Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A07
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: 92880876
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2857347 characters in sequence are not A, C, G, or T
File 173 of 290
Found at i:56275029 original size:44 final size:44
Alignment explanation
Indices: 56274961--56275128 Score: 225
Period size: 44 Copynumber: 3.8 Consensus size: 44
56274951 TACGGTACTA
* *
56274961 ATCGAGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAAATGAT
1 ATCGGGCCTTCGAGCCTAGCAGGCTATAATGCCGGTGAAATGAT
* *
56275005 ATCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAGAT-ACT
1 ATCGGGCCTTCGAGCCTAGCAGGCTATAATGCCGGTGAAATGA-T
*
56275049 ATTCGGGCCTTCGAGCCTAGCAAGCTATAATGCCGGTGAAATGAT
1 A-TCGGGCCTTCGAGCCTAGCAGGCTATAATGCCGGTGAAATGAT
** *
56275094 ATTTGG-CTTCGAGCCTAGCAGGCGA-AATGCCGGTG
1 ATCGGGCCTTCGAGCCTAGCAGGCTATAATGCCGGTG
56275129 GATGAATTTG
Statistics
Matches: 112, Mismatches: 9, Indels: 8
0.87 0.07 0.06
Matches are distributed among these distances:
42 10 0.09
43 18 0.16
44 44 0.39
45 39 0.35
46 1 0.01
ACGTcount: A:0.24, C:0.22, G:0.29, T:0.24
Consensus pattern (44 bp):
ATCGGGCCTTCGAGCCTAGCAGGCTATAATGCCGGTGAAATGAT
Found at i:56275070 original size:45 final size:45
Alignment explanation
Indices: 56274966--56275128 Score: 228
Period size: 45 Copynumber: 3.7 Consensus size: 45
56274956 TACTAATCGA
*
56274966 GCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAAATGATA-TCGG
1 GCCTTCGAGCCTAGCAGGCTATAATGCCGGTGAAATGATATTCGG
* *
56275010 GCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAGAT-ACTATTCGG
1 GCCTTCGAGCCTAGCAGGCTATAATGCCGGTGAAATGA-TATTCGG
* *
56275055 GCCTTCGAGCCTAGCAAGCTATAATGCCGGTGAAATGATATT-TG
1 GCCTTCGAGCCTAGCAGGCTATAATGCCGGTGAAATGATATTCGG
*
56275099 G-CTTCGAGCCTAGCAGGCGA-AATGCCGGTG
1 GCCTTCGAGCCTAGCAGGCTATAATGCCGGTG
56275129 GATGAATTTG
Statistics
Matches: 109, Mismatches: 7, Indels: 8
0.88 0.06 0.06
Matches are distributed among these distances:
42 10 0.09
43 18 0.17
44 39 0.36
45 41 0.38
46 1 0.01
ACGTcount: A:0.24, C:0.22, G:0.29, T:0.25
Consensus pattern (45 bp):
GCCTTCGAGCCTAGCAGGCTATAATGCCGGTGAAATGATATTCGG
Found at i:56279226 original size:27 final size:27
Alignment explanation
Indices: 56279196--56279385 Score: 222
Period size: 27 Copynumber: 7.1 Consensus size: 27
56279186 CTGAAATGCA
**
56279196 CTCGATTTGTAGAATTACCATTTTACC
1 CTCGATTTACAGAATTACCATTTTACC
** * *
56279223 CTCGATTTGTAGAATTACCGTTTCACC
1 CTCGATTTACAGAATTACCATTTTACC
* *
56279250 CTCGATTTACAAAATTGCCATTTTACC
1 CTCGATTTACAGAATTACCATTTTACC
* *
56279277 CTCAATTTATAGAATTACCATTTTACC
1 CTCGATTTACAGAATTACCATTTTACC
*
56279304 CT-GATTTACAGAATTACCGTTTTACC
1 CTCGATTTACAGAATTACCATTTTACC
*
56279330 CTCGATTTACAAAATTACCATTTTACC
1 CTCGATTTACAGAATTACCATTTTACC
* * *
56279357 CTC-AGTTTAAAAAATTACCGTTTTACC
1 CTCGA-TTTACAGAATTACCATTTTACC
56279384 CT
1 CT
56279386 TAATTGTGAA
Statistics
Matches: 142, Mismatches: 19, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
26 24 0.17
27 118 0.83
ACGTcount: A:0.29, C:0.24, G:0.08, T:0.38
Consensus pattern (27 bp):
CTCGATTTACAGAATTACCATTTTACC
Found at i:56279338 original size:80 final size:81
Alignment explanation
Indices: 56279200--56279385 Score: 284
Period size: 80 Copynumber: 2.3 Consensus size: 81
56279190 AATGCACTCG
* **
56279200 ATTTGTAGAATTACCATTTTACCCTCGATTTGTAGAATTACCGTTTCACCCTCGATTTACAAAAT
1 ATTTATAGAATTACCATTTTACCCTCGATTTACAGAATTACCGTTTCACCCTCGATTTACAAAAT
*
56279265 TGCCATTTTACCCTCA
66 TACCATTTTACCCTCA
*
56279281 ATTTATAGAATTACCATTTTACCCT-GATTTACAGAATTACCGTTTTACCCTCGATTTACAAAAT
1 ATTTATAGAATTACCATTTTACCCTCGATTTACAGAATTACCGTTTCACCCTCGATTTACAAAAT
56279345 TACCATTTTACCCTCA
66 TACCATTTTACCCTCA
* * * *
56279361 GTTTAAAAAATTACCGTTTTACCCT
1 ATTTATAGAATTACCATTTTACCCT
56279386 TAATTGTGAA
Statistics
Matches: 96, Mismatches: 9, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
80 72 0.75
81 24 0.25
ACGTcount: A:0.30, C:0.24, G:0.08, T:0.39
Consensus pattern (81 bp):
ATTTATAGAATTACCATTTTACCCTCGATTTACAGAATTACCGTTTCACCCTCGATTTACAAAAT
TACCATTTTACCCTCA
Found at i:56279514 original size:54 final size:53
Alignment explanation
Indices: 56279389--56279541 Score: 168
Period size: 54 Copynumber: 2.8 Consensus size: 53
56279379 TTACCCTTAA
* ** *
56279389 TTGTGAAATTACTGAAATACCCCT-GTAGGATAGAATTACCAAAAT-CACCTAGT
1 TTGTGAAATTACCGAAATA-CCCTAGTTTG-TAAAATTACCAAAATACACCTAGT
* * *
56279442 TTGTAAAATTACCAAAATATCCCTAGTTTGTAAAATTACCAAAATAC-CACTGGT
1 TTGTGAAATTACCGAAATA-CCCTAGTTTGTAAAATTACCAAAATACAC-CTAGT
*
56279496 TTGTGAAATTACCGAAATACCCTCAATTTGTAAAATTACCAAAATA
1 TTGTGAAATTACCGAAATACCCT-AGTTTGTAAAATTACCAAAATA
56279542 TCTCTAATTT
Statistics
Matches: 85, Mismatches: 11, Indels: 7
0.83 0.11 0.07
Matches are distributed among these distances:
53 39 0.46
54 46 0.54
ACGTcount: A:0.41, C:0.18, G:0.11, T:0.30
Consensus pattern (53 bp):
TTGTGAAATTACCGAAATACCCTAGTTTGTAAAATTACCAAAATACACCTAGT
Found at i:56279551 original size:27 final size:26
Alignment explanation
Indices: 56279422--56279541 Score: 161
Period size: 27 Copynumber: 4.5 Consensus size: 26
56279412 TGTAGGATAG
56279422 AATTACCAAAAT-CACCTAGTTTGTAA
1 AATTACCAAAATAC-CCTAGTTTGTAA
56279448 AATTACCAAAATATCCCTAGTTTGTAA
1 AATTACCAAAATA-CCCTAGTTTGTAA
* *
56279475 AATTACCAAAATACCACTGGTTTGTGA
1 AATTACCAAAATACC-CTAGTTTGTAA
* *
56279502 AATTACCGAAATACCCTCAATTTGTAA
1 AATTACCAAAATACCCT-AGTTTGTAA
56279529 AATTACCAAAATA
1 AATTACCAAAATA
56279542 TCTCTAATTT
Statistics
Matches: 83, Mismatches: 7, Indels: 7
0.86 0.07 0.07
Matches are distributed among these distances:
26 16 0.19
27 66 0.80
28 1 0.01
ACGTcount: A:0.42, C:0.19, G:0.08, T:0.30
Consensus pattern (26 bp):
AATTACCAAAATACCCTAGTTTGTAA
Found at i:56279557 original size:27 final size:27
Alignment explanation
Indices: 56279422--56279560 Score: 142
Period size: 27 Copynumber: 5.2 Consensus size: 27
56279412 TGTAGGATAG
*
56279422 AATTACC-AAA-ATCACCTAGTTTGTAA
1 AATTACCAAAATATC-CCTAATTTGTAA
*
56279448 AATTACCAAAATATCCCTAGTTTGTAA
1 AATTACCAAAATATCCCTAATTTGTAA
** *
56279475 AATTACCAAAATA-CCACTGGTTTGTGA
1 AATTACCAAAATATCC-CTAATTTGTAA
*
56279502 AATTACCGAAATA-CCCTCAATTTGTAA
1 AATTACCAAAATATCCCT-AATTTGTAA
* **
56279529 AATTACCAAAATATCTCTAATTTACAA
1 AATTACCAAAATATCCCTAATTTGTAA
56279556 AATTA
1 AATTA
56279561 TAGAAATACC
Statistics
Matches: 98, Mismatches: 10, Indels: 9
0.84 0.09 0.08
Matches are distributed among these distances:
26 11 0.11
27 81 0.83
28 6 0.06
ACGTcount: A:0.42, C:0.19, G:0.07, T:0.32
Consensus pattern (27 bp):
AATTACCAAAATATCCCTAATTTGTAA
Found at i:56279559 original size:54 final size:53
Alignment explanation
Indices: 56279446--56279628 Score: 143
Period size: 54 Copynumber: 3.4 Consensus size: 53
56279436 CCTAGTTTGT
* * ** **
56279446 AAAATTACCAAAATATCCCTAGTTTGTAAAATTACCAAAATACCACTGGTTTGT
1 AAAATTACCGAAATA-CCCTAATTTGTAAAATTACCAAAATACCACTAATTTAC
* * *
56279500 GAAATTACCGAAATACCCTCAATTTGTAAAATTACCAAAATATCTCTAATTTAC
1 AAAATTACCGAAATACCCT-AATTTGTAAAATTACCAAAATACCACTAATTTAC
** * * * * **
56279554 AAAATTATAGAAATACCCTTGACTTTCTAAAAATTA-TAGAAATACCATTGGTTTAC
1 AAAATTACCGAAATACCC-T-AATTTGT-AAAATTACCA-AAATACCACTAATTTAC
*
56279610 AAAATTACTGAAATACCCT
1 AAAATTACCGAAATACCCT
56279629 TGGTTTGTAG
Statistics
Matches: 102, Mismatches: 23, Indels: 7
0.77 0.17 0.05
Matches are distributed among these distances:
53 4 0.04
54 55 0.54
55 8 0.08
56 35 0.34
ACGTcount: A:0.43, C:0.18, G:0.08, T:0.32
Consensus pattern (53 bp):
AAAATTACCGAAATACCCTAATTTGTAAAATTACCAAAATACCACTAATTTAC
Found at i:56279622 original size:27 final size:27
Alignment explanation
Indices: 56279549--56279634 Score: 104
Period size: 27 Copynumber: 3.1 Consensus size: 27
56279539 ATATCTCTAA
*
56279549 TTTACAAAATTATAGAAATACCCTTGAC
1 TTTACAAAATTATAGAAATACCCTTG-G
*
56279577 TTT-CTAAAAATTATAGAAATACCATTGG
1 TTTAC--AAAATTATAGAAATACCCTTGG
56279605 TTTACAAAATTACT-GAAATACCCTTGG
1 TTTACAAAATTA-TAGAAATACCCTTGG
56279632 TTT
1 TTT
56279635 GTAGATTTAC
Statistics
Matches: 51, Mismatches: 3, Indels: 9
0.81 0.05 0.14
Matches are distributed among these distances:
27 23 0.45
28 7 0.14
29 21 0.41
ACGTcount: A:0.40, C:0.15, G:0.09, T:0.36
Consensus pattern (27 bp):
TTTACAAAATTATAGAAATACCCTTGG
Found at i:56279779 original size:27 final size:27
Alignment explanation
Indices: 56279688--56279779 Score: 116
Period size: 27 Copynumber: 3.4 Consensus size: 27
56279678 ACCCCTATTA
* *
56279688 GGTAAAAAGACCGTAAAGCTCCTGTAG
1 GGTAAAATGACCGTAAAGCCCCTGTAG
56279715 GGTAAAGA-GACCGTAAAGCCCCTGTAG
1 GGTAAA-ATGACCGTAAAGCCCCTGTAG
* *
56279742 GGTAAAGTGACCGTAATA-CCCCTGTAT
1 GGTAAAATGACCGTAA-AGCCCCTGTAG
56279769 GGTAAAATGAC
1 GGTAAAATGAC
56279780 GAATATGCCC
Statistics
Matches: 58, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
27 56 0.97
28 2 0.03
ACGTcount: A:0.35, C:0.20, G:0.26, T:0.20
Consensus pattern (27 bp):
GGTAAAATGACCGTAAAGCCCCTGTAG
Found at i:56280608 original size:27 final size:26
Alignment explanation
Indices: 56280578--56280691 Score: 183
Period size: 27 Copynumber: 4.3 Consensus size: 26
56280568 TAGGAAGTGC
*
56280578 AAAAGGGCTTATGCCCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTATCG
56280604 AAAAAGGGCTTATGCCCCAGTTTATCG
1 -AAAAGGGCTTATGCCCCAGTTTATCG
*
56280631 AAAAGGGCTTATGCCCCAAGTTTACCG
1 AAAAGGGCTTATGCCCC-AGTTTATCG
*
56280658 AAAAGGGCTTATGCCCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTATCG
56280684 AAAAGGGC
1 AAAAGGGC
56280692 ATAATTGAAA
Statistics
Matches: 82, Mismatches: 4, Indels: 3
0.92 0.04 0.03
Matches are distributed among these distances:
26 32 0.39
27 50 0.61
ACGTcount: A:0.30, C:0.21, G:0.24, T:0.25
Consensus pattern (26 bp):
AAAAGGGCTTATGCCCCAGTTTATCG
Found at i:56280662 original size:53 final size:53
Alignment explanation
Indices: 56280578--56280792 Score: 255
Period size: 53 Copynumber: 4.3 Consensus size: 53
56280568 TAGGAAGTGC
56280578 AAAAGGGCTTATGCCCC-AGTTTATTGAAAAAGGGCTTATGCCCCAGTTTATCG
1 AAAAGGGCTTATGCCCCAAGTTTATTG-AAAAGGGCTTATGCCCCAGTTTATCG
** *
56280631 AAAAGGGCTTATGCCCCAAGTTTACCGAAAAGGGCTTATGCCCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAAGTTTATTGAAAAGGGCTTATGCCCCAGTTTATCG
* * *
56280684 AAAAGGGC--AT------A----ATTGAAAAGGGATTATGCCCCCGTTTACCG
1 AAAAGGGCTTATGCCCCAAGTTTATTGAAAAGGGCTTATGCCCCAGTTTATCG
56280725 AAAAGGGCTTATGCCCC-AGTTTATTGAAAAGGGCTT-TGCCCCAGTTTATCG
1 AAAAGGGCTTATGCCCCAAGTTTATTGAAAAGGGCTTATGCCCCAGTTTATCG
56280776 AAAAGGGCTT-TGCCCCA
1 AAAAGGGCTTATGCCCCA
56280793 GTTATTAAAG
Statistics
Matches: 137, Mismatches: 12, Indels: 28
0.77 0.07 0.16
Matches are distributed among these distances:
41 32 0.23
43 2 0.01
45 1 0.01
48 1 0.01
50 6 0.04
51 25 0.18
52 13 0.09
53 50 0.36
54 7 0.05
ACGTcount: A:0.29, C:0.22, G:0.23, T:0.26
Consensus pattern (53 bp):
AAAAGGGCTTATGCCCCAAGTTTATTGAAAAGGGCTTATGCCCCAGTTTATCG
Found at i:56280739 original size:67 final size:68
Alignment explanation
Indices: 56280630--56280758 Score: 233
Period size: 67 Copynumber: 1.9 Consensus size: 68
56280620 CCAGTTTATC
*
56280630 GAAAAGGGCTTATGCCCCAAGTTTACCGAAAAGGGCTTATGCCCCAGTTTATTGAAAAGGGCATA
1 GAAAAGGGATTATGCCCCAAGTTTACCGAAAAGGGCTTATGCCCCAGTTTATTGAAAAGGGCATA
56280695 ATT
66 ATT
*
56280698 GAAAAGGGATTATGCCCC-CGTTTACCGAAAAGGGCTTATGCCCCAGTTTATTGAAAAGGGC
1 GAAAAGGGATTATGCCCCAAGTTTACCGAAAAGGGCTTATGCCCCAGTTTATTGAAAAGGGC
