Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr1
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: 106989029
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 3754247 characters in sequence are not A, C, G, or T
File 148 of 322
Found at i:48693592 original size:22 final size:22
Alignment explanation
Indices: 48693522--48693592 Score: 54
Period size: 22 Copynumber: 3.1 Consensus size: 22
48693512 GATAAGGCCT
*
48693522 AATGGCCGATGTGATGAAAGTG
1 AATGGCCAATGTGATGAAAGTG
** *
48693544 AAAGTGTACATATGTGAT-AAGGCTG
1 -AA-TGGCCA-ATGTGATGAAAG-TG
*
48693569 AATGGCCAATGTGATGAATGTG
1 AATGGCCAATGTGATGAAAGTG
48693591 AA
1 AA
48693593 AGTGTATATA
Statistics
Matches: 37, Mismatches: 7, Indels: 9
0.70 0.13 0.17
Matches are distributed among these distances:
22 11 0.30
23 9 0.24
24 8 0.22
25 9 0.24
ACGTcount: A:0.35, C:0.08, G:0.31, T:0.25
Consensus pattern (22 bp):
AATGGCCAATGTGATGAAAGTG
Found at i:48693688 original size:22 final size:22
Alignment explanation
Indices: 48693618--48693688 Score: 54
Period size: 22 Copynumber: 3.1 Consensus size: 22
48693608 GATAAGGCCT
*
48693618 AATGGCCGATGTGATGAAAGTG
1 AATGGCCAATGTGATGAAAGTG
** *
48693640 AAAGTGTACATATGTGAT-AAGGCTG
1 -AA-TGGCCA-ATGTGATGAAAG-TG
*
48693665 AATGGCCAATGTGATGAATGTG
1 AATGGCCAATGTGATGAAAGTG
48693687 AA
1 AA
48693689 AGTGTATATA
Statistics
Matches: 37, Mismatches: 7, Indels: 9
0.70 0.13 0.17
Matches are distributed among these distances:
22 11 0.30
23 9 0.24
24 8 0.22
25 9 0.24
ACGTcount: A:0.35, C:0.08, G:0.31, T:0.25
Consensus pattern (22 bp):
AATGGCCAATGTGATGAAAGTG
Found at i:48693784 original size:22 final size:22
Alignment explanation
Indices: 48693714--48693784 Score: 54
Period size: 22 Copynumber: 3.1 Consensus size: 22
48693704 GATAAGGCCT
*
48693714 AATGGCCGATGTGATGAAAGTG
1 AATGGCCAATGTGATGAAAGTG
** *
48693736 AAAGTGTACATATGTGAT-AAGGCTG
1 -AA-TGGCCA-ATGTGATGAAAG-TG
*
48693761 AATGGCCAATGTGATGAATGTG
1 AATGGCCAATGTGATGAAAGTG
48693783 AA
1 AA
48693785 AGTGTATATA
Statistics
Matches: 37, Mismatches: 7, Indels: 9
0.70 0.13 0.17
Matches are distributed among these distances:
22 11 0.30
23 9 0.24
24 8 0.22
25 9 0.24
ACGTcount: A:0.35, C:0.08, G:0.31, T:0.25
Consensus pattern (22 bp):
AATGGCCAATGTGATGAAAGTG
Found at i:48693880 original size:22 final size:22
Alignment explanation
Indices: 48693810--48693880 Score: 54
Period size: 22 Copynumber: 3.1 Consensus size: 22
48693800 GATAAGGCCT
*
48693810 AATGGCCGATGTGATGAAAGTG
1 AATGGCCAATGTGATGAAAGTG
** *
48693832 AAAGTGTACATATGTGAT-AAGGCTG
1 -AA-TGGCCA-ATGTGATGAAAG-TG
*
48693857 AATGGCCAATGTGATGAATGTG
1 AATGGCCAATGTGATGAAAGTG
48693879 AA
1 AA
48693881 AGTGTATATA
Statistics
Matches: 37, Mismatches: 7, Indels: 9
0.70 0.13 0.17
Matches are distributed among these distances:
22 11 0.30
23 9 0.24
24 8 0.22
25 9 0.24
ACGTcount: A:0.35, C:0.08, G:0.31, T:0.25
Consensus pattern (22 bp):
AATGGCCAATGTGATGAAAGTG
Found at i:48693976 original size:22 final size:22
Alignment explanation
Indices: 48693906--48693976 Score: 54
Period size: 22 Copynumber: 3.1 Consensus size: 22
48693896 GATAAGGCCT
*
48693906 AATGGCCGATGTGATGAAAGTG
1 AATGGCCAATGTGATGAAAGTG
** *
48693928 AAAGTGTACATATGTGAT-AAGGCTG
1 -AA-TGGCCA-ATGTGATGAAAG-TG
*
48693953 AATGGCCAATGTGATGAATGTG
1 AATGGCCAATGTGATGAAAGTG
48693975 AA
1 AA
48693977 AGTGTATATA
Statistics
Matches: 37, Mismatches: 7, Indels: 9
0.70 0.13 0.17
Matches are distributed among these distances:
22 11 0.30
23 9 0.24
24 8 0.22
25 9 0.24
ACGTcount: A:0.35, C:0.08, G:0.31, T:0.25
Consensus pattern (22 bp):
AATGGCCAATGTGATGAAAGTG
Found at i:48694072 original size:22 final size:22
Alignment explanation
Indices: 48694002--48694072 Score: 54
Period size: 22 Copynumber: 3.1 Consensus size: 22
48693992 GATAAGGCCT
*
48694002 AATGGCCGATGTGATGAAAGTG
1 AATGGCCAATGTGATGAAAGTG
** *
48694024 AAAGTGTACATATGTGAT-AAGGCTG
1 -AA-TGGCCA-ATGTGATGAAAG-TG
*
48694049 AATGGCCAATGTGATGAATGTG
1 AATGGCCAATGTGATGAAAGTG
48694071 AA
1 AA
48694073 AGTGTATATA
Statistics
Matches: 37, Mismatches: 7, Indels: 9
0.70 0.13 0.17
Matches are distributed among these distances:
22 11 0.30
23 9 0.24
24 8 0.22
25 9 0.24
ACGTcount: A:0.35, C:0.08, G:0.31, T:0.25
Consensus pattern (22 bp):
AATGGCCAATGTGATGAAAGTG
Found at i:48694168 original size:22 final size:22
Alignment explanation
Indices: 48694098--48694168 Score: 54
Period size: 22 Copynumber: 3.1 Consensus size: 22
48694088 GATAAGGCCT
*
48694098 AATGGCCGATGTGATGAAAGTG
1 AATGGCCAATGTGATGAAAGTG
** *
48694120 AAAGTGTACATATGTGAT-AAGGCTG
1 -AA-TGGCCA-ATGTGATGAAAG-TG
*
48694145 AATGGCCAATGTGATGAATGTG
1 AATGGCCAATGTGATGAAAGTG
48694167 AA
1 AA
48694169 AGTGTATATA
Statistics
Matches: 37, Mismatches: 7, Indels: 9
0.70 0.13 0.17
Matches are distributed among these distances:
22 11 0.30
23 9 0.24
24 8 0.22
25 9 0.24
ACGTcount: A:0.35, C:0.08, G:0.31, T:0.25
Consensus pattern (22 bp):
AATGGCCAATGTGATGAAAGTG
Found at i:48694264 original size:22 final size:22
Alignment explanation
Indices: 48694194--48694264 Score: 54
Period size: 22 Copynumber: 3.1 Consensus size: 22
48694184 GATAAGGCCT
*
48694194 AATGGCCGATGTGATGAAAGTG
1 AATGGCCAATGTGATGAAAGTG
** *
48694216 AAAGTGTACATATGTGAT-AAGGCTG
1 -AA-TGGCCA-ATGTGATGAAAG-TG
*
48694241 AATGGCCAATGTGATGAATGTG
1 AATGGCCAATGTGATGAAAGTG
48694263 AA
1 AA
48694265 AGTGTATATA
Statistics
Matches: 37, Mismatches: 7, Indels: 9
0.70 0.13 0.17
Matches are distributed among these distances:
22 11 0.30
23 9 0.24
24 8 0.22
25 9 0.24
ACGTcount: A:0.35, C:0.08, G:0.31, T:0.25
Consensus pattern (22 bp):
AATGGCCAATGTGATGAAAGTG
Found at i:48697341 original size:29 final size:29
Alignment explanation
Indices: 48697308--48697410 Score: 120
Period size: 29 Copynumber: 3.6 Consensus size: 29
48697298 GCCTACTAAG
* *
48697308 CCAAATCATATTCATATGGCCTATTAGGC
1 CCAAATCACATTCATATGGCCCATTAGGC
* *
48697337 CCAAATCAC-CTCTATATAGCCCATTAGGC
1 CCAAATCACATTC-ATATGGCCCATTAGGC
* * *
48697366 CCAAATCACATTTACATGGCCCGTTAGGC
1 CCAAATCACATTCATATGGCCCATTAGGC
48697395 CC-AATCACATTCATAT
1 CCAAATCACATTCATAT
48697411 TCATGCTCAC
Statistics
Matches: 61, Mismatches: 11, Indels: 5
0.79 0.14 0.06
Matches are distributed among these distances:
28 14 0.23
29 46 0.75
30 1 0.02
ACGTcount: A:0.31, C:0.30, G:0.12, T:0.27
Consensus pattern (29 bp):
CCAAATCACATTCATATGGCCCATTAGGC
Found at i:48697640 original size:8 final size:8
Alignment explanation
Indices: 48697629--48697664 Score: 54
Period size: 8 Copynumber: 4.5 Consensus size: 8
48697619 ATTTTCGGCT
48697629 TTTCAGCA
1 TTTCAGCA
*
48697637 TTTCAGCT
1 TTTCAGCA
*
48697645 TTTCAGCT
1 TTTCAGCA
48697653 TTTCAGCA
1 TTTCAGCA
48697661 TTTC
1 TTTC
48697665 GGCTTTTGCT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
8 26 1.00
ACGTcount: A:0.17, C:0.25, G:0.11, T:0.47
Consensus pattern (8 bp):
TTTCAGCA
Found at i:48697653 original size:24 final size:24
Alignment explanation
Indices: 48697620--48697671 Score: 86
Period size: 24 Copynumber: 2.2 Consensus size: 24
48697610 CGTAGCCAAA
*
48697620 TTTTCGGCTTTTCAGCATTTCAGC
1 TTTTCAGCTTTTCAGCATTTCAGC
*
48697644 TTTTCAGCTTTTCAGCATTTCGGC
1 TTTTCAGCTTTTCAGCATTTCAGC
48697668 TTTT
1 TTTT
48697672 GCTGATACAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.12, C:0.23, G:0.15, T:0.50
Consensus pattern (24 bp):
TTTTCAGCTTTTCAGCATTTCAGC
Found at i:48697671 original size:16 final size:16
Alignment explanation
Indices: 48697621--48697664 Score: 61
Period size: 16 Copynumber: 2.8 Consensus size: 16
48697611 GTAGCCAAAT
*
48697621 TTTCGGCTTTTCAGCA
1 TTTCAGCTTTTCAGCA
*
48697637 TTTCAGCTTTTCAGCT
1 TTTCAGCTTTTCAGCA
*
48697653 TTTCAGCATTTC
1 TTTCAGCTTTTC
48697665 GGCTTTTGCT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.14, C:0.25, G:0.14, T:0.48
Consensus pattern (16 bp):
TTTCAGCTTTTCAGCA
Found at i:48698906 original size:16 final size:16
Alignment explanation
Indices: 48698885--48698918 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
48698875 TAATTTTCCC
48698885 TAAAAATAGACTCATA
1 TAAAAATAGACTCATA
48698901 TAAAAATAGACTCATA
1 TAAAAATAGACTCATA
48698917 TA
1 TA
48698919 TCTTCAAACC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.56, C:0.12, G:0.06, T:0.26
Consensus pattern (16 bp):
TAAAAATAGACTCATA
Found at i:48700030 original size:28 final size:28
Alignment explanation
Indices: 48699962--48700040 Score: 95
Period size: 28 Copynumber: 2.8 Consensus size: 28
48699952 GAATCATTCG
*
48699962 ATATTTTGCACACTAAGTGTCATTCTCA
1 ATATTTTGCACACTAAGTGCCATTCTCA
** *
48699990 ATAGCTCGCACACTAAGTGCCATTCTCA
1 ATATTTTGCACACTAAGTGCCATTCTCA
* * *
48700018 ATATTTTGTACACTGAGTACCAT
1 ATATTTTGCACACTAAGTGCCAT
48700041 ATTTGATTGC
Statistics
Matches: 41, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
28 41 1.00
ACGTcount: A:0.29, C:0.24, G:0.13, T:0.34
Consensus pattern (28 bp):
ATATTTTGCACACTAAGTGCCATTCTCA
Found at i:48704339 original size:57 final size:57
Alignment explanation
Indices: 48704275--48704576 Score: 406
Period size: 57 Copynumber: 5.3 Consensus size: 57
48704265 TGATCTCATT
** * * * * *
48704275 TCACACACTTAGTGCCCCAACAACCGATCTTGCACATACAGTGCTTGGTTACGGAGC
1 TCACACACACAGTGCCTCAACAACCGATCTCGCACACACAGTGCTCGGTTACGGAAC
* * * *
48704332 TCACACACACAGTGCCTCAACAACTGATATTGCACACATAGTGCTCGGTTACGGAAC
1 TCACACACACAGTGCCTCAACAACCGATCTCGCACACACAGTGCTCGGTTACGGAAC
* * * * *
48704389 TCGCACACACAGTACCTCAACAACCGATCTCGTACACACAGTGTTTGGTTACGGAAC
1 TCACACACACAGTGCCTCAACAACCGATCTCGCACACACAGTGCTCGGTTACGGAAC
* * *
48704446 TCGCACACACAGTGCCTCAACAACCGATCTCGCACACAAAGTGCTCGGTTATGGAAC
1 TCACACACACAGTGCCTCAACAACCGATCTCGCACACACAGTGCTCGGTTACGGAAC
* * *
48704503 TCACACACACAGTGCCTCAACAACCGGTCTCACACACACAGTGCTCGGTTACGAAAC
1 TCACACACACAGTGCCTCAACAACCGATCTCGCACACACAGTGCTCGGTTACGGAAC
48704560 TCACACACACAGTGCCT
1 TCACACACACAGTGCCT
48704577 ATGTTCACTT
Statistics
Matches: 215, Mismatches: 30, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
57 215 1.00
ACGTcount: A:0.30, C:0.33, G:0.18, T:0.20
Consensus pattern (57 bp):
TCACACACACAGTGCCTCAACAACCGATCTCGCACACACAGTGCTCGGTTACGGAAC
Found at i:48704483 original size:29 final size:29
Alignment explanation
Indices: 48704335--48704546 Score: 124
Period size: 29 Copynumber: 7.4 Consensus size: 29
48704325 ACGGAGCTCA
* * *
48704335 CACACACAGTGCCTCAACAACTGATATTG
1 CACACACAGTGCCTCAACAACCGATCTCG
* **** * *
48704364 CACACATAGTG-CTCGGTTACGGAACTCG
1 CACACACAGTGCCTCAACAACCGATCTCG
*
48704392 CACACACAGTACCTCAACAACCGATCTCG
1 CACACACAGTGCCTCAACAACCGATCTCG
* * ***** * *
48704421 TACACACAGTG-TTTGGTTACGGAACTCG
1 CACACACAGTGCCTCAACAACCGATCTCG
48704449 CACACACAGTGCCTCAACAACCGATCTCG
1 CACACACAGTGCCTCAACAACCGATCTCG
* **** ** * *
48704478 CACACAAAGTG-CTCGGTTATGGAACTCA
1 CACACACAGTGCCTCAACAACCGATCTCG
* *
48704506 CACACACAGTGCCTCAACAACCGGTCTCA
1 CACACACAGTGCCTCAACAACCGATCTCG
48704535 CACACACAGTGC
1 CACACACAGTGC
48704547 TCGGTTACGA
Statistics
Matches: 126, Mismatches: 54, Indels: 6
0.68 0.29 0.03
Matches are distributed among these distances:
28 56 0.44
29 70 0.56
ACGTcount: A:0.31, C:0.33, G:0.17, T:0.18
