Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr2
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: 61750188
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1877335 characters in sequence are not A, C, G, or T
File 60 of 186
Found at i:18700036 original size:18 final size:18
Alignment explanation
Indices: 18700013--18700052 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
18700003 ATATTTATTC
18700013 ATTTA-TTCATTCATTTTT
1 ATTTATTTCATT-ATTTTT
*
18700031 ATTTATTTTATTATTTTT
1 ATTTATTTCATTATTTTT
18700049 ATTT
1 ATTT
18700053 TGAAAAAGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 15 0.75
19 5 0.25
ACGTcount: A:0.23, C:0.05, G:0.00, T:0.72
Consensus pattern (18 bp):
ATTTATTTCATTATTTTT
Found at i:18701713 original size:46 final size:46
Alignment explanation
Indices: 18701660--18701835 Score: 160
Period size: 46 Copynumber: 3.8 Consensus size: 46
18701650 TATTTGGGTA
*
18701660 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* * * *
18701706 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAA--A--CG
* * * * *
18701753 TCCGAGCTCGTTGAGTTGAGTCTGAGTTCACTCATGGATGCGAACA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* * * * *
18701799 CCCGAGCTCATTGAGTTGAGTCTGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
18701836 GCGGGTTACA
Statistics
Matches: 108, Mismatches: 15, Indels: 14
0.79 0.11 0.10
Matches are distributed among these distances:
43 6 0.06
45 3 0.03
46 64 0.59
47 27 0.25
48 3 0.03
50 5 0.05
ACGTcount: A:0.22, C:0.20, G:0.28, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
Found at i:18701780 original size:93 final size:93
Alignment explanation
Indices: 18701659--18701828 Score: 250
Period size: 93 Copynumber: 1.8 Consensus size: 93
18701649 ATATTTGGGT
* *** *
18701659 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCCGAACTCGTTGAGTTG
1 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCAAACACCCGAACTCATTGAGTTG
18701724 AGTCCGAGTTCGTGAGATGTAACTAGGC
66 AGTCCGAGTTCGTGAGATGTAACTAGGC
* * * *
18701752 ATCCGAGCTCGTTGAGTTGAGTCTGAGTTCACTCATGGATGCGAACACCCGAGCTCATTGAGTTG
1 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCAAACACCCGAACTCATTGAGTTG
*
18701817 AGTCTGAGTTCG
66 AGTCCGAGTTCG
18701829 CTTATGGGCG
Statistics
Matches: 67, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
93 67 1.00
ACGTcount: A:0.22, C:0.21, G:0.28, T:0.29
Consensus pattern (93 bp):
ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCAAACACCCGAACTCATTGAGTTG
AGTCCGAGTTCGTGAGATGTAACTAGGC
Found at i:18703784 original size:20 final size:20
Alignment explanation
Indices: 18703759--18703801 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
18703749 ATGTCACGCA
* *
18703759 TTCACACGGGCCTGTGTTTC
1 TTCACACGGGCCTATGCTTC
18703779 TTCACACGGGCCTATGCTTC
1 TTCACACGGGCCTATGCTTC
18703799 TTC
1 TTC
18703802 CACATGGGTG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.12, C:0.33, G:0.21, T:0.35
Consensus pattern (20 bp):
TTCACACGGGCCTATGCTTC
Found at i:18706654 original size:29 final size:29
Alignment explanation
Indices: 18706593--18706662 Score: 88
Period size: 29 Copynumber: 2.4 Consensus size: 29
18706583 GTGAGCATGA
* * *
18706593 ATAT-AATATGATTTGGGCCTAATGGGCC
1 ATATGAATATGAATTGGGCCTAATAGACC
* *
18706621 TTATGAATGTGAATTGGGCCTAATAGACC
1 ATATGAATATGAATTGGGCCTAATAGACC
18706650 ATATGAATATGAA
1 ATATGAATATGAA
18706663 CTAGGCCAGA
Statistics
Matches: 34, Mismatches: 7, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
28 3 0.09
29 31 0.91
ACGTcount: A:0.34, C:0.11, G:0.23, T:0.31
Consensus pattern (29 bp):
ATATGAATATGAATTGGGCCTAATAGACC
Found at i:18706669 original size:29 final size:29
Alignment explanation
Indices: 18706608--18706669 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 29
18706598 ATATGATTTG
* * * * * *
18706608 GGCCTAATGGGCCTTATGAATGTGAATTG
1 GGCCTAATAGACCATATGAATATGAACTA
18706637 GGCCTAATAGACCATATGAATATGAACTA
1 GGCCTAATAGACCATATGAATATGAACTA
18706666 GGCC
1 GGCC
18706670 AGATGGGCCA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.31, C:0.18, G:0.26, T:0.26
Consensus pattern (29 bp):
GGCCTAATAGACCATATGAATATGAACTA
Found at i:18713766 original size:6 final size:6
Alignment explanation
Indices: 18713750--18713814 Score: 94
Period size: 6 Copynumber: 10.5 Consensus size: 6
18713740 AGTTATTTAG
* *
18713750 TTTATT TATTATT ATTATT ATTTATT TTTACT TTTATT TTTATT TTTATT
1 TTTATT T-TTATT TTTATT -TTTATT TTTATT TTTATT TTTATT TTTATT
18713800 TTTATT TTTATT TTT
1 TTTATT TTTATT TTT
18713815 TATTCATCTT
Statistics
Matches: 53, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
6 43 0.81
7 10 0.19
ACGTcount: A:0.20, C:0.02, G:0.00, T:0.78
Consensus pattern (6 bp):
TTTATT
Found at i:18713770 original size:25 final size:24
Alignment explanation
Indices: 18713742--18713818 Score: 88
Period size: 24 Copynumber: 3.2 Consensus size: 24
18713732 GTTAAAATAG
*
18713742 TTATTTA-GTTTATTTATTATTATTA
1 TTATTTATTTTTATTT-TTATT-TTA
*
18713767 TTATTTATTTTTACTTTTATTTTTA
1 TTATTTATTTTTATTTTTA-TTTTA
18713792 TT-TTTATTTTTATTTTTATTTT-
1 TTATTTATTTTTATTTTTATTTTA
18713814 TTATT
1 TTATT
18713819 CATCTTCCTT
Statistics
Matches: 46, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
22 2 0.04
23 6 0.13
24 15 0.33
25 15 0.33
26 8 0.17
ACGTcount: A:0.21, C:0.01, G:0.01, T:0.77
Consensus pattern (24 bp):
TTATTTATTTTTATTTTTATTTTA
Found at i:18714789 original size:14 final size:14
Alignment explanation
Indices: 18714770--18714803 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
18714760 TTCTAAATTG
18714770 GTACATCTGCATAC
1 GTACATCTGCATAC
*
18714784 GTACATTTGCATAC
1 GTACATCTGCATAC
*
18714798 ATACAT
1 GTACAT
18714804 ACATATGCAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.32, C:0.24, G:0.12, T:0.32
Consensus pattern (14 bp):
GTACATCTGCATAC
Found at i:18714806 original size:18 final size:18
Alignment explanation
Indices: 18714779--18714814 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
18714769 GGTACATCTG
* *
18714779 CATACGTACATTTGCATA
1 CATACATACATATGCATA
18714797 CATACATACATATGCATA
1 CATACATACATATGCATA
18714815 AACTATTTTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.39, C:0.22, G:0.08, T:0.31
Consensus pattern (18 bp):
CATACATACATATGCATA
Found at i:18716821 original size:207 final size:207
Alignment explanation
Indices: 18716466--18716878 Score: 826
Period size: 207 Copynumber: 2.0 Consensus size: 207
18716456 GTTCTAAAAG
18716466 TTCTTTCCATCTTTCCTCTATCGTCTAATATTACTAGATTGTTCAATAAAGAGTTATTGCAAAAA
1 TTCTTTCCATCTTTCCTCTATCGTCTAATATTACTAGATTGTTCAATAAAGAGTTATTGCAAAAA
18716531 ATCTTTATAGAAATTGATTTTCTTGTTATACGATGCTTAGTGAACTATTTTCATTAATGCAAAAC
66 ATCTTTATAGAAATTGATTTTCTTGTTATACGATGCTTAGTGAACTATTTTCATTAATGCAAAAC
18716596 ACAAATAGTCATCAGGCTTCATTGTATCCTTGAGGTTCATTTGTGCATTGAGTATAGGTACGGGT
131 ACAAATAGTCATCAGGCTTCATTGTATCCTTGAGGTTCATTTGTGCATTGAGTATAGGTACGGGT
18716661 GAATATAACCAC
196 GAATATAACCAC
18716673 TTCTTTCCATCTTTCCTCTATCGTCTAATATTACTAGATTGTTCAATAAAGAGTTATTGCAAAAA
1 TTCTTTCCATCTTTCCTCTATCGTCTAATATTACTAGATTGTTCAATAAAGAGTTATTGCAAAAA
18716738 ATCTTTATAGAAATTGATTTTCTTGTTATACGATGCTTAGTGAACTATTTTCATTAATGCAAAAC
66 ATCTTTATAGAAATTGATTTTCTTGTTATACGATGCTTAGTGAACTATTTTCATTAATGCAAAAC
18716803 ACAAATAGTCATCAGGCTTCATTGTATCCTTGAGGTTCATTTGTGCATTGAGTATAGGTACGGGT