56280759 TTTGCCCCAG
Statistics
Matches: 59, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
67 42 0.71
68 17 0.29
ACGTcount: A:0.31, C:0.20, G:0.25, T:0.24
Consensus pattern (68 bp):
GAAAAGGGATTATGCCCCAAGTTTACCGAAAAGGGCTTATGCCCCAGTTTATTGAAAAGGGCATA
ATT
Found at i:56280764 original size:25 final size:26
Alignment explanation
Indices: 56280698--56280795 Score: 146
Period size: 25 Copynumber: 3.8 Consensus size: 26
56280688 GGGCATAATT
* * *
56280698 GAAAAGGGATTATGCCCCCGTTTACC
1 GAAAAGGGCTTATGCCCCAGTTTATC
*
56280724 GAAAAGGGCTTATGCCCCAGTTTATT
1 GAAAAGGGCTTATGCCCCAGTTTATC
56280750 GAAAAGGGCTT-TGCCCCAGTTTATC
1 GAAAAGGGCTTATGCCCCAGTTTATC
56280775 GAAAAGGGCTT-TGCCCCAGTT
1 GAAAAGGGCTTATGCCCCAGTT
56280796 ATTAAAGAGG
Statistics
Matches: 67, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
25 34 0.51
26 33 0.49
ACGTcount: A:0.26, C:0.23, G:0.24, T:0.27
Consensus pattern (26 bp):
GAAAAGGGCTTATGCCCCAGTTTATC
Found at i:56280772 original size:51 final size:51
Alignment explanation
Indices: 56280695--56280795 Score: 159
Period size: 51 Copynumber: 2.0 Consensus size: 51
56280685 AAAGGGCATA
*
56280695 ATTGAAAAGGGATTATGCCCCCGTTTACCGAAAAGGGCTTATGCCCCAGTTT
1 ATTGAAAAGGGATTATGCCCCAGTTTACCGAAAAGGGCTT-TGCCCCAGTTT
* *
56280747 ATTGAAAAGGGCTT-TGCCCCAGTTTATCGAAAAGGGCTTTGCCCCAGTT
1 ATTGAAAAGGGATTATGCCCCAGTTTACCGAAAAGGGCTTTGCCCCAGTT
56280796 ATTAAAGAGG
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
50 10 0.22
51 23 0.50
52 13 0.28
ACGTcount: A:0.26, C:0.23, G:0.24, T:0.28
Consensus pattern (51 bp):
ATTGAAAAGGGATTATGCCCCAGTTTACCGAAAAGGGCTTTGCCCCAGTTT
Found at i:56281064 original size:31 final size:31
Alignment explanation
Indices: 56281013--56281091 Score: 122
Period size: 31 Copynumber: 2.5 Consensus size: 31
56281003 CGTTTACAGT
* *
56281013 AAAGGCTTCGACCCAATGATATGATTTATGA
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
*
56281044 AAAGGATTCGGCCCAGTGATATGATTTATGA
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
*
56281075 AAAGGCTTCAGCCCAGT
1 AAAGGCTTCGGCCCAGT
56281092 AACCGTTAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 43 1.00
ACGTcount: A:0.33, C:0.18, G:0.23, T:0.27
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTGATATGATTTATGA
Found at i:56286209 original size:30 final size:30
Alignment explanation
Indices: 56286175--56286232 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
56286165 CCGAGCCTAG
56286175 GGGCAAAAGTGTAAATATGCAAAAGTTTAA
1 GGGCAAAAGTGTAAATATGCAAAAGTTTAA
* * *
56286205 GGGCAAAATTGTAATTTTGCAAAAGTTT
1 GGGCAAAAGTGTAAATATGCAAAAGTTT
56286233 GAGTTAAGGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.41, C:0.07, G:0.22, T:0.29
Consensus pattern (30 bp):
GGGCAAAAGTGTAAATATGCAAAAGTTTAA
Found at i:56291843 original size:25 final size:23
Alignment explanation
Indices: 56291810--56291867 Score: 62
Period size: 25 Copynumber: 2.4 Consensus size: 23
56291800 TGAGCATTAT
* *
56291810 ACTTATCTTTACTCTTCTAGCATGA
1 ACTTGTCTTAACT-TTCTAGCAT-A
*
56291835 ACTTGTCTTAACTTTTTAGCATA
1 ACTTGTCTTAACTTTCTAGCATA
*
56291858 ACTCGTCTTA
1 ACTTGTCTTA
56291868 CCTAACCTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
23 10 0.34
24 8 0.28
25 11 0.38
ACGTcount: A:0.24, C:0.22, G:0.09, T:0.45
Consensus pattern (23 bp):
ACTTGTCTTAACTTTCTAGCATA
Found at i:56292130 original size:55 final size:53
Alignment explanation
Indices: 56291987--56292194 Score: 231
Period size: 55 Copynumber: 3.8 Consensus size: 53
56291977 ATCCTTTTGA
* *
56291987 AACTTACCATTGCCATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTATG
1 AACTTACCAATGCCATGTCTTGACATGGTCTTACATGGGATCCTTGCCTTATG
* * *
56292040 AACTCACCAATGCCATGCCTTGGCATGGTCTTACATGGGA-CCTTTGCCTTATAG
1 AACTTACCAATGCCATGTCTTGACATGGTCTTACATGGGATCC-TTGCCTTAT-G
* ***
56292094 TAACTTATCAATGCCATGTCTTGACATGGTCTTACATGATTTCCTTGCCTTA-G
1 -AACTTACCAATGCCATGTCTTGACATGGTCTTACATGGGATCCTTGCCTTATG
* * * *
56292147 AAACCTTACCAATTTCCATGCCTTGGCATGGTCTTACATGGTATCCTT
1 -AA-CTTACCAA-TGCCATGTCTTGACATGGTCTTACATGGGATCCTT
56292195 AAACCCTAAT
Statistics
Matches: 130, Mismatches: 19, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
52 2 0.02
53 47 0.36
54 8 0.06
55 71 0.55
56 2 0.02
ACGTcount: A:0.22, C:0.25, G:0.17, T:0.36
Consensus pattern (53 bp):
AACTTACCAATGCCATGTCTTGACATGGTCTTACATGGGATCCTTGCCTTATG
Found at i:56292139 original size:108 final size:110
Alignment explanation
Indices: 56291987--56292187 Score: 318
Period size: 108 Copynumber: 1.8 Consensus size: 110
56291977 ATCCTTTTGA
* *
56291987 AACTTACCATTGCCATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTATG-AA-CTCACCAA
1 AACTTACCAATGCCATGTCTTGACATGGTCTTACATGATATCCTTGCCTTA-GAAACCTCACCAA
56292050 -TGCCATGCCTTGGCATGGTCTTACATGGGACCTTTGCCTTATAGT
65 TTGCCATGCCTTGGCATGGTCTTACATGGGACCTTTGCCTTATAGT
* * *
56292095 AACTTATCAATGCCATGTCTTGACATGGTCTTACATGATTTCCTTGCCTTAGAAACCTTACCAAT
1 AACTTACCAATGCCATGTCTTGACATGGTCTTACATGATATCCTTGCCTTAGAAACCTCACCAAT
*
56292160 TTCCATGCCTTGGCATGGTCTTACATGG
66 TGCCATGCCTTGGCATGGTCTTACATGG
56292188 TATCCTTAAA
Statistics
Matches: 84, Mismatches: 6, Indels: 4
0.89 0.06 0.04
Matches are distributed among these distances:
107 1 0.01
108 49 0.58
109 7 0.08
110 27 0.32
ACGTcount: A:0.22, C:0.25, G:0.17, T:0.35
Consensus pattern (110 bp):
AACTTACCAATGCCATGTCTTGACATGGTCTTACATGATATCCTTGCCTTAGAAACCTCACCAAT
TGCCATGCCTTGGCATGGTCTTACATGGGACCTTTGCCTTATAGT
Found at i:56299141 original size:23 final size:24
Alignment explanation
Indices: 56299101--56299145 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
56299091 TTTGCTCTTC
* *
56299101 TAGCATGAACTTGTCTTACCTTTT
1 TAGCATGAACTCGCCTTACCTTTT
56299125 TAGCAT-AACTCGCCTTACCTT
1 TAGCATGAACTCGCCTTACCTT
56299146 ACCTTACCTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 13 0.68
24 6 0.32
ACGTcount: A:0.22, C:0.27, G:0.11, T:0.40
Consensus pattern (24 bp):
TAGCATGAACTCGCCTTACCTTTT
Found at i:56299343 original size:53 final size:54
Alignment explanation
Indices: 56299214--56299468 Score: 256
Period size: 55 Copynumber: 4.8 Consensus size: 54
56299204 ACACGGGTAC
* * * * *
56299214 CTTACCATTTCCATGACTTGTCATGGTCTTACGTGGTATCC-T---TT-TGAAA
1 CTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATGAAA
* *
56299263 CTTACCATTGCCATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTATG-AA
1 CTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATGAAA
* * * *
56299316 CTCACCAATGCCATGCCTTGGCATGGTCTTACATGGGA-CCTTTGCCTTATAGTAA
1 CTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCC-TTGCCTTAT-GAAA
* * * * * *
56299371 CTTATCAATGCCATGTCTTGACTTGGTCTTACATGATTTCCTTGCCTTA-AAAA
1 CTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATGAAA
*
56299424 CCTTACCAATTGCCATGCCTTGGCATGGTCTTACATGGTATCCTT
1 -CTTACCAA-TGCCATGCCTTGACATGGTCTTACATGGTATCCTT
56299469 AAACCCTAAT
Statistics
Matches: 170, Mismatches: 25, Indels: 16
0.81 0.12 0.08
Matches are distributed among these distances:
49 37 0.22
50 1 0.01
52 2 0.01
53 48 0.28
54 10 0.06
55 70 0.41
56 2 0.01
ACGTcount: A:0.21, C:0.25, G:0.17, T:0.37
Consensus pattern (54 bp):
CTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATGAAA
Found at i:56299413 original size:108 final size:110
Alignment explanation
Indices: 56299261--56299461 Score: 316
Period size: 108 Copynumber: 1.8 Consensus size: 110
56299251 ATCCTTTTGA
* * **
56299261 AACTTACCATTGCCATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTATGAA-CTCACCAA-
1 AACTTACCAATGCCATGTCTTGACATGGTCTTACATGATATCCTTGCCTTAAAAACCTCACCAAT
56299324 TGCCATGCCTTGGCATGGTCTTACATGGGACCTTTGCCTTATAGT
66 TGCCATGCCTTGGCATGGTCTTACATGGGACCTTTGCCTTATAGT
* * * *
56299369 AACTTATCAATGCCATGTCTTGACTTGGTCTTACATGATTTCCTTGCCTTAAAAACCTTACCAAT
1 AACTTACCAATGCCATGTCTTGACATGGTCTTACATGATATCCTTGCCTTAAAAACCTCACCAAT
56299434 TGCCATGCCTTGGCATGGTCTTACATGG
66 TGCCATGCCTTGGCATGGTCTTACATGG
56299462 TATCCTTAAA
Statistics
Matches: 83, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
108 48 0.58
109 7 0.08
110 28 0.34
ACGTcount: A:0.22, C:0.25, G:0.17, T:0.35
Consensus pattern (110 bp):
AACTTACCAATGCCATGTCTTGACATGGTCTTACATGATATCCTTGCCTTAAAAACCTCACCAAT
TGCCATGCCTTGGCATGGTCTTACATGGGACCTTTGCCTTATAGT
Found at i:56300756 original size:11 final size:11
Alignment explanation
Indices: 56300740--56300767 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
56300730 GCTGAAGCCC
56300740 ATATCACAATA
1 ATATCACAATA
56300751 ATATCACAATA
1 ATATCACAATA
56300762 ATATCA
1 ATATCA
56300768 TACATGCAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.54, C:0.18, G:0.00, T:0.29
Consensus pattern (11 bp):
ATATCACAATA
Found at i:56301271 original size:27 final size:27
Alignment explanation
Indices: 56301223--56301315 Score: 98
Period size: 27 Copynumber: 3.4 Consensus size: 27
56301213 AGGGCAAAAT
* * *
56301223 AGTCATTTTAC-CTTATAGGGGTATGTG
1 AGTCATTTTACAC-TACAAGGGTATGTC
*
56301250 AGTCATTTTACACTACAAGGGTATTTC
1 AGTCATTTTACACTACAAGGGTATGTC
* *
56301277 AGTAATTTTACACTACAAGGGTATTTC
1 AGTCATTTTACACTACAAGGGTATGTC
* *
56301304 AATAATTTTACA
1 AGTCATTTTACA
56301316 AATCAGAGGT
Statistics
Matches: 59, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
27 58 0.98
28 1 0.02
ACGTcount: A:0.31, C:0.14, G:0.16, T:0.39
Consensus pattern (27 bp):
AGTCATTTTACACTACAAGGGTATGTC
Found at i:56301330 original size:27 final size:28
Alignment explanation
Indices: 56301267--56301635 Score: 329
Period size: 27 Copynumber: 13.7 Consensus size: 28
56301257 TTACACTACA
* *
56301267 AGGGTATTTCAGTAATTTTAC-ACTACA-
1 AGGGTATTTCGGTAATTTTACAAAT-CAG
**
56301294 AGGGTATTTCAATAATTTTACAAATCAG
1 AGGGTATTTCGGTAATTTTACAAATCAG
*
56301322 A-GGTGTTTCGGTAATTTTACAAATC-G
1 AGGGTATTTCGGTAATTTTACAAATCAG
* *
56301348 AGGGTATTTCGATAATTTTACAAAT-TG
1 AGGGTATTTCGGTAATTTTACAAATCAG
* *
56301375 AGGGTATTTCGATAATTTTACAAAT-TG
1 AGGGTATTTCGGTAATTTTACAAATCAG
*
56301402 AGGGTATTTCAGTAATTTTACAAATC-G
1 AGGGTATTTCGGTAATTTTACAAATCAG
* * * *
56301429 AGGGTGTTTCAGTAATTTTAAAAAT-TG
1 AGGGTATTTCGGTAATTTTACAAATCAG
* *
56301456 AGGGTGTTTTGGTAATTTTACAAATCA-
1 AGGGTATTTCGGTAATTTTACAAATCAG
* * * * *
56301483 AGGGTGTTTCGATAATTTCATAAAT-TG
1 AGGGTATTTCGGTAATTTTACAAATCAG
* * *
56301510 GGGGTATTTTGGTAATTCTACAAATCA-
1 AGGGTATTTCGGTAATTTTACAAATCAG
**
56301537 AGGGTATTTTAGT-ATTTT-CACAATC-G
1 AGGGTATTTCGGTAATTTTACA-AATCAG
* *
56301563 AGGGTATTTCAGTAATTTTATAAATCAG
1 AGGGTATTTCGGTAATTTTACAAATCAG
*
56301591 -GGGTATTTCGATAATTTTACAAATCA-
1 AGGGTATTTCGGTAATTTTACAAATCAG
**
56301617 AGGGTATTTTAGTAATTTT
1 AGGGTATTTCGGTAATTTT
56301636 TCTTTATTAT
Statistics
Matches: 288, Mismatches: 39, Indels: 30
0.81 0.11 0.08
Matches are distributed among these distances:
25 2 0.01
26 22 0.08
27 259 0.90
28 5 0.02
ACGTcount: A:0.32, C:0.09, G:0.19, T:0.40
Consensus pattern (28 bp):
AGGGTATTTCGGTAATTTTACAAATCAG
Found at i:56301352 original size:81 final size:81
Alignment explanation
Indices: 56301267--56301635 Score: 371
Period size: 81 Copynumber: 4.6 Consensus size: 81
56301257 TTACACTACA
* * * *
56301267 AGGGTATTTCAGTAATTTTAC-ACTACAAGGGTATTTCAATAATTTTACAAATCAGA-GGTGTTT
1 AGGGTATTTC-GTAATTTTACAAAT-CAAGGGTATTTTAGTAATTTTACAAATCAGAGGGTATTT
*
56301330 CGGTAATTTTACAAATCG
64 CAGTAATTTTACAAATCG
** * *
56301348 AGGGTATTTCGATAATTTTACAAATTGAGGGTA-TTTCGATAATTTTACAAAT-TGAGGGTATTT
1 AGGGTATTTCG-TAATTTTACAAATCAAGGGTATTTTAG-TAATTTTACAAATCAGAGGGTATTT