Consensus pattern (29 bp):
CACACACAGTGCCTCAACAACCGATCTCG
Found at i:48704516 original size:28 final size:28
Alignment explanation
Indices: 48704364--48704574 Score: 118
Period size: 28 Copynumber: 7.4 Consensus size: 28
48704354 ACTGATATTG
* *
48704364 CACACATAGTGCTCGGTTACGGAACTCG
1 CACACACAGTGCTCGGTTACGGAACTCA
* **** * * *
48704392 CACACACAGTACCTCAACAACCGATCTCG
1 CACACACAGT-GCTCGGTTACGGAACTCA
* * * *
48704421 TACACACAGTGTTTGGTTACGGAACTCG
1 CACACACAGTGCTCGGTTACGGAACTCA
**** * * *
48704449 CACACACAGTGCCTCAACAACCGATCTCG
1 CACACACAGTG-CTCGGTTACGGAACTCA
* *
48704478 CACACAAAGTGCTCGGTTATGGAACTCA
1 CACACACAGTGCTCGGTTACGGAACTCA
**** *
48704506 CACACACAGTGCCTCAACAACCGG-TCTCA
1 CACACACAGTG-CTCGGTTA-CGGAACTCA
*
48704535 CACACACAGTGCTCGGTTACGAAACTCA
1 CACACACAGTGCTCGGTTACGGAACTCA
48704563 CACACACAGTGC
1 CACACACAGTGC
48704575 CTATGTTCAC
Statistics
Matches: 129, Mismatches: 49, Indels: 10
0.69 0.26 0.05
Matches are distributed among these distances:
27 2 0.02
28 67 0.52
29 58 0.45
30 2 0.02
ACGTcount: A:0.30, C:0.34, G:0.18, T:0.18
Consensus pattern (28 bp):
CACACACAGTGCTCGGTTACGGAACTCA
Found at i:48710952 original size:29 final size:29
Alignment explanation
Indices: 48710915--48710991 Score: 86
Period size: 29 Copynumber: 2.7 Consensus size: 29
48710905 ATATTCATAT
* *
48710915 GGCCAATTAGGCCCAAGTCACCTATATAG
1 GGCCCATTAGGCCCAAGTCACATATATAG
* * *
48710944 GGCCCATTAGGCCCAAATCACATTTATAT
1 GGCCCATTAGGCCCAAGTCACATATATAG
48710973 GGCCCGA-TAGGCCC-AGTCA
1 GGCCC-ATTAGGCCCAAGTCA
48710992 TGTTCATATT
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
28 4 0.10
29 36 0.88
30 1 0.02
ACGTcount: A:0.29, C:0.30, G:0.21, T:0.21
Consensus pattern (29 bp):
GGCCCATTAGGCCCAAGTCACATATATAG
Found at i:48714787 original size:40 final size:40
Alignment explanation
Indices: 48714732--48714808 Score: 154
Period size: 40 Copynumber: 1.9 Consensus size: 40
48714722 GATACATAAT
48714732 GACTCTACAGGCAAAGTCTTACTGTGTACTAAATTCAGTA
1 GACTCTACAGGCAAAGTCTTACTGTGTACTAAATTCAGTA
48714772 GACTCTACAGGCAAAGTCTTACTGTGTACTAAATTCA
1 GACTCTACAGGCAAAGTCTTACTGTGTACTAAATTCA
48714809 TATAGATATA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.32, C:0.21, G:0.17, T:0.30
Consensus pattern (40 bp):
GACTCTACAGGCAAAGTCTTACTGTGTACTAAATTCAGTA
Found at i:48724506 original size:25 final size:25
Alignment explanation
Indices: 48724478--48724525 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
48724468 TTATAATATG
* * *
48724478 AAAATGACTATTTTGCCCCTAGGTA
1 AAAATGACCATTATACCCCTAGGTA
48724503 AAAATGACCATTATACCCCTAGG
1 AAAATGACCATTATACCCCTAGG
48724526 GTTTAATTAT
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:0.35, C:0.23, G:0.15, T:0.27
Consensus pattern (25 bp):
AAAATGACCATTATACCCCTAGGTA
Found at i:48724588 original size:11 final size:11
Alignment explanation
Indices: 48724572--48724609 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
48724562 ACACGATTGG
48724572 ACATGATATGC
1 ACATGATATGC
48724583 ACATGATATG-
1 ACATGATATGC
*
48724593 -TATGATATGC
1 ACATGATATGC
48724603 ACATGAT
1 ACATGAT
48724610 GTATTCATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
9 8 0.35
11 15 0.65
ACGTcount: A:0.37, C:0.13, G:0.18, T:0.32
Consensus pattern (11 bp):
ACATGATATGC
Found at i:48724695 original size:24 final size:25
Alignment explanation
Indices: 48724657--48724726 Score: 79
Period size: 24 Copynumber: 2.8 Consensus size: 25
48724647 GAGGAAGTGC
* *
48724657 AAAAGGGTTTTTGCCCCAGTTTACCG
1 AAAAGGG-CTTTGCCCCAGTTTACCA
* *
48724683 AAAA-GGCTTTGCCCCAATTTATCA
1 AAAAGGGCTTTGCCCCAGTTTACCA
*
48724707 AAAAGGGCTTTGGCCCAGTT
1 AAAAGGGCTTTGCCCCAGTT
48724727 ATTAAAAGAG
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
24 18 0.49
25 15 0.41
26 4 0.11
ACGTcount: A:0.27, C:0.23, G:0.21, T:0.29
Consensus pattern (25 bp):
AAAAGGGCTTTGCCCCAGTTTACCA
Found at i:48724728 original size:24 final size:24
Alignment explanation
Indices: 48724666--48724739 Score: 62
Period size: 24 Copynumber: 3.0 Consensus size: 24
48724656 CAAAAGGGTT
* *
48724666 TTTGCCCC-AGTTTACCGAAAAGGC
1 TTTGCCCCAAG-TTATCAAAAAGGC
*
48724690 TTTGCCCCAATTTATCAAAAAGGGC
1 TTTGCCCCAAGTTATCAAAAA-GGC
* *
48724715 TTTGGCCC-AGTTATTAAAAGAGGC
1 TTTGCCCCAAGTTATCAAAA-AGGC
48724739 T
1 T
48724740 AGGCCTCCAG
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
24 29 0.71
25 12 0.29
ACGTcount: A:0.28, C:0.23, G:0.20, T:0.28
Consensus pattern (24 bp):
TTTGCCCCAAGTTATCAAAAAGGC
Found at i:48725012 original size:31 final size:30
Alignment explanation
Indices: 48724945--48725014 Score: 95
Period size: 30 Copynumber: 2.3 Consensus size: 30
48724935 ACCGTTTACA
* *
48724945 GTAAAGGCTTCGGCCCAGTGATATGATAAT
1 GTAAAGGCTTCAGCCCAGTGACATGATAAT
* *
48724975 GAAAAGGCTTCAGCCTAGTGACATGAATAAT
1 GTAAAGGCTTCAGCCCAGTGACATG-ATAAT
48725006 GTAAAGGCT
1 GTAAAGGCT
48725015 GATATTGTTT
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
30 21 0.62
31 13 0.38
ACGTcount: A:0.34, C:0.16, G:0.26, T:0.24
Consensus pattern (30 bp):
GTAAAGGCTTCAGCCCAGTGACATGATAAT
Found at i:48728358 original size:39 final size:40
Alignment explanation
Indices: 48728214--48728459 Score: 295
Period size: 40 Copynumber: 6.2 Consensus size: 40
48728204 CGGATGATAA
* **
48728214 CCGGGCTAAGTCCCG-AGAGCATTTGTGCTAGTGGCTA-ATT
1 CCGGGCTAAGTCCCGAAG-GCATTTGTGCGAGTTACTATA-T
* * *
48728254 CCGGGCTAAGTCCCGAAGGCATTCGTGTGAGCTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
48728294 CCGGGCTAAGTCCCGAAGGCGTTTGTGCGAGTTATTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
48728334 CCGGGCT-AGTCCTGAAGGCATTTGTGCGAGTTATTATA-
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
48728372 CCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* * **
48728412 CCGGGCTAAGTCCCGAAGGCATTTGAGCTAGTGGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
48728452 CC-GGCTAA
1 CCGGGCTAA
48728460 ACTCCGAAGG
Statistics
Matches: 181, Mismatches: 21, Indels: 9
0.86 0.10 0.04
Matches are distributed among these distances:
38 7 0.04
39 63 0.35
40 108 0.60
41 3 0.02
ACGTcount: A:0.22, C:0.22, G:0.28, T:0.27
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:48733551 original size:40 final size:40
Alignment explanation
Indices: 48733498--48734409 Score: 1509
Period size: 40 Copynumber: 22.8 Consensus size: 40
48733488 CAGCCGCAAA
* * * *
48733498 CATATTTGCCTTCGGGTCTTAACCCGGACATATGAACTCG
1 CATAATTGCCTTCGGGTCTTAGCCCGGATATATCAACTCG
* *
48733538 CATAATTGCCTTCGGGTCTTAGCCCGGATATATCATCCCG
1 CATAATTGCCTTCGGGTCTTAGCCCGGATATATCAACTCG
*
48733578 CATAATTGCCTTCGGGTCATAGCCCGGATATATCAACTCG
1 CATAATTGCCTTCGGGTCTTAGCCCGGATATATCAACTCG
* *
48733618 CATAATTGCCTTCGGGTCTTAGCCCGGATATATCATCCCG
1 CATAATTGCCTTCGGGTCTTAGCCCGGATATATCAACTCG
*
48733658 CATAATTGCCTTCGGGTCATAGCCCGGATATATCAACTCG
1 CATAATTGCCTTCGGGTCTTAGCCCGGATATATCAACTCG
* *
48733698 CATAATTGCCTTCGGGTCTTAGCCCGGATATATCATCCCG
1 CATAATTGCCTTCGGGTCTTAGCCCGGATATATCAACTCG
*
48733738 CATAATTGCCTTCGGGTCATAGCCCGGATATATCAACTCG
1 CATAATTGCCTTCGGGTCTTAGCCCGGATATATCAACTCG
* *
48733778 CATAATTGCCTTCGGGTCTTAGCCCGGATATATCATCCCG
1 CATAATTGCCTTCGGGTCTTAGCCCGGATATATCAACTCG
*
48733818 CATAATTGCCTTCGGGTCATAGCCCGGATATATCAACTCG
1 CATAATTGCCTTCGGGTCTTAGCCCGGATATATCAACTCG
* *
48733858 CATAATTGCCTTCGGGTCTTAGCCCGGATATATCATCCCG
1 CATAATTGCCTTCGGGTCTTAGCCCGGATATATCAACTCG
*
48733898 CATAATTGCCTTCGGGTCATAGCCCGGATATATCAACTCG
1 CATAATTGCCTTCGGGTCTTAGCCCGGATATATCAACTCG
* *
48733938 CATAATTGCCTTCGGGTCTTAGCCCGGATATATCATCCCG
1 CATAATTGCCTTCGGGTCTTAGCCCGGATATATCAACTCG
*
48733978 CATAATTGCCTTCGGGTCATAGCCCGGATATATCAACTCG
1 CATAATTGCCTTCGGGTCTTAGCCCGGATATATCAACTCG
* *
48734018 CATAATTGCCTTCGGGTCTTAGCCCGGATATATCATCCCG
1 CATAATTGCCTTCGGGTCTTAGCCCGGATATATCAACTCG
*
48734058 CATAATTGCCTTCGGGTCATAGCCCGGATATATCAACTCG
1 CATAATTGCCTTCGGGTCTTAGCCCGGATATATCAACTCG
* *
48734098 CATAATTGCCTTCGGGTCTTAGCCCGGATATATCATCCCG
1 CATAATTGCCTTCGGGTCTTAGCCCGGATATATCAACTCG
*
48734138 CATAATTGCCTTCGGGTCATAGCCCGGATATATCAACTCG
1 CATAATTGCCTTCGGGTCTTAGCCCGGATATATCAACTCG
* *
48734178 CATAATTGCCTTCGGGTCTTAGCCCGGATATATCATCCCG
1 CATAATTGCCTTCGGGTCTTAGCCCGGATATATCAACTCG
*
48734218 CATAATTGCCTTCGGGTCATAGCCCGGATATATCAACTCG
1 CATAATTGCCTTCGGGTCTTAGCCCGGATATATCAACTCG
* *
48734258 CATAATTGCCTTCGGGTCTTAGCCCGGATATATCATCCCG
1 CATAATTGCCTTCGGGTCTTAGCCCGGATATATCAACTCG
*
48734298 CATAATTGCCTTCGGGTCATAGCCCGGATATATCAACTCG
1 CATAATTGCCTTCGGGTCTTAGCCCGGATATATCAACTCG
*
48734338 CATAATTGCCTTCGGGTCTTAGCCCGGATATGTCAACTCG
1 CATAATTGCCTTCGGGTCTTAGCCCGGATATATCAACTCG
48734378 CATAATTGCCTTCGGGTCTTAGCCCGGATATA
1 CATAATTGCCTTCGGGTCTTAGCCCGGATATA
48734410 ATCCAATGTT
Statistics
Matches: 806, Mismatches: 66, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 806 1.00
ACGTcount: A:0.22, C:0.29, G:0.20, T:0.29
Consensus pattern (40 bp):
CATAATTGCCTTCGGGTCTTAGCCCGGATATATCAACTCG
Found at i:48733604 original size:80 final size:80
Alignment explanation
Indices: 48733498--48734409 Score: 1743
Period size: 80 Copynumber: 11.4 Consensus size: 80
48733488 CAGCCGCAAA
* * * * *
48733498 CATATTTGCCTTCGGGTCTTAACCCGGACATATGAACTCGCATAATTGCCTTCGGGTCTTAGCCC
1 CATAATTGCCTTCGGGTCATAGCCCGGATATATCAACTCGCATAATTGCCTTCGGGTCTTAGCCC
48733563 GGATATATCATCCCG
66 GGATATATCATCCCG
48733578 CATAATTGCCTTCGGGTCATAGCCCGGATATATCAACTCGCATAATTGCCTTCGGGTCTTAGCCC
1 CATAATTGCCTTCGGGTCATAGCCCGGATATATCAACTCGCATAATTGCCTTCGGGTCTTAGCCC
48733643 GGATATATCATCCCG
66 GGATATATCATCCCG
48733658 CATAATTGCCTTCGGGTCATAGCCCGGATATATCAACTCGCATAATTGCCTTCGGGTCTTAGCCC
1 CATAATTGCCTTCGGGTCATAGCCCGGATATATCAACTCGCATAATTGCCTTCGGGTCTTAGCCC
48733723 GGATATATCATCCCG
66 GGATATATCATCCCG
48733738 CATAATTGCCTTCGGGTCATAGCCCGGATATATCAACTCGCATAATTGCCTTCGGGTCTTAGCCC
1 CATAATTGCCTTCGGGTCATAGCCCGGATATATCAACTCGCATAATTGCCTTCGGGTCTTAGCCC
48733803 GGATATATCATCCCG
66 GGATATATCATCCCG
48733818 CATAATTGCCTTCGGGTCATAGCCCGGATATATCAACTCGCATAATTGCCTTCGGGTCTTAGCCC
1 CATAATTGCCTTCGGGTCATAGCCCGGATATATCAACTCGCATAATTGCCTTCGGGTCTTAGCCC
48733883 GGATATATCATCCCG
66 GGATATATCATCCCG
48733898 CATAATTGCCTTCGGGTCATAGCCCGGATATATCAACTCGCATAATTGCCTTCGGGTCTTAGCCC
1 CATAATTGCCTTCGGGTCATAGCCCGGATATATCAACTCGCATAATTGCCTTCGGGTCTTAGCCC
48733963 GGATATATCATCCCG
66 GGATATATCATCCCG
48733978 CATAATTGCCTTCGGGTCATAGCCCGGATATATCAACTCGCATAATTGCCTTCGGGTCTTAGCCC
1 CATAATTGCCTTCGGGTCATAGCCCGGATATATCAACTCGCATAATTGCCTTCGGGTCTTAGCCC
48734043 GGATATATCATCCCG
66 GGATATATCATCCCG
48734058 CATAATTGCCTTCGGGTCATAGCCCGGATATATCAACTCGCATAATTGCCTTCGGGTCTTAGCCC
1 CATAATTGCCTTCGGGTCATAGCCCGGATATATCAACTCGCATAATTGCCTTCGGGTCTTAGCCC
48734123 GGATATATCATCCCG
66 GGATATATCATCCCG
48734138 CATAATTGCCTTCGGGTCATAGCCCGGATATATCAACTCGCATAATTGCCTTCGGGTCTTAGCCC
1 CATAATTGCCTTCGGGTCATAGCCCGGATATATCAACTCGCATAATTGCCTTCGGGTCTTAGCCC
48734203 GGATATATCATCCCG
66 GGATATATCATCCCG
48734218 CATAATTGCCTTCGGGTCATAGCCCGGATATATCAACTCGCATAATTGCCTTCGGGTCTTAGCCC
1 CATAATTGCCTTCGGGTCATAGCCCGGATATATCAACTCGCATAATTGCCTTCGGGTCTTAGCCC
48734283 GGATATATCATCCCG
66 GGATATATCATCCCG
48734298 CATAATTGCCTTCGGGTCATAGCCCGGATATATCAACTCGCATAATTGCCTTCGGGTCTTAGCCC
1 CATAATTGCCTTCGGGTCATAGCCCGGATATATCAACTCGCATAATTGCCTTCGGGTCTTAGCCC
* * *