131 ACAAATAGTCATCAGGCTTCATTGTATCCTTGAGGTTCATTTGTGCATTGAGTATAGGTACGGGT
18716868 GAATATAACCA
196 GAATATAACCA
18716879 TTAAGATAGT
Statistics
Matches: 206, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
207 206 1.00
ACGTcount: A:0.31, C:0.16, G:0.15, T:0.39
Consensus pattern (207 bp):
TTCTTTCCATCTTTCCTCTATCGTCTAATATTACTAGATTGTTCAATAAAGAGTTATTGCAAAAA
ATCTTTATAGAAATTGATTTTCTTGTTATACGATGCTTAGTGAACTATTTTCATTAATGCAAAAC
ACAAATAGTCATCAGGCTTCATTGTATCCTTGAGGTTCATTTGTGCATTGAGTATAGGTACGGGT
GAATATAACCAC
Found at i:18717118 original size:233 final size:233
Alignment explanation
Indices: 18716776--18717943 Score: 2088
Period size: 233 Copynumber: 5.0 Consensus size: 233
18716766 TACGATGCTT
*
18716776 AGTGAACTATTTTCATTAATGCAAAACACAAATAGTCATCAGGCTTCATTGTATCCTTGAGGTTC
1 AGTGGACTATTTTCATTAATGCAAAACACAAATAGTCATCAGGCTTCATTGTATCCTTGAGGTTC
18716841 ATTTGTGCATTGAGTATAGGTACGGGTGAATATAACCATTAAGATAGTGGCTTGATACATGCATT
66 ATTTGTGCATTGAGTATAGGTACGGGTGAATATAACCATTAAGATAGTGGCTTGATACATGCATT
* * *
18716906 GGAGTCTTGTCCTATTTCTTTGTTTTTTGTTATAGCTT-TTGTTCATATGTTCTAGATTTTCTTC
131 GGAGTCTTGTCCTATTTCTTTGTTTTCTGTTATAG-TTGTTGTTCATATGTTCAAGATTTTCCTC
* *
18716970 ACTGAAATTTTGAATTAACAGGAAGAAATACTAAATGGA
195 ACTGAAATTTTGTATTAACAGGAAGAAATACTAAAAGGA
18717009 AGTGGACTATTTTCATTAATGCAAAACACAAATAGTCATCAGGCTTCATTGTATCCTTGAGGTTC
1 AGTGGACTATTTTCATTAATGCAAAACACAAATAGTCATCAGGCTTCATTGTATCCTTGAGGTTC
* * * * *
18717074 ATTTGTGCACTGAGTATAGCTAGGGGTGAATATAATCATTAAGATAGTGGTTTGATACATGCATT
66 ATTTGTGCATTGAGTATAGGTACGGGTGAATATAACCATTAAGATAGTGGCTTGATACATGCATT
18717139 GGAGTCTTGTCCTATTTCTTTGTTTTCTGTTATAGTTGTTGTTCATATGTTCAAGATTTTCCTCA
131 GGAGTCTTGTCCTATTTCTTTGTTTTCTGTTATAGTTGTTGTTCATATGTTCAAGATTTTCCTCA
18717204 CTGAAATTTTGTATTAACAGGAAGAAATACTAAAAGGA
196 CTGAAATTTTGTATTAACAGGAAGAAATACTAAAAGGA
*
18717242 AGTGGACTGTTTTCATTAATGCAAAACACAAATAGTCATCAGGCTTCATTGTATCCTTGAGGTTC
1 AGTGGACTATTTTCATTAATGCAAAACACAAATAGTCATCAGGCTTCATTGTATCCTTGAGGTTC
* * * * *
18717307 ATTTGTGCACTGAGTATAGCTAGGGGTGAATATAATCATTAAGATAGTGGTTTGATACATGCATT
66 ATTTGTGCATTGAGTATAGGTACGGGTGAATATAACCATTAAGATAGTGGCTTGATACATGCATT
18717372 GGAGTCTTGTCCTATTTCTTTGTTTTCTGTTATAGTTGTTGTTCATATGTTCAAGATTTTCCTCA
131 GGAGTCTTGTCCTATTTCTTTGTTTTCTGTTATAGTTGTTGTTCATATGTTCAAGATTTTCCTCA
18717437 CTGAAATTTTGTATTAACAGGAAGAAATACTAAAAGGA
196 CTGAAATTTTGTATTAACAGGAAGAAATACTAAAAGGA
*
18717475 AGTGGACTGTTTTCATTAATGCAAAACACAAATAGTCATCAGGCTTCATTGTATCCTTGAGGTTC
1 AGTGGACTATTTTCATTAATGCAAAACACAAATAGTCATCAGGCTTCATTGTATCCTTGAGGTTC
18717540 ATTTGTGCATTGAGTATAGGTACGGGTGAATATAACCATTAAGATAGTGGCTTGATACATGCATT
66 ATTTGTGCATTGAGTATAGGTACGGGTGAATATAACCATTAAGATAGTGGCTTGATACATGCATT
* * *
18717605 GGAGTCTTGTCCTATTTCTTTGTTTTTTGTTATAGCTT-TTGTTCATATGTTCTAGATTTTCTTC
131 GGAGTCTTGTCCTATTTCTTTGTTTTCTGTTATAG-TTGTTGTTCATATGTTCAAGATTTTCCTC
* *
18717669 ACTGAAATTTTGAATTAACAGGAAGAAATACTAAATGGA
195 ACTGAAATTTTGTATTAACAGGAAGAAATACTAAAAGGA
18717708 AGTGGACTATTTTCATTAATGCAAAACACAAATAGTCATCAGGCTTCATTGTATCCTTGAGGTTC
1 AGTGGACTATTTTCATTAATGCAAAACACAAATAGTCATCAGGCTTCATTGTATCCTTGAGGTTC
18717773 ATTTGTGCATTGAGTATAGGTACGGGTGAATATAACCATTAAGATAGTGGCTTGATACATGCATT
66 ATTTGTGCATTGAGTATAGGTACGGGTGAATATAACCATTAAGATAGTGGCTTGATACATGCATT
*
18717838 GGAGTCTTGTCCTATTTCTTTGTTTTCTGTTATAGTTGTTGTTCGTATGTTCAAGATTTTCCTCA
131 GGAGTCTTGTCCTATTTCTTTGTTTTCTGTTATAGTTGTTGTTCATATGTTCAAGATTTTCCTCA
18717903 CTGAAATTTTGTATTAACAGGAAGAAATACTAAAAGGA
196 CTGAAATTTTGTATTAACAGGAAGAAATACTAAAAGGA
18717941 AGT
1 AGT
18717944 TGAGGATTGA
Statistics
Matches: 903, Mismatches: 29, Indels: 6
0.96 0.03 0.01
Matches are distributed among these distances:
232 4 0.00
233 897 0.99
234 2 0.00
ACGTcount: A:0.29, C:0.13, G:0.19, T:0.38
Consensus pattern (233 bp):
AGTGGACTATTTTCATTAATGCAAAACACAAATAGTCATCAGGCTTCATTGTATCCTTGAGGTTC
ATTTGTGCATTGAGTATAGGTACGGGTGAATATAACCATTAAGATAGTGGCTTGATACATGCATT
GGAGTCTTGTCCTATTTCTTTGTTTTCTGTTATAGTTGTTGTTCATATGTTCAAGATTTTCCTCA
CTGAAATTTTGTATTAACAGGAAGAAATACTAAAAGGA
Found at i:18719940 original size:48 final size:46
Alignment explanation
Indices: 18719869--18720367 Score: 440
Period size: 48 Copynumber: 10.6 Consensus size: 46
18719859 GGTGAATTGT
* * *
18719869 CGATGCCATGTCCCAAACATGGTCTTACACTGGCTCGCAT-GCCGAGAC
1 CGATGCCATGT-CC-AACATGGTCTTACACTGGCTCTCATAACAGAG-C
* * **
18719917 CGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCGTCTCA-ATGC
1 CGATGCCATGT-CCA-ACATGGTCTTACACTGGCTCTCATAACAGA-GC
* * * ** *
18719965 AGAGGCCATGTCCAACATGGACTTACACTGGCTCTCAT-ATGGTGGC
1 CGATGCCATGTCCAACATGGTCTTACACTGGCTCTCATAACAG-AGC
* * *
18720011 CGATGCCATTTCCAACATGGTCTTACACAGGCT-T-ATAGTCA-ATGC
1 CGATGCCATGTCCAACATGGTCTTACACTGGCTCTCATA-ACAGA-GC
* * *
18720056 CGATGCCAGGTCCAACATGGTCTTACACTGGCTCTCATAACATAGT
1 CGATGCCATGTCCAACATGGTCTTACACTGGCTCTCATAACAGAGC
* * * * *
18720102 CGATGTCATGTTCCAAACATGGTCCTACACTAGCTCTCATAACATAGT
1 CGATGCCATG-TCC-AACATGGTCTTACACTGGCTCTCATAACAGAGC
* *
18720150 CGATGCCATGTCCAACATGGTCTTACACTGGCTCTCATAACATAGT
1 CGATGCCATGTCCAACATGGTCTTACACTGGCTCTCATAACAGAGC
* *
18720196 CGATGTCATGTCCAACATAGTCTTACACTGGCTCTCATAACAGAGC
1 CGATGCCATGTCCAACATGGTCTTACACTGGCTCTCATAACAGAGC
* *
18720242 CGATGCCATGTTCCAAACATGGTCTTACACTGACTCTCATAACATAGC
1 CGATGCCATG-TCC-AACATGGTCTTACACTGGCTCTCATAACAGAGC
* * * * * *
18720290 CAATTCTATGTTCCAAACATGGTCTTACACTGGCATAC-GA-AA-TGTGGC
1 CGATGCCATG-TCC-AACATGGTCTTACACTGGC-T-CTCATAACAG-AGC
18720338 CGATGCCATGTCCAGACATGGTCTTACACT
1 CGATGCCATGTCCA-ACATGGTCTTACACT
18720368 AGCTACATGT
Statistics
Matches: 378, Mismatches: 54, Indels: 39
0.80 0.11 0.08
Matches are distributed among these distances:
44 2 0.01
45 33 0.09
46 146 0.39
47 35 0.09
48 157 0.42
49 4 0.01
50 1 0.00
ACGTcount: A:0.26, C:0.28, G:0.19, T:0.27
Consensus pattern (46 bp):
CGATGCCATGTCCAACATGGTCTTACACTGGCTCTCATAACAGAGC
Found at i:18720173 original size:94 final size:93
Alignment explanation
Indices: 18719867--18720320 Score: 469
Period size: 94 Copynumber: 4.8 Consensus size: 93
18719857 AGGGTGAATT
* * ** * *
18719867 GTCGATGCCATGTCCCAAACATGGTCTTACACTGGCTCGCAT-GCCGAGACCGATGCCATGTCCC
1 GTCGATGCCATGT-CC-AACATGGTCTTACACTGGCTCTCATAACATAG-CCGATGTCATGTTCC
* * **
18719931 AGACATGGTCTTACACTAGCTCTCGTCTCAA
63 AAACATGGTCTTACACTAGCTCTCATAACAA
* * *** * *
18719962 -TGCAGAGGCCATGTCCAACATGGACTTACACTGGCTCTCATATGGTGGCCGATGCCAT-TTCC-
1 GT-C-GATGCCATGTCCAACATGGTCTTACACTGGCTCTCATAACATAGCCGATGTCATGTTCCA
*
18720024 AACATGGTCTTACAC-AGGCT-T-ATAGTCAA
64 AACATGGTCTTACACTA-GCTCTCATA-ACAA
* * *
18720053 TGCCGATGCCAGGTCCAACATGGTCTTACACTGGCTCTCATAACATAGTCGATGTCATGTTCCAA
1 -GTCGATGCCATGTCCAACATGGTCTTACACTGGCTCTCATAACATAGCCGATGTCATGTTCCAA
*
18720118 ACATGGTCCTACACTAGCTCTCATAACATA
65 ACATGGTCTTACACTAGCTCTCATAACA-A
*
18720148 GTCGATGCCATGTCCAACATGGTCTTACACTGGCTCTCATAACATAGTCGATGTCATG-TCC-AA
1 GTCGATGCCATGTCCAACATGGTCTTACACTGGCTCTCATAACATAGCCGATGTCATGTTCCAAA
* *
18720211 CATAGTCTTACACTGGCTCTCATAACAGA
66 CATGGTCTTACACTAGCTCTCATAACA-A
* * *
18720240 GCCGATGCCATGTTCCAAACATGGTCTTACACTGACTCTCATAACATAGCCAAT-TCTATGTTCC
1 GTCGATGCCATG-TCC-AACATGGTCTTACACTGGCTCTCATAACATAGCCGATGTC-ATGTTCC
18720304 AAACATGGTCTTACACT
63 AAACATGGTCTTACACT
18720321 GGCATACGAA
Statistics
Matches: 306, Mismatches: 35, Indels: 35
0.81 0.09 0.09
Matches are distributed among these distances:
90 1 0.00
91 51 0.17
92 60 0.20
93 28 0.09
94 131 0.43
95 11 0.04
96 24 0.08