56301411 CAGTAATTTTACAAATCG
64 CAGTAATTTTACAAATCG
* * ** * * *
56301429 AGGGTGTTTCAGTAATTTTAAAAATTGAGGGTGTTTTGGTAATTTTACAAATCA-AGGGTGTTTC
1 AGGGTATTTC-GTAATTTTACAAATCAAGGGTATTTTAGTAATTTTACAAATCAGAGGGTATTTC
* * *
56301493 -GATAATTTCATAAATTG
65 AG-TAATTTTACAAATCG
* * *
56301510 GGGGTATTTTGGTAATTCTACAAATCAAGGGTATTTTAGT-ATTTT-CACAATC-GAGGGTATTT
1 AGGGTA-TTTCGTAATTTTACAAATCAAGGGTATTTTAGTAATTTTACA-AATCAGAGGGTATTT
*
56301572 CAGTAATTTTATAAATC-
64 CAGTAATTTTACAAATCG
56301589 AGGGGTATTTCGATAATTTTACAAATCAAGGGTATTTTAGTAATTTT
1 A-GGGTATTTCG-TAATTTTACAAATCAAGGGTATTTTAGTAATTTT
56301636 TCTTTATTAT
Statistics
Matches: 240, Mismatches: 33, Indels: 30
0.79 0.11 0.10
Matches are distributed among these distances:
79 6 0.03
80 68 0.28
81 156 0.65
82 10 0.04
ACGTcount: A:0.32, C:0.09, G:0.19, T:0.40
Consensus pattern (81 bp):
AGGGTATTTCGTAATTTTACAAATCAAGGGTATTTTAGTAATTTTACAAATCAGAGGGTATTTCA
GTAATTTTACAAATCG
Found at i:56305191 original size:16 final size:16
Alignment explanation
Indices: 56305170--56305200 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
56305160 AAAATGATAT
*
56305170 ATGTTTTCATAACATC
1 ATGTTTTCACAACATC
56305186 ATGTTTTCACAACAT
1 ATGTTTTCACAACAT
56305201 TGTTGAAATG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.32, C:0.19, G:0.06, T:0.42
Consensus pattern (16 bp):
ATGTTTTCACAACATC
Found at i:56313724 original size:29 final size:29
Alignment explanation
Indices: 56313653--56313776 Score: 124
Period size: 29 Copynumber: 4.3 Consensus size: 29
56313643 AAATTCACAT
* * * *
56313653 ACATGTATATGGCCCACTAGACCC-AATT
1 ACATTTATATGGCCCATTAGGCCCAAATC
* * * *
56313681 ATATTCACATGGCCCATTAGGCCAAAATC
1 ACATTTATATGGCCCATTAGGCCCAAATC
*
56313710 ACATTTATATGGCCCTTTAGGCCCAAATC
1 ACATTTATATGGCCCATTAGGCCCAAATC
* * *
56313739 ACATTTATATGGCACATCAGGCCCAATTC
1 ACATTTATATGGCCCATTAGGCCCAAATC
*
56313768 AAATTTATA
1 ACATTTATA
56313777 GTCATGCTCA
Statistics
Matches: 77, Mismatches: 18, Indels: 1
0.80 0.19 0.01
Matches are distributed among these distances:
28 17 0.22
29 60 0.78
ACGTcount: A:0.33, C:0.26, G:0.13, T:0.28
Consensus pattern (29 bp):
ACATTTATATGGCCCATTAGGCCCAAATC
Found at i:56314031 original size:16 final size:16
Alignment explanation
Indices: 56313989--56314023 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
56313979 ATAGTCAAAC
*
56313989 TTTCAGCTTTTCGATA
1 TTTCAGCTTTTCGACA
56314005 TTTCAGCTTTTCGACA
1 TTTCAGCTTTTCGACA
56314021 TTT
1 TTT
56314024 TGGCTTTTAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.17, C:0.20, G:0.11, T:0.51
Consensus pattern (16 bp):
TTTCAGCTTTTCGACA
Found at i:56317564 original size:27 final size:26
Alignment explanation
Indices: 56317516--56317575 Score: 75
Period size: 27 Copynumber: 2.3 Consensus size: 26
56317506 GCGAGGCTGC
*
56317516 CAGATATTGTGACGAAGTCACCAGATA
1 CAGATATTGTGACGAAGCCACCAGA-A
* * *
56317543 CAGATATTGTGGCTAGGCCACCAGAA
1 CAGATATTGTGACGAAGCCACCAGAA
56317569 CAGATAT
1 CAGATAT
56317576 ATATATGTGG
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 8 0.28
27 21 0.72
ACGTcount: A:0.35, C:0.20, G:0.23, T:0.22
Consensus pattern (26 bp):
CAGATATTGTGACGAAGCCACCAGAA
Found at i:56317622 original size:71 final size:67
Alignment explanation
Indices: 56317543--56317683 Score: 183
Period size: 67 Copynumber: 2.0 Consensus size: 67
56317533 TCACCAGATA
* * * * *
56317543 CAGATATTGTGGCTAGGCCACCAGAACAGATATATATATGTGGCGAAGCCACCAGATTGCGGTGA
1 CAGATATTGTGACGAAGCCACCAGAACAG----ATATATGTGGCGAAGCCACCAGATTGCAGCGA
56317608 GGCTGC
62 GGCTGC
* *
56317614 CAGATATTGTGACGAAGTCACCAGAACAGATATATGTGGCGAGGCCACCAGATTGCAGCGAGGCT
1 CAGATATTGTGACGAAGCCACCAGAACAGATATATGTGGCGAAGCCACCAGATTGCAGCGAGGCT
56317679 GC
66 GC
56317681 CAG
1 CAG
56317684 GACGCTTCCT
Statistics
Matches: 63, Mismatches: 7, Indels: 4
0.85 0.09 0.05
Matches are distributed among these distances:
67 38 0.60
71 25 0.40
ACGTcount: A:0.29, C:0.22, G:0.30, T:0.19
Consensus pattern (67 bp):
CAGATATTGTGACGAAGCCACCAGAACAGATATATGTGGCGAAGCCACCAGATTGCAGCGAGGCT
GC
Found at i:56317662 original size:27 final size:26
Alignment explanation
Indices: 56317614--56317665 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
56317604 GTGAGGCTGC
*
56317614 CAGATATTGTGACGAAGTCACCAGAA
1 CAGATATTGTGACGAAGCCACCAGAA
* *
56317640 CAGATATATGTGGCGAGGCCACCAGA
1 CAGATAT-TGTGACGAAGCCACCAGA
56317666 TTGCAGCGAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.35, C:0.21, G:0.27, T:0.17
Consensus pattern (26 bp):
CAGATATTGTGACGAAGCCACCAGAA
Found at i:56318337 original size:27 final size:27
Alignment explanation
Indices: 56318307--56318398 Score: 121
Period size: 27 Copynumber: 3.4 Consensus size: 27
56318297 AGGGCAAAAT
* *
56318307 GGTAATTTTACCCCACAAGGGTATCTC
1 GGTAATTCTACCCTACAAGGGTATCTC
* *
56318334 GGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATCTC
*
56318361 GGTAATTCTACCCTACAAGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATCTC
**
56318388 AATAATTCTAC
1 GGTAATTCTAC
56318399 AACTTATCCA
Statistics
Matches: 58, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 58 1.00
ACGTcount: A:0.27, C:0.23, G:0.17, T:0.33
Consensus pattern (27 bp):
GGTAATTCTACCCTACAAGGGTATCTC
Found at i:56323906 original size:15 final size:15
Alignment explanation
Indices: 56323886--56323919 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
56323876 GAATGAAACC
56323886 GATAGGCCCATAGTA
1 GATAGGCCCATAGTA
56323901 GATAGGCCCATAGTA
1 GATAGGCCCATAGTA
56323916 GATA
1 GATA
56323920 TAGAACAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.35, C:0.18, G:0.26, T:0.21
Consensus pattern (15 bp):
GATAGGCCCATAGTA
Found at i:56324202 original size:27 final size:26
Alignment explanation
Indices: 56324154--56324205 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
56324144 GCGAGGCTGC
*
56324154 CAGATATTGTGACGAAGTCACCAGAA
1 CAGATATTGTGACGAAGCCACCAGAA
* *
56324180 CAGATATATGTGGCGAGGCCACCAGA
1 CAGATAT-TGTGACGAAGCCACCAGA
56324206 TTGCAGCGAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.35, C:0.21, G:0.27, T:0.17
Consensus pattern (26 bp):
CAGATATTGTGACGAAGCCACCAGAA
Found at i:56324928 original size:27 final size:27
Alignment explanation
Indices: 56324848--56324939 Score: 123
Period size: 27 Copynumber: 3.4 Consensus size: 27
56324838 AGGGCAAAAT
* *
56324848 GGTAATTTTACCCCACAAGGGTATCTT-
1 GGTAATTCTACCCTACAAGGGTAT-TTC
*
56324875 GGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
56324902 GGTAATTCTACCCTACAAGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
**
56324929 AATAATTCTAC
1 GGTAATTCTAC
56324940 AACTTATCCA
Statistics
Matches: 58, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
26 2 0.03
27 56 0.97
ACGTcount: A:0.27, C:0.22, G:0.17, T:0.34
Consensus pattern (27 bp):
GGTAATTCTACCCTACAAGGGTATTTC
Found at i:56327773 original size:53 final size:53
Alignment explanation
Indices: 56327598--56327801 Score: 183
Period size: 53 Copynumber: 3.8 Consensus size: 53
56327588 AGGGTTTAAG
* * * * * * *
56327598 GATACCAAGTAAGACCATGCCAAGGCGTGGCATTGGTAAGGTTTACAAGGCAAG
1 GATACCATGTAAGACCATGCCAAGACATGGCAATGGTAA-GTTCATAAGGCAAA
* * ** * * * *
56327652 GAAATCATGTAAGACCATTTCAAGACATGGCTATGATAAACTACGATAAGGCAAA
1 GATACCATGTAAGACCATGCCAAGACATGGCAATGGT-AAGTTC-ATAAGGCAAA
* * * *
56327707 GATCCCATGTAAGACCATGCCAAGGCATGGCAATGTTAAGTTCATAAGGCAAC
1 GATACCATGTAAGACCATGCCAAGACATGGCAATGGTAAGTTCATAAGGCAAA
* * *
56327760 GATACCATGTAAGACCATGTCAATACATGGAAATGGTAAGTT
1 GATACCATGTAAGACCATGCCAAGACATGGCAATGGTAAGTT
56327802 TAAAAAGGAA
Statistics
Matches: 116, Mismatches: 32, Indels: 5
0.76 0.21 0.03
Matches are distributed among these distances:
53 45 0.39
54 32 0.28
55 39 0.34
ACGTcount: A:0.37, C:0.18, G:0.23, T:0.22
Consensus pattern (53 bp):
GATACCATGTAAGACCATGCCAAGACATGGCAATGGTAAGTTCATAAGGCAAA
Found at i:56333161 original size:27 final size:27
Alignment explanation
Indices: 56333123--56333177 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
56333113 CCACCAGAGT
56333123 TAGAGAAGATTCATGATGTGTTCCATG
1 TAGAGAAGATTCATGATGTGTTCCATG
56333150 TAGAGAAGATTCATGATGTGTTCCATG
1 TAGAGAAGATTCATGATGTGTTCCATG
56333177 T
1 T
56333178 GTCTATGTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.29, C:0.11, G:0.25, T:0.35
Consensus pattern (27 bp):
TAGAGAAGATTCATGATGTGTTCCATG
Found at i:56334834 original size:53 final size:54
Alignment explanation
Indices: 56334653--56334855 Score: 194
Period size: 53 Copynumber: 3.8 Consensus size: 54
56334643 ATTAGGGTTT
* * * * * *
56334653 AAGGATACCAAGTAAGACCATGCCAAGGCATGGCATTGGTAAATTTTACAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAATGGTAAAGTTCATAAGGC
*** * * * * *
56334707 AAGGA-AATTTGTAAGACCATGTCAAGACATGGCATTGATAAACTACGATAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAATGGTAAAGTTC-ATAAGGC
* * * *
56334761 AAAGATCCCATGTAAGACCATGCCAAGGCATGGCAATGGT-GAGTTCATAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAATGGTAAAGTTCATAAGGC
* * *
56334814 AAGGATACCACGTAAGACCATGTCAAGACATGACAATGGTAA
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAATGGTAA
56334856 GTTTAAAAAG
Statistics
Matches: 116, Mismatches: 30, Indels: 6
0.76 0.20 0.04
Matches are distributed among these distances:
53 72 0.62
54 18 0.16
55 26 0.22
ACGTcount: A:0.38, C:0.18, G:0.24, T:0.20
Consensus pattern (54 bp):
AAGGATACCATGTAAGACCATGCCAAGACATGGCAATGGTAAAGTTCATAAGGC
Found at i:56337750 original size:35 final size:35
Alignment explanation
Indices: 56337711--56337781 Score: 124
Period size: 35 Copynumber: 2.0 Consensus size: 35
56337701 ATCTATGAGG
*
56337711 AGATACGAACTAAAGGTATCGGGGTTGAATGCTAC
1 AGATACGAACTAAAGGTATCGGGGTTGAACGCTAC
*
56337746 AGATAGGAACTAAAGGTATCGGGGTTGAACGCTAC
1 AGATACGAACTAAAGGTATCGGGGTTGAACGCTAC
56337781 A
1 A
56337782 CTAAAAGAGT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.35, C:0.14, G:0.30, T:0.21
Consensus pattern (35 bp):
AGATACGAACTAAAGGTATCGGGGTTGAACGCTAC
Found at i:56338778 original size:39 final size:39
Alignment explanation
Indices: 56338735--56338811 Score: 145
Period size: 39 Copynumber: 2.0 Consensus size: 39
56338725 ATGTAGAAAA
56338735 CATATTAATGATGTTCAAACTATAACATAATTAAAGACT
1 CATATTAATGATGTTCAAACTATAACATAATTAAAGACT
*
56338774 CATATTAATGATGTTCAAACTATGACATAATTAAAGAC
1 CATATTAATGATGTTCAAACTATAACATAATTAAAGAC
56338812 ACAAACTAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.45, C:0.13, G:0.09, T:0.32
Consensus pattern (39 bp):
CATATTAATGATGTTCAAACTATAACATAATTAAAGACT
Found at i:56340952 original size:93 final size:93
Alignment explanation
Indices: 56340825--56340995 Score: 270
Period size: 93 Copynumber: 1.8 Consensus size: 93
56340815 CGCATAAGCG
* * * *
56340825 AACTCGGACTCAACTCAATGAGATCAGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAAC
1 AACTCGGACTCAACTCAACGAGATCAGACATTCGCATCCACAAGTGAACTCGGACTCAACTCAAC
*
56340890 GAGTTCGGATGCCTAGTTACATTTCACA
66 GAGTTCAGATGCCTAGTTACATTTCACA
* * *
56340918 AACTCGGCCTCAACTCAACGAGTTCAGACATTCGCATCCACAAGTGAACTCGGACTCAACTCAAT
1 AACTCGGACTCAACTCAACGAGATCAGACATTCGCATCCACAAGTGAACTCGGACTCAACTCAAC
56340983 GAGTTCAGATGCC
66 GAGTTCAGATGCC
56340996 CAAATATCTG
Statistics
Matches: 70, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
93 70 1.00
ACGTcount: A:0.30, C:0.29, G:0.19, T:0.22
Consensus pattern (93 bp):
AACTCGGACTCAACTCAACGAGATCAGACATTCGCATCCACAAGTGAACTCGGACTCAACTCAAC