48734363 GGATATGTCAACTCG
66 GGATATATCATCCCG
*
48734378 CATAATTGCCTTCGGGTCTTAGCCCGGATATA
1 CATAATTGCCTTCGGGTCATAGCCCGGATATA
48734410 ATCCAATGTT
Statistics
Matches: 823, Mismatches: 9, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
80 823 1.00
ACGTcount: A:0.22, C:0.29, G:0.20, T:0.29
Consensus pattern (80 bp):
CATAATTGCCTTCGGGTCATAGCCCGGATATATCAACTCGCATAATTGCCTTCGGGTCTTAGCCC
GGATATATCATCCCG
Found at i:48739560 original size:84 final size:84
Alignment explanation
Indices: 48739419--48739585 Score: 316
Period size: 84 Copynumber: 2.0 Consensus size: 84
48739409 TATTACAGCT
* *
48739419 GGCAACCCATCCAAGTCCGTAGACTCAACTCGGATTACTTCGTTATTTGCGCACCTCAAATCAAT
1 GGCAACCCATCCAAATCCGTAGACTCAACTCGGATTACTTCGTTATTTGCACACCTCAAATCAAT
48739484 AGTCTTGCTTTTGCAATTG
66 AGTCTTGCTTTTGCAATTG
48739503 GGCAACCCATCCAAATCCGTAGACTCAACTCGGATTACTTCGTTATTTGCACACCTCAAATCAAT
1 GGCAACCCATCCAAATCCGTAGACTCAACTCGGATTACTTCGTTATTTGCACACCTCAAATCAAT
48739568 AGTCTTGCTTTTGCAATT
66 AGTCTTGCTTTTGCAATT
48739586 CACAACCGCA
Statistics
Matches: 81, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
84 81 1.00
ACGTcount: A:0.26, C:0.28, G:0.15, T:0.31
Consensus pattern (84 bp):
GGCAACCCATCCAAATCCGTAGACTCAACTCGGATTACTTCGTTATTTGCACACCTCAAATCAAT
AGTCTTGCTTTTGCAATTG
Found at i:48741048 original size:62 final size:62
Alignment explanation
Indices: 48740951--48741075 Score: 232
Period size: 62 Copynumber: 2.0 Consensus size: 62
48740941 TATTGTAGGT
48740951 GCGGGGGTGGTATTAGTCGGGAATGGAGGTTGTGGAACAGCCGTATTAGTTCGAATGTATTG
1 GCGGGGGTGGTATTAGTCGGGAATGGAGGTTGTGGAACAGCCGTATTAGTTCGAATGTATTG
* *
48741013 GCGGGGGTGGTGTTTGTCGGGAATGGAGGTTGTGGAACAGCCGTATTAGTTCGAATGTATTG
1 GCGGGGGTGGTATTAGTCGGGAATGGAGGTTGTGGAACAGCCGTATTAGTTCGAATGTATTG
48741075 G
1 G
48741076 TTGAACCAAT
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
62 61 1.00
ACGTcount: A:0.19, C:0.10, G:0.42, T:0.30
Consensus pattern (62 bp):
GCGGGGGTGGTATTAGTCGGGAATGGAGGTTGTGGAACAGCCGTATTAGTTCGAATGTATTG
Found at i:48742797 original size:40 final size:40
Alignment explanation
Indices: 48742749--48743180 Score: 702
Period size: 40 Copynumber: 10.8 Consensus size: 40
48742739 GCAAACACAC
* * * * *
48742749 TTGCCTTCGGGTCTTAACCCGGACATATCAACTTGCCTAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATTAACTCGCATAA
* ***
48742789 TTGCCTTCGGGTCTTAGCCCAGATATATCGTCTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATTAACTCGCATAA
* * * *
48742829 TTGCCTTCGGGTCATAGCCCGGACATATTAACTTGCCTAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATTAACTCGCATAA
***
48742869 TTGCCTTCGGGTCTTAGCCCGGATATATCGTCTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATTAACTCGCATAA
* *
48742909 TTGCCTTCGGGTCATAGCCCGGACATATTAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATTAACTCGCATAA
48742949 TTGCCTTCGGGTCTTAGCCCGGATATATTAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATTAACTCGCATAA
48742989 TTGCCTTCGGGTCTTAGCCCGGATATATTAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATTAACTCGCATAA
48743029 TTGCCTTCGGGTCTTAGCCCGGATATATTAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATTAACTCGCATAA
48743069 TTGCCTTCGGGTCTTAGCCCGGATATATTAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATTAACTCGCATAA
48743109 TTGCCTTCGGGTCTTAGCCCGGATATATTAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATTAACTCGCATAA
48743149 TTGCCTTCGGGTCTTAGCCCGGATATATTAAC
1 TTGCCTTCGGGTCTTAGCCCGGATATATTAAC
48743181 ATGCTCATGC
Statistics
Matches: 363, Mismatches: 29, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 363 1.00
ACGTcount: A:0.22, C:0.26, G:0.20, T:0.32
Consensus pattern (40 bp):
TTGCCTTCGGGTCTTAGCCCGGATATATTAACTCGCATAA
Found at i:48759661 original size:26 final size:24
Alignment explanation
Indices: 48759627--48759675 Score: 62
Period size: 26 Copynumber: 2.0 Consensus size: 24
48759617 TGAATAAAAA
* *
48759627 ATTTGAAAATATAATAAATCAAATAC
1 ATTTAAAAACATAA-AAA-CAAATAC
48759653 ATTTAAAAACATAAAAACAAATA
1 ATTTAAAAACATAAAAACAAATA
48759676 TTAAAACAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 6 0.29
25 3 0.14
26 12 0.57
ACGTcount: A:0.63, C:0.08, G:0.02, T:0.27
Consensus pattern (24 bp):
ATTTAAAAACATAAAAACAAATAC
Found at i:48759919 original size:11 final size:11
Alignment explanation
Indices: 48759905--48759979 Score: 64
Period size: 11 Copynumber: 6.9 Consensus size: 11
48759895 CAAAAAGTAG
48759905 CACCAAAACAA
1 CACCAAAACAA
*
48759916 CACCAAATA-AG
1 CACCAAA-ACAA
** *
48759927 CATTAAAACAG
1 CACCAAAACAA
*
48759938 CACCAAAACAG
1 CACCAAAACAA
*
48759949 CAACAAAACAA
1 CACCAAAACAA
48759960 CACC-AAACAA
1 CACCAAAACAA
*
48759970 CAACAAAACA
1 CACCAAAACA
48759980 TCACAAAAAA
Statistics
Matches: 52, Mismatches: 9, Indels: 6
0.78 0.13 0.09
Matches are distributed among these distances:
10 10 0.19
11 41 0.79
12 1 0.02
ACGTcount: A:0.61, C:0.31, G:0.04, T:0.04
Consensus pattern (11 bp):
CACCAAAACAA
Found at i:48759934 original size:22 final size:22
Alignment explanation
Indices: 48759903--48759988 Score: 86
Period size: 22 Copynumber: 4.0 Consensus size: 22
48759893 CACAAAAAGT
*
48759903 AGCACCAAAACAACACCAAATA-
1 AGCAACAAAACAACACCAAA-AC
** *
48759925 AGCATTAAAACAGCACCAAAAC
1 AGCAACAAAACAACACCAAAAC
48759947 AGCAACAAAACAACACC-AAAC
1 AGCAACAAAACAACACCAAAAC
* * *
48759968 AACAACAAAACATCACAAAAA
1 AGCAACAAAACAACACCAAAA
48759989 ATAGCATAAA
Statistics
Matches: 53, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
21 19 0.36
22 34 0.64
ACGTcount: A:0.62, C:0.29, G:0.05, T:0.05
Consensus pattern (22 bp):
AGCAACAAAACAACACCAAAAC
Found at i:48773326 original size:20 final size:20
Alignment explanation
Indices: 48773301--48773350 Score: 91
Period size: 20 Copynumber: 2.5 Consensus size: 20
48773291 TTATGCTAAG
48773301 ATATTTCTAATGAAATACCA
1 ATATTTCTAATGAAATACCA
48773321 ATATTTCTAATGAAATACCA
1 ATATTTCTAATGAAATACCA
*
48773341 AAATTTCTAA
1 ATATTTCTAA
48773351 GTACATATCC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.46, C:0.14, G:0.04, T:0.36
Consensus pattern (20 bp):
ATATTTCTAATGAAATACCA
Found at i:48775632 original size:48 final size:48
Alignment explanation
Indices: 48775552--48775807 Score: 213
Period size: 48 Copynumber: 5.4 Consensus size: 48
48775542 GAGTTGATGA
* * * *
48775552 GATCCCGTATAAGACCATATCTGGGATATGGCATCGGCATCGATATGT
1 GATCCCATGTAAGACCATGTCTGGGACATGGCATCGGCATCGATATGT
** * * *
48775600 GATTTCATGTAAGACCATGTTTAGGACATGGCATTGGCATC-ATTATGT
1 GATCCCATGTAAGACCATGTCTGGGACATGGCATCGGCATCGA-TATGT
*
48775648 GATCCCATGTAAGACCATGTCTGGGACATGGCA-CTGGCATCGATATGA
1 GATCCCATGTAAGACCATGTCTGGGACATGGCATC-GGCATCGATATGT
* * * * *
48775696 GAGCATCGTGTAAGACCATAG-CTGGG-C-T---ATTGGCTTCGATATGT
1 GATC-CCATGTAAGACCAT-GTCTGGGACATGGCATCGGCATCGATATGT
* * * *
48775740 GCGATCCCATGTAAGACCATGTCTGGGACATGACATTGACATCGATAAGT
1 --GATCCCATGTAAGACCATGTCTGGGACATGGCATCGGCATCGATATGT
* *
48775790 GGTCCCATGTAATACCAT
1 GATCCCATGTAAGACCAT
48775808 ATCCGAGATA
Statistics
Matches: 165, Mismatches: 29, Indels: 28
0.74 0.13 0.13
Matches are distributed among these distances:
44 13 0.08
45 17 0.10
46 4 0.02
47 3 0.02
48 96 0.58
49 18 0.11
50 14 0.08
ACGTcount: A:0.27, C:0.20, G:0.25, T:0.28
Consensus pattern (48 bp):
GATCCCATGTAAGACCATGTCTGGGACATGGCATCGGCATCGATATGT
Found at i:48781378 original size:20 final size:18
Alignment explanation
Indices: 48781351--48781402 Score: 59
Period size: 20 Copynumber: 2.7 Consensus size: 18
48781341 ATTCTTTTTT
48781351 ATAATTTTAATAAGTTTA
1 ATAATTTTAATAAGTTTA
* *
48781369 TATGAATTTTAATGATTTTA
1 -AT-AATTTTAATAAGTTTA
48781389 ATAATATTTAATAA
1 ATAAT-TTTAATAA
48781403 TTTTTGATGG
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
18 3 0.11
19 11 0.39
20 14 0.50
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (18 bp):
ATAATTTTAATAAGTTTA
Found at i:48781398 original size:10 final size:9
Alignment explanation
Indices: 48781346--48781406 Score: 68
Period size: 9 Copynumber: 6.4 Consensus size: 9
48781336 TATAAATTCT
*
48781346 TTTTTATAA
1 TTTTAATAA
48781355 TTTTAATAA
1 TTTTAATAA
*
48781364 GTTTATATGAA
1 TTTTA-AT-AA
*
48781375 TTTTAATGA
1 TTTTAATAA
48781384 TTTTAATAA
1 TTTTAATAA
48781393 TATTTAATAA
1 T-TTTAATAA
48781403 TTTT
1 TTTT
48781407 TGATGGAAAA
Statistics
Matches: 44, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
9 25 0.57
10 13 0.30
11 6 0.14
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (9 bp):
TTTTAATAA
Found at i:48781407 original size:29 final size:30
Alignment explanation
Indices: 48781345--48781407 Score: 69
Period size: 29 Copynumber: 2.2 Consensus size: 30
48781335 TTATAAATTC
* *
48781345 TTTTTTATAATTTTAATAAGTTTATATGAA
1 TTTTTAATAATTTTAATAAATTTATATGAA
*
48781375 -TTTTAATGATTTTAATAATATTTA-AT-AA
1 TTTTTAATAATTTTAATAA-ATTTATATGAA
48781403 TTTTT
1 TTTTT
48781408 GATGGAAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
28 2 0.07
29 22 0.79
30 4 0.14
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.59
Consensus pattern (30 bp):
TTTTTAATAATTTTAATAAATTTATATGAA
Found at i:48783294 original size:27 final size:28
Alignment explanation
Indices: 48783249--48783327 Score: 83
Period size: 28 Copynumber: 2.8 Consensus size: 28
48783239 TAATTTGAAT
*
48783249 AAAATATAAAATATGAAAAAT-AGGGGCA
1 AAAATATAAAATATGAAAAATAAAGGG-A
* *
48783277 AAACTATAAAATCT-AAAAATAAAGGGA
1 AAAATATAAAATATGAAAAATAAAGGGA
48783304 AAAATTATAAAACT-TGAAAAATAA
1 AAAA-TATAAAA-TATGAAAAATAA
48783328 GAGACATATG
Statistics
Matches: 43, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
27 10 0.23
28 24 0.56
29 9 0.21
ACGTcount: A:0.63, C:0.05, G:0.11, T:0.20
Consensus pattern (28 bp):
AAAATATAAAATATGAAAAATAAAGGGA
Found at i:48788239 original size:6 final size:6
Alignment explanation
Indices: 48788228--48788272 Score: 74
Period size: 6 Copynumber: 7.5 Consensus size: 6
48788218 ATCTTGTGGC
48788228 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAATG -AAAAG AAA
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAA-G AAAAAG AAA
48788273 GAGATGGTAA
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
5 1 0.03
6 35 0.95
7 1 0.03
ACGTcount: A:0.82, C:0.00, G:0.16, T:0.02
Consensus pattern (6 bp):
AAAAAG
Found at i:48790093 original size:16 final size:16
Alignment explanation
Indices: 48790067--48790106 Score: 62
Period size: 16 Copynumber: 2.4 Consensus size: 16
48790057 TAACAGATCA
48790067 ACATCATACACATATAT
1 ACAT-ATACACATATAT
48790084 ACATATACACATATAT
1 ACATATACACATATAT
48790100 ATCATAT
1 A-CATAT
48790107 TAGAAATCTC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
16 13 0.59
17 9 0.41
ACGTcount: A:0.47, C:0.20, G:0.00, T:0.33
Consensus pattern (16 bp):
ACATATACACATATAT
Found at i:48793208 original size:84 final size:84
Alignment explanation
Indices: 48793092--48793245 Score: 220
Period size: 84 Copynumber: 1.8 Consensus size: 84
48793082 GATAAAAAAC
* * * *
48793092 ATTTGTAGTTCCTGCCACTTCTTGTGAGTGCACAACATGGTT-GCAGATTAAACAAATTGCCACT
1 ATTTGCAGTTACTGCCACTTCTTGTGAGTGCACAACAT-ATTCGCAGATTAAACAAACTGCCACT
48793156 AGGTTTGTGACGAGCCACAT
65 AGGTTTGTGACGAGCCACAT
* * * *
48793176 ATTTGCAGTTACTGTCACTTGTTGTGAGTGCACAACATATTCGTAGATTAAACAAACTGCTACTA