ACGTcount: A:0.26, C:0.29, G:0.18, T:0.27
Consensus pattern (93 bp):
GTCGATGCCATGTCCAACATGGTCTTACACTGGCTCTCATAACATAGCCGATGTCATGTTCCAAA
CATGGTCTTACACTAGCTCTCATAACAA
Found at i:18721097 original size:23 final size:23
Alignment explanation
Indices: 18721067--18721114 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
18721057 AATAGTTCAT
18721067 TTGAGGTGTTTCCATGAAAATCC
1 TTGAGGTGTTTCCATGAAAATCC
18721090 TTGAGGTGTTTCCATGAAAATCC
1 TTGAGGTGTTTCCATGAAAATCC
18721113 TT
1 TT
18721115 TCACAAAAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.25, C:0.17, G:0.21, T:0.38
Consensus pattern (23 bp):
TTGAGGTGTTTCCATGAAAATCC
Found at i:18723189 original size:20 final size:20
Alignment explanation
Indices: 18723166--18723203 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
18723156 ATTTTATCAT
*
18723166 TTTTATTTTTATTTTAATAA
1 TTTTATTTTTAATTTAATAA
*
18723186 TTTTGTTTTTAATTTAAT
1 TTTTATTTTTAATTTAAT
18723204 TTTTACATTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (20 bp):
TTTTATTTTTAATTTAATAA
Found at i:18726998 original size:28 final size:28
Alignment explanation
Indices: 18726967--18727037 Score: 106
Period size: 28 Copynumber: 2.5 Consensus size: 28
18726957 ATATGGCACG
18726967 TAGTGTGTGAAATATTGAGAATGACACT
1 TAGTGTGTGAAATATTGAGAATGACACT
* * * *
18726995 TAGTATGCGAGATATTGAGAATGGCACT
1 TAGTGTGTGAAATATTGAGAATGACACT
18727023 TAGTGTGTGAAATAT
1 TAGTGTGTGAAATAT
18727038 CGAATGATTC
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 36 1.00
ACGTcount: A:0.34, C:0.07, G:0.27, T:0.32
Consensus pattern (28 bp):
TAGTGTGTGAAATATTGAGAATGACACT
Found at i:18730115 original size:18 final size:18
Alignment explanation
Indices: 18730075--18730116 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
18730065 TTTAATACTT
*
18730075 TTATTTTTTTTCATTTTA
1 TTATTATTTTTCATTTTA
*
18730093 GTATTATTTTT-ATTGTTA
1 TTATTATTTTTCATT-TTA
18730111 TTATTA
1 TTATTA
18730117 CTCTACTTAC
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
17 3 0.15
18 17 0.85
ACGTcount: A:0.21, C:0.02, G:0.05, T:0.71
Consensus pattern (18 bp):
TTATTATTTTTCATTTTA
Found at i:18730179 original size:21 final size:19
Alignment explanation
Indices: 18730162--18730209 Score: 66
Period size: 17 Copynumber: 2.7 Consensus size: 19
18730152 ATTAGTTTTA
18730162 AATTATT-TTATTTTAGTT
1 AATTATTATTATTTTAGTT
18730180 AATTATTATTATTTT-GTT
1 AATTATTATTATTTTAGTT
*
18730198 -ATTTTTATTATT
1 AATTATTATTATT
18730210 ACTACTATTA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
17 11 0.39
18 10 0.36
19 7 0.25
ACGTcount: A:0.27, C:0.00, G:0.04, T:0.69
Consensus pattern (19 bp):
AATTATTATTATTTTAGTT
Found at i:18730189 original size:3 final size:3
Alignment explanation
Indices: 18730163--18730256 Score: 54
Period size: 3 Copynumber: 31.7 Consensus size: 3
18730153 TTAGTTTTAA
* *
18730163 ATT ATT -TT ATT -TT AGTT AATT ATT ATT ATT -TT GTT ATT TTT ATT
1 ATT ATT ATT ATT ATT A-TT -ATT ATT ATT ATT ATT ATT ATT ATT ATT
* * * * *
18730207 ATT ACT ACT ATT ATT ATT GTGT -TT ATT CTT -TGT ATT ATA ATT ATT
1 ATT ATT ATT ATT ATT ATT AT-T ATT ATT ATT AT-T ATT ATT ATT ATT
18730252 ATT AT
1 ATT AT
18730257 CACTGCAATT
Statistics
Matches: 73, Mismatches: 9, Indels: 18
0.73 0.09 0.18
Matches are distributed among these distances:
2 8 0.11
3 58 0.79
4 6 0.08
5 1 0.01
ACGTcount: A:0.27, C:0.03, G:0.05, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:18734761 original size:64 final size:64
Alignment explanation
Indices: 18734654--18735515 Score: 1681
Period size: 64 Copynumber: 13.5 Consensus size: 64
18734644 CCTGCTCATT
** *
18734654 TTATCTTTGGTTGTGAGTATGTCAACTTGATTTGT-TATTCTCAAGTTGACATACCACATTATTG
1 TTATCTTTGGTTGTGAGTATGTCAACTTGAGGTGTGT-TCCTCAAGTTGACATACCACATTATTG
18734718 TTATCTTTGGTTGTGAGTATGTCAACTTGAGGTGTGTTCCTCAAGTTGACATACCACATTATTG
1 TTATCTTTGGTTGTGAGTATGTCAACTTGAGGTGTGTTCCTCAAGTTGACATACCACATTATTG
18734782 TTATCTTTGGTTGTGAGTATGTCAACTTGAGGTGTGTTCCTCAAGTTGACATACCACATTATTG
1 TTATCTTTGGTTGTGAGTATGTCAACTTGAGGTGTGTTCCTCAAGTTGACATACCACATTATTG
18734846 TTATCTTTGGTTGTGAGTATGTCAACTTGAGGTGTGTTCCTCAAGTTGACATACCACATTATTG
1 TTATCTTTGGTTGTGAGTATGTCAACTTGAGGTGTGTTCCTCAAGTTGACATACCACATTATTG
18734910 TTATCTTTGGTTGTGAGTATGTCAACTTGAGGTGTGTTCCTCAAGTTGACATACCACATTATTG
1 TTATCTTTGGTTGTGAGTATGTCAACTTGAGGTGTGTTCCTCAAGTTGACATACCACATTATTG
18734974 TTATCTTTGGTTGTGAGTATGTCAACTTGAGGTGTGTTCCTCAAGTTGACATACCACATTATTG
1 TTATCTTTGGTTGTGAGTATGTCAACTTGAGGTGTGTTCCTCAAGTTGACATACCACATTATTG
18735038 TTATCTTTGGTTGTGAGTATGTCAACTTGAGGTGTGTTCCTCAAGTTGACATACCACATTATTG
1 TTATCTTTGGTTGTGAGTATGTCAACTTGAGGTGTGTTCCTCAAGTTGACATACCACATTATTG
18735102 TTATCTTTGGTTGTGAGTATGTCAACTTGAGGTGTGTTCCTCAAGTTGACATACCACATTATTG
1 TTATCTTTGGTTGTGAGTATGTCAACTTGAGGTGTGTTCCTCAAGTTGACATACCACATTATTG
18735166 TTATCTTTGGTTGTGAGTATGTCAACTTGAGGTGTGTTCCTCAAGTTGACATACCACATTATTG
1 TTATCTTTGGTTGTGAGTATGTCAACTTGAGGTGTGTTCCTCAAGTTGACATACCACATTATTG
18735230 TTATCTTTGGTTGTGAGTATGTCAACTTGAGGTGTGTTCCTCAAGTTGACATACCACATTATTG
1 TTATCTTTGGTTGTGAGTATGTCAACTTGAGGTGTGTTCCTCAAGTTGACATACCACATTATTG
18735294 TTATCTTTGGTTGTGAGTATGTCAACTTGAGGTGTGTTCCTCAAGTTGACATACCACATTATTG
1 TTATCTTTGGTTGTGAGTATGTCAACTTGAGGTGTGTTCCTCAAGTTGACATACCACATTATTG
18735358 TTATCTTTGGTTGTGAGTATGTCAACTTGAGGTGTGTTCCTCAAGTTGACATACCACATTATTG
1 TTATCTTTGGTTGTGAGTATGTCAACTTGAGGTGTGTTCCTCAAGTTGACATACCACATTATTG
18735422 TTATCTTTGGTTGTGAGTATGTCAACTTGAGGTGTGTTCCTCAAGTTGACATACCACATTATTG
1 TTATCTTTGGTTGTGAGTATGTCAACTTGAGGTGTGTTCCTCAAGTTGACATACCACATTATTG
18735486 TTATCTTTGGTTGTGAGTATGTCAACTTGA
1 TTATCTTTGGTTGTGAGTATGTCAACTTGA
18735516 TTTGTTATTC
Statistics
Matches: 794, Mismatches: 3, Indels: 2
0.99 0.00 0.00
Matches are distributed among these distances:
64 793 1.00
65 1 0.00
ACGTcount: A:0.22, C:0.15, G:0.22, T:0.41
Consensus pattern (64 bp):
TTATCTTTGGTTGTGAGTATGTCAACTTGAGGTGTGTTCCTCAAGTTGACATACCACATTATTG
Found at i:18739169 original size:11 final size:11
Alignment explanation
Indices: 18739153--18739182 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
18739143 TCAATTGCAT
18739153 GATTATCTGTA
1 GATTATCTGTA
*
18739164 GATTATCCGTA
1 GATTATCTGTA
18739175 GATTATCT
1 GATTATCT
18739183 TAAGACATTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.27, C:0.13, G:0.17, T:0.43
Consensus pattern (11 bp):
GATTATCTGTA
Found at i:18741912 original size:11 final size:11
Alignment explanation
Indices: 18741896--18741920 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
18741886 AAACTGTAAA
18741896 AAAATAAAAAT
1 AAAATAAAAAT
18741907 AAAATAAAAAT
1 AAAATAAAAAT
18741918 AAA
1 AAA
18741921 TCAGTAGTGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (11 bp):
AAAATAAAAAT
Found at i:18747181 original size:11 final size:11
Alignment explanation
Indices: 18747165--18747201 Score: 56
Period size: 11 Copynumber: 3.2 Consensus size: 11
18747155 ATTCATATAT
18747165 TTAATTGTGAA
1 TTAATTGTGAA
18747176 TTAATTGTGAAAA
1 TTAATTGTG--AA
18747189 TTAATTGTGAA
1 TTAATTGTGAA
18747200 TT
1 TT
18747202 CATATGGAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
11 13 0.54
13 11 0.46
ACGTcount: A:0.38, C:0.00, G:0.16, T:0.46
Consensus pattern (11 bp):
TTAATTGTGAA
Found at i:18747192 original size:13 final size:13
Alignment explanation
Indices: 18747165--18747199 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
18747155 ATTCATATAT
18747165 TTAATTGTG--AA