GAGTTCAGATGCCTAGTTACATTTCACA
Found at i:56340981 original size:46 final size:46
Alignment explanation
Indices: 56340824--56340991 Score: 157
Period size: 46 Copynumber: 3.6 Consensus size: 46
56340814 ACGCATAAGC
* * * * *
56340824 GAACTCGGACTCAACTCAATGAGATCAGGCGTTCGCATCCATAAGT
1 GAACTCGGACTCAACTCAACGAGTTCAGACATTCGCATCCACAAGT
* * *
56340870 GAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACATTTCAC-A--
1 GAACTCGGACTCAACTCAACGAGTTC--A-GAC-A-TTCGCA-TCCACAAGT
*
56340918 -AACTCGGCCTCAACTCAACGAGTTCAGACATTCGCATCCACAAGT
1 GAACTCGGACTCAACTCAACGAGTTCAGACATTCGCATCCACAAGT
*
56340963 GAACTCGGACTCAACTCAATGAGTTCAGA
1 GAACTCGGACTCAACTCAACGAGTTCAGA
56340992 TGCCCAAATA
Statistics
Matches: 98, Mismatches: 13, Indels: 22
0.74 0.10 0.17
Matches are distributed among these distances:
42 6 0.06
43 4 0.04
44 2 0.02
45 1 0.01
46 50 0.51
47 24 0.24
48 1 0.01
49 2 0.02
50 3 0.03
51 5 0.05
ACGTcount: A:0.31, C:0.28, G:0.19, T:0.22
Consensus pattern (46 bp):
GAACTCGGACTCAACTCAACGAGTTCAGACATTCGCATCCACAAGT
Found at i:56350179 original size:34 final size:33
Alignment explanation
Indices: 56350116--56350181 Score: 80
Period size: 34 Copynumber: 2.0 Consensus size: 33
56350106 TATCTCAGTG
* *
56350116 ACAGTTCAGTATCAGTTAGGGACTTAGCCCATT
1 ACAGTTCAGAATCAGTTAGGGACTGAGCCCATT
*
56350149 ACAGTATCAGAATCAGTTTGGG-CTAGAGCCCAT
1 ACAGT-TCAGAATCAGTTAGGGACT-GAGCCCAT
56350182 CTCAATGACA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
33 7 0.25
34 21 0.75
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.27
Consensus pattern (33 bp):
ACAGTTCAGAATCAGTTAGGGACTGAGCCCATT
Found at i:56364407 original size:19 final size:21
Alignment explanation
Indices: 56364374--56364417 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 21
56364364 AAGTGATTAA
56364374 AAAACTAAGTAAAAT-AAAAT
1 AAAACTAAGTAAAATAAAAAT
*
56364394 AAAA-TAAGTTAAATAAAAAT
1 AAAACTAAGTAAAATAAAAAT
56364414 AAAA
1 AAAA
56364418 GTTCCAATGC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 9 0.41
20 13 0.59
ACGTcount: A:0.73, C:0.02, G:0.05, T:0.20
Consensus pattern (21 bp):
AAAACTAAGTAAAATAAAAAT
Found at i:56372770 original size:40 final size:40
Alignment explanation
Indices: 56372699--56372919 Score: 297
Period size: 40 Copynumber: 5.6 Consensus size: 40
56372689 AAACCAAGTA
** * * *
56372699 CCTTCGGGGTTTAG-CCGGATATAGCT-ACTCGCTCAAATG
1 CCTTCGGGACTTAGCCCGGTTATAG-TAACTCGCACAATTG
*
56372738 CCTTCAGGACTTAGCCCGGTTATAGTAACTCGCACAATTG
1 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAATTG
*
56372778 CCTTCGGGACTTACCCCGGTTATAGTAACTCGCACAATTG
1 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAATTG
56372818 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAATTG
1 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAATTG
* * * *
56372858 CCTTCGGG-CTTAGCCCGG-AATTAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGTTA-TAGTAACTCGCACAATTG
56372897 CCTTCGGGACTTAGCCCGGTTAT
1 CCTTCGGGACTTAGCCCGGTTAT
56372920 CATCCGAATA
Statistics
Matches: 163, Mismatches: 14, Indels: 9
0.88 0.08 0.05
Matches are distributed among these distances:
38 1 0.01
39 45 0.28
40 116 0.71
41 1 0.01
ACGTcount: A:0.22, C:0.28, G:0.23, T:0.27
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAATTG
Found at i:56372915 original size:119 final size:119
Alignment explanation
Indices: 56372699--56372919 Score: 295
Period size: 119 Copynumber: 1.9 Consensus size: 119
56372689 AAACCAAGTA
** * *
56372699 CCTTCGGGGTTTAGCCGGATATAGCTACTCGCTCAAATGCCTTCAGGACTTAGCCCGGTTATAGT
1 CCTTCGGGACTTAGCCGGATATAGCTACTCGCACAAATGCCTTCAGGACTTAGCCCGGATATAGT
* *
56372764 AACTCGCACAATTGCCTTCGGGACTTACCCCGGTTATAGTAACTCGCACAATTG
66 AACTAGCACAAATGCCTTCGGGACTTACCCCGGTTATAGTAACTCGCACAATTG
* * *
56372818 CCTTCGGGACTTAGCCCGGTTATAG-TAACTCGCACAATTGCCTTC-GGGCTTAGCCCGGA-ATT
1 CCTTCGGGACTTAG-CCGGATATAGCT-ACTCGCACAAATGCCTTCAGGACTTAGCCCGGATA-T
* *
56372880 AGTCACTAGCACAAATGCCTTCGGGACTTAGCCCGGTTAT
63 AGTAACTAGCACAAATGCCTTCGGGACTTACCCCGGTTAT
56372920 CATCCGAATA
Statistics
Matches: 88, Mismatches: 11, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
118 1 0.01
119 62 0.70
120 25 0.28
ACGTcount: A:0.22, C:0.28, G:0.23, T:0.27
Consensus pattern (119 bp):
CCTTCGGGACTTAGCCGGATATAGCTACTCGCACAAATGCCTTCAGGACTTAGCCCGGATATAGT
AACTAGCACAAATGCCTTCGGGACTTACCCCGGTTATAGTAACTCGCACAATTG
Found at i:56374182 original size:34 final size:34
Alignment explanation
Indices: 56374139--56374206 Score: 118
Period size: 34 Copynumber: 2.0 Consensus size: 34
56374129 TCTTCTATTC
56374139 GGCCAAGTTGAAACATGAGAACTTATTTCTTTTT
1 GGCCAAGTTGAAACATGAGAACTTATTTCTTTTT
* *
56374173 GGCCAAGTTGAAACATGATAACTTTTTTCTTTTT
1 GGCCAAGTTGAAACATGAGAACTTATTTCTTTTT
56374207 CTTTTTTCTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.28, C:0.15, G:0.16, T:0.41
Consensus pattern (34 bp):
GGCCAAGTTGAAACATGAGAACTTATTTCTTTTT
Found at i:56381791 original size:40 final size:40
Alignment explanation
Indices: 56381731--56381914 Score: 224
Period size: 40 Copynumber: 4.6 Consensus size: 40
56381721 GATAAATTAA
* *
56381731 TTATTTATGGCACTTAGTGTGCGATACGACATAGCTTTGG
1 TTATATATGGCACTTAGTGTGCGATACGACATAGCTTCGG
* *
56381771 TTGTATATGGCACTTAGTGTGCAATACGACATAGCTTCGG
1 TTATATATGGCACTTAGTGTGCGATACGACATAGCTTCGG
* * * *
56381811 CTATATATGGCACTTAGTGTGAGATTCGACATAGCTTCGA
1 TTATATATGGCACTTAGTGTGCGATACGACATAGCTTCGG
* ** * *
56381851 TTATATATGGCACTTAGTGTGCAATTTGAGATAGCTTCAG
1 TTATATATGGCACTTAGTGTGCGATACGACATAGCTTCGG
* * *
56381891 CTATGTATGGCACTTAATGTGCGA
1 TTATATATGGCACTTAGTGTGCGA
56381915 GACATTGAGT
Statistics
Matches: 123, Mismatches: 21, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 123 1.00
ACGTcount: A:0.26, C:0.16, G:0.24, T:0.35
Consensus pattern (40 bp):
TTATATATGGCACTTAGTGTGCGATACGACATAGCTTCGG
Found at i:56381841 original size:80 final size:80
Alignment explanation
Indices: 56381736--56381911 Score: 253
Period size: 80 Copynumber: 2.2 Consensus size: 80
56381726 ATTAATTATT
* * * *
56381736 TATGGCACTTAGTGTGCGATACGACATAGCTTTGGTTGTATATGGCACTTAGTGTGCAATACGAC
1 TATGGCACTTAGTGTGAGATACGACATAGCTTCGATTATATATGGCACTTAGTGTGCAATACGAC
*
56381801 ATAGCTTCGGCTATA
66 ATAGCTTCAGCTATA
* ** *
56381816 TATGGCACTTAGTGTGAGATTCGACATAGCTTCGATTATATATGGCACTTAGTGTGCAATTTGAG
1 TATGGCACTTAGTGTGAGATACGACATAGCTTCGATTATATATGGCACTTAGTGTGCAATACGAC
*
56381881 ATAGCTTCAGCTATG
66 ATAGCTTCAGCTATA
*
56381896 TATGGCACTTAATGTG
1 TATGGCACTTAGTGTG
56381912 CGAGACATTG
Statistics
Matches: 85, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
80 85 1.00
ACGTcount: A:0.26, C:0.16, G:0.24, T:0.34
Consensus pattern (80 bp):
TATGGCACTTAGTGTGAGATACGACATAGCTTCGATTATATATGGCACTTAGTGTGCAATACGAC
ATAGCTTCAGCTATA
Found at i:56386275 original size:22 final size:20
Alignment explanation
Indices: 56386247--56386291 Score: 63
Period size: 22 Copynumber: 2.1 Consensus size: 20
56386237 CATTTATGAG
*
56386247 AATGAATGCTTTATGCTTGATA
1 AATGAATGCTATATG-TTG-TA
56386269 AATGAATGCTATATGTTGTA
1 AATGAATGCTATATGTTGTA
56386289 AAT
1 AAT
56386292 TGATCGGTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 5 0.23
21 3 0.14
22 14 0.64
ACGTcount: A:0.36, C:0.07, G:0.18, T:0.40
Consensus pattern (20 bp):
AATGAATGCTATATGTTGTA
Found at i:56386927 original size:19 final size:18
Alignment explanation
Indices: 56386890--56386928 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
56386880 ATGCCTCAAT
*
56386890 TTTTGAAAGTGTTGATGA
1 TTTTGAAAGTGTTCATGA
*
56386908 TTTTGAAAGTTTTCATTGA
1 TTTTGAAAGTGTTCA-TGA
56386927 TT
1 TT
56386929 AATTCATGTG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 13 0.72
19 5 0.28
ACGTcount: A:0.26, C:0.03, G:0.21, T:0.51
Consensus pattern (18 bp):
TTTTGAAAGTGTTCATGA
Found at i:56387615 original size:43 final size:43
Alignment explanation
Indices: 56387550--56387761 Score: 261
Period size: 43 Copynumber: 5.0 Consensus size: 43
56387540 GTTACCGAAA
*
56387550 TGTGATTACATGTAAGACCATGTCTGGGATATTGGCATTGTAT
1 TGTGAATACATGTAAGACCATGTCTGGGATATTGGCATTGTAT
* *
56387593 TGTGAATACATGTAAGATCATGTCCGGGATATTGGCATTGTAT
1 TGTGAATACATGTAAGACCATGTCTGGGATATTGGCATTGTAT
* *
56387636 TGTGGATACATGTAAGACCATGTCTGGGACATTGGCATTGTTAT
1 TGTGAATACATGTAAGACCATGTCTGGGATATTGGCATTG-TAT
* * * * * *
56387680 T-TGATTTCGTGTAAGACCATGTCTGGGATAGTGGCGTCG-AT
1 TGTGAATACATGTAAGACCATGTCTGGGATATTGGCATTGTAT
*
56387721 ATGTG-ATAACATGTAAGACCATATCTGGGATA-TGGCATTGT
1 -TGTGAAT-ACATGTAAGACCATGTCTGGGATATTGGCATTGT
56387762 TCGAGCTTAT
Statistics
Matches: 143, Mismatches: 21, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
41 2 0.01
42 8 0.06
43 129 0.90
44 4 0.03
ACGTcount: A:0.26, C:0.13, G:0.27, T:0.34
Consensus pattern (43 bp):
TGTGAATACATGTAAGACCATGTCTGGGATATTGGCATTGTAT
Found at i:56391694 original size:14 final size:14
Alignment explanation
Indices: 56391677--56391706 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
56391667 AAAGTAGTTT
*
56391677 TAAAAAGATAAAAA
1 TAAAAACATAAAAA
56391691 TAAAAACATAAAAA
1 TAAAAACATAAAAA
56391705 TA
1 TA
56391707 CTAAATAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.77, C:0.03, G:0.03, T:0.17
Consensus pattern (14 bp):
TAAAAACATAAAAA
Found at i:56393358 original size:18 final size:19
Alignment explanation
Indices: 56393325--56393363 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
56393315 TGAGGTGCGC
*
56393325 AAGGGTGAGAAGAGGGGAG
1 AAGGGAGAGAAGAGGGGAG
56393344 AAGGGAGAG-AGAGGGGAG
1 AAGGGAGAGAAGAGGGGAG
56393362 AA
1 AA
56393364 AAATGAAAGG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 11 0.58
19 8 0.42
ACGTcount: A:0.41, C:0.00, G:0.56, T:0.03
Consensus pattern (19 bp):
AAGGGAGAGAAGAGGGGAG
Found at i:56401000 original size:28 final size:28
Alignment explanation
Indices: 56400965--56401023 Score: 118
Period size: 28 Copynumber: 2.1 Consensus size: 28
56400955 CCATGAGCCA
56400965 TATCATAAGATTATATACACAAAATGAG
1 TATCATAAGATTATATACACAAAATGAG
56400993 TATCATAAGATTATATACACAAAATGAG
1 TATCATAAGATTATATACACAAAATGAG
56401021 TAT
1 TAT
56401024 AATGCTATAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.49, C:0.10, G:0.10, T:0.31
Consensus pattern (28 bp):
TATCATAAGATTATATACACAAAATGAG
Found at i:56403879 original size:35 final size:36
Alignment explanation
Indices: 56403833--56403908 Score: 127
Period size: 35 Copynumber: 2.1 Consensus size: 36
56403823 CAAAACCGTG
56403833 AGGTAAACCTCAGATCTCTATCT-AATGATCAACAA
1 AGGTAAACCTCAGATCTCTATCTAAATGATCAACAA
*
56403868 AGGTAAACCTCAGATCTCTATCTGAAATGATCGACAA
1 AGGTAAACCTCAGATCTCTATCT-AAATGATCAACAA
56403905 AGGT
1 AGGT
56403909 GCTCTATGAA
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
35 23 0.61
37 15 0.39
ACGTcount: A:0.38, C:0.21, G:0.16, T:0.25
Consensus pattern (36 bp):
AGGTAAACCTCAGATCTCTATCTAAATGATCAACAA
Found at i:56408104 original size:24 final size:24
Alignment explanation
Indices: 56407950--56408104 Score: 211
Period size: 24 Copynumber: 6.4 Consensus size: 24
56407940 CTAGAGGCCT
* * *
56407950 AGCCTCTTTTAATAAGTGGGGCAAA
1 AGCC-CTTTTGATAACTGGGGCATA
* *
56407975 AACCCTTTTAATAACTGGGGCATA
1 AGCCCTTTTGATAACTGGGGCATA
*
56407999 AGCCCTTTTGATAACTGGGGCGTA
1 AGCCCTTTTGATAACTGGGGCATA
*
56408023 AGCCCTTTTAATAACTGGGGCATA
1 AGCCCTTTTGATAACTGGGGCATA
* *
56408047 AGGCCTTTTGATAGCTGGGGCATA
1 AGCCCTTTTGATAACTGGGGCATA
*
56408071 AGCCCTTTTGATAACTGAGGCATA
1 AGCCCTTTTGATAACTGGGGCATA