1 ATTTGCAGTTACTGCCACTTCTTGTGAGTGCACAACATATTCGCAGATTAAACAAACTGCCACTA
48793241 GGTTT
66 GGTTT
48793246 TGTGGACAAG
Statistics
Matches: 61, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
83 2 0.03
84 59 0.97
ACGTcount: A:0.27, C:0.19, G:0.20, T:0.33
Consensus pattern (84 bp):
ATTTGCAGTTACTGCCACTTCTTGTGAGTGCACAACATATTCGCAGATTAAACAAACTGCCACTA
GGTTTGTGACGAGCCACAT
Found at i:48800351 original size:28 final size:28
Alignment explanation
Indices: 48800320--48800409 Score: 126
Period size: 28 Copynumber: 3.2 Consensus size: 28
48800310 GGAATCAATC
*
48800320 AGGGGAAAAACTGTAAAATCTAAAAAAT
1 AGGGGAAAAACTATAAAATCTAAAAAAT
* *
48800348 AGGGGCAAAACTATAAATTCTAAAAAAT
1 AGGGGAAAAACTATAAAATCTAAAAAAT
* * *
48800376 AAGAGAAAAACTATAAAATCTAGAAAAT
1 AGGGGAAAAACTATAAAATCTAAAAAAT
48800404 AGGGGA
1 AGGGGA
48800410 CACGCGACTG
Statistics
Matches: 52, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 52 1.00
ACGTcount: A:0.57, C:0.08, G:0.18, T:0.18
Consensus pattern (28 bp):
AGGGGAAAAACTATAAAATCTAAAAAAT
Found at i:48804478 original size:68 final size:64
Alignment explanation
Indices: 48804280--48804510 Score: 193
Period size: 68 Copynumber: 3.5 Consensus size: 64
48804270 ACATGGTGAA
* * * * * *
48804280 CACTCAGTACCACCCATGTGACCTAGCCA-ATTTATCTCGTAGCTCTCTTGTCTACATGGTGT-
1 CACTCAGCACCACACATGTGACCTAGCTACATATATCCCGTAGCTCTCTTGTCTACATGATGTG
* * *
48804342 C-CTTCACCTGGAGCCACGCATGTGACCTAGCTACATATATCCCGTAGCTCTCTTGTCTACATGG
1 CAC-TCA---GCA-CCACACATGTGACCTAGCTACATATATCCCGTAGCTCTCTTGTCTACATGA
48804406 TGTG
61 TGTG
* * * **
48804410 CACAT-AGTATCACCCATGTGACCTAGCTACATCATAATGTCTTGTAGCTCTCTTGTAC-ACATG
1 CAC-TCAGCACCACACATGTGACCTAGCTACAT-AT-A--TCCCGTAGCTCTCTTGT-CTACATG
48804473 ATGTG
60 ATGTG
*
48804478 CACTCAGCACCATACATGTGACCTAGCTACATA
1 CACTCAGCACCACACATGTGACCTAGCTACATA
48804511 CTATTTGTAT
Statistics
Matches: 139, Mismatches: 16, Indels: 23
0.78 0.09 0.13
Matches are distributed among these distances:
61 1 0.01
62 4 0.03
64 21 0.15
65 6 0.04
66 19 0.14
67 33 0.24
68 52 0.37
69 3 0.02
ACGTcount: A:0.24, C:0.29, G:0.17, T:0.30
Consensus pattern (64 bp):
CACTCAGCACCACACATGTGACCTAGCTACATATATCCCGTAGCTCTCTTGTCTACATGATGTG
Found at i:48805212 original size:30 final size:30
Alignment explanation
Indices: 48805176--48805236 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
48805166 TCCTTAACTC
48805176 AAACTTTGGAAAATTTACAATTTTGCCCCT
1 AAACTTTGGAAAATTTACAATTTTGCCCCT
* * * *
48805206 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTGGAAAATTTACAATTTTGCCCCT
48805236 A
1 A
48805237 GGCTCGGGAA
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:0.30, C:0.23, G:0.08, T:0.39
Consensus pattern (30 bp):
AAACTTTGGAAAATTTACAATTTTGCCCCT
Found at i:48809744 original size:22 final size:22
Alignment explanation
Indices: 48809700--48809740 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
48809690 ATATTTGATA
*
48809700 TTTATATTTATTTTTGAATTGT
1 TTTATATTTATTATTGAATTGT
48809722 TTTATA-TTATTATTGAATT
1 TTTATATTTATTATTGAATT
48809741 TGTTAACGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.27, C:0.00, G:0.07, T:0.66
Consensus pattern (22 bp):
TTTATATTTATTATTGAATTGT
Found at i:48811759 original size:28 final size:28
Alignment explanation
Indices: 48811702--48811759 Score: 82
Period size: 28 Copynumber: 2.0 Consensus size: 28
48811692 TACAGGGGTT
*
48811702 TTCACACGGCCAAGCACATGCCCGTGTCC
1 TTCACACGGCCAA-CACACGCCCGTGTCC
48811731 TTCACACGGCCTAA-ACACGCCCGTGTCC
1 TTCACACGGCC-AACACACGCCCGTGTCC
48811759 T
1 T
48811760 CGCCTATGTC
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
28 14 0.52
29 11 0.41
30 2 0.07
ACGTcount: A:0.21, C:0.41, G:0.19, T:0.19
Consensus pattern (28 bp):
TTCACACGGCCAACACACGCCCGTGTCC
Found at i:48813203 original size:51 final size:51
Alignment explanation
Indices: 48813062--48813204 Score: 205
Period size: 51 Copynumber: 2.8 Consensus size: 51
48813052 ACATGTAATA
* * ** *
48813062 CATCCATAATGAACTCGGACCTCTCAACGAGCTCAGATATTACGTGAATCG
1 CATCCATCATGAACTCGGACCACTCAACGAGCTCAGATGCTACATGAATCG
* * *
48813113 CATCCATCATGAACTCGGACCACTCAATGAGCTCGGATGCTACATGAATCT
1 CATCCATCATGAACTCGGACCACTCAACGAGCTCAGATGCTACATGAATCG
*
48813164 CATCCATCATGAACTCGAACCACTCAACGAGCTCAGATGCT
1 CATCCATCATGAACTCGGACCACTCAACGAGCTCAGATGCT
48813205 CGCATCTATA
Statistics
Matches: 81, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
51 81 1.00
ACGTcount: A:0.31, C:0.30, G:0.17, T:0.22
Consensus pattern (51 bp):
CATCCATCATGAACTCGGACCACTCAACGAGCTCAGATGCTACATGAATCG
Found at i:48817687 original size:41 final size:40
Alignment explanation
Indices: 48817642--48817719 Score: 104
Period size: 40 Copynumber: 1.9 Consensus size: 40
48817632 ATAGTAGCAC
48817642 AATAGAATAGAACAAAAC-CAAAGCAGAACAAAACAGAATAG
1 AATAGAATAGAAC-AAACTCAAA-CAGAACAAAACAGAATAG
* * *
48817683 AATAGAGTAGAACAAACTTAAACAGAACAAAGCAGAA
1 AATAGAATAGAACAAACTCAAACAGAACAAAACAGAA
48817720 CCGAACAGAA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
40 18 0.55
41 15 0.45
ACGTcount: A:0.62, C:0.14, G:0.15, T:0.09
Consensus pattern (40 bp):
AATAGAATAGAACAAACTCAAACAGAACAAAACAGAATAG
Found at i:48818520 original size:29 final size:29
Alignment explanation
Indices: 48818478--48818538 Score: 104
Period size: 29 Copynumber: 2.1 Consensus size: 29
48818468 ATAGCTTAAA
* *
48818478 ACAGATTATACAGACCCTGCGGAAGGCCT
1 ACAGATCATACAGACCCTACGGAAGGCCT
48818507 ACAGATCATACAGACCCTACGGAAGGCCT
1 ACAGATCATACAGACCCTACGGAAGGCCT
48818536 ACA
1 ACA
48818539 TTCGAACCAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.34, C:0.30, G:0.21, T:0.15
Consensus pattern (29 bp):
ACAGATCATACAGACCCTACGGAAGGCCT
Found at i:48822608 original size:18 final size:18
Alignment explanation
Indices: 48822582--48822625 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
48822572 TTAATAAATA
*
48822582 AAAACAAAAGAAAGTATT
1 AAAACAAAAGAAAATATT
* *
48822600 AAAATAAAATAAAATATT
1 AAAACAAAAGAAAATATT
*
48822618 AAATCAAA
1 AAAACAAA
48822626 CATTTTTTCT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.70, C:0.05, G:0.05, T:0.20
Consensus pattern (18 bp):
AAAACAAAAGAAAATATT
Found at i:48825600 original size:20 final size:20
Alignment explanation
Indices: 48825572--48825611 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
48825562 CATGTTTACC
* *
48825572 AAATATTATTCTTTTTATCA
1 AAATATTATACTTCTTATCA
*
48825592 AAATCTTATACTTCTTATCA
1 AAATATTATACTTCTTATCA
48825612 TATCACATAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.35, C:0.15, G:0.00, T:0.50
Consensus pattern (20 bp):
AAATATTATACTTCTTATCA
Found at i:48830090 original size:12 final size:12
Alignment explanation
Indices: 48830073--48830103 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
48830063 GGAATTGTTT
48830073 TTTTTTTCTTTC
1 TTTTTTTCTTTC
48830085 TTTTTTTCTTTC
1 TTTTTTTCTTTC
48830097 TTTTTTT
1 TTTTTTT
48830104 TTTAAATAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (12 bp):
TTTTTTTCTTTC
Found at i:48830091 original size:16 final size:15
Alignment explanation
Indices: 48830070--48830106 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
48830060 AGTGGAATTG
48830070 TTTTTTTTTTCTTTC
1 TTTTTTTTTTCTTTC
48830085 TTTTTTTCTTTCTTT-
1 TTTTTTT-TTTCTTTC
48830100 TTTTTTT
1 TTTTTTT
48830107 AAATAATAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 14 0.67
16 7 0.33
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (15 bp):
TTTTTTTTTTCTTTC
Found at i:48830369 original size:3 final size:3
Alignment explanation
Indices: 48830361--48830578 Score: 56
Period size: 3 Copynumber: 73.0 Consensus size: 3
48830351 ATATATAACT
* * * *
48830361 ATA ATA ATA ATA ATA GTA GTA GTT ATA ATA A-A AGTA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A-TA ATA ATA ATA
* * * * * ***
48830406 CTA A-A TATA ATA ATA ATA GTA TTA GTG ATA A-A ATA ATA GCG ATA
1 ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * * * *
48830450 AAA ATA GA-A ATA ATG ACA ATA ACA ATA A-A GAGTA ATG GTA ATA ATA
1 ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA -A-TA ATA ATA ATA ATA
* * * * * * *
48830496 ATA ATA ATGA A-A ATA AGA GTA ATA TTA GTA ATA CATT A-A ATT ACA
1 ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA
* * * *
48830541 ATA GTA A-A GTA ATA ATA ATA ATA TTA ATA GTA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
48830579 CAAGTAATAA
Statistics
Matches: 149, Mismatches: 51, Indels: 30
0.65 0.22 0.13
Matches are distributed among these distances:
2 11 0.07
3 128 0.86
4 9 0.06
5 1 0.01
ACGTcount: A:0.57, C:0.03, G:0.10, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:48830410 original size:18 final size:18
Alignment explanation
Indices: 48830361--48830423 Score: 65
Period size: 18 Copynumber: 3.5 Consensus size: 18
48830351 ATATATAACT
*
48830361 ATAATAATAATAATAGTA
1 ATAATAATAATAAAAGTA
* * *
48830379 GTAGTTATAATAAAAGTA
1 ATAATAATAATAAAAGTA
*
48830397 ATAATAATACTAAATA-TA
1 ATAATAATAATAAA-AGTA
48830415 ATAATAATA
1 ATAATAATA
48830424 GTATTAGTGA
Statistics
Matches: 36, Mismatches: 8, Indels: 2
0.78 0.17 0.04
Matches are distributed among these distances:
18 35 0.97
19 1 0.03
ACGTcount: A:0.59, C:0.02, G:0.06, T:0.33
Consensus pattern (18 bp):
ATAATAATAATAAAAGTA
Found at i:48831006 original size:3 final size:3
Alignment explanation
Indices: 48831000--48831042 Score: 63
Period size: 3 Copynumber: 15.0 Consensus size: 3
48830990 AAATAAGATG
*
48831000 ATA ATA A-A A-A ATA ATA ATA ATA ATA ACA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
48831043 TATTATGAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
2 4 0.11
3 33 0.89
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (3 bp):
ATA
Found at i:48832704 original size:44 final size:44
Alignment explanation
Indices: 48832649--48832793 Score: 139
Period size: 44 Copynumber: 3.3 Consensus size: 44
48832639 TCTGTTTCCA
48832649 CTACTGCTTAGGGAGACAAGATTTGTAATTTTCAACCTGTTACT
1 CTACTGCTTAGGGAGACAAGATTTGTAATTTTCAACCTGTTACT
* ** *** ** * * ** * * *
48832693 CTACTGCTTAGGGGGTTAAGGCCCT-TCGTCTTCGATTTGCTCCA
1 CTACTGCTTAGGGAGACAA-GATTTGTAATTTTCAACCTGTTACT
48832737 CTACTGCTTAGGGAGACAAGATTTGTAATTTTCAACCTGTTACT
1 CTACTGCTTAGGGAGACAAGATTTGTAATTTTCAACCTGTTACT
48832781 CTACTGCTTAGGG
1 CTACTGCTTAGGG
48832794 GGTTAAGGCC
Statistics
Matches: 69, Mismatches: 30, Indels: 4
0.67 0.29 0.04
Matches are distributed among these distances:
43 2 0.03
44 65 0.94
45 2 0.03
ACGTcount: A:0.22, C:0.21, G:0.21, T:0.35
Consensus pattern (44 bp):
CTACTGCTTAGGGAGACAAGATTTGTAATTTTCAACCTGTTACT
Found at i:48832829 original size:44 final size:44
Alignment explanation
Indices: 48832693--48832837 Score: 139
Period size: 44 Copynumber: 3.3 Consensus size: 44
48832683 ACCTGTTACT
48832693 CTACTGCTTAGGGGGTTAAGGCCCTTCGTCTTCGATTTGCTCCA
1 CTACTGCTTAGGGGGTTAAGGCCCTTCGTCTTCGATTTGCTCCA
* ** *** ** * * ** * * *
48832737 CTACTGCTTAGGGAGACAA-GATTTGTAATTTTCAACCTGTTACT
1 CTACTGCTTAGGGGGTTAAGGCCCT-TCGTCTTCGATTTGCTCCA
48832781 CTACTGCTTAGGGGGTTAAGGCCCTTCGTCTTCGATTTGCTCCA
1 CTACTGCTTAGGGGGTTAAGGCCCTTCGTCTTCGATTTGCTCCA
48832825 CTACTGCTTAGGG
1 CTACTGCTTAGGG
48832838 AGACAAGATC
Statistics