1 TTAATTGTGAAAA
18747176 TTAATTGTGAAAA
1 TTAATTGTGAAAA
18747189 TTAATTGTGAA
1 TTAATTGTGAA
18747200 TTCATATGGA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 9 0.41
13 13 0.59
ACGTcount: A:0.40, C:0.00, G:0.17, T:0.43
Consensus pattern (13 bp):
TTAATTGTGAAAA
Found at i:18747969 original size:43 final size:43
Alignment explanation
Indices: 18747861--18748000 Score: 142
Period size: 43 Copynumber: 3.3 Consensus size: 43
18747851 GCTGCTATAA
* * *
18747861 AACATGACCTTTAGC-A-GCATTTCTCACAAAAATG-CTACTATAG
1 AACATGACCTTTAGCAACGC-TTTC-CCCAAAAACGTC-ACTAAAG
* * *
18747904 AACATGACCTTTAGCAACGCTTTTCCCACAAACGTCGCTAAAG
1 AACATGACCTTTAGCAACGCTTTCCCCAAAAACGTCACTAAAG
***
18747947 AACATGACCTTTAGCGGTGCTTTCCCCAAAAACGTCACTAAAG
1 AACATGACCTTTAGCAACGCTTTCCCCAAAAACGTCACTAAAG
*
18747990 AACGTGACCTT
1 AACATGACCTT
18748001 GCTTTTCCCA
Statistics
Matches: 81, Mismatches: 13, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
43 74 0.91
44 5 0.06
45 2 0.02
ACGTcount: A:0.34, C:0.27, G:0.14, T:0.25
Consensus pattern (43 bp):
AACATGACCTTTAGCAACGCTTTCCCCAAAAACGTCACTAAAG
Found at i:18748011 original size:36 final size:38
Alignment explanation
Indices: 18747922--18748025 Score: 104
Period size: 43 Copynumber: 2.7 Consensus size: 38
18747912 CTTTAGCAAC
* *
18747922 GCTTTTCCCACAAACGTCGCTAAAGAACATGACCTTTA
1 GCTTTTCCCAAAAACGTCACTAAAGAACATGACCTTTA
*
18747960 GCGGTGCTTTCCCCAAAAACGTCACTAAAGAACGTGACC-TT-
1 GC--T--TTT-CCCAAAAACGTCACTAAAGAACATGACCTTTA
**
18748001 GCTTTTCCCAAAAACACCACTAAAG
1 GCTTTTCCCAAAAACGTCACTAAAG
18748026 GTCATGTTCT
Statistics
Matches: 56, Mismatches: 5, Indels: 12
0.77 0.07 0.16
Matches are distributed among these distances:
36 17 0.30
37 3 0.05
38 2 0.04
39 1 0.02
40 1 0.02
41 2 0.04
42 5 0.09
43 25 0.45
ACGTcount: A:0.33, C:0.30, G:0.14, T:0.23
Consensus pattern (38 bp):
GCTTTTCCCAAAAACGTCACTAAAGAACATGACCTTTA
Found at i:18748216 original size:35 final size:35
Alignment explanation
Indices: 18748169--18748235 Score: 107
Period size: 35 Copynumber: 1.9 Consensus size: 35
18748159 TTTTATTATT
*
18748169 CTTTAAATGTTTATATAAGTTATGATAATCATAAA
1 CTTTAAACGTTTATATAAGTTATGATAATCATAAA
* *
18748204 CTTTAAACGTTTATGTAAGTTATGATTATCAT
1 CTTTAAACGTTTATATAAGTTATGATAATCAT
18748236 CTTTAAATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 29 1.00
ACGTcount: A:0.37, C:0.07, G:0.10, T:0.45
Consensus pattern (35 bp):
CTTTAAACGTTTATATAAGTTATGATAATCATAAA
Found at i:18748705 original size:34 final size:35
Alignment explanation
Indices: 18748667--18748732 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
18748657 CTATGAAAAT
18748667 TTTAAATTTAAAA-CTAAATATAA-AAATTAATGAA
1 TTTAAATTTAAAATCTAAA-ATAATAAATTAATGAA
*
18748701 TTTAAATTTAAAATTTAAAATAATAAATTAAT
1 TTTAAATTTAAAATCTAAAATAATAAATTAAT
18748733 AACACAATTA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.39
Consensus pattern (35 bp):
TTTAAATTTAAAATCTAAAATAATAAATTAATGAA
Found at i:18751741 original size:31 final size:29
Alignment explanation
Indices: 18751705--18751763 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 29
18751695 GATCAGTTGT
18751705 TTATTTTAGCTT-TAACCTTTTTTTTCTTTTG
1 TTATTTTAG-TTGTAA--TTTTTTTTCTTTTG
18751736 TTATTTTAGTTGTAATTTTTTTTCTTTT
1 TTATTTTAGTTGTAATTTTTTTTCTTTT
18751764 TTCTAATTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
29 13 0.48
30 2 0.07
31 12 0.44
ACGTcount: A:0.14, C:0.08, G:0.07, T:0.71
Consensus pattern (29 bp):
TTATTTTAGTTGTAATTTTTTTTCTTTTG
Found at i:18759064 original size:15 final size:16
Alignment explanation
Indices: 18759024--18759065 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
18759014 TGTAATTATA
18759024 TTTAATATTAAATACCT
1 TTTAAT-TTAAATACCT
*
18759041 TTTAA-TTAAATA-TT
1 TTTAATTTAAATACCT
18759055 TTTAATTTAAA
1 TTTAATTTAAA
18759066 AATAATGGAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 6 0.26
15 12 0.52
17 5 0.22
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.52
Consensus pattern (16 bp):
TTTAATTTAAATACCT
Found at i:18762715 original size:14 final size:14
Alignment explanation
Indices: 18762698--18762724 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
18762688 TAATATTAGA
18762698 TTTTTATTTTTATT
1 TTTTTATTTTTATT
18762712 TTTTTATTTTTAT
1 TTTTTATTTTTAT
18762725 AAATTATAAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (14 bp):
TTTTTATTTTTATT
Found at i:18776076 original size:71 final size:70
Alignment explanation
Indices: 18775961--18776096 Score: 236
Period size: 71 Copynumber: 1.9 Consensus size: 70
18775951 CACAAACGTT
*
18775961 AGAATTTGAAAGGCTTTCTTTTTCAACAGTGAAGCATTTTATCGAACACTTCGCTCGACGAAAAG
1 AGAATTTGAAAGGCTTTCCTTTTCAACAGTGAAGCATTTTATCGAACACTTCGCTCGACGAAAAG
18776026 ATGAA
66 ATGAA
* *
18776031 AGAATTTGAAAGGCCTTTCCTTTTCATCAGTGAAGCATTTTATCGAACACTTCGCTTGACGAAAA
1 AGAATTTGAAAGG-CTTTCCTTTTCAACAGTGAAGCATTTTATCGAACACTTCGCTCGACGAAAA
18776096 G
65 G
18776097 TTGGAGGAAG
Statistics
Matches: 62, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
70 13 0.21
71 49 0.79
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.31
Consensus pattern (70 bp):
AGAATTTGAAAGGCTTTCCTTTTCAACAGTGAAGCATTTTATCGAACACTTCGCTCGACGAAAAG
ATGAA
Found at i:18778183 original size:71 final size:70
Alignment explanation
Indices: 18778068--18778203 Score: 236
Period size: 71 Copynumber: 1.9 Consensus size: 70
18778058 CACAAACGTT
*
18778068 AGAATTTGAAAGGCTTTCTTTTTCAACAGTGAAGCATTTTATCGAACACTTCGCTCGACGAAAAG
1 AGAATTTGAAAGGCTTTCCTTTTCAACAGTGAAGCATTTTATCGAACACTTCGCTCGACGAAAAG
18778133 ATGAA
66 ATGAA
* *
18778138 AGAATTTGAAAGGCCTTTCCTTTTCATCAGTGAAGCATTTTATCGAACACTTCGCTTGACGAAAA
1 AGAATTTGAAAGG-CTTTCCTTTTCAACAGTGAAGCATTTTATCGAACACTTCGCTCGACGAAAA
18778203 G
65 G
18778204 TTGGAGGAAG
Statistics
Matches: 62, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
70 13 0.21
71 49 0.79
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.31
Consensus pattern (70 bp):
AGAATTTGAAAGGCTTTCCTTTTCAACAGTGAAGCATTTTATCGAACACTTCGCTCGACGAAAAG
ATGAA
Found at i:18781735 original size:29 final size:32
Alignment explanation
Indices: 18781675--18781734 Score: 90
Period size: 31 Copynumber: 1.9 Consensus size: 32
18781665 CTCAGAATCA
18781675 AAAAGTATGTACCATAACATCATAAGATTTTG
1 AAAAGTATGTACCATAACATCATAAGATTTTG
18781707 AAAA-TATGTACCATAATCATC-TAA-ATTT
1 AAAAGTATGTACCATAA-CATCATAAGATTT
18781735 GCCAAAAAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
30 4 0.15
31 15 0.56
32 8 0.30
ACGTcount: A:0.45, C:0.13, G:0.08, T:0.33
Consensus pattern (32 bp):
AAAAGTATGTACCATAACATCATAAGATTTTG
Found at i:18795683 original size:28 final size:28
Alignment explanation
Indices: 18795647--18795702 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
18795637 TCTAGTGAGA
18795647 TGATCGTTCTCATTCAAGAGATTAATGT
1 TGATCGTTCTCATTCAAGAGATTAATGT
*
18795675 TGATTGTTCTCATTCAAGAGATTAATGT
1 TGATCGTTCTCATTCAAGAGATTAATGT
18795703 GTGCTCAAAG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.29, C:0.12, G:0.18, T:0.41
Consensus pattern (28 bp):
TGATCGTTCTCATTCAAGAGATTAATGT
Found at i:18800278 original size:8 final size:8
Alignment explanation
Indices: 18800265--18800293 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
18800255 TTATGTTTAA
18800265 TATATTAT
1 TATATTAT
18800273 TATATTAT
1 TATATTAT
18800281 TATATTAT
1 TATATTAT
18800289 TATAT
1 TATAT
