGGGCTAAGTCCCGAGGAGCATT
1 TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATATATCCGGGCTAAGTCCCGAAGAGCATT
* *
55055242 CGTGCTAGTGATGTA
66 CGTGCGAGTGATATA
* * * ** *
55055257 TCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATATATCCGTGCTAAACCCCAAAGAGCATT
1 TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATATATCCGGGCTAAGTCCCGAAGAGCATT
*
55055322 CGTGCTG-GTGTTATA
66 CGTGC-GAGTGATATA
* * * *
55055337 TCCGGGCTAGGTCCCGAAGAGTAATCATGCTGGTGA
1 TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGA
55055373 CGTGTATTCG
Statistics
Matches: 237, Mismatches: 34, Indels: 10
0.84 0.12 0.04
Matches are distributed among these distances:
79 1 0.00
80 212 0.89
81 18 0.08
82 6 0.03
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.25
Consensus pattern (80 bp):
TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATATATCCGGGCTAAGTCCCGAAGAGCATT
CGTGCGAGTGATATA
Found at i:55055565 original size:25 final size:25
Alignment explanation
Indices: 55055536--55055586 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
55055526 GTGTATTAAC
55055536 GAATGAATAAGA-GCACTATGTATGT
1 GAATG-ATAAGAGGCACTATGTATGT
* *
55055561 GAATGATTAGAGGCACTATGTGTGT
1 GAATGATAAGAGGCACTATGTATGT
55055586 G
1 G
55055587 CGAATTCCTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 5 0.22
25 18 0.78
ACGTcount: A:0.33, C:0.08, G:0.29, T:0.29
Consensus pattern (25 bp):
GAATGATAAGAGGCACTATGTATGT
Found at i:55058840 original size:47 final size:47
Alignment explanation
Indices: 55058774--55059140 Score: 689
Period size: 47 Copynumber: 7.7 Consensus size: 47
55058764 GAAATGATAG
55058774 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
55058821 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
55058868 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
55058915 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
55058962 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
55059009 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
55059056 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGA
* *
55059105 TAGGGCCTAATGGCCAATGTGATGAATGTGATAAGT
1 TAAGGCCTAATGGCCGATGTGATGAATGTGA-AAGT
55059141 CCCGAAGGGC
Statistics
Matches: 315, Mismatches: 2, Indels: 3
0.98 0.01 0.01
Matches are distributed among these distances:
47 271 0.86
49 40 0.13
50 4 0.01
ACGTcount: A:0.32, C:0.09, G:0.30, T:0.30
Consensus pattern (47 bp):
TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
Found at i:55059313 original size:37 final size:37
Alignment explanation
Indices: 55059257--55059335 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
55059247 CCGAGCTCTA
* * *
55059257 AAGACCCGATGACTACGTGTGGGGATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
*
55059294 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
55059331 AAGAC
1 AAGAC
55059336 TTCGTAATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.24, C:0.19, G:0.32, T:0.25
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:55066030 original size:46 final size:46
Alignment explanation
Indices: 55065963--55066223 Score: 163
Period size: 46 Copynumber: 5.5 Consensus size: 46
55065953 TATGTGTGCT
55065963 AGTGTAAGACATGTCTGGGACATGCATCGGCCACATTATGAGAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCACATTATGAGAGCC
* * * * * *
55066009 AGTGTAAGACATGTCTGGGACATGCAT-TGTCATATAGACGAGAGCT
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCACAT-TATGAGAGCC