Matches: 69, Mismatches: 30, Indels: 4
0.67 0.29 0.04
Matches are distributed among these distances:
43 2 0.03
44 65 0.94
45 2 0.03
ACGTcount: A:0.18, C:0.24, G:0.23, T:0.34
Consensus pattern (44 bp):
CTACTGCTTAGGGGGTTAAGGCCCTTCGTCTTCGATTTGCTCCA
Found at i:48832917 original size:44 final size:44
Alignment explanation
Indices: 48832860--48833363 Score: 276
Period size: 44 Copynumber: 11.5 Consensus size: 44
48832850 TAAATTTAGC
* * *
48832860 CTGTTACCCTACTGCTTAAGGGTTTAAGGCCCATTGCCTTCGAT
1 CTGTTTCCCTACTGCTTAGGGGTTTAAGGCCCATAGCCTTCGAT
* * ** ** *** * *
48832904 CTGTTTCCGTACTGCTTA-GGGTGATAAGATCTGTAAATTTAG-C
1 CTGTTTCCCTACTGCTTAGGGGT-TTAAGGCCCATAGCCTTCGAT
*
48832947 CTGTTAT-CCTACTGCTTAGGGGTTTAAGGCCCATCGCCTTCGAT
1 CTGTT-TCCCTACTGCTTAGGGGTTTAAGGCCCATAGCCTTCGAT
** ** ** *** * *
48832991 CTGTTTCCCTACTGCTTAGGGGGATAAGATCTGTAAATTTAG-C
1 CTGTTTCCCTACTGCTTAGGGGTTTAAGGCCCATAGCCTTCGAT
*
48833034 CTGTTAT-CCTACTGCTTAGGGGTTTAAGGCCCATCGCCTTCGAT
1 CTGTT-TCCCTACTGCTTAGGGGTTTAAGGCCCATAGCCTTCGAT
** ** ** *** * *
48833078 CTGTTTCCCTACTGCTTAGGGGGATAAGATCTGTAAATTTAG-C
1 CTGTTTCCCTACTGCTTAGGGGTTTAAGGCCCATAGCCTTCGAT
* *
48833121 CTGTTACCCTACTGCTTAGGGGTTTAAGGCCCATCGCCTTCGAT
1 CTGTTTCCCTACTGCTTAGGGGTTTAAGGCCCATAGCCTTCGAT
* ** ** *** * *
48833165 CTGTTTCCCTACTGCTTA-GGGTGATAAGATCTGTAAATTTAG-C
1 CTGTTTCCCTACTGCTTAGGGGT-TTAAGGCCCATAGCCTTCGAT
* * *
48833208 CTGTTACCCTACTGCTTAGGCGTTTAAGGCCCATCA-CCTTCAAT
1 CTGTTTCCCTACTGCTTAGGGGTTTAAGGCCCAT-AGCCTTCGAT
* * ** ** ** *
48833252 CTATTTCCCTACTGCTTAGGGGGTTAAGATCTGTA-AATTC-AGC
1 CTGTTTCCCTACTGCTTAGGGGTTTAAGGCCCATAGCCTTCGA-T
* *
48833295 CTGTTACCCTACTGCTTAGGGGTTTAAGGTCCATCA-CCTTCGAT
1 CTGTTTCCCTACTGCTTAGGGGTTTAAGGCCCAT-AGCCTTCGAT
48833339 CTGTTTCCCTACTGCTTAAGGGGTT
1 CTGTTTCCCTACTGCTT-AGGGGTT
48833364 AAGATCTGTA
Statistics
Matches: 324, Mismatches: 119, Indels: 33
0.68 0.25 0.07
Matches are distributed among these distances:
42 1 0.00
43 150 0.46
44 165 0.51
45 8 0.02
ACGTcount: A:0.20, C:0.24, G:0.22, T:0.35
Consensus pattern (44 bp):
CTGTTTCCCTACTGCTTAGGGGTTTAAGGCCCATAGCCTTCGAT
Found at i:48832918 original size:87 final size:87
Alignment explanation
Indices: 48832552--48833411 Score: 1188
Period size: 87 Copynumber: 9.8 Consensus size: 87
48832542 AATTTCCAGC
* * * * * *
48832552 CTGTTACCCTACTGCTTAGGGTGATAAGATATGTAATTTTCAGCCTGTTTCCCTACTACTTAGGG
1 CTGTTTCCCTACTGCTTAGGGAGATAAGATCTGTAAATTT-AGCCTGTTACCCTACTGCTTAGGG
*
48832617 GTTTAAGGCCCATTGCCTTCGAT
65 GTTTAAGGCCCATCGCCTTCGAT
* * * * *
48832640 CTGTTTCCACTACTGCTTAGGGAGACAAGATTTGTAATTTTCAACCTGTTACTCTACTGCTTAGG
1 CTGTTTCC-CTACTGCTTAGGGAGATAAGATCTGTAAATTT-AGCCTGTTACCCTACTGCTTAGG
* * *
48832705 GGGTTAAGGCCCTTCGTCTTCGAT
64 GGTTTAAGGCCCATCGCCTTCGAT
* * * * * * *
48832729 TTG-CTCCACTACTGCTTAGGGAGACAAGATTTGTAATTTTCAACCTGTTACTCTACTGCTTAGG
1 CTGTTTCC-CTACTGCTTAGGGAGATAAGATCTGTAAATTT-AGCCTGTTACCCTACTGCTTAGG
* * *
48832793 GGGTTAAGGCCCTTCGTCTTCGAT
64 GGTTTAAGGCCCATCGCCTTCGAT
* * * *
48832817 TTG-CTCCACTACTGCTTAGGGAGACAAGATCTGTAAATTTAGCCTGTTACCCTACTGCTTAAGG
1 CTGTTTCC-CTACTGCTTAGGGAGATAAGATCTGTAAATTTAGCCTGTTACCCTACTGCTTAGGG
*
48832881 GTTTAAGGCCCATTGCCTTCGAT
65 GTTTAAGGCCCATCGCCTTCGAT
* * *
48832904 CTGTTTCCGTACTGCTTAGGGTGATAAGATCTGTAAATTTAGCCTGTTATCCTACTGCTTAGGGG
1 CTGTTTCCCTACTGCTTAGGGAGATAAGATCTGTAAATTTAGCCTGTTACCCTACTGCTTAGGGG
48832969 TTTAAGGCCCATCGCCTTCGAT
66 TTTAAGGCCCATCGCCTTCGAT
* *
48832991 CTGTTTCCCTACTGCTTAGGGGGATAAGATCTGTAAATTTAGCCTGTTATCCTACTGCTTAGGGG
1 CTGTTTCCCTACTGCTTAGGGAGATAAGATCTGTAAATTTAGCCTGTTACCCTACTGCTTAGGGG
48833056 TTTAAGGCCCATCGCCTTCGAT
66 TTTAAGGCCCATCGCCTTCGAT
*
48833078 CTGTTTCCCTACTGCTTAGGGGGATAAGATCTGTAAATTTAGCCTGTTACCCTACTGCTTAGGGG
1 CTGTTTCCCTACTGCTTAGGGAGATAAGATCTGTAAATTTAGCCTGTTACCCTACTGCTTAGGGG
48833143 TTTAAGGCCCATCGCCTTCGAT
66 TTTAAGGCCCATCGCCTTCGAT
* *
48833165 CTGTTTCCCTACTGCTTAGGGTGATAAGATCTGTAAATTTAGCCTGTTACCCTACTGCTTAGGCG
1 CTGTTTCCCTACTGCTTAGGGAGATAAGATCTGTAAATTTAGCCTGTTACCCTACTGCTTAGGGG
* *
48833230 TTTAAGGCCCATCACCTTCAAT
66 TTTAAGGCCCATCGCCTTCGAT
* * * *
48833252 CTATTTCCCTACTGCTTAGGGGGTTAAGATCTGTAAATTCAGCCTGTTACCCTACTGCTTAGGGG
1 CTGTTTCCCTACTGCTTAGGGAGATAAGATCTGTAAATTTAGCCTGTTACCCTACTGCTTAGGGG
* *
48833317 TTTAAGGTCCATCACCTTCGAT
66 TTTAAGGCCCATCGCCTTCGAT
* *
48833339 CTGTTTCCCTACTGCTTAAGGG-GTTAAGATCTGTAAATTTGGCCTGTTACCCTACTGCTTAAGG
1 CTGTTTCCCTACTGCTT-AGGGAGATAAGATCTGTAAATTTAGCCTGTTACCCTACTGCTT-AGG
48833403 GG-TTAAGGC
64 GGTTTAAGGC
48833412 TTGTGAATTT
Statistics
Matches: 719, Mismatches: 49, Indels: 9
0.93 0.06 0.01
Matches are distributed among these distances:
87 507 0.71
88 141 0.20
89 71 0.10
ACGTcount: A:0.21, C:0.23, G:0.22, T:0.35
Consensus pattern (87 bp):
CTGTTTCCCTACTGCTTAGGGAGATAAGATCTGTAAATTTAGCCTGTTACCCTACTGCTTAGGGG
TTTAAGGCCCATCGCCTTCGAT
Found at i:48833421 original size:43 final size:43
Alignment explanation
Indices: 48832825--48833409 Score: 216
Period size: 43 Copynumber: 13.5 Consensus size: 43
48832815 ATTTGCTCCA
** *
48832825 CTACTGCTT-AGGGAGACAAGATCTGTAAATTTAGCCTGTTACC
1 CTACTGCTTAAGGG-GTTAAGATCTGTAAATTTGGCCTGTTACC
* ** *** * ** *
48832868 CTACTGCTTAAGGGTTTAAGGCCCAT-TGCCTTCGATCTGTTTCC
1 CTACTGCTTAAGGGGTTAA-GATC-TGTAAATTTGGCCTGTTACC
* * * *
48832912 GTACTGCTT-AGGGTGATAAGATCTGTAAATTTAGCCTGTTATC
1 CTACTGCTTAAGGG-GTTAAGATCTGTAAATTTGGCCTGTTACC
** ** *** * ** *
48832955 CTACTGCTT-AGGGGTTTAAGGCCCATCGCCTTCGATCTGTTTCC
1 CTACTGCTTAAGGGG-TTAAGATCTGT-AAATTTGGCCTGTTACC
* * * *
48832999 CTACTGCTTAGGGGGATAAGATCTGTAAATTTAGCCTGTTATC
1 CTACTGCTTAAGGGGTTAAGATCTGTAAATTTGGCCTGTTACC
** ** *** * ** *
48833042 CTACTGCTT-AGGGGTTTAAGGCCCATCGCCTTCGATCTGTTTCC
1 CTACTGCTTAAGGGG-TTAAGATCTGT-AAATTTGGCCTGTTACC
* * *
48833086 CTACTGCTTAGGGGGATAAGATCTGTAAATTTAGCCTGTTACC
1 CTACTGCTTAAGGGGTTAAGATCTGTAAATTTGGCCTGTTACC
** ** *** * ** *
48833129 CTACTGCTT-AGGGGTTTAAGGCCCATCGCCTTCGATCTGTTTCC
1 CTACTGCTTAAGGGG-TTAAGATCTGT-AAATTTGGCCTGTTACC
* *
48833173 CTACTGCTT-AGGGTGATAAGATCTGTAAATTTAGCCTGTTACC
1 CTACTGCTTAAGGG-GTTAAGATCTGTAAATTTGGCCTGTTACC
* ** ** ** **** * *
48833216 CTACTGCTT-AGGCGTTTAAGGCCCATCACCTTCAATCTATTTCC
1 CTACTGCTTAAGG-GGTTAAGATCTGT-AAATTTGGCCTGTTACC
* **
48833260 CTACTGCTTAGGGGGTTAAGATCTGTAAATTCAGCCTGTTACC
1 CTACTGCTTAAGGGGTTAAGATCTGTAAATTTGGCCTGTTACC
* ** ** * ** *
48833303 CTACTGCTT-AGGGGTTTAAGGTCCATCACCTTCGATCTGTTTCC
1 CTACTGCTTAAGGGG-TTAAGATCTGT-AAATTTGGCCTGTTACC
48833347 CTACTGCTTAAGGGGTTAAGATCTGTAAATTTGGCCTGTTACC
1 CTACTGCTTAAGGGGTTAAGATCTGTAAATTTGGCCTGTTACC
48833390 CTACTGCTTAAGGGGTTAAG
1 CTACTGCTTAAGGGGTTAAG
48833410 GCTTGTGAAT
Statistics
Matches: 365, Mismatches: 157, Indels: 40
0.65 0.28 0.07
Matches are distributed among these distances:
42 14 0.04
43 177 0.48
44 157 0.43
45 17 0.05
ACGTcount: A:0.21, C:0.23, G:0.22, T:0.34
Consensus pattern (43 bp):
CTACTGCTTAAGGGGTTAAGATCTGTAAATTTGGCCTGTTACC
Found at i:48837746 original size:18 final size:19
Alignment explanation
Indices: 48837725--48837988 Score: 108
Period size: 18 Copynumber: 14.3 Consensus size: 19
48837715 GAACAATTAT
* *
48837725 TTATTCAG-TAACAGTCAC
1 TTATTCAGATAACAATCAA
48837743 TTATTC-GATAACAATCAA
1 TTATTCAGATAACAATCAA
* * *
48837761 TTATTCA-ATAATAACCAG
1 TTATTCAGATAACAATCAA
* *
48837779 TTATTCAGTATCGACCAATTGATCGA
1 TTATTCAG-AT--AAC-A---ATCAA
* *
48837805 TTATCCAG-TAACAGTCAA
1 TTATTCAGATAACAATCAA
*
48837823 TTATTTAG-TAA-AATCAGA
1 TTATTCAGATAACAATCA-A
** *
48837841 -TATTCAG-TAGTAATTAA
1 TTATTCAGATAACAATCAA
* * *
48837858 GTATTCAG-TAACAGTCAT
1 TTATTCAGATAACAATCAA
*
48837876 TTATTCAG-TGACAATCAA
1 TTATTCAGATAACAATCAA
* **
48837894 TGATTCAG-TAATGATCAA
1 TTATTCAGATAACAATCAA
* *
48837912 TTATTCAG-TAATATTCAA
1 TTATTCAGATAACAATCAA
*
48837930 TTATTCAG-TAACAGTCAA
1 TTATTCAGATAACAATCAA
* *
48837948 TTATTC-GGTAACAGTCAA
1 TTATTCAGATAACAATCAA
* *
48837966 TTATTCAG-TAATAATCAG
1 TTATTCAGATAACAATCAA
48837984 TTATT
1 TTATT
48837989 TTATACCTTT
Statistics
Matches: 190, Mismatches: 41, Indels: 30
0.73 0.16 0.11
Matches are distributed among these distances:
17 15 0.08
18 157 0.83
19 1 0.01
20 2 0.01
21 1 0.01
22 3 0.02
23 1 0.01
24 1 0.01
26 9 0.05
ACGTcount: A:0.38, C:0.15, G:0.11, T:0.36
Consensus pattern (19 bp):
TTATTCAGATAACAATCAA
Found at i:48837917 original size:54 final size:52
Alignment explanation
Indices: 48837798--48837976 Score: 171
Period size: 54 Copynumber: 3.3 Consensus size: 52
48837788 ATCGACCAAT
* * * * *
48837798 TGATCGATTATCCAGTAACAGTCAATTATTTAGTAAAATCAGATATTCAGTAG
1 TGATCAATTATTCAGTAACAGTCAATTATTCAGTACAATCA-ATATTCAGTAA
* * * *
48837851 TAATTAAGTATTCAGTAACAGTCATTTATTCAGTGACAATCAATGATTCAGTAA
1 TGATCAATTATTCAGTAACAGTCAATTATTCAGT-ACAATCAAT-ATTCAGTAA
* * * *
48837905 TGATCAATTATTCAGTAATATTCAATTATTCAGTAACAGTCAATTATTCGGTAA
1 TGATCAATTATTCAGTAACAGTCAATTATTCAGT-ACAATCAA-TATTCAGTAA
*
48837959 -CAGTCAATTATTCAGTAA
1 TGA-TCAATTATTCAGTAA
48837977 TAATCAGTTA
Statistics
Matches: 103, Mismatches: 19, Indels: 7
0.80 0.15 0.05
Matches are distributed among these distances:
53 30 0.29
54 72 0.70
55 1 0.01
ACGTcount: A:0.38, C:0.13, G:0.13, T:0.36
Consensus pattern (52 bp):
TGATCAATTATTCAGTAACAGTCAATTATTCAGTACAATCAATATTCAGTAA
Found at i:48837988 original size:36 final size:36
Alignment explanation
Indices: 48837804--48837988 Score: 167
Period size: 36 Copynumber: 5.2 Consensus size: 36
48837794 CAATTGATCG
* * *
48837804 ATTATCCAGTAACAGTCAATTATTTAGTAA-AATCA
1 ATTATTCAGTAACAATCAATTATTCAGTAACAATCA
** * * *
48837839 GA-TATTCAGTAGTAATTAAGTATTCAGTAACAGTCA
1 -ATTATTCAGTAACAATCAATTATTCAGTAACAATCA
* * * **
48837875 TTTATTCAGTGACAATCAATGATTCAGTAATGATCA
1 ATTATTCAGTAACAATCAATTATTCAGTAACAATCA
* * *
48837911 ATTATTCAGTAATATTCAATTATTCAGTAACAGTCA
1 ATTATTCAGTAACAATCAATTATTCAGTAACAATCA
* * *
48837947 ATTATTCGGTAACAGTCAATTATTCAGTAATAATCA
1 ATTATTCAGTAACAATCAATTATTCAGTAACAATCA
*
48837983 GTTATT
1 ATTATT
48837989 TTATACCTTT
Statistics
Matches: 115, Mismatches: 32, Indels: 4
0.76 0.21 0.03
Matches are distributed among these distances:
35 21 0.18
36 94 0.82
ACGTcount: A:0.38, C:0.13, G:0.12, T:0.37
Consensus pattern (36 bp):
ATTATTCAGTAACAATCAATTATTCAGTAACAATCA
Found at i:48838388 original size:21 final size:21
Alignment explanation
Indices: 48838354--48838404 Score: 59
Period size: 21 Copynumber: 2.3 Consensus size: 21
48838344 TTCAGTTTTC
*
48838354 AATTAATTTATATTTT-AATT
1 AATTAATGTATATTTTCAATT
48838374 AATTAACTGTATATTTTCAATT
1 AATTAA-TGTATATTTTCAATT
48838396 CAATATAAT
1 -AAT-TAAT
48838405 TCCATTCACT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
20 6 0.23
21 9 0.35
22 4 0.15
23 4 0.15
24 3 0.12
ACGTcount: A:0.41, C:0.06, G:0.02, T:0.51
Consensus pattern (21 bp):
AATTAATGTATATTTTCAATT
Found at i:48845458 original size:22 final size:22
Alignment explanation
Indices: 48845414--48845458 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
48845404 TGCAGCACTA
* *
48845414 TTTTAAGTTCTTCTATCTTCTC
1 TTTTAAGTTCTTCGATCTGCTC
48845436 TTTTAA-TTCTTCGATTCTGCTC
1 TTTTAAGTTCTTCGA-TCTGCTC
48845458 T
1 T
48845459 GACTAGCTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.13, C:0.22, G:0.07, T:0.58
Consensus pattern (22 bp):
TTTTAAGTTCTTCGATCTGCTC