18800294 AATAAAGATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (8 bp):
TATATTAT
Found at i:18800326 original size:5 final size:5
Alignment explanation
Indices: 18800316--18800367 Score: 104
Period size: 5 Copynumber: 10.4 Consensus size: 5
18800306 TTATGTTTTA
18800316 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT
1 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT
18800366 AT
1 AT
18800368 AAACTAAAGA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 47 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
ATTAT
Found at i:18802298 original size:5 final size:5
Alignment explanation
Indices: 18802290--18802316 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
18802280 TCTTTAGTTT
18802290 ATATA ATATA ATATA ATATA ATATA AT
1 ATATA ATATA ATATA ATATA ATATA AT
18802317 TAAAACATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (5 bp):
ATATA
Found at i:18807895 original size:5 final size:5
Alignment explanation
Indices: 18807885--18807913 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
18807875 GTTTATGGGT
18807885 TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
18807914 GTAAGTAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (5 bp):
TTTTA
Found at i:18811538 original size:27 final size:28
Alignment explanation
Indices: 18811475--18811538 Score: 69
Period size: 27 Copynumber: 2.3 Consensus size: 28
18811465 ATAAAATTTA
* *
18811475 AATATAATAAATTGAATATTTAATTTTT
1 AATATAAAAAAGTGAATATTTAATTTTT
* *
18811503 AACAAAAAAAAGTG-ATAATTT-ATTTTT
1 AATATAAAAAAGTGAAT-ATTTAATTTTT
18811530 AATATAAAA
1 AATATAAAA
18811539 GTTTAGATAA
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
27 15 0.52
28 14 0.48
ACGTcount: A:0.53, C:0.02, G:0.05, T:0.41
Consensus pattern (28 bp):
AATATAAAAAAGTGAATATTTAATTTTT
Found at i:18812663 original size:22 final size:21
Alignment explanation
Indices: 18812638--18812701 Score: 65
Period size: 22 Copynumber: 3.0 Consensus size: 21
18812628 ATTTTTTGAA
*
18812638 TTATTTTCTTTCTTTATTTATT
1 TTATTTTATTTCTTTATTT-TT
** *
18812660 TTATAGTATTTCTTTATCTTT
1 TTATTTTATTTCTTTATTTTT
*
18812681 TTATTTTGTTATCTTTATTTT
1 TTATTTTATT-TCTTTATTTT
18812702 CTTAAAAAAA
Statistics
Matches: 33, Mismatches: 8, Indels: 2
0.77 0.19 0.05
Matches are distributed among these distances:
21 9 0.27
22 24 0.73
ACGTcount: A:0.16, C:0.08, G:0.03, T:0.73
Consensus pattern (21 bp):
TTATTTTATTTCTTTATTTTT
Found at i:18813777 original size:17 final size:16
Alignment explanation
Indices: 18813748--18813802 Score: 58
Period size: 17 Copynumber: 3.4 Consensus size: 16
18813738 ACAGAGAAAT
*
18813748 ATAATAATAAATAATC
1 ATAATAATAAATAATA
18813764 ATAATAATTAAATAATA
1 ATAATAA-TAAATAATA
* * *
18813781 ATAA-ACTTATTAATA
1 ATAATAATAAATAATA
18813796 ATAATAA
1 ATAATAA
18813803 AAGAGTAACA
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
15 11 0.34
16 9 0.28
17 12 0.38
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.35
Consensus pattern (16 bp):
ATAATAATAAATAATA
Found at i:18815157 original size:230 final size:225
Alignment explanation
Indices: 18814740--18815162 Score: 491
Period size: 230 Copynumber: 1.9 Consensus size: 225
18814730 TCCCCTATGT
* * * *
18814740 CTTAACTGGATCACCAACTCAATTATGAAATTATAAAAATACCTCTTTATTATTATTATTATTAT
1 CTTAACTGGATCACCAAATCAATTATGAAATTACAAAAATACCTCTTTATTATAATTAATATTAT
* * * *
18814805 TATGAAGCTTTTGTGTTTTCGTACTTTTACATCAGCTTTAAATAAAAGAATTCAAAATTACAAAT
66 TATGAAGCTTTTATCTTTTCATACTTTTACATCAGATTTAAATAAAAGAATTCAAAATTACAAAT
* * ** * *
18814870 TTGATGATTGGACACTTGTTCAATTGTCTTAAAATATAAGTTCATTACCACTTTACCTATATTTG
131 TTGAAGATTGGACACATGTTCAATAATATTAAAATACAAGTTCATTACCACTTTACCTATATTTG
18814935 TTAGCTAATACTTGCATAGTTGGTGTCACC
196 TTAGCTAATACTTGCATAGTTGGTGTCACC
* * * *
18814965 CTTAACTGGATCATCAAATTAGTTATGAAATTACATAAATACCTCTTCTTTTAAATTATAATTAA
1 CTTAACTGGATCACCAAATCAATTATGAAATTACAAAAATA-C-C-TC-TTT--ATTATAATTAA
* * *
18815030 TATTATTATGACA-CTTTTATCTTTTCATATTTTTATATCATATTTAAATAAAA-AATT-ACAAA
60 TATTATTATGA-AGCTTTTATCTTTTCATACTTTTACATCAGATTTAAATAAAAGAATTCA-AAA
*
18815092 TTACAAATTT-AAGAATT-GA-ACATGCATTCAATAATATTAAAATACAAGTTCATTACTC-GTT
123 TTACAAATTTGAAG-ATTGGACACATG--TTCAATAATATTAAAATACAAGTTCATTAC-CACTT
18815153 TACCTATATT
184 TACCTATATT
18815163 CATTGTTGAA
Statistics
Matches: 164, Mismatches: 22, Indels: 19
0.80 0.11 0.09
Matches are distributed among these distances:
225 35 0.21
226 1 0.01
227 1 0.01
228 6 0.04
229 8 0.05
230 58 0.35
231 54 0.33
232 1 0.01
ACGTcount: A:0.37, C:0.14, G:0.08, T:0.41
Consensus pattern (225 bp):
CTTAACTGGATCACCAAATCAATTATGAAATTACAAAAATACCTCTTTATTATAATTAATATTAT
TATGAAGCTTTTATCTTTTCATACTTTTACATCAGATTTAAATAAAAGAATTCAAAATTACAAAT
TTGAAGATTGGACACATGTTCAATAATATTAAAATACAAGTTCATTACCACTTTACCTATATTTG
TTAGCTAATACTTGCATAGTTGGTGTCACC
Found at i:18824583 original size:3 final size:3
Alignment explanation
Indices: 18824575--18824604 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
18824565 TATTCCAATG
18824575 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
18824605 GTTTATGCTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:18825415 original size:146 final size:146
Alignment explanation
Indices: 18825151--18825442 Score: 575
Period size: 146 Copynumber: 2.0 Consensus size: 146
18825141 CTCACCTTGT
18825151 CGTATTCGTTATTGTTTTGTCAAGCATCGACACTAAACACCAAAAGGAAAATTTTTCTAAATAAG
1 CGTATTCGTTATTGTTTTGTCAAGCATCGACACTAAACACCAAAAGGAAAATTTTTCTAAATAAG
18825216 GCAATATTTCGCGTTTGGAAACTCGAGAAAACGTGCCCTAACGTGCTGGGTTTCGATTTCTCGTT
66 GCAATATTTCGCGTTTGGAAACTCGAGAAAACGTGCCCTAACGTGCTGGGTTTCGATTTCTCGTT
18825281 TGACTAAATAGCCAAA
131 TGACTAAATAGCCAAA
*
18825297 CGTATTCGTTATTGTTTTGTCAAGCATTGACACTAAACACCAAAAGGAAAATTTTTCTAAATAAG
1 CGTATTCGTTATTGTTTTGTCAAGCATCGACACTAAACACCAAAAGGAAAATTTTTCTAAATAAG
18825362 GCAATATTTCGCGTTTGGAAACTCGAGAAAACGTGCCCTAACGTGCTGGGTTTCGATTTCTCGTT
66 GCAATATTTCGCGTTTGGAAACTCGAGAAAACGTGCCCTAACGTGCTGGGTTTCGATTTCTCGTT
18825427 TGACTAAATAGCCAAA
131 TGACTAAATAGCCAAA
18825443 TATCCTCTTA
Statistics
Matches: 145, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
146 145 1.00
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Consensus pattern (146 bp):
CGTATTCGTTATTGTTTTGTCAAGCATCGACACTAAACACCAAAAGGAAAATTTTTCTAAATAAG
GCAATATTTCGCGTTTGGAAACTCGAGAAAACGTGCCCTAACGTGCTGGGTTTCGATTTCTCGTT
TGACTAAATAGCCAAA
Found at i:18831223 original size:44 final size:43
Alignment explanation
Indices: 18831095--18831611 Score: 459
Period size: 44 Copynumber: 11.7 Consensus size: 43
18831085 ATAGGTCCTA
* * *
18831095 TCTTCCTATATTGGTAGGAAGTGGATCAAAGAT-GCAGATCTTG
1 TCTTCCTATATTGG-CGGAAGTAGATCGAAGATAGCAGATCTTG
* * * * *
18831138 TCTTCCCATATTGGTGGCGAAGTAGATCGCAGAAAGTAGATCTTG
1 TCTTCCTATATTGG-CG-GAAGTAGATCGAAGATAGCAGATCTTG
* * * * *
18831183 TCTTCATGTATTGGCGTGAAGTAGATCGAAGGTAGCAGATCCTA
1 TCTTCCTATATTGGCG-GAAGTAGATCGAAGATAGCAGATCTTG
* * *
18831227 TCTTCCTATATTGGTAGGAAGTGGATCAAAGAT-GCAGATCTTG
1 TCTTCCTATATTGG-CGGAAGTAGATCGAAGATAGCAGATCTTG
* * * *
18831270 TCTTCCCATATTGGTGGCAAAGTAGATCGCAGAAAGCAGATCTTG
1 TCTTCCTATATTGGCGG--AAGTAGATCGAAGATAGCAGATCTTG
* * * * *
18831315 TCTTCATGTATTGGCGTGAAGTAGATCGAAGGTAGCAGATCCTA
1 TCTTCCTATATTGGCG-GAAGTAGATCGAAGATAGCAGATCTTG
* *
18831359 TCTTCCTATATTGGTAGGAAGTGGATCGAAGAT-GCAGATCTTG
1 TCTTCCTATATTGG-CGGAAGTAGATCGAAGATAGCAGATCTTG
* * * *