56408095 AGCCCTTTTG
1 AGCCCTTTTG
56408105 CTCTTCCTCC
Statistics
Matches: 116, Mismatches: 14, Indels: 1
0.89 0.11 0.01
Matches are distributed among these distances:
24 113 0.97
25 3 0.03
ACGTcount: A:0.26, C:0.20, G:0.24, T:0.30
Consensus pattern (24 bp):
AGCCCTTTTGATAACTGGGGCATA
Found at i:56408167 original size:11 final size:11
Alignment explanation
Indices: 56408153--56408208 Score: 57
Period size: 11 Copynumber: 5.5 Consensus size: 11
56408143 TTATGTATAC
56408153 ATCATGTGCAT
1 ATCATGTGCAT
*
56408164 ATCA--TACAT
1 ATCATGTGCAT
56408173 ATCATGTGCAT
1 ATCATGTGCAT
*
56408184 ATCA--TACAT
1 ATCATGTGCAT
*
56408193 GTCATGTGCAT
1 ATCATGTGCAT
56408204 ATCAT
1 ATCAT
56408209 ACATACCATG
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
9 15 0.43
11 20 0.57
ACGTcount: A:0.32, C:0.20, G:0.12, T:0.36
Consensus pattern (11 bp):
ATCATGTGCAT
Found at i:56408178 original size:20 final size:20
Alignment explanation
Indices: 56408153--56408219 Score: 116
Period size: 20 Copynumber: 3.4 Consensus size: 20
56408143 TTATGTATAC
56408153 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
56408173 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
*
56408193 GTCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
*
56408213 ACCATGT
1 ATCATGT
56408220 TTATCAAAAT
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.33, C:0.21, G:0.12, T:0.34
Consensus pattern (20 bp):
ATCATGTGCATATCATACAT
Found at i:56416298 original size:24 final size:24
Alignment explanation
Indices: 56416244--56416363 Score: 161
Period size: 24 Copynumber: 5.0 Consensus size: 24
56416234 GCTTTATCAT
* *
56416244 ATAACTGGAGGCCT-AGCCTCTGTTA
1 ATAACTGG-GGCATAAGCC-CTTTTA
*
56416269 ATAACTGGGGCAAAAGCCCTTTTA
1 ATAACTGGGGCATAAGCCCTTTTA
*
56416293 ATAACTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTA
* *
56416317 ATAGCTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTA
56416341 ATAACTGGGGCATAAGCCCTTTT
1 ATAACTGGGGCATAAGCCCTTTT
56416364 GCACTTCCTC
Statistics
Matches: 87, Mismatches: 7, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
24 75 0.86
25 12 0.14
ACGTcount: A:0.26, C:0.22, G:0.24, T:0.28
Consensus pattern (24 bp):
ATAACTGGGGCATAAGCCCTTTTA
Found at i:56416364 original size:24 final size:24
Alignment explanation
Indices: 56416269--56416364 Score: 165
Period size: 24 Copynumber: 4.0 Consensus size: 24
56416259 GCCTCTGTTA
* *
56416269 ATAACTGGGGCAAAAGCCCTTTTA
1 ATAACTGGGGCATAAGCCCTTTTG
56416293 ATAACTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTG
*
56416317 ATAGCTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTG
56416341 ATAACTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTG
56416365 CACTTCCTCC
Statistics
Matches: 68, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 68 1.00
ACGTcount: A:0.26, C:0.21, G:0.25, T:0.28
Consensus pattern (24 bp):
ATAACTGGGGCATAAGCCCTTTTG
Found at i:56416438 original size:20 final size:20
Alignment explanation
Indices: 56416413--56416479 Score: 107
Period size: 20 Copynumber: 3.4 Consensus size: 20
56416403 TTATGTATAC
56416413 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
56416433 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
* *
56416453 GTCATGCGCATATCATACAT
1 ATCATGTGCATATCATACAT
*
56416473 ACCATGT
1 ATCATGT
56416480 TTATCAAAAT
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.33, C:0.22, G:0.12, T:0.33
Consensus pattern (20 bp):
ATCATGTGCATATCATACAT
Found at i:56416544 original size:25 final size:25
Alignment explanation
Indices: 56416516--56416563 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
56416506 ATATATAAAC
* * *
56416516 CCTAGGGGTATAATGGTCATTTTTA
1 CCTAGGGGAAAAACGGTCATTTTTA
56416541 CCTAGGGGAAAAACGGTCATTTT
1 CCTAGGGGAAAAACGGTCATTTT
56416564 CATATCATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.27, C:0.15, G:0.25, T:0.33
Consensus pattern (25 bp):
CCTAGGGGAAAAACGGTCATTTTTA
Found at i:56421302 original size:79 final size:81
Alignment explanation
Indices: 56421158--56421336 Score: 224
Period size: 79 Copynumber: 2.2 Consensus size: 81
56421148 GCTACTCGTT
* *
56421158 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
* *
56421223 ATTTAGTAAC-TCGCA
66 ATATAGTAACTTAGCA
* **
56421238 CAAATGCCTTCGGG-CTTAGCCCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGTCC
1 CAAATGCCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCC
* *
56421300 GGATATGGTCACTTAGCA
64 GGATATAGTAACTTAGCA
56421318 CAAA-GCCTTCGGGACTTAG
1 CAAATGCCTTCGGGACTTAG
56421337 TGTGACAGCC
Statistics
Matches: 86, Mismatches: 9, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
78 4 0.05
79 55 0.64
80 27 0.31
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (81 bp):
CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
ATATAGTAACTTAGCA
Found at i:56421337 original size:40 final size:40
Alignment explanation
Indices: 56421139--56421336 Score: 226
Period size: 40 Copynumber: 5.0 Consensus size: 40
56421129 CAGAATTTAA
** *
56421139 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* *
56421179 CCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
56421219 CCGGATTTAGTAACTCGCACAAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
56421258 CCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
56421298 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAG
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAG
56421337 TGTGACAGCC
Statistics
Matches: 136, Mismatches: 15, Indels: 14
0.82 0.09 0.08
Matches are distributed among these distances:
38 2 0.01
39 33 0.24
40 89 0.65
41 12 0.09
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:56427007 original size:40 final size:39
Alignment explanation
Indices: 56426915--56427126 Score: 301
Period size: 40 Copynumber: 5.5 Consensus size: 39
56426905 TGGATGATAA
*
56426915 CCGGGCTAAGTCCCGAAGGCATT-TGCGTAGTGACTAT-T
1 CCGGGCTAAGTCCCGAAGGCATTGTGCG-AGTTACTATAT
56426953 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCA-TTGTGCGAGTTACTATAT
56426993 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCA-TTGTGCGAGTTACTATAT
56427033 CCGGGCTAAGTCCCGAAGGCATTGTGCGAGTTAC--TAT
1 CCGGGCTAAGTCCCGAAGGCATTGTGCGAGTTACTATAT
* *
56427070 CCGGGCTATGTCCCGAAGGCATTGAGCGAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTGTGCGAGTTA-CTATAT
* *
56427109 CC-GGTTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
56427127 TACTTGGCTT
Statistics
Matches: 162, Mismatches: 6, Indels: 12
0.90 0.03 0.07
Matches are distributed among these distances:
36 2 0.01
37 32 0.20
38 34 0.21
39 28 0.17
40 66 0.41
ACGTcount: A:0.23, C:0.24, G:0.29, T:0.25
Consensus pattern (39 bp):
CCGGGCTAAGTCCCGAAGGCATTGTGCGAGTTACTATAT
Found at i:56435112 original size:40 final size:40
Alignment explanation
Indices: 56435054--56435271 Score: 280
Period size: 40 Copynumber: 5.5 Consensus size: 40
56435044 TGGATGATAA
* * * *
56435054 CCGGGCTAAGTCCCGAAGGCATTTGCGCTAGTGACAAGT-T
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-TAT
*
56435094 CCAGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
56435134 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
56435174 CCGGGCTAAGTCTCGAAGGCATTGGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* * *
56435214 CCGGGCTATGTCCCGAAGGCATTCGAGCGAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT
* * *
56435254 TC-GGTTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
56435272 TACTTGGCTT
Statistics
Matches: 160, Mismatches: 16, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
39 16 0.10
40 144 0.90
ACGTcount: A:0.23, C:0.23, G:0.28, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:56452469 original size:30 final size:30
Alignment explanation
Indices: 56452435--56452531 Score: 97
Period size: 30 Copynumber: 3.2 Consensus size: 30
56452425 AGCTCACTTC
*
56452435 TAGCTCATA-TTCAGCTCATGAGCTAAACCT
1 TAGCTCA-ACTTCAGCTCACGAGCTAAACCT
* * * * *
56452465 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTCAGCTCACGAGCTAAACCT
* * *
56452495 CAGCTCAACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCAACTTCAGCTCACGAGCTAAACCT
56452525 TAGCTCA
1 TAGCTCA
56452532 TTTTAGTTTA
Statistics
Matches: 52, Mismatches: 14, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
29 1 0.02
30 51 0.98
ACGTcount: A:0.28, C:0.27, G:0.16, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTCAGCTCACGAGCTAAACCT
Found at i:56453421 original size:22 final size:20
Alignment explanation
Indices: 56453389--56453437 Score: 53
Period size: 20 Copynumber: 2.3 Consensus size: 20
56453379 GTCGAATTTA
56453389 TGAACTATTTTAATACATTAGTG
1 TGAAC-ATTTTAAT-CATT-GTG
* *
56453412 TGAACATTTTTATTATTGTG
1 TGAACATTTTAATCATTGTG
56453432 TGAACA
1 TGAACA
56453438 CCTAGATGCC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 9 0.38
21 3 0.12
22 7 0.29
23 5 0.21
ACGTcount: A:0.33, C:0.08, G:0.14, T:0.45
Consensus pattern (20 bp):
TGAACATTTTAATCATTGTG
Found at i:56456616 original size:46 final size:45
Alignment explanation
Indices: 56456532--56456651 Score: 116
Period size: 46 Copynumber: 2.6 Consensus size: 45
56456522 CTAGTAGCTA
* * *
56456532 ATGCATGTCCCAAACATGTCTTACACTGGCTTACGTCTTGAGGCCG
1 ATGCATGTCCCAGACATGTCTTACACTGACTTA-GTCTTGAGGACG
* * * *
56456578 ATGCATGTCCCGGACATGTCTTACATTAGAACTT-GTCTTGATGATG
1 ATGCATGTCCCAGACATGTCTTACACT-G-ACTTAGTCTTGAGGACG
*
56456624 ATGCCATGTCCAAGACATGGTCTTACAC
1 ATG-CATGTCCCAGACAT-GTCTTACAC
56456652 AGGCTCTCAT
Statistics
Matches: 60, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
46 36 0.60
47 13 0.22
48 11 0.18
ACGTcount: A:0.24, C:0.25, G:0.21, T:0.30
Consensus pattern (45 bp):
ATGCATGTCCCAGACATGTCTTACACTGACTTAGTCTTGAGGACG
Found at i:56464776 original size:44 final size:43
Alignment explanation
Indices: 56464728--56464881 Score: 136
Period size: 42 Copynumber: 3.6 Consensus size: 43
56464718 TGTGAATTCA
*
56464728 TGTAAGACCATGTCTGGGACATTGGCATCGACTACTATTTTACG
1 TGTAAGACCATATCTGGGACATTGGCATCGA-TACTATTTTACG
**
56464772 TGTAAGACCATATCTGGGACATCAGCATCG-TATCTGA-TTT-CG
1 TGTAAGACCATATCTGGGACATTGGCATCGATA-CT-ATTTTACG
* * * * * * * *
56464814 TGTAAGACCCTGTCTGGGATAGTGGCAACGAT-TTTTTATTACA
1 TGTAAGACCATATCTGGGACATTGGCATCGATACTATT-TTACG
*
56464857 TGTAAGACCACATCTGGGACATTGG
1 TGTAAGACCATATCTGGGACATTGG
56464882 TGTTGTATAT
Statistics
Matches: 86, Mismatches: 18, Indels: 13
0.74 0.15 0.11
Matches are distributed among these distances:
41 2 0.02
42 29 0.34
43 27 0.31
44 28 0.33
ACGTcount: A:0.26, C:0.19, G:0.23, T:0.31
Consensus pattern (43 bp):
TGTAAGACCATATCTGGGACATTGGCATCGATACTATTTTACG
Found at i:56464830 original size:42 final size:44
Alignment explanation
Indices: 56464728--56464832 Score: 128
Period size: 44 Copynumber: 2.4 Consensus size: 44
56464718 TGTGAATTCA
**
56464728 TGTAAGACCATGTCTGGGACATTGGCATCGACTACTATTTTACG
1 TGTAAGACCATGTCTGGGACATCAGCATCGACTACTATTTTACG
*
56464772 TGTAAGACCATATCTGGGACATCAGCATCG--TATCTGA-TTT-CG
1 TGTAAGACCATGTCTGGGACATCAGCATCGACTA-CT-ATTTTACG
*
56464814 TGTAAGACCCTGTCTGGGA
1 TGTAAGACCATGTCTGGGA
56464833 TAGTGGCAAC
Statistics
Matches: 54, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
42 21 0.39
43 5 0.09
44 28 0.52
ACGTcount: A:0.25, C:0.21, G:0.24, T:0.30
Consensus pattern (44 bp):
TGTAAGACCATGTCTGGGACATCAGCATCGACTACTATTTTACG
Found at i:56471123 original size:20 final size:20