* * * * * * *
55066055 AGTGTAAGACATGTCTGGGACATGTAACGACCTCGAGATAT-ACAAGCG
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCAC-A-TTATGA-GAGCC
* * * * **
55066103 AGTGTAAGACCTGTCTGGGACACGGCATCGGCCTCGATATATGAAAGTT
1 AGTGTAAGACATGTCTGGGACA-TGCATCGGCCAC-AT-TATGAGAGCC
* * * *
55066152 AGTGTAAGACTTGTATGGGACATGGCATC-G--ACTTTGATGTGTTAGCC
1 AGTGTAAGACATGTCTGGGACAT-GCATCGGCCACATT-ATGAG--AGCC
*
55066199 AATGTAAGACCATGTCTGGGACATG
1 AGTGTAAGA-CATGTCTGGGACATG
55066224 GCGTCTGCAT
Statistics
Matches: 164, Mismatches: 38, Indels: 25
0.72 0.17 0.11
Matches are distributed among these distances:
44 1 0.01
45 9 0.05
46 60 0.37
47 13 0.08
48 39 0.24
49 41 0.25
50 1 0.01
ACGTcount: A:0.29, C:0.18, G:0.28, T:0.25
Consensus pattern (46 bp):
AGTGTAAGACATGTCTGGGACATGCATCGGCCACATTATGAGAGCC
Found at i:55066159 original size:49 final size:47
Alignment explanation
Indices: 55065960--55066181 Score: 207
Period size: 46 Copynumber: 4.7 Consensus size: 47
55065950 TGATATGTGT
* *
55065960 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCACAT-TATGAGA
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCTCATATATGAAA
* * * * * * *
55066006 GCCAGTGTAAGACATGTCTGGGACATGCATTGTCAT-ATAGACGAGA
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCTCATATATGAAA
* * * *
55066052 GCTAGTGTAAGACATGTCTGGGACATGTAACGACCTCGAGATAT-ACAA
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCTC-ATATATGA-AA
* * *
55066100 GCGAGTGTAAGACCTGTCTGGGACACGGCATCGGCCTCGATATATGAAA
1 GCTAGTGTAAGACATGTCTGGGACA-TGCATCGGCCTC-ATATATGAAA
* * *
55066149 GTTAGTGTAAGACTTGTATGGGACATGGCATCG
1 GCTAGTGTAAGACATGTCTGGGACAT-GCATCG
55066182 ACTTTGATGT
Statistics
Matches: 140, Mismatches: 29, Indels: 11
0.78 0.16 0.06
Matches are distributed among these distances:
45 2 0.01
46 66 0.47
47 1 0.01
48 27 0.19
49 43 0.31
50 1 0.01
ACGTcount: A:0.29, C:0.18, G:0.29, T:0.24
Consensus pattern (47 bp):
GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCTCATATATGAAA
Found at i:55069859 original size:30 final size:30
Alignment explanation
Indices: 55069825--55069885 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
55069815 TTCCCGAGCC
55069825 TAGGGGCAAAAGTGTAAATATGCAAAAGTT
1 TAGGGGCAAAAGTGTAAATATGCAAAAGTT
* * * *
55069855 TAGGGGCAAAATTGTAATTTTTCAAAAGTT
1 TAGGGGCAAAAGTGTAAATATGCAAAAGTT
55069885 T
1 T
55069886 GAGTTAAGGA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.39, C:0.07, G:0.23, T:0.31
Consensus pattern (30 bp):
TAGGGGCAAAAGTGTAAATATGCAAAAGTT
Found at i:55070655 original size:68 final size:64
Alignment explanation
Indices: 55070539--55070794 Score: 207
Period size: 68 Copynumber: 3.9 Consensus size: 64
55070529 CGGATGATAC
** * * * *
55070539 AGATAGTATGTAGCTAGGTCACATGTATGGTGCTGA-ATGCACATCATGT-GTACAAGAGAGCTA
1 AGATA-TATGTAGCTAGGTCACATGGGTGGTACT-ATGTGTACACCATGTAG-ACAAGAGAGCTA
55070602 CAAG
63 C--G
* *
55070606 ACATTATGATGTAGCTAGGTCACATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTAC
1 AGA-TAT-ATGTAGCTAGGTCACATGGGTGGTACTATGTGTACACCATGTAGACAAGAGAGCTAC
55070671 G
64 G
* * * * * * *
55070672 GGATATATGTAGCTAGGTCGCATGCGTGGTTCCAGGTGAAGGACACCATGTAGACAAGAGAGCTA
1 AGATATATGTAGCTAGGTCACATGGGTGGTACTA--TG-TGTACACCATGTAGACAAGAGAGCTA
55070737 CG
63 CG
* * *
55070739 AGATAAAT-TGGCTAGGTCACATGGGTGGTACTGA-GTGTTCACCATGT-GTACAAGAG
1 AGATATATGTAGCTAGGTCACATGGGTGGTACT-ATGTGTACACCATGTAG-ACAAGAG
55070795 GGTCGAACTA
Statistics
Matches: 153, Mismatches: 27, Indels: 22