18831402 TCTTCCCATATTGGTGGCAAAGTAGATCGCAGAAAGCAGATCTTG
1 TCTTCCTATATTGGCGG--AAGTAGATCGAAGATAGCAGATCTTG
* * * *
18831447 TCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGGTCCTG
1 TCTTCCTATATTGGCG-GAAGTAGATCGAAGATAGCAGATCTTG
* * *
18831491 TCTTCCTATATTGGTAGGAAGTGGATCGACGAT-GCAGATCTTG
1 TCTTCCTATATTGG-CGGAAGTAGATCGAAGATAGCAGATCTTG
* * *
18831534 TCTTCCCATACTGGTGGC-GAAGTAGATCGAAGAAAGCAGATCTTA
1 TCTTCCTATA-T--TGGCGGAAGTAGATCGAAGATAGCAGATCTTG
* *
18831579 TCTTCATGTATTGGCGTGAAGTAGATCGAAGAT
1 TCTTCCTATATTGGCG-GAAGTAGATCGAAGAT
18831612 NNNNNNNNNN
Statistics
Matches: 377, Mismatches: 78, Indels: 37
0.77 0.16 0.08
Matches are distributed among these distances:
42 8 0.02
43 74 0.20
44 207 0.55
45 83 0.22
46 5 0.01
ACGTcount: A:0.27, C:0.16, G:0.26, T:0.30
Consensus pattern (43 bp):
TCTTCCTATATTGGCGGAAGTAGATCGAAGATAGCAGATCTTG
Found at i:18831327 original size:132 final size:132
Alignment explanation
Indices: 18831090--18831609 Score: 932
Period size: 132 Copynumber: 3.9 Consensus size: 132
18831080 CGTAAATAGG
18831090 TCCTATCTTCCTATATTGGTAGGAAGTGGATCAAAGATGCAGATCTTGTCTTCCCATATTGGTGG
1 TCCTATCTTCCTATATTGGTAGGAAGTGGATCAAAGATGCAGATCTTGTCTTCCCATATTGGTGG
* *
18831155 CGAAGTAGATCGCAGAAAGTAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGGTAGCA
66 CAAAGTAGATCGCAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGGTAGCA
18831220 GA
131 GA
18831222 TCCTATCTTCCTATATTGGTAGGAAGTGGATCAAAGATGCAGATCTTGTCTTCCCATATTGGTGG
1 TCCTATCTTCCTATATTGGTAGGAAGTGGATCAAAGATGCAGATCTTGTCTTCCCATATTGGTGG
18831287 CAAAGTAGATCGCAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGGTAGCA
66 CAAAGTAGATCGCAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGGTAGCA
18831352 GA
131 GA
*
18831354 TCCTATCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGG
1 TCCTATCTTCCTATATTGGTAGGAAGTGGATCAAAGATGCAGATCTTGTCTTCCCATATTGGTGG
*
18831419 CAAAGTAGATCGCAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCA
66 CAAAGTAGATCGCAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGGTAGCA
*
18831484 GG
131 GA
* * * *
18831486 TCCTGTCTTCCTATATTGGTAGGAAGTGGATCGACGATGCAGATCTTGTCTTCCCATACTGGTGG
1 TCCTATCTTCCTATATTGGTAGGAAGTGGATCAAAGATGCAGATCTTGTCTTCCCATATTGGTGG
* * *
18831551 CGAAGTAGATCGAAGAAAGCAGATCTTATCTTCATGTATTGGCGTGAAGTAGATCGAAG
66 CAAAGTAGATCGCAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAG
18831610 ATNNNNNNNN
Statistics
Matches: 377, Mismatches: 11, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
132 377 1.00
ACGTcount: A:0.27, C:0.17, G:0.26, T:0.30
Consensus pattern (132 bp):
TCCTATCTTCCTATATTGGTAGGAAGTGGATCAAAGATGCAGATCTTGTCTTCCCATATTGGTGG
CAAAGTAGATCGCAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGGTAGCA
GA
Found at i:18836311 original size:5 final size:5
Alignment explanation
Indices: 18836301--18836325 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
18836291 TGACTTGTGC
18836301 ATGTT ATGTT ATGTT ATGTT ATGTT
1 ATGTT ATGTT ATGTT ATGTT ATGTT
18836326 TTAATTTACT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.20, T:0.60
Consensus pattern (5 bp):
ATGTT
Found at i:18847115 original size:21 final size:21
Alignment explanation
Indices: 18847086--18847125 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
18847076 CGTGGTACTT
18847086 GTGGAAGGGGTAC-TAGAGGCC
1 GTGGAAGGGGT-CGTAGAGGCC
*
18847107 GTGGTAGGGGTCGTAGAGG
1 GTGGAAGGGGTCGTAGAGG
18847126 GGCTCGAGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.20, C:0.10, G:0.53, T:0.17
Consensus pattern (21 bp):
GTGGAAGGGGTCGTAGAGGCC
Found at i:18852431 original size:18 final size:18
Alignment explanation
Indices: 18852387--18852432 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
18852377 TCAACCAATT
*
18852387 GGGCCGTGTGGGCCACAC
1 GGGCTGTGTGGGCCACAC
*
18852405 GGGCT-TGTGGGCCCACAT
1 GGGCTGTGTGGG-CCACAC
18852423 GGG-TGTGTGG
1 GGGCTGTGTGG
18852433 AATTCTAGGC
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
17 7 0.29
18 17 0.71
ACGTcount: A:0.09, C:0.24, G:0.48, T:0.20
Consensus pattern (18 bp):
GGGCTGTGTGGGCCACAC
Found at i:18852505 original size:17 final size:18
Alignment explanation
Indices: 18852483--18852516 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
18852473 ACTTGGGCCG
18852483 TGTAGGCC-ACACGGGTT
1 TGTAGGCCTACACGGGTT
18852500 TGTAGGCCTACACGGGT
1 TGTAGGCCTACACGGGT
18852517 AGGCCACATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.18, C:0.24, G:0.35, T:0.24
Consensus pattern (18 bp):
TGTAGGCCTACACGGGTT
Found at i:18857778 original size:35 final size:35
Alignment explanation
Indices: 18857739--18857944 Score: 130
Period size: 35 Copynumber: 5.9 Consensus size: 35
18857729 CACAATACCA
* *
18857739 ATACTTCTTTCAATAAACATCCTACCACAACATTG
1 ATACTTCATTCAATTAACATCCTACCACAACATTG
* * * * *
18857774 ATACTTCAATCAAGTAACATTCTGCCACAACATCG
1 ATACTTCATTCAATTAACATCCTACCACAACATTG
* * *** * *
18857809 TTACTTCATTCATTTAATGCCCCACCACAACACTG
1 ATACTTCATTCAATTAACATCCTACCACAACATTG
* **
18857844 GTACTTCATTCAATTAACATTCC-ACCACAACACCG
1 ATACTTCATTCAATTAACA-TCCTACCACAACATTG
* * ** ***
18857879 TTACTTTATTC-ATGTAATGTCCTACCACAACACCA
1 ATACTTCATTCAAT-TAACATCCTACCACAACATTG
* *
18857914 ATACTTTATTCATTTAACAT-CTCACCACAAC
1 ATACTTCATTCAATTAACATCCT-ACCACAAC
18857945 GCCAAAATTT
Statistics
Matches: 132, Mismatches: 34, Indels: 10
0.75 0.19 0.06
Matches are distributed among these distances:
34 7 0.05
35 122 0.92
36 3 0.02
ACGTcount: A:0.34, C:0.31, G:0.05, T:0.31
Consensus pattern (35 bp):
ATACTTCATTCAATTAACATCCTACCACAACATTG
Found at i:18857919 original size:70 final size:70
Alignment explanation
Indices: 18857758--18857944 Score: 223
Period size: 70 Copynumber: 2.7 Consensus size: 70
18857748 TCAATAAACA
* * * ** * *
18857758 TCCTACCACAACATTGATACTTCAATCAAGTAACATTCTGCCACAACATCGTTACTTCATTCATT
1 TCCTACCACAACACTGATACTTCATTCAATTAACATTCCACCACAACACCGTTACTTCATTCATG
18857823 TAATG
66 TAATG
* * * *
18857828 CCCCACCACAACACTGGTACTTCATTCAATTAACATTCCACCACAACACCGTTACTTTATTCATG
1 TCCTACCACAACACTGATACTTCATTCAATTAACATTCCACCACAACACCGTTACTTCATTCATG
18857893 TAATG
66 TAATG
** * *
18857898 TCCTACCACAACACCAATACTTTATTCATTTAACA-TCTCACCACAAC
1 TCCTACCACAACACTGATACTTCATTCAATTAACATTC-CACCACAAC
18857945 GCCAAAATTT
Statistics
Matches: 98, Mismatches: 18, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
69 2 0.02
70 96 0.98
ACGTcount: A:0.33, C:0.32, G:0.05, T:0.30
Consensus pattern (70 bp):
TCCTACCACAACACTGATACTTCATTCAATTAACATTCCACCACAACACCGTTACTTCATTCATG
TAATG
Found at i:18858479 original size:22 final size:20
Alignment explanation
Indices: 18858446--18858487 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 20
18858436 GTTAGCTAAA
18858446 CAAAATAATCATTCATTAAT
1 CAAAATAATCATTCATTAAT
18858466 CAAAACTACATCATTCATTAAT
1 CAAAA-TA-ATCATTCATTAAT
18858488 GAGATAATCA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 5 0.25
21 2 0.10
22 13 0.65
ACGTcount: A:0.48, C:0.19, G:0.00, T:0.33
Consensus pattern (20 bp):
CAAAATAATCATTCATTAAT
Found at i:18860147 original size:17 final size:17
Alignment explanation
Indices: 18860125--18860159 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
18860115 AACCATTAAG
18860125 AAAATACAAAAAAAATC
1 AAAATACAAAAAAAATC
* *
18860142 AAAATAGAAAATAAATC
1 AAAATACAAAAAAAATC
18860159 A
1 A
18860160 TGTTAGTAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.74, C:0.09, G:0.03, T:0.14