Alignment explanation
Indices: 56471098--56471137 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
56471088 GCGACAGGTG
56471098 TTAGCATGAAAACACCTAAA
1 TTAGCATGAAAACACCTAAA
56471118 TTAGCATGAAAACACCTAAA
1 TTAGCATGAAAACACCTAAA
56471138 GGGACTATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.50, C:0.20, G:0.10, T:0.20
Consensus pattern (20 bp):
TTAGCATGAAAACACCTAAA
Found at i:56480042 original size:28 final size:28
Alignment explanation
Indices: 56480010--56480079 Score: 106
Period size: 28 Copynumber: 2.5 Consensus size: 28
56480000 AATGAGATTG
*
56480010 GCACTAAGTGTGCGAGTTTAATT-GTATA
1 GCACTAAGTGTGCGAGTTTAATTATTA-A
*
56480038 GCACTAAGTGTGCGAGTTTGATTATTAA
1 GCACTAAGTGTGCGAGTTTAATTATTAA
56480066 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
56480080 GACTTACTAT
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
28 37 0.95
29 2 0.05
ACGTcount: A:0.27, C:0.13, G:0.27, T:0.33
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTAATTATTAA
Found at i:56486410 original size:28 final size:28
Alignment explanation
Indices: 56486344--56486471 Score: 157
Period size: 28 Copynumber: 4.5 Consensus size: 28
56486334 CATGAGATTG
* * **
56486344 GCACTAAGTGTGCGGGTTTAAATTGCATA
1 GCACTAAGTGTGCGAGTTT-GATTATATA
*
56486373 GCACTAAGTGTGCAAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
* *
56486401 GCAATAAGTGTGCGAGTTTGATTATGTAA
1 GCACTAAGTGTGCGAGTTTGATTATAT-A
*
56486430 GCACTAAGTGTGTGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
56486458 ACACTAAGTGTGCG
1 GCACTAAGTGTGCG
56486472 GACTTACTAT
Statistics
Matches: 85, Mismatches: 13, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
28 43 0.51
29 42 0.49
ACGTcount: A:0.30, C:0.11, G:0.26, T:0.34
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGATTATATA
Found at i:56494433 original size:29 final size:28
Alignment explanation
Indices: 56494386--56494483 Score: 88
Period size: 28 Copynumber: 3.5 Consensus size: 28
56494376 CATGAGATTG
** *
56494386 GCACTAAGTGTGCGGGTTTAAATTGCATA
1 GCACTAAGTGTGCAAGTTT-AATTACATA
* *
56494415 GCACTAAGTGTGCAAGTTTGATTATATA
1 GCACTAAGTGTGCAAGTTTAATTACATA
** * *
56494443 GCACTAAGTGTGTGAGTTTGATTATATA
1 GCACTAAGTGTGCAAGTTTAATTACATA
* *
56494471 ACACTATGTGTGC
1 GCACTAAGTGTGC
56494484 GGACTTACTA
Statistics
Matches: 59, Mismatches: 10, Indels: 1
0.84 0.14 0.01
Matches are distributed among these distances:
28 42 0.71
29 17 0.29
ACGTcount: A:0.29, C:0.12, G:0.24, T:0.35
Consensus pattern (28 bp):
GCACTAAGTGTGCAAGTTTAATTACATA
Found at i:56494452 original size:28 final size:28
Alignment explanation
Indices: 56494412--56494483 Score: 108
Period size: 28 Copynumber: 2.6 Consensus size: 28
56494402 TTTAAATTGC
56494412 ATAGCACTAAGTGTGCAAGTTTGATTAT
1 ATAGCACTAAGTGTGCAAGTTTGATTAT
**
56494440 ATAGCACTAAGTGTGTGAGTTTGATTAT
1 ATAGCACTAAGTGTGCAAGTTTGATTAT
* *
56494468 ATAACACTATGTGTGC
1 ATAGCACTAAGTGTGC
56494484 GGACTTACTA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 39 1.00
ACGTcount: A:0.31, C:0.11, G:0.22, T:0.36
Consensus pattern (28 bp):
ATAGCACTAAGTGTGCAAGTTTGATTAT
Found at i:56510874 original size:37 final size:37
Alignment explanation
Indices: 56510824--56510902 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
56510814 TTATTACGAA
* * *
56510824 GTCTTACCCGGACATAATCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
*
56510861 GTCTTACCCGGACAAAATCCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
56510898 GTCTT
1 GTCTT
56510903 TAGAGCTCGG
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:0.25, C:0.32, G:0.19, T:0.24
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
Found at i:56511108 original size:47 final size:47
Alignment explanation
Indices: 56511021--56511496 Score: 691
Period size: 47 Copynumber: 10.1 Consensus size: 47
56511011 CCTTTCGGGA
* * * * * * * * *
56511021 CTTATCACATTTATGCACTTCCACATCCATTACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
56511068 CTTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
56511115 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * * *
56511162 CTTATCACACACATACACTTTCACATTCATCACGTCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
56511209 CTTATCACACATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * * *
56511256 CCTATCACACATATACACTTTCACATTCATCACGTCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * * *
56511303 CCTATCACACATATACACTTTCACATTCATCACGTCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
56511350 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
56511397 CTTATCACGTATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
56511444 CCTATCACATATATTTACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATA--TACACTTTCACATTCATCACATCGGCCATTAGGC
56511493 CTTA
1 CTTA
56511497 CTATCATTTG
Statistics
Matches: 400, Mismatches: 27, Indels: 2
0.93 0.06 0.00
Matches are distributed among these distances:
47 363 0.91
49 37 0.09
ACGTcount: A:0.28, C:0.31, G:0.10, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:56518708 original size:40 final size:40
Alignment explanation
Indices: 56518664--56518739 Score: 107
Period size: 40 Copynumber: 1.9 Consensus size: 40
56518654 ATTGTATGAT
* * *
56518664 TGCACATACGTGCTCTTGTTTGTACTTCGGTACCCCTAAA
1 TGCACATACGTGCCCCTATTTGTACTTCGGTACCCCTAAA
* *
56518704 TGCACATACGTGCCCCTATTTGTACTTTGGTGCCCC
1 TGCACATACGTGCCCCTATTTGTACTTCGGTACCCC
56518740 GATTCTGACG
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 31 1.00
ACGTcount: A:0.17, C:0.30, G:0.18, T:0.34
Consensus pattern (40 bp):
TGCACATACGTGCCCCTATTTGTACTTCGGTACCCCTAAA
Found at i:56521496 original size:40 final size:40
Alignment explanation
Indices: 56521420--56521527 Score: 99
Period size: 40 Copynumber: 2.7 Consensus size: 40
56521410 TGAAGATATC
* * * *** *
56521420 TCAAATCGCACACTAAATGCCATATATTGTCGAAGCTATG
1 TCAAATCACACACTAAGTGCCAAATATAACCAAAGCTATG
** * *
56521460 TTGAATCACACATTAAGTGCCATATATAACCAAAGCTATG
1 TCAAATCACACACTAAGTGCCAAATATAACCAAAGCTATG
**
56521500 TCAAATTGCACACTAAGTGCCAAATATA
1 TCAAATCACACACTAAGTGCCAAATATA
56521528 GTCAATTTGT
Statistics
Matches: 53, Mismatches: 15, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
40 53 1.00
ACGTcount: A:0.39, C:0.21, G:0.13, T:0.27
Consensus pattern (40 bp):
TCAAATCACACACTAAGTGCCAAATATAACCAAAGCTATG
Found at i:56521972 original size:21 final size:21
Alignment explanation
Indices: 56521925--56521972 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
56521915 CAAAACTTTC
*
56521925 ATTT-ATTTCACATTTCAACC
1 ATTTAATTTCACATTTCAACA
*
56521945 ATATAATTTGCACATTTC-ACA
1 ATTTAATTT-CACATTTCAACA
56521966 ATTTAAT
1 ATTTAAT
56521973 CCTTATTATG
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
20 3 0.13
21 12 0.52
22 8 0.35
ACGTcount: A:0.35, C:0.19, G:0.02, T:0.44
Consensus pattern (21 bp):
ATTTAATTTCACATTTCAACA
Found at i:56525466 original size:31 final size:31
Alignment explanation
Indices: 56525431--56525495 Score: 130
Period size: 31 Copynumber: 2.1 Consensus size: 31
56525421 TGGTATTTTT
56525431 GTGCTTAAATGGTTGGTGTTGAAATAATCAA
1 GTGCTTAAATGGTTGGTGTTGAAATAATCAA
56525462 GTGCTTAAATGGTTGGTGTTGAAATAATCAA
1 GTGCTTAAATGGTTGGTGTTGAAATAATCAA
56525493 GTG
1 GTG
56525496 AAAGTATATG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.31, C:0.06, G:0.28, T:0.35
Consensus pattern (31 bp):
GTGCTTAAATGGTTGGTGTTGAAATAATCAA
Found at i:56529080 original size:34 final size:33
Alignment explanation
Indices: 56528987--56529080 Score: 127
Period size: 34 Copynumber: 2.8 Consensus size: 33
56528977 GTGAATACAT
* *
56528987 TCTGGGCCTAAGCCCATATT-AGTAACAGTAGCAG
1 TCTGGG-CTTAGCCCAT-TTCAGTAATAGTAGCAG
56529021 TCTGGGGCTTAGCCCATTTCAGTAATAGTAGCAG
1 TCT-GGGCTTAGCCCATTTCAGTAATAGTAGCAG
56529055 TCTGGGCTTTAGCCCATTTCAGTAAT
1 TCTGGGC-TTAGCCCATTTCAGTAAT
56529081 CGTAATCAGT
Statistics
Matches: 55, Mismatches: 2, Indels: 6
0.87 0.03 0.10
Matches are distributed among these distances:
33 6 0.11
34 46 0.84
35 3 0.05
ACGTcount: A:0.24, C:0.22, G:0.23, T:0.30
Consensus pattern (33 bp):
TCTGGGCTTAGCCCATTTCAGTAATAGTAGCAG
Found at i:56529132 original size:18 final size:19
Alignment explanation
Indices: 56529082--56529132 Score: 61
Period size: 18 Copynumber: 2.8 Consensus size: 19
56529072 TTCAGTAATC
56529082 GTAATCAGTGTAGTAACCA
1 GTAATCAGTGTAGTAACCA
* *
56529101 -TGATCAATGTAGTAA-CA
1 GTAATCAGTGTAGTAACCA
*
56529118 GTAATCAGTGCAGTA
1 GTAATCAGTGTAGTA
56529133 TGCAAGCAGA
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
17 2 0.08
18 24 0.92
ACGTcount: A:0.37, C:0.14, G:0.22, T:0.27
Consensus pattern (19 bp):
GTAATCAGTGTAGTAACCA
Found at i:56529411 original size:23 final size:23
Alignment explanation
Indices: 56529385--56529434 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 23
56529375 ACCCCATGCA
56529385 ATGCAACATA-ATATTATACATGG-
1 ATGCAACATACATA-TA-ACATGGC
56529408 ATGCAACATACATATAACATGGC
1 ATGCAACATACATATAACATGGC
56529431 ATGC
1 ATGC
56529435 TCGAATACAG
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
22 6 0.24
23 16 0.64
24 3 0.12
ACGTcount: A:0.42, C:0.18, G:0.14, T:0.26
Consensus pattern (23 bp):
ATGCAACATACATATAACATGGC
Found at i:56529527 original size:27 final size:27
Alignment explanation
Indices: 56529469--56529584 Score: 81
Period size: 27 Copynumber: 4.3 Consensus size: 27
56529459 GAACAAATCT
* ** **
56529469 GTCATTTTACCTTACCGGGGTATTAAA
1 GTCATTTTACCCTACAAGGGTATTTCA
*
56529496 ATCATTTTACCCTACAAGGGTATTTCA
1 GTCATTTTACCCTACAAGGGTATTTCA
* *** * *
56529523 GTCATTCTA-CCTTGTAGGGCATTTCG
1 GTCATTTTACCCTACAAGGGTATTTCA
** * *
56529549 GTCATTTTACCCTATGAGTGTATTTCG
1 GTCATTTTACCCTACAAGGGTATTTCA
56529576 GTCATTTTA
1 GTCATTTTA
56529585 TCACATAAGG
Statistics
Matches: 69, Mismatches: 19, Indels: 2
0.77 0.21 0.02
Matches are distributed among these distances:
26 20 0.29
27 49 0.71
ACGTcount: A:0.22, C:0.20, G:0.17, T:0.41
Consensus pattern (27 bp):
GTCATTTTACCCTACAAGGGTATTTCA
Found at i:56529606 original size:27 final size:27
Alignment explanation
Indices: 56529576--56529916 Score: 447
Period size: 27 Copynumber: 12.7 Consensus size: 27
56529566 GTGTATTTCG
* *
56529576 GTCATTTTATCACATAAGGGCCAAATC
1 GTCATTTTATCACATGAGGGCAAAATC
* * *
56529603 GTCATTTTATCACATAAGGGCCAAATT
1 GTCATTTTATCACATGAGGGCAAAATC
* *
56529630 TTCATTTTAACACATGAGGGCAAAATC
1 GTCATTTTATCACATGAGGGCAAAATC
*
56529657 -TCCATTTTATCACATG-GGACAAAATC
1 GT-CATTTTATCACATGAGGGCAAAATC
* * *
56529683 GTCATTTTATCACATAAAGGTAAAATC
1 GTCATTTTATCACATGAGGGCAAAATC
* * *
56529710 ATCATTTTATCAC--GAGGGAAAAATA
1 GTCATTTTATCACATGAGGGCAAAATC
* *
56529735 GTCATTTTATCATATGAGGGAAAAATC
1 GTCATTTTATCACATGAGGGCAAAATC
*
56529762 GTCATTTTATCACATGAGGGCAAAATA
1 GTCATTTTATCACATGAGGGCAAAATC
*
56529789 GTCATTTTATCACATGAGGGCAAAATA
1 GTCATTTTATCACATGAGGGCAAAATC
56529816 GTCATTTTATCACATGAGGGCAAAATC
1 GTCATTTTATCACATGAGGGCAAAATC
56529843 GTCATTTTATCACATGAGGGCAAAATC
1 GTCATTTTATCACATGAGGGCAAAATC
* *
56529870 ATCATTTTATCACATGAGGGAAAAATC
1 GTCATTTTATCACATGAGGGCAAAATC
* *
56529897 TTCATTTTATCAAATGAGGG
1 GTCATTTTATCACATGAGGG
56529917 TTCAAGTACG
Statistics
Matches: 281, Mismatches: 28, Indels: 10
0.88 0.09 0.03
Matches are distributed among these distances:
25 19 0.07
26 23 0.08
27 239 0.85
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.31
Consensus pattern (27 bp):
GTCATTTTATCACATGAGGGCAAAATC