Found at i:48848715 original size:3 final size:3
Alignment explanation
Indices: 48848707--48848924 Score: 56
Period size: 3 Copynumber: 73.0 Consensus size: 3
48848697 CATGATAACT
* * * *
48848707 ATA ATA ATA ATA ATA GTA GTA GTT ATA ATA A-A AGTA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A-TA ATA ATA ATA
* * * * * ***
48848752 CTA A-A TATA ATA ATA ATA GTA TTA GTG ATA A-A ATA ATA GCG ATA
1 ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * * * *
48848796 AAA ATA GA-A ATA ATG ACA ATA ACA ATA A-A GAGTA ATG GTA ATA ATA
1 ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA -A-TA ATA ATA ATA ATA
* * * * * * *
48848842 ATA ATA ATGA A-A ATA AGA GTA ATA TTA GTA ATA CATT A-A ATT ACA
1 ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA
* * * *
48848887 ATA GTA A-A GTA ATA ATA ATA ATA TTA ATA GTA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
48848925 CAAGTAATAA
Statistics
Matches: 149, Mismatches: 51, Indels: 30
0.65 0.22 0.13
Matches are distributed among these distances:
2 11 0.07
3 128 0.86
4 9 0.06
5 1 0.01
ACGTcount: A:0.57, C:0.03, G:0.10, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:48848756 original size:18 final size:18
Alignment explanation
Indices: 48848707--48848769 Score: 65
Period size: 18 Copynumber: 3.5 Consensus size: 18
48848697 CATGATAACT
*
48848707 ATAATAATAATAATAGTA
1 ATAATAATAATAAAAGTA
* * *
48848725 GTAGTTATAATAAAAGTA
1 ATAATAATAATAAAAGTA
*
48848743 ATAATAATACTAAATA-TA
1 ATAATAATAATAAA-AGTA
48848761 ATAATAATA
1 ATAATAATA
48848770 GTATTAGTGA
Statistics
Matches: 36, Mismatches: 8, Indels: 2
0.78 0.17 0.04
Matches are distributed among these distances:
18 35 0.97
19 1 0.03
ACGTcount: A:0.59, C:0.02, G:0.06, T:0.33
Consensus pattern (18 bp):
ATAATAATAATAAAAGTA
Found at i:48849352 original size:3 final size:3
Alignment explanation
Indices: 48849346--48849388 Score: 63
Period size: 3 Copynumber: 15.0 Consensus size: 3
48849336 AAATAAGATG
*
48849346 ATA ATA A-A A-A ATA ATA ATA ATA ATA ACA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
48849389 TATTATGAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
2 4 0.11
3 33 0.89
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (3 bp):
ATA
Found at i:48853817 original size:7 final size:7
Alignment explanation
Indices: 48853807--48853900 Score: 64
Period size: 7 Copynumber: 13.4 Consensus size: 7
48853797 AGTTTAAGAT
48853807 TTAGGGG
1 TTAGGGG
*
48853814 TTAGAGG
1 TTAGGGG
* **
48853821 TTAAGAA
1 TTAGGGG
48853828 TTAGGGG
1 TTAGGGG
*
48853835 TTAGGAGA
1 TTAGG-GG
* *
48853843 TAAGGAG
1 TTAGGGG
48853850 -TAGGGG
1 TTAGGGG
*
48853856 TTATGGG
1 TTAGGGG
* * *
48853863 ATAAGGA
1 TTAGGGG
48853870 TTAGGGG
1 TTAGGGG
48853877 TTAGGGG
1 TTAGGGG
48853884 TTAGGGG
1 TTAGGGG
*
48853891 TTAAGGG
1 TTAGGGG
48853898 TTA
1 TTA
48853901 AGAGTTTATG
Statistics
Matches: 63, Mismatches: 22, Indels: 4
0.71 0.25 0.04
Matches are distributed among these distances:
6 4 0.06
7 54 0.86
8 5 0.08
ACGTcount: A:0.28, C:0.00, G:0.45, T:0.28
Consensus pattern (7 bp):
TTAGGGG
Found at i:48853846 original size:21 final size:21
Alignment explanation
Indices: 48853801--48853881 Score: 85
Period size: 21 Copynumber: 3.9 Consensus size: 21
48853791 AGTTGGAGTT
* *
48853801 TAAGATTTAGGGGTTA-GAGGT
1 TAAGAATTAGGGGTTAGGA-GA
48853822 TAAGAATTAGGGGTTAGGAGA
1 TAAGAATTAGGGGTTAGGAGA
* *
48853843 TAAGGAGTAGGGGTTATGG-GA
1 TAAGAATTAGGGGTTA-GGAGA
*
48853864 TAAGGATTAGGGGTTAGG
1 TAAGAATTAGGGGTTAGG
48853882 GGTTAGGGGT
Statistics
Matches: 53, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
20 2 0.04
21 47 0.89
22 4 0.08
ACGTcount: A:0.31, C:0.00, G:0.42, T:0.27
Consensus pattern (21 bp):
TAAGAATTAGGGGTTAGGAGA
Found at i:48853923 original size:14 final size:14
Alignment explanation
Indices: 48853870--48853922 Score: 52
Period size: 14 Copynumber: 3.7 Consensus size: 14
48853860 GGGATAAGGA
*
48853870 TTAGGGGTTAGGGG
1 TTAGGGGTTAGGGT
48853884 TTAGGGGTTAAGGGT
1 TTAGGGGTT-AGGGT
* * * *
48853899 TAAGAGTTTATGGT
1 TTAGGGGTTAGGGT
48853913 TTAGGGGTTA
1 TTAGGGGTTA
48853923 TAGTCTAAGG
Statistics
Matches: 30, Mismatches: 8, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
14 20 0.67
15 10 0.33
ACGTcount: A:0.21, C:0.00, G:0.43, T:0.36
Consensus pattern (14 bp):
TTAGGGGTTAGGGT
Found at i:48857231 original size:3 final size:3
Alignment explanation
Indices: 48857209--48857278 Score: 81
Period size: 3 Copynumber: 24.0 Consensus size: 3
48857199 GTTTAAAAAG
* * *
48857209 AGA AAA AGA AGA A-A AAA AGA AGA AGA AGA AGA AGA AAA AGA AGA AG-
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
* *
48857255 AGG AGA AGA AAA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA
48857279 GAAAAAATAG
Statistics
Matches: 57, Mismatches: 8, Indels: 4
0.83 0.12 0.06
Matches are distributed among these distances:
2 4 0.07
3 53 0.93
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:48857232 original size:20 final size:21
Alignment explanation
Indices: 48857203--48857285 Score: 95
Period size: 20 Copynumber: 4.2 Consensus size: 21
48857193 TTTAGGGTTT
48857203 AAAAAG-AGAAAAAGAAGAA-
1 AAAAAGAAGAAAAAGAAGAAG
*
48857222 AAAAAGAAGAAGAAGAAGAAG
1 AAAAAGAAGAAAAAGAAGAAG
* *
48857243 AAAAAGAAG-AAGAGGAGAAG
1 AAAAAGAAGAAAAAGAAGAAG
*
48857263 AAAAAGAAGAAGAAG-AGAA-
1 AAAAAGAAGAAAAAGAAGAAG
48857282 AAAA
1 AAAA
48857286 TAGAGATGTA
Statistics
Matches: 55, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
19 10 0.18
20 33 0.60
21 12 0.22
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (21 bp):
AAAAAGAAGAAAAAGAAGAAG
Found at i:48857245 original size:32 final size:32
Alignment explanation
Indices: 48857209--48857276 Score: 100
Period size: 32 Copynumber: 2.1 Consensus size: 32
48857199 GTTTAAAAAG
*
48857209 AGAAAAAGAAGAAAAAAAGAAGAAGAAGAAGA
1 AGAAAAAGAAGAAAAAAAGAAGAAAAAGAAGA
* **
48857241 AGAAAAAGAAGAAGAGGAGAAGAAAAAGAAGA
1 AGAAAAAGAAGAAAAAAAGAAGAAAAAGAAGA
48857273 AGAA
1 AGAA
48857277 GAGAAAAAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (32 bp):
AGAAAAAGAAGAAAAAAAGAAGAAAAAGAAGA
Found at i:48858571 original size:3 final size:3
Alignment explanation
Indices: 48858565--48858618 Score: 99
Period size: 3 Copynumber: 18.0 Consensus size: 3
48858555 TTTTACAATC
*
48858565 TCT TCT TTT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
48858613 TCT TCT
1 TCT TCT
48858619 CTGTTATTAA
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TCT
Found at i:48858721 original size:21 final size:21
Alignment explanation
Indices: 48858695--48858734 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
48858685 AACGTGGCAA
48858695 GTTAACTTGCCACATCAGCTG
1 GTTAACTTGCCACATCAGCTG
48858716 GTTAACTTGCCACATCAGC
1 GTTAACTTGCCACATCAGC
48858735 AGTCCCGTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.25, C:0.30, G:0.17, T:0.28
Consensus pattern (21 bp):
GTTAACTTGCCACATCAGCTG
Found at i:48858822 original size:30 final size:31
Alignment explanation
Indices: 48858770--48858837 Score: 95
Period size: 30 Copynumber: 2.2 Consensus size: 31
48858760 CTGTTAATCG
*
48858770 GTGACTGTTTTGTCACTTTTTTATAACGTT-A
1 GTGACTGTTTTGTCACTTTTTTA-AAAGTTGA
*
48858801 GTGACTGTTTTGTTA-TTTTTTAAAAGTTGA
1 GTGACTGTTTTGTCACTTTTTTAAAAGTTGA
48858831 GTGACTG
1 GTGACTG
48858838 ATATGAAACC
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
29 5 0.15
30 15 0.44
31 14 0.41
ACGTcount: A:0.21, C:0.09, G:0.21, T:0.50
Consensus pattern (31 bp):
GTGACTGTTTTGTCACTTTTTTAAAAGTTGA
Found at i:48859989 original size:23 final size:22
Alignment explanation
Indices: 48859963--48860009 Score: 67
Period size: 23 Copynumber: 2.1 Consensus size: 22
48859953 TGGATTAATA
*
48859963 AAAGTAAAAGACATGTCTATATT
1 AAAGCAAAAGACATGT-TATATT
*
48859986 AAAGCAAAAGACATGTTATTTT
1 AAAGCAAAAGACATGTTATATT
48860008 AA
1 AA
48860010 TTATTATAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 7 0.32
23 15 0.68
ACGTcount: A:0.49, C:0.09, G:0.13, T:0.30
Consensus pattern (22 bp):
AAAGCAAAAGACATGTTATATT
Found at i:48860030 original size:19 final size:19
Alignment explanation
Indices: 48860006--48860108 Score: 65
Period size: 19 Copynumber: 5.3 Consensus size: 19
48859996 ACATGTTATT
48860006 TTAATTATTATAATTTGGA
1 TTAATTATTATAATTTGGA
48860025 TTAATTTATGTA-AATATT--A
1 TTAA-TTAT-TATAAT-TTGGA
* *
48860044 TTTATTTAATATAATTTGGA
1 -TTAATTATTATAATTTGGA
48860064 TTAATTTATT-TAAATATT--A
1 TTAA-TTATTAT-AAT-TTGGA
*
48860083 TTTAATTAATATAATTTGGA
1 -TTAATTATTATAATTTGGA
48860103 TTAATT
1 TTAATT
48860109 TATTTAAATA
Statistics
Matches: 65, Mismatches: 5, Indels: 28
0.66 0.05 0.29
Matches are distributed among these distances:
18 6 0.09
19 29 0.45
20 24 0.37
21 6 0.09
ACGTcount: A:0.39, C:0.00, G:0.07, T:0.54
Consensus pattern (19 bp):
TTAATTATTATAATTTGGA
Found at i:48860058 original size:39 final size:39
Alignment explanation
Indices: 48860005--48860119 Score: 203
Period size: 39 Copynumber: 2.9 Consensus size: 39
48859995 GACATGTTAT
* *
48860005 TTTAATTATTATAATTTGGATTAATTTATGTAAATATTA
1 TTTAATTAATATAATTTGGATTAATTTATTTAAATATTA
*
48860044 TTTATTTAATATAATTTGGATTAATTTATTTAAATATTA
1 TTTAATTAATATAATTTGGATTAATTTATTTAAATATTA
48860083 TTTAATTAATATAATTTGGATTAATTTATTTAAATAT
1 TTTAATTAATATAATTTGGATTAATTTATTTAAATAT
48860120 ATAAGAATTT
Statistics
Matches: 72, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 72 1.00
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (39 bp):
TTTAATTAATATAATTTGGATTAATTTATTTAAATATTA
Found at i:48860090 original size:24 final size:24
Alignment explanation
Indices: 48860043--48860092 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
48860033 TGTAAATATT
*
48860043 ATTTATTTAATATAATTTGGATTA
1 ATTTATTTAATATAATTTGAATTA
*
48860067 ATTTATTTAAATATTATTT-AATTA
1 ATTTATTT-AATATAATTTGAATTA
48860091 AT
1 AT
48860093 ATAATTTGGA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 14 0.61
25 9 0.39
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (24 bp):
ATTTATTTAATATAATTTGAATTA
Found at i:48860243 original size:18 final size:18
Alignment explanation
Indices: 48860220--48860320 Score: 166
Period size: 18 Copynumber: 5.6 Consensus size: 18
48860210 TATATAATTG
48860220 AACTTACATAACTCACAT
1 AACTTACATAACTCACAT
* *
48860238 AACTTACATAACTTATAT
1 AACTTACATAACTCACAT
*
48860256 AACTCACATAACTCACAT
1 AACTTACATAACTCACAT
48860274 AACTTACATAACTCACAT
1 AACTTACATAACTCACAT
*
48860292 AACTCACATAACTCACAT
1 AACTTACATAACTCACAT
48860310 AACTTACATAA
1 AACTTACATAA
48860321 TACATAAGTA
Statistics
Matches: 75, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 75 1.00
ACGTcount: A:0.46, C:0.27, G:0.00, T:0.28
Consensus pattern (18 bp):
AACTTACATAACTCACAT
Found at i:48860355 original size:9 final size:9
Alignment explanation
Indices: 48860220--48860358 Score: 149
Period size: 9 Copynumber: 15.7 Consensus size: 9
48860210 TATATAATTG
48860220 AACTTACAT
1 AACTTACAT
*
48860229 AACTCACAT
1 AACTTACAT
48860238 AACTTACAT
1 AACTTACAT
*
48860247 AACTTATAT
1 AACTTACAT
*
48860256 AACTCACAT
1 AACTTACAT
*
48860265 AACTCACAT
1 AACTTACAT
48860274 AACTTACAT
1 AACTTACAT
*
48860283 AACTCACAT
1 AACTTACAT