Consensus pattern (17 bp):
AAAATACAAAAAAAATC
Found at i:18864009 original size:15 final size:15
Alignment explanation
Indices: 18863989--18864030 Score: 66
Period size: 15 Copynumber: 2.8 Consensus size: 15
18863979 CTCGAAAATC
18863989 CATAAACCAAATTCA
1 CATAAACCAAATTCA
18864004 CATAAACCAAATTCA
1 CATAAACCAAATTCA
* *
18864019 CGTAAATCAAAT
1 CATAAACCAAAT
18864031 CCGTATACTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.52, C:0.24, G:0.02, T:0.21
Consensus pattern (15 bp):
CATAAACCAAATTCA
Found at i:18864665 original size:56 final size:56
Alignment explanation
Indices: 18864578--18864737 Score: 230
Period size: 56 Copynumber: 2.9 Consensus size: 56
18864568 GTAACCACAT
*
18864578 ATATCGATGCCAACGTACTAGACGTGGTCTAACTCGCACACATATATCAAAATCAA
1 ATATCGATGCCAACGTACTAGATGTGGTCTAACTCGCACACATATATCAAAATCAA
* * * *
18864634 ATATCGATGTCAACGTACTAGATGTGCTCTAACTTGCACACATATATCAAAATCAC
1 ATATCGATGCCAACGTACTAGATGTGGTCTAACTCGCACACATATATCAAAATCAA
* * * * *
18864690 ATATCGATGCCAATGTACTAAATGTGGTCTTACTGGCTCACATATATC
1 ATATCGATGCCAACGTACTAGATGTGGTCTAACTCGCACACATATATC
18864738 GATGCCATGG
Statistics
Matches: 92, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
56 92 1.00
ACGTcount: A:0.34, C:0.23, G:0.14, T:0.28
Consensus pattern (56 bp):
ATATCGATGCCAACGTACTAGATGTGGTCTAACTCGCACACATATATCAAAATCAA
Found at i:18877216 original size:20 final size:20
Alignment explanation
Indices: 18877173--18877217 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
18877163 TAACATATGA
*
18877173 TTAAATAAGTTTAATTAAAC
1 TTAATTAAGTTTAATTAAAC
18877193 -TAATTAAGTTTTAATT-AAC
1 TTAATTAAG-TTTAATTAAAC
18877212 TTAATT
1 TTAATT
18877218 TGTAACACCC
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
19 10 0.45
20 12 0.55
ACGTcount: A:0.44, C:0.04, G:0.04, T:0.47
Consensus pattern (20 bp):
TTAATTAAGTTTAATTAAAC
Found at i:18883501 original size:47 final size:47
Alignment explanation
Indices: 18883449--18883546 Score: 178
Period size: 47 Copynumber: 2.1 Consensus size: 47
18883439 AATCTTTTTG
* *
18883449 TTAAAATTTTTCATTTATTTTTATTGTTAAAAATTAGTCATTGTATA
1 TTAAAATTTTTCATTAATTTATATTGTTAAAAATTAGTCATTGTATA
18883496 TTAAAATTTTTCATTAATTTATATTGTTAAAAATTAGTCATTGTATA
1 TTAAAATTTTTCATTAATTTATATTGTTAAAAATTAGTCATTGTATA
18883543 TTAA
1 TTAA
18883547 TATGAGATAC
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 49 1.00
ACGTcount: A:0.37, C:0.04, G:0.06, T:0.53
Consensus pattern (47 bp):
TTAAAATTTTTCATTAATTTATATTGTTAAAAATTAGTCATTGTATA
Found at i:18887738 original size:27 final size:28
Alignment explanation
Indices: 18887708--18887768 Score: 108
Period size: 27 Copynumber: 2.2 Consensus size: 28
18887698 TGGATATTCA
18887708 TTATAATCAACATTTCACTTTTCAT-TT
1 TTATAATCAACATTTCACTTTTCATCTT
18887735 TTATAATCAACATTTCACTTTTCATCTT
1 TTATAATCAACATTTCACTTTTCATCTT
18887763 TT-TAAT
1 TTATAAT
18887769 TCTTTCTCTT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
27 29 0.88
28 4 0.12
ACGTcount: A:0.30, C:0.18, G:0.00, T:0.52
Consensus pattern (28 bp):
TTATAATCAACATTTCACTTTTCATCTT
Found at i:18887779 original size:24 final size:24
Alignment explanation
Indices: 18887747--18887813 Score: 75
Period size: 24 Copynumber: 2.8 Consensus size: 24
18887737 ATAATCAACA
* *
18887747 TTTCACTTTTCATCTTTTTAATTC
1 TTTCTCTTTTCATATTTTTAATTC
*
18887771 TTTCTCTTTT-ATTTTTCTTAATTC
1 TTTCTCTTTTCATATTT-TTAATTC
*
18887795 TTTATC-TTTCATATTTTTA
1 TTTCTCTTTTCATATTTTTA
18887814 TAACCCTTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
23 11 0.30
24 26 0.70
ACGTcount: A:0.16, C:0.16, G:0.00, T:0.67
Consensus pattern (24 bp):
TTTCTCTTTTCATATTTTTAATTC
Found at i:18888375 original size:15 final size:15
Alignment explanation
Indices: 18888355--18888384 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
18888345 TATAGAGACA
18888355 CACATGATTTGTGAG
1 CACATGATTTGTGAG
18888370 CACATGATTTGTGAG
1 CACATGATTTGTGAG
18888385 TATAAATGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.13, G:0.27, T:0.33
Consensus pattern (15 bp):
CACATGATTTGTGAG
Found at i:18894301 original size:23 final size:22
Alignment explanation
Indices: 18894275--18894389 Score: 63
Period size: 23 Copynumber: 5.0 Consensus size: 22
18894265 TTAGGCTATA
18894275 CAGAACTTACCACAAAGGCATTG
1 CAGAA-TTACCACAAAGGCATTG
* * *
18894298 CAGAA-CACGCCACAAAAGTATTG
1 CAGAATTA--CCACAAAGGCATTG
* *
18894321 CAGAATAAGCCATAAAGGCATTG
1 CAGAATTA-CCACAAAGGCATTG
* ** *
18894344 TAGAATATGTCACAAAGGCATTA
1 CAGAAT-TACCACAAAGGCATTG
*
18894367 CA-AAATACGCCACAAAGGCATTG
1 CAGAATTA--CCACAAAGGCATTG
18894390 TAAGTAACTT
Statistics
Matches: 68, Mismatches: 18, Indels: 12
0.69 0.18 0.12
Matches are distributed among these distances:
21 2 0.03
22 2 0.03
23 63 0.93
24 1 0.01
ACGTcount: A:0.43, C:0.22, G:0.18, T:0.17
Consensus pattern (22 bp):
CAGAATTACCACAAAGGCATTG
Found at i:18894390 original size:46 final size:46
Alignment explanation
Indices: 18894284--18894391 Score: 126
Period size: 46 Copynumber: 2.3 Consensus size: 46
18894274 ACAGAACTTA
* * * *
18894284 CCACAAAGGCATTGCAGAACACGCCACAAAAGTATTGCAGAATAAG
1 CCACAAAGGCATTGTAGAACACGCCACAAAAGCATTACAAAATAAG
* * * * * *
18894330 CCATAAAGGCATTGTAGAATATGTCACAAAGGCATTACAAAATACG
1 CCACAAAGGCATTGTAGAACACGCCACAAAAGCATTACAAAATAAG
18894376 CCACAAAGGCATTGTA
1 CCACAAAGGCATTGTA
18894392 AGTAACTTGC
Statistics
Matches: 51, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
46 51 1.00
ACGTcount: A:0.43, C:0.21, G:0.19, T:0.18
Consensus pattern (46 bp):
CCACAAAGGCATTGTAGAACACGCCACAAAAGCATTACAAAATAAG
Found at i:18902420 original size:23 final size:23
Alignment explanation
Indices: 18902394--18902450 Score: 96
Period size: 23 Copynumber: 2.5 Consensus size: 23
18902384 TTGTTACATA
*
18902394 CCACAAAGGCATTGTAGAATACG
1 CCACAAAGGCATTGCAGAATACG
*
18902417 CCACAAAGGCATTGCAGCATACG
1 CCACAAAGGCATTGCAGAATACG
18902440 CCACAAAGGCA
1 CCACAAAGGCA
18902451 GAGTACGACA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.39, C:0.28, G:0.21, T:0.12
Consensus pattern (23 bp):
CCACAAAGGCATTGCAGAATACG
Found at i:18903385 original size:22 final size:20
Alignment explanation
Indices: 18903344--18903386 Score: 50
Period size: 22 Copynumber: 2.0 Consensus size: 20
18903334 AATACTTAGG
*
18903344 TTTAGAAAGAAGAACCAAAT
1 TTTAGAAAGAAGAACAAAAT
*
18903364 TTTAGAACAGAAAGAAGAAAAT
1 TTTAGAA-AG-AAGAACAAAAT
18903386 T
1 T
18903387 AAAACATTTG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 7 0.37
21 2 0.11
22 10 0.53
ACGTcount: A:0.56, C:0.07, G:0.16, T:0.21
Consensus pattern (20 bp):
TTTAGAAAGAAGAACAAAAT
Found at i:18906318 original size:18 final size:18
Alignment explanation
Indices: 18906295--18906354 Score: 75
Period size: 18 Copynumber: 3.3 Consensus size: 18
18906285 CAGTCAGTCA
*
18906295 TCAGTATTAATCAGTTAT
1 TCAGTAATAATCAGTTAT
* *
18906313 TCAGTAATAGTCAATTAT
1 TCAGTAATAATCAGTTAT
*
18906331 TTAGTAATAATCAGTTAT
1 TCAGTAATAATCAGTTAT
*
18906349 TTAGTA
1 TCAGTA
18906355 CCTTTATTTA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 36 1.00
ACGTcount: A:0.37, C:0.08, G:0.12, T:0.43
Consensus pattern (18 bp):
TCAGTAATAATCAGTTAT
Found at i:18906531 original size:45 final size:45
Alignment explanation
Indices: 18906481--18906587 Score: 117
Period size: 45 Copynumber: 2.4 Consensus size: 45
18906471 AACAGTAGCA
* * *
18906481 GTAACAGTAACATTAATAGTATTCAACACACAAAGTG-CTGAATCT