Found at i:56537596 original size:40 final size:41
Alignment explanation
Indices: 56537541--56537642 Score: 127
Period size: 40 Copynumber: 2.5 Consensus size: 41
56537531 AAAACTATCT
56537541 CAATATTGCACACTTAGTGCCACATATAGCCGAAGCTA-TTC
1 CAAT-TTGCACACTTAGTGCCACATATAGCCGAAGCTATTTC
* ** *
56537582 CAATTTGCACACTTAGTGCTATTTATAGTCGAAGCTATTTC
1 CAATTTGCACACTTAGTGCCACATATAGCCGAAGCTATTTC
* *
56537623 AAATCT-CACACTTAGTGCCA
1 CAATTTGCACACTTAGTGCCA
56537643 AACATAGTCT
Statistics
Matches: 53, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
40 42 0.79
41 11 0.21
ACGTcount: A:0.30, C:0.25, G:0.14, T:0.31
Consensus pattern (41 bp):
CAATTTGCACACTTAGTGCCACATATAGCCGAAGCTATTTC
Found at i:56540353 original size:27 final size:27
Alignment explanation
Indices: 56540321--56540382 Score: 88
Period size: 27 Copynumber: 2.3 Consensus size: 27
56540311 TAGTGTAGCC
56540321 AAATTACCGAAATACCCCTGTAGGGTA
1 AAATTACCGAAATACCCCTGTAGGGTA
* * * *
56540348 GAATTACCGAGATACCCTTGTGGGGTA
1 AAATTACCGAAATACCCCTGTAGGGTA
56540375 AAATTACC
1 AAATTACC
56540383 ATTTTTCCCT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.34, C:0.21, G:0.21, T:0.24
Consensus pattern (27 bp):
AAATTACCGAAATACCCCTGTAGGGTA
Found at i:56540692 original size:24 final size:25
Alignment explanation
Indices: 56540585--56540679 Score: 145
Period size: 25 Copynumber: 3.8 Consensus size: 25
56540575 AGGAAGTGCT
* * * *
56540585 AAAAGGGCTATGCCCCAATTTACCG
1 AAAAGGGCTTTGCCCCAGTTTATCA
56540610 AAAAGGGCTTTGCCCCAGTTTATCA
1 AAAAGGGCTTTGCCCCAGTTTATCA
*
56540635 AAAAGGGCTTTGCCCTAGTTTATCA
1 AAAAGGGCTTTGCCCCAGTTTATCA
56540660 AAAAGGGCTTTGCCCCAGTT
1 AAAAGGGCTTTGCCCCAGTT
56540680 ATTAAAAGAG
Statistics
Matches: 64, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 64 1.00
ACGTcount: A:0.28, C:0.24, G:0.21, T:0.26
Consensus pattern (25 bp):
AAAAGGGCTTTGCCCCAGTTTATCA
Found at i:56540703 original size:50 final size:50
Alignment explanation
Indices: 56540585--56540704 Score: 136
Period size: 50 Copynumber: 2.4 Consensus size: 50
56540575 AGGAAGTGCT
* * * * *
56540585 AAAAGGGCTATGCCCCAATTTACCGAAAAGGGCTTTGCCCCAGTTTATCA
1 AAAAGGGCTAGGCCCTAGTTTATCAAAAAGGGCTTTGCCCCAGTTTATCA
** *
56540635 AAAAGGGCTTTGCCCTAGTTTATCAAAAAGGGCTTTGCCCCAG-TTAT-T
1 AAAAGGGCTAGGCCCTAGTTTATCAAAAAGGGCTTTGCCCCAGTTTATCA
56540683 AAAAGAGGCTAGGCCTCTAGTT
1 AAAAG-GGCTAGGCC-CTAGTT
56540705 ATATGATAAA
Statistics
Matches: 60, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
48 5 0.08
49 11 0.18
50 44 0.73
ACGTcount: A:0.29, C:0.23, G:0.22, T:0.27
Consensus pattern (50 bp):
AAAAGGGCTAGGCCCTAGTTTATCAAAAAGGGCTTTGCCCCAGTTTATCA
Found at i:56546510 original size:30 final size:29
Alignment explanation
Indices: 56546454--56546517 Score: 92
Period size: 30 Copynumber: 2.2 Consensus size: 29
56546444 ATGAATCGAA
***
56546454 AGCTTTGGCACTAAGTGTGTGGTTTAAACT
1 AGCTTTGGCACTAAGTGTGCAATTT-AACT
56546484 AGCTTTGGCACTAAGTGTGCAATTTAACT
1 AGCTTTGGCACTAAGTGTGCAATTTAACT
56546513 AGCTT
1 AGCTT
56546518 CGGCTACTTG
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
29 9 0.29
30 22 0.71
ACGTcount: A:0.25, C:0.16, G:0.23, T:0.36
Consensus pattern (29 bp):
AGCTTTGGCACTAAGTGTGCAATTTAACT
Found at i:56548506 original size:29 final size:29
Alignment explanation
Indices: 56548449--56548530 Score: 121
Period size: 29 Copynumber: 2.9 Consensus size: 29
56548439 CCTGTATATT
* *
56548449 GCCCACTAGGCCC-AATCACATTTATATG
1 GCCCATTAGGCCCAAATCACATTTACATG
56548477 GCCCATTAGGCCCAAATCACATTTACATG
1 GCCCATTAGGCCCAAATCACATTTACATG
* *
56548506 GCCCATCAGGCCCAATTCACATTTA
1 GCCCATTAGGCCCAAATCACATTTA
56548531 TAGTCATGCT
Statistics
Matches: 49, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
28 12 0.24
29 37 0.76
ACGTcount: A:0.29, C:0.33, G:0.13, T:0.24
Consensus pattern (29 bp):
GCCCATTAGGCCCAAATCACATTTACATG
Found at i:56552378 original size:17 final size:17
Alignment explanation
Indices: 56552356--56552405 Score: 55
Period size: 17 Copynumber: 2.8 Consensus size: 17
56552346 ATTCATAAGC
56552356 AAATAAACAAATTAATA
1 AAATAAACAAATTAATA
* * *
56552373 AAATAATCAAATCATTA
1 AAATAAACAAATTAATA
56552390 AAATTAAACCAAATTA
1 AAA-TAAA-CAAATTA
56552406 TACTATCATA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
17 17 0.65
18 3 0.12
19 6 0.23
ACGTcount: A:0.64, C:0.10, G:0.00, T:0.26
Consensus pattern (17 bp):
AAATAAACAAATTAATA
Found at i:56561478 original size:50 final size:50
Alignment explanation
Indices: 56561402--56561577 Score: 241
Period size: 49 Copynumber: 3.5 Consensus size: 50
56561392 CCATGGCAAC
*
56561402 AAGTGATAAGTGATAGCTTCGACTACACTTATTTGATCAAGGACAAATGA
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATTTGATCAAGGACAAATGA
* *
56561452 AAGTGATAAGTAATTA-CTTCGGCTACA-TTATCTT-ATCAAGGACAAGTGA
1 AAGTGATAAGTGA-TAGCTTCGGCTACACTTAT-TTGATCAAGGACAAATGA
* *
56561501 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTACAAATGA
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATTTGATCAAGGACAAATGA
* *
56561551 CAAGTGAAAAGTGGTAGCTTCGGCTAC
1 -AAGTGATAAGTGATAGCTTCGGCTAC
56561578 CTGATCAGTG
Statistics
Matches: 111, Mismatches: 9, Indels: 11
0.85 0.07 0.08
Matches are distributed among these distances:
48 2 0.02
49 42 0.38
50 41 0.37
51 26 0.23
ACGTcount: A:0.36, C:0.15, G:0.21, T:0.28
Consensus pattern (50 bp):
AAGTGATAAGTGATAGCTTCGGCTACACTTATTTGATCAAGGACAAATGA
Found at i:56561507 original size:49 final size:50
Alignment explanation
Indices: 56561402--56561577 Score: 241
Period size: 50 Copynumber: 3.5 Consensus size: 50
56561392 CCATGGCAAC
*
56561402 AAGTGATAAGTGATAGCTTCGACTACACTTAT-TTGATCAAGGACAAATGA
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTT-ATCAAGGACAAATGA
* *
56561452 AAGTGATAAGTAATTA-CTTCGGCTACA-TTATCTTATCAAGGACAAGTGA
1 AAGTGATAAGTGA-TAGCTTCGGCTACACTTATCTTATCAAGGACAAATGA
* *
56561501 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTACAAATGA
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTTATCAAGGACAAATGA
* *
56561551 CAAGTGAAAAGTGGTAGCTTCGGCTAC
1 -AAGTGATAAGTGATAGCTTCGGCTAC
56561578 CTGATCAGTG
Statistics
Matches: 112, Mismatches: 9, Indels: 9
0.86 0.07 0.07
Matches are distributed among these distances:
48 2 0.02
49 41 0.37
50 43 0.38
51 26 0.23
ACGTcount: A:0.36, C:0.15, G:0.21, T:0.28
Consensus pattern (50 bp):
AAGTGATAAGTGATAGCTTCGGCTACACTTATCTTATCAAGGACAAATGA
Found at i:56561591 original size:31 final size:31
Alignment explanation
Indices: 56561553--56561639 Score: 129
Period size: 31 Copynumber: 2.8 Consensus size: 31
56561543 ACAAATGACA
56561553 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
* * *
56561584 AGTGAAAAATGGTAGCTCCGGCTACCTGATT
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
* *
56561615 AGTGAATAGTGGTAGCTTCAGCTAC
1 AGTGAAAAGTGGTAGCTTCGGCTAC
56561640 ATGTGACAAG
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 49 1.00
ACGTcount: A:0.28, C:0.18, G:0.28, T:0.26
Consensus pattern (31 bp):
AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
Found at i:56561806 original size:49 final size:47
Alignment explanation
Indices: 56561740--56561912 Score: 206
Period size: 42 Copynumber: 3.9 Consensus size: 47
56561730 AATTAGTGAG
56561740 ATGTGATTCGTGTAAGACCATAGCTGGGCTATGGCATCGATATATGA
1 ATGTGATTCGTGTAAGACCATAGCTGGGCTATGGCATCGATATATGA
56561787 TATGTGATTACGTGTAAGACCATAGCTGGGCTATGGCATCGATATATGA
1 -ATGTGATT-CGTGTAAGACCATAGCTGGGCTATGGCATCGATATATGA
56561836 A--T-A-T-GTGTAAGACCATAGCTGGGCTATGGCATC-AT-TATG-
1 ATGTGATTCGTGTAAGACCATAGCTGGGCTATGGCATCGATATATGA
* * **
56561875 -TGAAGA-T-ATGTAAGACCATAGCTGAACTATGGCATCGA
1 ATG-TGATTCGTGTAAGACCATAGCTGGGCTATGGCATCGA
56561913 GAAAATGAAG
Statistics
Matches: 115, Mismatches: 4, Indels: 17
0.85 0.03 0.12
Matches are distributed among these distances:
40 4 0.03
41 2 0.02
42 57 0.50
43 1 0.01
44 1 0.01
45 1 0.01
46 1 0.01
48 9 0.08
49 39 0.34
ACGTcount: A:0.30, C:0.15, G:0.26, T:0.29
Consensus pattern (47 bp):
ATGTGATTCGTGTAAGACCATAGCTGGGCTATGGCATCGATATATGA
Found at i:56564714 original size:28 final size:29
Alignment explanation
Indices: 56564671--56564785 Score: 110
Period size: 29 Copynumber: 4.0 Consensus size: 29
56564661 TACCTGTATC
** *
56564671 TGGCCCATTAAACCC-AATCATATTCATA
1 TGGCCCATTAGGCCCAAATCACATTCATA
*
56564699 TGGCCCATTAGGCCCAAATCACCTAT-ATA
1 TGGCCCATTAGGCCCAAATCACAT-TCATA
* * *
56564728 TGGTCCAATAGGCCCAAATCACATTTATA
1 TGGCCCATTAGGCCCAAATCACATTCATA
* * *
56564757 TGGCTCGTTAGGCCC-AGTCACATTCATA
1 TGGCCCATTAGGCCCAAATCACATTCATA
56564785 T
1 T
56564786 TCATGCTCAC
Statistics
Matches: 71, Mismatches: 13, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
28 26 0.37
29 44 0.62
30 1 0.01
ACGTcount: A:0.30, C:0.28, G:0.14, T:0.28
Consensus pattern (29 bp):
TGGCCCATTAGGCCCAAATCACATTCATA
Found at i:56565022 original size:16 final size:16
Alignment explanation
Indices: 56565003--56565033 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
56564993 AACTTTCAGC
56565003 TTTTCGGCATTTCAAT
1 TTTTCGGCATTTCAAT
*
56565019 TTTTCGGTATTTCAA
1 TTTTCGGCATTTCAA
56565034 AATTTTGGGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.19, C:0.16, G:0.13, T:0.52
Consensus pattern (16 bp):
TTTTCGGCATTTCAAT
Found at i:56572423 original size:29 final size:29
Alignment explanation
Indices: 56572325--56572439 Score: 117
Period size: 29 Copynumber: 4.0 Consensus size: 29
56572315 TAACTGTATC
* * * *
56572325 TGGCCCATTAAGCCC-AATCATAATCATA
1 TGGCCCATTAGGCCCAAATCACATTTATA
* * *
56572353 TGGCCCATTAGGACCAAATCACCTATATA
1 TGGCCCATTAGGCCCAAATCACATTTATA
*
56572382 TGGTCCATTAGGCCCAAATCACATTTATA
1 TGGCCCATTAGGCCCAAATCACATTTATA
* * *
56572411 TGGCCCGTTAGGCCC-AGTCACATTCATA
1 TGGCCCATTAGGCCCAAATCACATTTATA
56572439 T
1 T
56572440 TCATTTTCAC
Statistics
Matches: 71, Mismatches: 15, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
28 25 0.35
29 46 0.65
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (29 bp):
TGGCCCATTAGGCCCAAATCACATTTATA
Found at i:56572683 original size:16 final size:16
Alignment explanation
Indices: 56572664--56572694 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
56572654 AAATTTTTGG
56572664 CATTTCGGCATTTCAA
1 CATTTCGGCATTTCAA
*
56572680 CATTTCGGTATTTCA
1 CATTTCGGCATTTCA
56572695 GATTTTGCCG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.23, C:0.23, G:0.13, T:0.42
Consensus pattern (16 bp):
CATTTCGGCATTTCAA
Found at i:56588316 original size:29 final size:29
Alignment explanation
Indices: 56588281--56588359 Score: 106
Period size: 29 Copynumber: 2.8 Consensus size: 29
56588271 AGGAATAGAT
*
56588281 TTGGCTTGGGGCCATGCATATTGAATATG
1 TTGGCTTCGGGCCATGCATATTGAATATG
* * *
56588310 TTGGCTTCGGGCCATGCATATCGCATGTG
1 TTGGCTTCGGGCCATGCATATTGAATATG
*
56588339 TTGGCTTCGAGCCATG-ATATT
1 TTGGCTTCGGGCCATGCATATT
56588360 AGCACTTTAG
Statistics
Matches: 44, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
28 4 0.09
29 40 0.91
ACGTcount: A:0.18, C:0.19, G:0.29, T:0.34
Consensus pattern (29 bp):
TTGGCTTCGGGCCATGCATATTGAATATG
Found at i:56593353 original size:47 final size:46
Alignment explanation
Indices: 56593285--56593416 Score: 219
Period size: 47 Copynumber: 2.8 Consensus size: 46
56593275 GTTGAATTTA
* *
56593285 AAGCTTGTTCAATTGCTCTTAATATTTCCGGATAAGTTACTTAGTT
1 AAGCTTGTTAAATTGCTCTTAATATTTCCGGACAAGTTACTTAGTT
56593331 AAGCTTGTTAAATCTGCTCTTAATATTTCCGGACAAGTTACTTAGTT