*
48860292 AACTCACAT
1 AACTTACAT
*
48860301 AACTCACAT
1 AACTTACAT
48860310 AACTTACAT
1 AACTTACAT
48860319 AA--TACAT
1 AACTTACAT
* *
48860326 AA-GTAGAT
1 AACTTACAT
* *
48860334 AGCATATCAT
1 AACTTA-CAT
48860344 AACTTACAT
1 AACTTACAT
48860353 AACTTA
1 AACTTA
48860359 ATTATACTTA
Statistics
Matches: 113, Mismatches: 14, Indels: 6
0.85 0.11 0.05
Matches are distributed among these distances:
7 7 0.06
8 5 0.04
9 95 0.84
10 6 0.05
ACGTcount: A:0.45, C:0.24, G:0.02, T:0.29
Consensus pattern (9 bp):
AACTTACAT
Found at i:48865432 original size:13 final size:14
Alignment explanation
Indices: 48865416--48865444 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
48865406 TTATAAATAT
48865416 TTATAAT-GTTTAA
1 TTATAATGGTTTAA
48865429 TTATAATGGTTTAA
1 TTATAATGGTTTAA
48865443 TT
1 TT
48865445 CCTCATTAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.34, C:0.00, G:0.10, T:0.55
Consensus pattern (14 bp):
TTATAATGGTTTAA
Found at i:48865907 original size:21 final size:21
Alignment explanation
Indices: 48865863--48865915 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
48865853 AGGCAGTAGA
* *
48865863 GAGGGAGGGAGCGACAGCAAC
1 GAGGGAGGCAGCGACAACAAC
*
48865884 GAGGGAGGCAGCGACAACAGC
1 GAGGGAGGCAGCGACAACAAC
*
48865905 GAGAGAGGCAG
1 GAGGGAGGCAG
48865916 AAGCAGTAGC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.34, C:0.19, G:0.47, T:0.00
Consensus pattern (21 bp):
GAGGGAGGCAGCGACAACAAC
Found at i:48866348 original size:29 final size:29
Alignment explanation
Indices: 48866305--48866360 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
48866295 AAGCCATGAT
*
48866305 TTTTAGCGGCACTTTTCCCACAAACACAC
1 TTTTAGCAGCACTTTTCCCACAAACACAC
*
48866334 TTTTAGCAGCGCTTTTCCCACAAACAC
1 TTTTAGCAGCACTTTTCCCACAAACAC
48866361 GCCGCTAAAA
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:0.27, C:0.34, G:0.11, T:0.29
Consensus pattern (29 bp):
TTTTAGCAGCACTTTTCCCACAAACACAC
Found at i:48869686 original size:46 final size:47
Alignment explanation
Indices: 48869588--48869758 Score: 185
Period size: 46 Copynumber: 3.7 Consensus size: 47
48869578 CACTCGTGTG
**
48869588 AGCTAGTGTAAGACATGTCTGGGACATGGCATCCATATT-GAGACG-A
1 AGCTAGTGTAAGACATGTCTGGGACATGGCAT-CAGCTTCGAGACGTA
* *
48869634 GTGCTAGTGTAAGACATGTTTGGGACAT-GCATCAGCTTCGAGACGTA
1 -AGCTAGTGTAAGACATGTCTGGGACATGGCATCAGCTTCGAGACGTA
* * * *
48869681 AGCTAGTGTAAGACATGTCTGGAACAT-GCATCGGCTACGAGATGT-
1 AGCTAGTGTAAGACATGTCTGGGACATGGCATCAGCTTCGAGACGTA
48869726 -G-TCAGTGTAAGACCATGTCTGGGACATGGCATC
1 AGCT-AGTGTAAGA-CATGTCTGGGACATGGCATC
48869759 GGCACAGATA
Statistics
Matches: 108, Mismatches: 11, Indels: 11
0.83 0.08 0.08
Matches are distributed among these distances:
43 1 0.01
44 10 0.09
45 17 0.16
46 54 0.50
47 26 0.24
ACGTcount: A:0.27, C:0.18, G:0.29, T:0.25
Consensus pattern (47 bp):
AGCTAGTGTAAGACATGTCTGGGACATGGCATCAGCTTCGAGACGTA
Found at i:48873203 original size:11 final size:11
Alignment explanation
Indices: 48873168--48873195 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
48873158 GAGAGTAAGA
48873168 AATTTTAATGT
1 AATTTTAATGT
48873179 AATTTTAATGT
1 AATTTTAATGT
48873190 AATTTT
1 AATTTT
48873196 GATATAATGT
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:0.36, C:0.00, G:0.07, T:0.57
Consensus pattern (11 bp):
AATTTTAATGT
Found at i:48878875 original size:16 final size:16
Alignment explanation
Indices: 48878856--48878891 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
48878846 AAAATATAAT
48878856 AAAATAATAATATTAA
1 AAAATAATAATATTAA
* *
48878872 AAAATTATATTATTAA
1 AAAATAATAATATTAA
48878888 AAAA
1 AAAA
48878892 ATAAGTCGCG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (16 bp):
AAAATAATAATATTAA
Found at i:48880405 original size:24 final size:25
Alignment explanation
Indices: 48880359--48880405 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
48880349 ATATTTATTT
48880359 TTATATCATAAAAGATTAAAATTAA
1 TTATATCATAAAAGATTAAAATTAA
*
48880384 TTATAT-ATTAAAA-ATTAGAATT
1 TTATATCA-TAAAAGATTAAAATT
48880406 TGATTCAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 9 0.45
25 11 0.55
ACGTcount: A:0.53, C:0.02, G:0.04, T:0.40
Consensus pattern (25 bp):
TTATATCATAAAAGATTAAAATTAA
Found at i:48882975 original size:49 final size:49
Alignment explanation
Indices: 48882918--48883019 Score: 177
Period size: 49 Copynumber: 2.1 Consensus size: 49
48882908 CCAGAGGAAT
*
48882918 CCATAACACGAAGGGAAAGTTGGAGTATATTCATTATGATCTGTGGGGG
1 CCATAACACGAAGGGAAAGTTGGAGTATATTCATTATGATCTGTGGCGG
* *
48882967 CCATAACACGAAGGGAACGTTGGAGTATATTCATTCTGATCTGTGGCGG
1 CCATAACACGAAGGGAAAGTTGGAGTATATTCATTATGATCTGTGGCGG
48883016 CCAT
1 CCAT
48883020 CTAGAGTGCC
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
49 50 1.00
ACGTcount: A:0.28, C:0.17, G:0.28, T:0.26
Consensus pattern (49 bp):
CCATAACACGAAGGGAAAGTTGGAGTATATTCATTATGATCTGTGGCGG
Found at i:48886778 original size:30 final size:30
Alignment explanation
Indices: 48886731--48886809 Score: 103
Period size: 30 Copynumber: 2.8 Consensus size: 30
48886721 TTTAAATAAC
* *
48886731 TTTTAAA-T-AAT-TAAATTATTTGTTAAA
1 TTTTAAATTAAATATAAATTACTTGTGAAA
48886758 TTTTAAATTAAATATAAATTACTTGTGAAA
1 TTTTAAATTAAATATAAATTACTTGTGAAA
*
48886788 TTTTAAATTAAA-ATAATTTACT
1 TTTTAAATTAAATATAAATTACT
48886810 AATTAAATTT
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
27 7 0.15
28 1 0.02
29 12 0.26
30 26 0.57
ACGTcount: A:0.46, C:0.03, G:0.04, T:0.48
Consensus pattern (30 bp):
TTTTAAATTAAATATAAATTACTTGTGAAA
Found at i:48886817 original size:29 final size:30
Alignment explanation
Indices: 48886753--48886819 Score: 91
Period size: 29 Copynumber: 2.3 Consensus size: 30
48886743 AAATTATTTG
**
48886753 TTAAATTTTAAATTAAATATAAATTACTTG
1 TTAAATTTTAAATTAAATATAAATTACTAA
* *
48886783 TGAAATTTTAAATTAAA-ATAATTTACTAA
1 TTAAATTTTAAATTAAATATAAATTACTAA
48886812 TTAAATTT
1 TTAAATTT
48886820 AATAATTTTA
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
29 16 0.50
30 16 0.50
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.46
Consensus pattern (30 bp):
TTAAATTTTAAATTAAATATAAATTACTAA
Found at i:48887330 original size:32 final size:31
Alignment explanation
Indices: 48887269--48887330 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 31
48887259 ATAATTTACA
*
48887269 TATTATAATATTAAATTATTTAAATATTATT
1 TATTATAATATTAAATTATTTAAAAATTATT
*
48887300 TATTATTATATTTAAA-TATTTAAAAAATTAT
1 TATTATAATA-TTAAATTATTT-AAAAATTAT
48887331 ATATAAATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
31 14 0.52
32 13 0.48
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (31 bp):
TATTATAATATTAAATTATTTAAAAATTATT
Found at i:48887332 original size:22 final size:23
Alignment explanation
Indices: 48887304--48887357 Score: 67
Period size: 22 Copynumber: 2.3 Consensus size: 23
48887294 ATTATTTATT
48887304 ATTATATTTAAATATTTA-AAA-A
1 ATTATATTTAAAT-TTTACAAATA
*
48887326 ATTATATATAAATTTTACAAATA
1 ATTATATTTAAATTTTACAAATA
48887349 ATTTATATT
1 A-TTATATT
48887358 AATTACTTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
21 4 0.15
22 15 0.56
23 2 0.07
24 6 0.22
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (23 bp):
ATTATATTTAAATTTTACAAATA
Found at i:48888087 original size:11 final size:13
Alignment explanation
Indices: 48888061--48888092 Score: 50
Period size: 11 Copynumber: 2.6 Consensus size: 13
48888051 CTTGAAATTG
48888061 TTAAATATATGAA
1 TTAAATATATGAA
48888074 TTAAAT-TA-GAA
1 TTAAATATATGAA
48888085 TTAAATAT
1 TTAAATAT
48888093 TATCAGTTGG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 9 0.50
12 3 0.17
13 6 0.33
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.41
Consensus pattern (13 bp):
TTAAATATATGAA
Found at i:48899108 original size:8 final size:8
Alignment explanation
Indices: 48899097--48899121 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
48899087 TTTAATAAGA
48899097 TATTTTAT
1 TATTTTAT
48899105 TATTTTAT
1 TATTTTAT
48899113 TATTTTAT
1 TATTTTAT
48899121 T
1 T
48899122 TAGTATATAT
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:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (8 bp):
TATTTTAT
Found at i:48901897 original size:28 final size:26
Alignment explanation
Indices: 48901824--48901936 Score: 136
Period size: 27 Copynumber: 4.2 Consensus size: 26
48901814 TGGAGGAAGC
*
48901824 GTTCTGGTGGCTCTGCCACAAATATCT
1 GTTCTAGTGGCTCTGCCAC-AATATCT
*
48901851 GATCTAGTGGCTCTGCCACAAATATCT
1 GTTCTAGTGGCTCTGCCAC-AATATCT
*
48901878 GTTCCTGGTGGCTCTGCCACAATATCT
1 GTT-CTAGTGGCTCTGCCACAATATCT
* *
48901905 GTATCTAGTGACTCTGTCACAATATCT
1 GT-TCTAGTGGCTCTGCCACAATATCT
*
48901932 ATTCT
1 GTTCT
48901937 GGCAGCCATG
Statistics
Matches: 76, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
26 3 0.04
27 57 0.75
28 16 0.21
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.35
Consensus pattern (26 bp):
GTTCTAGTGGCTCTGCCACAATATCT
Found at i:48901911 original size:55 final size:54
Alignment explanation
Indices: 48901827--48901931 Score: 167
Period size: 55 Copynumber: 1.9 Consensus size: 54
48901817 AGGAAGCGTT
*
48901827 CTGGTGGCTCTGCCACAAATATCTGATCTAGTGGCTCTGCCACAAATATCTGTTC
1 CTGGTGGCTCTGCCACAAATATCTGATCTAGTGACTCTGCCAC-AATATCTGTTC
*
48901882 CTGGTGGCTCTGCCAC-AATATCTGTATCTAGTGACTCTGTCACAATATCT
1 CTGGTGGCTCTGCCACAAATATCTG-ATCTAGTGACTCTGCCACAATATCT
48901932 ATTCTGGCAG
Statistics
Matches: 47, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
54 15 0.32
55 32 0.68
ACGTcount: A:0.22, C:0.27, G:0.19, T:0.32
Consensus pattern (54 bp):
CTGGTGGCTCTGCCACAAATATCTGATCTAGTGACTCTGCCACAATATCTGTTC
Found at i:48904741 original size:46 final size:46
Alignment explanation
Indices: 48904663--48904755 Score: 125
Period size: 46 Copynumber: 2.0 Consensus size: 46
48904653 GAGTTCGCCC
*
48904663 AGGTTCCGAGCTCTTGAATATATAGCGAACTCGAGAATACATGAAT
1 AGGTTCCGAGCTCTTGAATATATAGCGAACTCGAGAATACAGGAAT
* * * *
48904709 AGGTTCCGAGCT-TCTGCATATGTTGCGGACTCGAGAATACAGGAAT
1 AGGTTCCGAGCTCT-TGAATATATAGCGAACTCGAGAATACAGGAAT
48904755 A
1 A
48904756 TTAAGCCTTG
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
45 1 0.02
46 40 0.98
ACGTcount: A:0.31, C:0.18, G:0.25, T:0.26
Consensus pattern (46 bp):
AGGTTCCGAGCTCTTGAATATATAGCGAACTCGAGAATACAGGAAT
Found at i:48906269 original size:5 final size:5
Alignment explanation
Indices: 48906255--48906295 Score: 75
Period size: 5 Copynumber: 8.4 Consensus size: 5
48906245 TTTTATTTAG
48906255 ATTAT A-TAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT AT
1 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT AT
48906296 AATTGATTAT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
4 4 0.11
5 31 0.89
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
ATTAT
Found at i:48906304 original size:12 final size:12
Alignment explanation
Indices: 48906255--48906316 Score: 53
Period size: 12 Copynumber: 5.3 Consensus size: 12
48906245 TTTTATTTAG
48906255 ATTA-TATATATT
1 ATTATTATA-ATT
48906267 A-TATTAT-ATT
1 ATTATTATAATT
*
48906277 A-TATTATATTAT
1 ATTATTATAAT-T
48906289 ATTA-TATAATT
1 ATTATTATAATT
48906300 GATTATTATAATT
1 -ATTATTATAATT
48906313 ATTA
1 ATTA
48906317 ATTGTTATGG