0.76 0.13 0.11
Matches are distributed among these distances:
62 1 0.01
63 16 0.10
64 24 0.16
65 3 0.02
66 23 0.15
67 37 0.24
68 48 0.31
69 1 0.01
ACGTcount: A:0.30, C:0.16, G:0.29, T:0.25
Consensus pattern (64 bp):
AGATATATGTAGCTAGGTCACATGGGTGGTACTATGTGTACACCATGTAGACAAGAGAGCTACG
Found at i:55079033 original size:49 final size:48
Alignment explanation
Indices: 55078929--55079051 Score: 149
Period size: 49 Copynumber: 2.5 Consensus size: 48
55078919 TTGAGACGAG
* * *
55078929 AGCTAGTGTAAGACATGTCTAGGACATGCATCAGCCTCAAGATATACA
1 AGCTAGTGTAAGACCTGTCTGGGACAGGCATCAGCCTCAAGATATACA
* * * *
55078977 AGCTAGTGTACGACCTGTCTGGGACACGGCATCGGCCTCGATATATGA-A
1 AGCTAGTGTAAGACCTGTCTGGGACA-GGCATCAGCCTCAAGATAT-ACA
*
55079026 AGTTAGTGTAAGACCTGTCTGGGACA
1 AGCTAGTGTAAGACCTGTCTGGGACA
55079052 TGACATCGAC
Statistics
Matches: 64, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
48 23 0.36
49 40 0.62
50 1 0.02
ACGTcount: A:0.29, C:0.21, G:0.26, T:0.24
Consensus pattern (48 bp):
AGCTAGTGTAAGACCTGTCTGGGACAGGCATCAGCCTCAAGATATACA
Found at i:55079059 original size:49 final size:48
Alignment explanation
Indices: 55078838--55079059 Score: 222
Period size: 46 Copynumber: 4.7 Consensus size: 48
55078828 TGATATGTGT
*
55078838 GCTAGTGTAAGACATGTCTGGGACATGCA-CTGGCCAC-AT-TATGAAA
1 GCTAGTGTAAGACATGTCTGGGACATGCATC-GGCCTCGATATATGAAA
* * * * * *
55078884 GCCAGTGTAAGACATGTCTGGGACATGCATCGGCATTG--AGACGAGA
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGATATATGAAA
* * * *
55078930 GCTAGTGTAAGACATGTCTAGGACATGCATCAGCCTCAAGATAT-ACAA
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGATATATGA-AA
* * *
55078978 GCTAGTGTACGACCTGTCTGGGACACGGCATCGGCCTCGATATATGAAA
1 GCTAGTGTAAGACATGTCTGGGACA-TGCATCGGCCTCGATATATGAAA
* *
55079027 GTTAGTGTAAGACCTGTCTGGGACATGACATCG
1 GCTAGTGTAAGACATGTCTGGGACATG-CATCG
55079060 ACTTTGATGT
Statistics
Matches: 141, Mismatches: 26, Indels: 15
0.77 0.14 0.08
Matches are distributed among these distances:
46 67 0.48
47 2 0.01
48 26 0.18
49 45 0.32
50 1 0.01
ACGTcount: A:0.29, C:0.21, G:0.27, T:0.23
Consensus pattern (48 bp):
GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGATATATGAAA
Found at i:55084379 original size:48 final size:48
Alignment explanation
Indices: 55084305--55084437 Score: 178
Period size: 48 Copynumber: 2.8 Consensus size: 48
55084295 GTGCGAATTA
* * * * *
55084305 TACCTTGATTTTGCTTCAGGCTATGGTATAGGTATTTCGGAGATGAGT
1 TACCTTGATTTGGCTTCGGGCCATGGTATAGGTACTTCGGAGATAAGT
* *
55084353 TACCTTGATTTGGCTACGGGCCATGGTATAGGTACTTCGGGGATAAGT
1 TACCTTGATTTGGCTTCGGGCCATGGTATAGGTACTTCGGAGATAAGT
*
55084401 TACCTTGATTTGGCTTCAGAG-CATGGTATAGGTACTT
1 TACCTTGATTTGGCTTC-GGGCCATGGTATAGGTACTT
55084438 ATCGATTGAG
Statistics
Matches: 75, Mismatches: 9, Indels: 2
0.87 0.10 0.02
Matches are distributed among these distances:
48 73 0.97
49 2 0.03
ACGTcount: A:0.21, C:0.15, G:0.28, T:0.36
Consensus pattern (48 bp):
TACCTTGATTTGGCTTCGGGCCATGGTATAGGTACTTCGGAGATAAGT
Found at i:55090817 original size:19 final size:19
Alignment explanation
Indices: 55090795--55090832 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
55090785 AACCACTGCC
*
55090795 ACCCAGCATAATCAAATTT
1 ACCCACCATAATCAAATTT
*
55090814 ACCCACCATAATTAAATTT
1 ACCCACCATAATCAAATTT
55090833 GTTATTAACT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.42, C:0.26, G:0.03, T:0.29
Consensus pattern (19 bp):
ACCCACCATAATCAAATTT
Done.