1 AAGCTTGTTAAAT-TGCTCTTAATATTTCCGGACAAGTTACTTAGTT
*
56593378 AAGCTTGTTAAATTTGCTCTTAATATATCCGGACAAGTT
1 AAGCTTGTTAAA-TTGCTCTTAATATTTCCGGACAAGTT
56593417 TGTAACATCC
Statistics
Matches: 81, Mismatches: 3, Indels: 3
0.93 0.03 0.03
Matches are distributed among these distances:
46 12 0.15
47 68 0.84
48 1 0.01
ACGTcount: A:0.28, C:0.16, G:0.15, T:0.41
Consensus pattern (46 bp):
AAGCTTGTTAAATTGCTCTTAATATTTCCGGACAAGTTACTTAGTT
Found at i:56596884 original size:45 final size:44
Alignment explanation
Indices: 56596820--56596935 Score: 155
Period size: 45 Copynumber: 2.6 Consensus size: 44
56596810 CGCACAGTAT
*
56596820 TATTCGGGCCTTTGAGCCTAGCAGGCTATAATGTCGGTGAGAT-A
1 TATTCGGG-CTTTGAGCCTAGCAGGCTATAATGTCGGTGAAATGA
56596864 CTATTCGGGCTTTCGAGCCTAGCAGGCTATAATGTCGGTGAAATGA
1 -TATTCGGGCTTT-GAGCCTAGCAGGCTATAATGTCGGTGAAATGA
* *
56596910 TA-TCGGGCTTTTAAACCTAGCAGGCT
1 TATTCGGGC-TTTGAGCCTAGCAGGCT
56596936 GAATGTCAGT
Statistics
Matches: 65, Mismatches: 3, Indels: 7
0.87 0.04 0.09
Matches are distributed among these distances:
44 22 0.34
45 42 0.65
46 1 0.02
ACGTcount: A:0.23, C:0.20, G:0.28, T:0.29
Consensus pattern (44 bp):
TATTCGGGCTTTGAGCCTAGCAGGCTATAATGTCGGTGAAATGA
Found at i:56602422 original size:47 final size:47
Alignment explanation
Indices: 56602350--56602491 Score: 225
Period size: 47 Copynumber: 3.0 Consensus size: 47
56602340 GTTGAATTTA
56602350 AAGCTTGTTAAA-TTGCTCTTAATATTTCTGGATCAGTTACTTAGTT
1 AAGCTTGTTAAATTTGCTCTTAATATTTCTGGATCAGTTACTTAGTT
*
56602396 AAGCTTGTTAAATTTGCTCTTAATATTTCCGGA-CAAGTTACTTAGTT
1 AAGCTTGTTAAATTTGCTCTTAATATTTCTGGATC-AGTTACTTAGTT
* * *
56602443 AAGCTTGTTAAATTTGCCCTTAATATTTGTGGATAAGTTACTTAGTT
1 AAGCTTGTTAAATTTGCTCTTAATATTTCTGGATCAGTTACTTAGTT
56602490 AA
1 AA
56602492 AGAAAATCTT
Statistics
Matches: 88, Mismatches: 5, Indels: 5
0.90 0.05 0.05
Matches are distributed among these distances:
46 13 0.15
47 75 0.85
ACGTcount: A:0.28, C:0.13, G:0.15, T:0.44
Consensus pattern (47 bp):
AAGCTTGTTAAATTTGCTCTTAATATTTCTGGATCAGTTACTTAGTT
Found at i:56607763 original size:31 final size:31
Alignment explanation
Indices: 56607723--56607805 Score: 143
Period size: 31 Copynumber: 2.7 Consensus size: 31
56607713 TCAGTCTCGA
56607723 CATA-TACTGGGCCGAAGCCTTTTCATAAAT
1 CATATTACTGGGCCGAAGCCTTTTCATAAAT
56607753 CATATTACTGGGCCGAAGCCTTTTCATAAAT
1 CATATTACTGGGCCGAAGCCTTTTCATAAAT
*
56607784 CATATCACT-GGCCGAAGCCTTT
1 CATATTACTGGGCCGAAGCCTTT
56607806 ACTGTAAGCG
Statistics
Matches: 51, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
30 17 0.33
31 34 0.67
ACGTcount: A:0.28, C:0.25, G:0.17, T:0.30
Consensus pattern (31 bp):
CATATTACTGGGCCGAAGCCTTTTCATAAAT
Found at i:56608063 original size:25 final size:25
Alignment explanation
Indices: 56608031--56608094 Score: 92
Period size: 25 Copynumber: 2.6 Consensus size: 25
56608021 TTAATAACGG
*
56608031 GGCAAAGCCCTTTTTGATAAACTGC
1 GGCAAAGCCCTTTTCGATAAACTGC
* *
56608056 GGCAAAGCCCTTTTCGGTAAACTGG
1 GGCAAAGCCCTTTTCGATAAACTGC
*
56608081 GGCATAGCCCTTTT
1 GGCAAAGCCCTTTT
56608095 AGCACTTCCT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 35 1.00
ACGTcount: A:0.23, C:0.25, G:0.23, T:0.28
Consensus pattern (25 bp):
GGCAAAGCCCTTTTCGATAAACTGC
Found at i:56608336 original size:27 final size:27
Alignment explanation
Indices: 56608297--56608540 Score: 265
Period size: 27 Copynumber: 9.0 Consensus size: 27
56608287 GGGGCAAAAT
* * *
56608297 GGTAATTTTTACCCCACAAGGGTATCTC
1 GGTAA-TTCTACCCTACAAGGGTATTTC
* ***
56608325 GGCAATTCTACCCTATTGGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
* *
56608352 GGTATTTTTACCCTACAAGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
* *
56608379 GGTAATTCTACCCTACAGGGGTATTTT
1 GGTAATTCTACCCTACAAGGGTATTTC
*
56608406 AGTAATTCTACCCTACAAGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
* *
56608433 GGTAATTCTACCCTA-TAGGGTTGTTTC
1 GGTAATTCTACCCTACAAGGG-TATTTC
* * * *
56608460 AGTAATTCTACCCAATAGGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
* *
56608487 GGTAATTCTACTCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
* *
56608514 GATAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
56608541 AATATTTTAC
Statistics
Matches: 180, Mismatches: 34, Indels: 5
0.82 0.16 0.02
Matches are distributed among these distances:
26 4 0.02
27 169 0.94
28 7 0.04
ACGTcount: A:0.24, C:0.20, G:0.20, T:0.36
Consensus pattern (27 bp):
GGTAATTCTACCCTACAAGGGTATTTC
Found at i:56608364 original size:54 final size:54
Alignment explanation
Indices: 56608306--56608540 Score: 301
Period size: 54 Copynumber: 4.4 Consensus size: 54
56608296 TGGTAATTTT
* * * ** * * *
56608306 TACCCCACAAGGGTATCTCGGCAATTCTACCCTATTGGGGTATTTCGGTATTTT
1 TACCCTACAAGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTCAGTAATTC
*
56608360 TACCCTACAAGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTTAGTAATTC
1 TACCCTACAAGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTCAGTAATTC
* * *
56608414 TACCCTACAAGGGTATTTCGGTAATTCTACCCTATAGGGTTGTTTCAGTAATTC
1 TACCCTACAAGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTCAGTAATTC
* * * *
56608468 TACCCAATAGGGGTATTTCGGTAATTCTACTCTACAGGGGTATTTC-GATAATTC
1 TACCCTACAAGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTCAG-TAATTC
*
56608522 TACCCTACAGGGGTATTTC
1 TACCCTACAAGGGTATTTC
56608541 AATATTTTAC
Statistics
Matches: 158, Mismatches: 22, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
53 1 0.01
54 157 0.99
ACGTcount: A:0.24, C:0.21, G:0.20, T:0.35
Consensus pattern (54 bp):
TACCCTACAAGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTCAGTAATTC
Found at i:56608589 original size:26 final size:26
Alignment explanation
Indices: 56608532--56608591 Score: 77
Period size: 26 Copynumber: 2.3 Consensus size: 26
56608522 TACCCTACAG
*
56608532 GGGTATTTCAATATTTTACAAATCGA
1 GGGTATTTCAATATTTCACAAATCGA
* *
56608558 GAGTATTTCGATAATTTCACAAATC-A
1 GGGTATTTCAAT-ATTTCACAAATCGA
56608584 GGGTATTT
1 GGGTATTT
56608592 TGGTAATCTT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
26 18 0.62
27 11 0.38
ACGTcount: A:0.33, C:0.12, G:0.17, T:0.38
Consensus pattern (26 bp):
GGGTATTTCAATATTTCACAAATCGA
Found at i:56608598 original size:26 final size:27
Alignment explanation
Indices: 56608544--56608750 Score: 130
Period size: 27 Copynumber: 7.7 Consensus size: 27
56608534 GTATTTCAAT
* * *
56608544 ATTTTACAAATCGAGAGTATTTCGATA
1 ATTTTACAAATCGAGGGTATTTTGGTA
*
56608571 ATTTCACAAATC-AGGGTATTTTGGTA
1 ATTTTACAAATCGAGGGTATTTTGGTA
* * *
56608597 ATCTTAC-AAGCTAGGGCTATTTTGGTA
1 ATTTTACAAATCGAGGG-TATTTTGGTA
***
56608624 ATTTTATTGATCGAGGGTATTTTGGTA
1 ATTTTACAAATCGAGGGTATTTTGGTA
** * * * *
56608651 ATTTTGTAAACCAAGGGTATTGTAGTA
1 ATTTTACAAATCGAGGGTATTTTGGTA
** ***
56608678 ATTTTGTAAATCGAGGGTAAAATGGTA
1 ATTTTACAAATCGAGGGTATTTTGGTA
* * *** *
56608705 ATTCTATAAATCGAGGGTAAAATGATA
1 ATTTTACAAATCGAGGGTATTTTGGTA
* *
56608732 ATTCTATAAATCGAGGGTA
1 ATTTTACAAATCGAGGGTA
56608751 AAACAGTAAT
Statistics
Matches: 149, Mismatches: 28, Indels: 6
0.81 0.15 0.03
Matches are distributed among these distances:
25 3 0.02
26 20 0.13
27 120 0.81
28 6 0.04
ACGTcount: A:0.33, C:0.09, G:0.21, T:0.37
Consensus pattern (27 bp):
ATTTTACAAATCGAGGGTATTTTGGTA
Found at i:56608704 original size:54 final size:52
Alignment explanation
Indices: 56608646--56608804 Score: 156
Period size: 54 Copynumber: 2.9 Consensus size: 52
56608636 GAGGGTATTT
* * * * * *
56608646 TGGTAATTTTGTAAACCAAGGGTATTGTAGTAATTTTGTAAATCGAGGGTAAAA
1 TGGTAATTCTATAAATCAAGGGTAATG-A-TAATTCTATAAATCGAGGGTAAAA
*
56608700 TGGTAATTCTATAAATCGAGGGTAAAATGATAATTCTATAAATCGAGGGTAAAA
1 TGGTAATTCTATAAATCAAGGGT--AATGATAATTCTATAAATCGAGGGTAAAA
** ** *
56608754 CAGTAATTCTATAAATCAAGGGTAAAACAGTAATTCTATAAATCGATGGTA
1 TGGTAATTCTATAAATCAAGGGT-AATGA-TAATTCTATAAATCGAGGGTA
56608805 CTTTGGTAAT
Statistics
Matches: 89, Mismatches: 13, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
53 4 0.04
54 81 0.91
55 1 0.01
56 3 0.03
ACGTcount: A:0.40, C:0.08, G:0.20, T:0.31
Consensus pattern (52 bp):
TGGTAATTCTATAAATCAAGGGTAATGATAATTCTATAAATCGAGGGTAAAA
Found at i:56608718 original size:81 final size:81
Alignment explanation
Indices: 56608619--56608818 Score: 202
Period size: 81 Copynumber: 2.5 Consensus size: 81
56608609 AGGGCTATTT
* ** * * **** * *
56608619 TGGTAATTTTATTGATCGAGGGTATTTTGGTAATTTTGTAAACCAAGGGTATTGTAGTAATTTTG
1 TGGTAATTCTATAAATCGAGGGTAATTTGGTAATTTTATAAACCAAGGGTAAAACAGTAATTCTA
*
56608684 TAAATCGAGGGTAAAA
66 TAAATCAAGGGTAAAA
** * * * *
56608700 TGGTAATTCTATAAATCGAGGGTAAAATGATAATTCTATAAATCGAGGGTAAAACAGTAATTCTA
1 TGGTAATTCTATAAATCGAGGGTAATTTGGTAATTTTATAAACCAAGGGTAAAACAGTAATTCTA
56608765 TAAATCAAGGGTAAAA
66 TAAATCAAGGGTAAAA
** * *
56608781 CAGTAATTCTATAAATCGATGGTACTTTGGTAATTTTA
1 TGGTAATTCTATAAATCGAGGGTAATTTGGTAATTTTA
56608819 CAAGTCGAGG
Statistics
Matches: 93, Mismatches: 26, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
81 93 1.00
ACGTcount: A:0.36, C:0.07, G:0.20, T:0.35
Consensus pattern (81 bp):
TGGTAATTCTATAAATCGAGGGTAATTTGGTAATTTTATAAACCAAGGGTAAAACAGTAATTCTA
TAAATCAAGGGTAAAA
Found at i:56608751 original size:27 final size:27
Alignment explanation
Indices: 56608674--56608804 Score: 183
Period size: 27 Copynumber: 4.9 Consensus size: 27
56608664 AGGGTATTGT
* * *
56608674 AGTAATTTTGTAAATCGAGGGTAAAAT
1 AGTAATTCTATAAATCGAGGGTAAAAC
*
56608701 GGTAATTCTATAAATCGAGGGTAAAA-
1 AGTAATTCTATAAATCGAGGGTAAAAC
*
56608727 TGATAATTCTATAAATCGAGGGTAAAAC
1 AG-TAATTCTATAAATCGAGGGTAAAAC
*
56608755 AGTAATTCTATAAATCAAGGGTAAAAC
1 AGTAATTCTATAAATCGAGGGTAAAAC
*
56608782 AGTAATTCTATAAATCGATGGTA
1 AGTAATTCTATAAATCGAGGGTA
56608805 CTTTGGTAAT
Statistics
Matches: 94, Mismatches: 8, Indels: 4
0.89 0.08 0.04
Matches are distributed among these distances:
26 1 0.01
27 92 0.98
28 1 0.01
ACGTcount: A:0.43, C:0.08, G:0.19, T:0.30
Consensus pattern (27 bp):
AGTAATTCTATAAATCGAGGGTAAAAC
Found at i:56616325 original size:44 final size:44
Alignment explanation
Indices: 56616277--56616379 Score: 170
Period size: 44 Copynumber: 2.3 Consensus size: 44
56616267 ATTGAGATGG
* *
56616277 CACTAAGTGTGCAAGATTGTAACAGCTTTGGCTAATCATTAATA
1 CACTAAGTGTGCAAGATCGTAACAGCTTTGACTAATCATTAATA
* *
56616321 CACTAAGTGTGCGAGATCGTAACAGCTTTGACTAATCATTAATG
1 CACTAAGTGTGCAAGATCGTAACAGCTTTGACTAATCATTAATA
56616365 CACTAAGTGTGCAAG
1 CACTAAGTGTGCAAG
56616380 CTCTTAAAGT
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
44 54 1.00
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.29
Consensus pattern (44 bp):
CACTAAGTGTGCAAGATCGTAACAGCTTTGACTAATCATTAATA
Found at i:56620170 original size:40 final size:39
Alignment explanation
Indices: 56620087--56620200 Score: 106
Period size: 40 Copynumber: 2.8 Consensus size: 39
56620077 ATGATCTCGT
* **
56620087 ACACTTAGTGCCATCACATTAAACCGAAGCTATATCGTATCAC
1 ACACTTAGTGCC-TCATA-T-AACCGAAGCTAT-TCCAATCAC
56620130 ACACTTAGTGCCTCATATAACCGAAGCTATTCCAATTCAC
1 ACACTTAGTGCCTCATATAACCGAAGCTATTCCAA-TCAC
* *
56620170 ACACTAAGTG--TTATATATAGCCGAAGCTATT
1 ACACTTAGTGCCTCATATA-A-CCGAAGCTATT
56620201 TTGAAACACA
Statistics
Matches: 63, Mismatches: 5, Indels: 9
0.82 0.06 0.12
Matches are distributed among these distances:
38 6 0.10
39 4 0.06
40 36 0.57
41 1 0.02
42 4 0.06
43 12 0.19
ACGTcount: A:0.34, C:0.25, G:0.12, T:0.28
Consensus pattern (39 bp):
ACACTTAGTGCCTCATATAACCGAAGCTATTCCAATCAC
Done.