Statistics
Matches: 42, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
10 10 0.24
11 4 0.10
12 19 0.45
13 9 0.21
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (12 bp):
ATTATTATAATT
Found at i:48906306 original size:20 final size:20
Alignment explanation
Indices: 48906263--48906324 Score: 69
Period size: 20 Copynumber: 3.1 Consensus size: 20
48906253 AGATTATATA
48906263 TATTATATTATATTATATT-A-
1 TATTATATTATA-TA-ATTGAT
48906283 TATTATATTATATAATTGAT
1 TATTATATTATATAATTGAT
48906303 TATTATAATTAT-TAATTG-T
1 TATTAT-ATTATATAATTGAT
48906322 TAT
1 TAT
48906325 GGTTTTATAT
Statistics
Matches: 39, Mismatches: 0, Indels: 7
0.85 0.00 0.15
Matches are distributed among these distances:
18 3 0.08
19 7 0.18
20 24 0.62
21 5 0.13
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (20 bp):
TATTATATTATATAATTGAT
Found at i:48907929 original size:12 final size:12
Alignment explanation
Indices: 48907912--48907936 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
48907902 GTCGACTACT
48907912 GTTACTGTTACC
1 GTTACTGTTACC
48907924 GTTACTGTTACC
1 GTTACTGTTACC
48907936 G
1 G
48907937 ATTCGACACT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.24, G:0.20, T:0.40
Consensus pattern (12 bp):
GTTACTGTTACC
Found at i:48907964 original size:45 final size:45
Alignment explanation
Indices: 48907914--48908007 Score: 154
Period size: 45 Copynumber: 2.1 Consensus size: 45
48907904 CGACTACTGT
*
48907914 TACTGTTACCGTTACTGTTACCGATTC-GACACTTTGTGTGTAGAA
1 TACTGTTACCGTTACTGTTACAGATTCAG-CACTTTGTGTGTAGAA
*
48907959 TACTGTTACCGTTACTGTTACAGATTCAGCACTTTGTGTGTTGAA
1 TACTGTTACCGTTACTGTTACAGATTCAGCACTTTGTGTGTAGAA
48908004 TACT
1 TACT
48908008 ATTAATGTTA
Statistics
Matches: 46, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
45 45 0.98
46 1 0.02
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.39
Consensus pattern (45 bp):
TACTGTTACCGTTACTGTTACAGATTCAGCACTTTGTGTGTAGAA
Found at i:48908017 original size:51 final size:49
Alignment explanation
Indices: 48907899--48908018 Score: 124
Period size: 45 Copynumber: 2.4 Consensus size: 49
48907889 CAGGCACTTA
* * *
48907899 TGTGTCGACTACTGTTACTGTTACCGTTACTGTTACCGATTCGACACTTTG
1 TGTGTAGAATACT-TTA-TGTTACCGTTACTGTTACAGATTCGACACTTTG
48907950 TGTGTAGAATAC----TGTTACCGTTACTGTTACAGATTC-AGCACTTTG
1 TGTGTAGAATACTTTATGTTACCGTTACTGTTACAGATTCGA-CACTTTG
*
48907995 TGTGTTGAATACTATTAATGTTAC
1 TGTGTAGAATACT-TT-ATGTTAC
48908019 TGCTACTGCT
Statistics
Matches: 58, Mismatches: 4, Indels: 14
0.76 0.05 0.18
Matches are distributed among these distances:
44 1 0.02
45 41 0.71
51 16 0.28
ACGTcount: A:0.23, C:0.18, G:0.19, T:0.40
Consensus pattern (49 bp):
TGTGTAGAATACTTTATGTTACCGTTACTGTTACAGATTCGACACTTTG
Found at i:48908018 original size:45 final size:45
Alignment explanation
Indices: 48907914--48908020 Score: 135
Period size: 45 Copynumber: 2.4 Consensus size: 45
48907904 CGACTACTGT
* * *
48907914 TACTGTTACCGTTACTGTTACCGATTCGACACTTTGTGTGTAGAA
1 TACTATTAACGTTACTGTTACAGATTCGACACTTTGTGTGTAGAA
* * *
48907959 TACTGTTACCGTTACTGTTACAGATTC-AGCACTTTGTGTGTTGAA
1 TACTATTAACGTTACTGTTACAGATTCGA-CACTTTGTGTGTAGAA
*
48908004 TACTATTAATGTTACTG
1 TACTATTAACGTTACTG
48908021 CTACTGCTAC
Statistics
Matches: 56, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
44 1 0.02
45 55 0.98
ACGTcount: A:0.23, C:0.18, G:0.19, T:0.40
Consensus pattern (45 bp):
TACTATTAACGTTACTGTTACAGATTCGACACTTTGTGTGTAGAA
Found at i:48915642 original size:13 final size:13
Alignment explanation
Indices: 48915616--48915679 Score: 65
Period size: 13 Copynumber: 4.9 Consensus size: 13
48915606 AGTTTGGCAA
*
48915616 TGCTTTTAAAAAG
1 TGCTTTTGAAAAG
*
48915629 TGCTTTTGAGAAG
1 TGCTTTTGAAAAG
* ***
48915642 TGATGGGGAAAAG
1 TGCTTTTGAAAAG
*
48915655 TGCTTTTGAGAAG
1 TGCTTTTGAAAAG
48915668 TGCTTTTGAAAA
1 TGCTTTTGAAAA
48915680 ATTTAGTTTA
Statistics
Matches: 38, Mismatches: 13, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
13 38 1.00
ACGTcount: A:0.31, C:0.06, G:0.28, T:0.34
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Found at i:48915678 original size:26 final size:26
Alignment explanation
Indices: 48915616--48915679 Score: 83
Period size: 26 Copynumber: 2.5 Consensus size: 26
48915606 AGTTTGGCAA
*
48915616 TGCTTTTAAAAAGTGCTTTTGAGAAG
1 TGCTTTTGAAAAGTGCTTTTGAGAAG
* ***
48915642 TGATGGGGAAAAGTGCTTTTGAGAAG
1 TGCTTTTGAAAAGTGCTTTTGAGAAG
48915668 TGCTTTTGAAAA
1 TGCTTTTGAAAA
48915680 ATTTAGTTTA
Statistics
Matches: 29, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.31, C:0.06, G:0.28, T:0.34
Consensus pattern (26 bp):
TGCTTTTGAAAAGTGCTTTTGAGAAG
Found at i:48917183 original size:37 final size:37
Alignment explanation
Indices: 48917122--48917200 Score: 106
Period size: 37 Copynumber: 2.1 Consensus size: 37
48917112 TTATTACGAA
* *
48917122 GTCTTACCCAGACATAATCTCCACACGAAGTTATCGG
1 GTCTTACCCAGACAAAATCTCCACACGAAGTCATCGG
* *
48917159 GTCTTACCCGGACAAAAT-TCCCACACGTAGTCATCGG
1 GTCTTACCCAGACAAAATCT-CCACACGAAGTCATCGG
48917196 GTCTT
1 GTCTT
48917201 TAGAGCTCGG
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
36 1 0.03
37 36 0.97
ACGTcount: A:0.27, C:0.30, G:0.18, T:0.25
Consensus pattern (37 bp):
GTCTTACCCAGACAAAATCTCCACACGAAGTCATCGG
Found at i:48917397 original size:47 final size:47
Alignment explanation
Indices: 48917320--48917745 Score: 744
Period size: 47 Copynumber: 9.1 Consensus size: 47
48917310 CCTTCGGGAT
* * * * * * *
48917320 TTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGCC
1 TTATCACGTATATACACTTTCACATTCATCACATCGGCCATTAGGCC
* * *
48917367 CTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCC
1 TTATCACGTATATACACTTTCACATTCATCACATCGGCCATTAGGCC
48917414 TTATCACGTATATACACTTTCACATTCATCACATCGGCCATTAGGCC
1 TTATCACGTATATACACTTTCACATTCATCACATCGGCCATTAGGCC
48917461 TTATCACGTATATACACTTTCACATTCATCACATCGGCCATTAGGCC
1 TTATCACGTATATACACTTTCACATTCATCACATCGGCCATTAGGCC
48917508 TTATCACGTATATACACTTTCACATTCATCACATCGGCCATTAGGCC
1 TTATCACGTATATACACTTTCACATTCATCACATCGGCCATTAGGCC
48917555 TTATCACGTATATACACTTTCACATTCATCACATCGGCCATTAGGCC
1 TTATCACGTATATACACTTTCACATTCATCACATCGGCCATTAGGCC
48917602 TTATCACGTATATACACTTTCACATTCATCACATCGGCCATTAGGCC
1 TTATCACGTATATACACTTTCACATTCATCACATCGGCCATTAGGCC
48917649 TTATCACGTATATACACTTTCACATTCATCACATCGGCCATTAGGCC
1 TTATCACGTATATACACTTTCACATTCATCACATCGGCCATTAGGCC
* *
48917696 TTATCTCATATATACACTTTCACATTCATCACATCGGCCATTAGGCC
1 TTATCACGTATATACACTTTCACATTCATCACATCGGCCATTAGGCC
48917743 TTA
1 TTA
48917746 CTATCATTTC
Statistics
Matches: 366, Mismatches: 13, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
47 366 1.00
ACGTcount: A:0.27, C:0.30, G:0.10, T:0.32
Consensus pattern (47 bp):
TTATCACGTATATACACTTTCACATTCATCACATCGGCCATTAGGCC
Found at i:48923219 original size:20 final size:20
Alignment explanation
Indices: 48923194--48923264 Score: 97
Period size: 20 Copynumber: 3.5 Consensus size: 20
48923184 GGTTCATTGG
48923194 ATGGAAAATGGATGTATGAA
1 ATGGAAAATGGATGTATGAA
* *
48923214 ATGGAAAATAGATGTATGGA
1 ATGGAAAATGGATGTATGAA
* * *
48923234 ATGAAAAATGGTTATATGAA
1 ATGGAAAATGGATGTATGAA
48923254 ATGGAAAATGG
1 ATGGAAAATGG
48923265 TTATTTGAAT
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.46, C:0.00, G:0.28, T:0.25
Consensus pattern (20 bp):
ATGGAAAATGGATGTATGAA
Found at i:48923265 original size:20 final size:20
Alignment explanation
Indices: 48923194--48923278 Score: 89
Period size: 20 Copynumber: 4.2 Consensus size: 20
48923184 GGTTCATTGG
*
48923194 ATGGAAAATGGATGTATGAA
1 ATGGAAAATGGATATATGAA
* * *
48923214 ATGGAAAATAGATGTATGGA
1 ATGGAAAATGGATATATGAA
* *
48923234 ATGAAAAATGGTTATATGAA
1 ATGGAAAATGGATATATGAA
* *
48923254 ATGGAAAATGGTTATTTGAA
1 ATGGAAAATGGATATATGAA
*
48923274 TTGGA
1 ATGGA
48923279 GATGATTGTA
Statistics
Matches: 55, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 55 1.00
ACGTcount: A:0.44, C:0.00, G:0.27, T:0.29
Consensus pattern (20 bp):
ATGGAAAATGGATATATGAA
Found at i:48926055 original size:27 final size:28
Alignment explanation
Indices: 48926027--48926115 Score: 96
Period size: 25 Copynumber: 3.2 Consensus size: 28
48926017 ACTTGGTTTT
48926027 AATAAAACTATATTTCATGCTTTAATTA
1 AATAAAACTATATTTCATGCTTTAATTA
* * * *
48926055 AATAAAAACAATAGTTTAAAG-GTT--TT-
1 AAT-AAAACTATA-TTTCATGCTTTAATTA
48926081 AATAAAACTATATTTCATGCTTTAATTA
1 AATAAAACTATATTTCATGCTTTAATTA
48926109 AATAAAA
1 AATAAAA
48926116 ACCATATGTT
Statistics
Matches: 47, Mismatches: 8, Indels: 12
0.70 0.12 0.18
Matches are distributed among these distances:
24 5 0.11
25 10 0.21
26 3 0.06
27 4 0.09
28 10 0.21
29 10 0.21
30 5 0.11
ACGTcount: A:0.48, C:0.08, G:0.06, T:0.38
Consensus pattern (28 bp):
AATAAAACTATATTTCATGCTTTAATTA
Found at i:48927461 original size:49 final size:49
Alignment explanation
Indices: 48927389--48927486 Score: 178
Period size: 49 Copynumber: 2.0 Consensus size: 49
48927379 AAGTTTTGGG
* *
48927389 CTGCTAGAGGTCCTTATGATATTCGACCATATATGGGTTTGTTGAAATT
1 CTGCTAGAGGTCCCTATGATATTCGACCATAAATGGGTTTGTTGAAATT
48927438 CTGCTAGAGGTCCCTATGATATTCGACCATAAATGGGTTTGTTGAAATT
1 CTGCTAGAGGTCCCTATGATATTCGACCATAAATGGGTTTGTTGAAATT
48927487 ATGTGTATTT
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 47 1.00
ACGTcount: A:0.26, C:0.15, G:0.22, T:0.37
Consensus pattern (49 bp):
CTGCTAGAGGTCCCTATGATATTCGACCATAAATGGGTTTGTTGAAATT
Found at i:48933930 original size:30 final size:29
Alignment explanation
Indices: 48933896--48933957 Score: 88
Period size: 29 Copynumber: 2.1 Consensus size: 29
48933886 AATTCTGGGT
*
48933896 AAAACTATAAAAATCTAAAAAATAGGGGCA
1 AAAACTAT-AAAACCTAAAAAATAGGGGCA
* *
48933926 AAAACTGTAAAACCTAAAAAATATGGGCA
1 AAAACTATAAAACCTAAAAAATAGGGGCA
48933955 AAA
1 AAA
48933958 TTGTAAAATA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 22 0.76
30 7 0.24
ACGTcount: A:0.60, C:0.11, G:0.13, T:0.16
Consensus pattern (29 bp):
AAAACTATAAAACCTAAAAAATAGGGGCA
Found at i:48933957 original size:28 final size:28
Alignment explanation
Indices: 48933891--48933965 Score: 87
Period size: 29 Copynumber: 2.6 Consensus size: 28
48933881 CGTAAAATTC
* * *
48933891 TGGGTAAAACTATAAAAATCTAAAAAATA
1 TGGGCAAAACTGT-AAAACCTAAAAAATA
*
48933920 GGGGCAAAAACTGTAAAACCTAAAAAATA
1 TGGGC-AAAACTGTAAAACCTAAAAAATA
*
48933949 TGGGCAAAATTGTAAAA
1 TGGGCAAAACTGTAAAA
48933966 TACAAAAAAT
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
28 11 0.28
29 21 0.54
30 7 0.18
ACGTcount: A:0.55, C:0.09, G:0.16, T:0.20
Consensus pattern (28 bp):
TGGGCAAAACTGTAAAACCTAAAAAATA
Found at i:48933972 original size:28 final size:29
Alignment explanation
Indices: 48933896--48933976 Score: 94
Period size: 28 Copynumber: 2.8 Consensus size: 29
48933886 AATTCTGGGT
*
48933896 AAAACTATAAAAATCTAAAAAATAGGGGCA
1 AAAACTGTAAAAA-CTAAAAAATAGGGGCA
* *
48933926 AAAACTGTAAAACCTAAAAAATATGGGC-
1 AAAACTGTAAAAACTAAAAAATAGGGGCA
*
48933954 AAAATTGTAAAATAC-AAAAAATA
1 AAAACTGTAAAA-ACTAAAAAATA
48933977 AGGGACACAC
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
28 19 0.42
29 15 0.33
30 11 0.24
ACGTcount: A:0.60, C:0.10, G:0.11, T:0.19
Consensus pattern (29 bp):
AAAACTGTAAAAACTAAAAAATAGGGGCA
Done.