1 GTAACAGTAACAGTAATAGAATTCAACACACAAAGTGTC-GAATCG
* * ** * *
18906526 GTAACAATAACGGTAATAGAATTTGACACACAAATTGTCGAGTCG
1 GTAACAGTAACAGTAATAGAATTCAACACACAAAGTGTCGAATCG
18906571 GTAACAGTAACAGTAAT
1 GTAACAGTAACAGTAAT
18906588 CGACACATAA
Statistics
Matches: 50, Mismatches: 11, Indels: 2
0.79 0.17 0.03
Matches are distributed among these distances:
45 49 0.98
46 1 0.02
ACGTcount: A:0.42, C:0.16, G:0.17, T:0.25
Consensus pattern (45 bp):
GTAACAGTAACAGTAATAGAATTCAACACACAAAGTGTCGAATCG
Found at i:18906736 original size:20 final size:20
Alignment explanation
Indices: 18906711--18906750 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
18906701 TTCAGTTTTC
18906711 AATCAGTATATATT-TCAATT
1 AATCAG-ATATATTCTCAATT
18906731 AATCAGATATATTCTCAATT
1 AATCAGATATATTCTCAATT
18906751 CAATATATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 7 0.37
20 12 0.63
ACGTcount: A:0.40, C:0.12, G:0.05, T:0.42
Consensus pattern (20 bp):
AATCAGATATATTCTCAATT
Found at i:18906758 original size:16 final size:15
Alignment explanation
Indices: 18906718--18906767 Score: 55
Period size: 15 Copynumber: 3.0 Consensus size: 15
18906708 TTCAATCAGT
18906718 ATATATTTCAATTAATCA
1 ATATATTTCAA-T--TCA
18906736 GATATATTCTCAATTCA
1 -ATATATT-TCAATTCA
18906753 ATATATTTCAATTCA
1 ATATATTTCAATTCA
18906768 CTTTATATTA
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
15 8 0.27
16 7 0.23
17 3 0.10
19 8 0.27
20 4 0.13
ACGTcount: A:0.40, C:0.14, G:0.02, T:0.44
Consensus pattern (15 bp):
ATATATTTCAATTCA
Found at i:18907665 original size:18 final size:18
Alignment explanation
Indices: 18907644--18907678 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
18907634 GAGCATTCTG
* *
18907644 TTTCTTTTCTTTGTTTCC
1 TTTCCTTTCTTTCTTTCC
18907662 TTTCCTTTCTTTCTTTC
1 TTTCCTTTCTTTCTTTC
18907679 TTTACTATAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.00, C:0.26, G:0.03, T:0.71
Consensus pattern (18 bp):
TTTCCTTTCTTTCTTTCC
Found at i:18907824 original size:16 final size:16
Alignment explanation
Indices: 18907800--18907867 Score: 50
Period size: 16 Copynumber: 4.1 Consensus size: 16
18907790 TTAAATTTAT
*
18907800 TTATTATATAAATATC
1 TTATAATATAAATATC
*
18907816 TTATAATATAATTA-C
1 TTATAATATAAATATC
*
18907831 TTAGTTA-ATAAATATC
1 TTA-TAATATAAATATC
18907847 TTTTATAAATAGTAAATATC
1 --TTAT-AATA-TAAATATC
18907867 T
1 T
18907868 ATTAGTAATT
Statistics
Matches: 40, Mismatches: 5, Indels: 12
0.70 0.09 0.21
Matches are distributed among these distances:
15 10 0.25
16 15 0.38
17 1 0.03
18 5 0.12
19 1 0.03
20 8 0.20
ACGTcount: A:0.44, C:0.06, G:0.03, T:0.47
Consensus pattern (16 bp):
TTATAATATAAATATC
Found at i:18907970 original size:9 final size:9
Alignment explanation
Indices: 18907951--18907985 Score: 54
Period size: 9 Copynumber: 3.9 Consensus size: 9
18907941 CACATTTGTC
18907951 TTTATTTTAT
1 TTTA-TTTAT
18907961 TTTATTTA-
1 TTTATTTAT
18907969 TTTATTTAT
1 TTTATTTAT
18907978 TTTATTTA
1 TTTATTTA
18907986 ATTAATATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
8 8 0.33
9 12 0.50
10 4 0.17
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (9 bp):
TTTATTTAT
Found at i:18913001 original size:18 final size:18
Alignment explanation
Indices: 18912978--18913066 Score: 117
Period size: 18 Copynumber: 4.9 Consensus size: 18
18912968 TCATCAATAT
18912978 TAATCAGTTATTCAGTAA
1 TAATCAGTTATTCAGTAA
*
18912996 TAATCATTTATTCAGTAA
1 TAATCAGTTATTCAGTAA
* *
18913014 CAGTC-GTTTATTCAGTAA
1 TAATCAG-TTATTCAGTAA
* *
18913032 TAGTCAATTATTCAGTAA
1 TAATCAGTTATTCAGTAA
18913050 TAATCAGTTATTCAGTA
1 TAATCAGTTATTCAGTA
18913067 CCTTTATTTA
Statistics
Matches: 61, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
18 61 1.00
ACGTcount: A:0.36, C:0.12, G:0.11, T:0.40
Consensus pattern (18 bp):
TAATCAGTTATTCAGTAA
Found at i:18913245 original size:45 final size:45
Alignment explanation
Indices: 18913193--18913298 Score: 124
Period size: 45 Copynumber: 2.4 Consensus size: 45
18913183 AATGGTAGCA
* * * *
18913193 GTAACAGTAACATTGATAGTATTCAACACACAAAGTGTTGAATCTG
1 GTAACAGTAACAGTAACAGTATTCAACACACAAAGTGTCGAATC-G
* ** *
18913239 G-AACAGTAACGGTAACAGTATTTGACACACAAAGTGTCGAGTCG
1 GTAACAGTAACAGTAACAGTATTCAACACACAAAGTGTCGAATCG
18913283 GTAACAGTAACAGTAA
1 GTAACAGTAACAGTAA
18913299 TGGTAACAGT
Statistics
Matches: 50, Mismatches: 9, Indels: 3
0.81 0.15 0.05
Matches are distributed among these distances:
44 2 0.04
45 47 0.94
46 1 0.02
ACGTcount: A:0.40, C:0.16, G:0.21, T:0.24
Consensus pattern (45 bp):
GTAACAGTAACAGTAACAGTATTCAACACACAAAGTGTCGAATCG
Found at i:18913457 original size:16 final size:16
Alignment explanation
Indices: 18913436--18913487 Score: 50
Period size: 16 Copynumber: 2.9 Consensus size: 16
18913426 AACTTTCAGT
18913436 TTTCAATCAATATATA
1 TTTCAATCAATATATA
*
18913452 TTTCAATTAATCAGATATA
1 TTTCAATCAAT---ATATA
18913471 TTCTCAATTCAATATAT
1 TT-TCAA-TCAATATAT
18913488 TTCAATTCAC
Statistics
Matches: 29, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
16 10 0.34
18 4 0.14
19 7 0.24
20 4 0.14
21 4 0.14
ACGTcount: A:0.40, C:0.13, G:0.02, T:0.44
Consensus pattern (16 bp):
TTTCAATCAATATATA
Found at i:18913488 original size:16 final size:15
Alignment explanation
Indices: 18913447--18913496 Score: 55
Period size: 15 Copynumber: 3.0 Consensus size: 15
18913437 TTCAATCAAT
18913447 ATATATTTCAATTAATCA
1 ATATATTTCAA-T--TCA
18913465 GATATATTCTCAATTCA
1 -ATATATT-TCAATTCA
18913482 ATATATTTCAATTCA
1 ATATATTTCAATTCA
18913497 CTTTATATTA
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
15 8 0.27
16 7 0.23
17 3 0.10
19 8 0.27
20 4 0.13
ACGTcount: A:0.40, C:0.14, G:0.02, T:0.44
Consensus pattern (15 bp):
ATATATTTCAATTCA
Found at i:18918408 original size:35 final size:35
Alignment explanation
Indices: 18918369--18918439 Score: 142
Period size: 35 Copynumber: 2.0 Consensus size: 35
18918359 AAAATTGAAG
18918369 AAGGGCTAAATGAAGATATCAAGCTGTTAATTGGA
1 AAGGGCTAAATGAAGATATCAAGCTGTTAATTGGA
18918404 AAGGGCTAAATGAAGATATCAAGCTGTTAATTGGA
1 AAGGGCTAAATGAAGATATCAAGCTGTTAATTGGA
18918439 A
1 A
18918440 TTTTGGAATT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.41, C:0.08, G:0.25, T:0.25
Consensus pattern (35 bp):
AAGGGCTAAATGAAGATATCAAGCTGTTAATTGGA
Found at i:18922325 original size:49 final size:49
Alignment explanation
Indices: 18922216--18922346 Score: 142
Period size: 49 Copynumber: 2.7 Consensus size: 49
18922206 GATAAGTTGC
* * *
18922216 CGATGCCATGTACCAAACATGGTCTTACACTAGCTATCATCATCGAGGT
1 CGATGCCATGTCCCAAACATGGTCTTACACTAGCTATCATCATAGACGT
* * *
18922265 CGATGCCATGTCCCAAACATGGTCTTATACTAGCTCTCAT-ATATACGT
1 CGATGCCATGTCCCAAACATGGTCTTACACTAGCTATCATCATAGACGT
* **
18922313 ACTGATG-TATGTCCCGGACAT-GTCTTACACTAGC
1 -C-GATGCCATGTCCCAAACATGGTCTTACACTAGC
18922347 ACAACTCTTA
Statistics
Matches: 70, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
48 17 0.24
49 49 0.70
50 4 0.06
ACGTcount: A:0.27, C:0.27, G:0.18, T:0.29
Consensus pattern (49 bp):
CGATGCCATGTCCCAAACATGGTCTTACACTAGCTATCATCATAGACGT
Found at i:18925491 original size:34 final size:34
Alignment explanation
Indices: 18925415--18925494 Score: 90
Period size: 34 Copynumber: 2.4 Consensus size: 34
18925405 TTGTTTGGAT
* *
18925415 ACTG-TACTGAAATGGGCTAAGGCCCAGACTGCC
1 ACTGCTACTGAAACGGGCTAAGGCCCAGAATGCC
* * * *
18925448 ACTGTTACTGAAACGGGCTCAGGCCCGGAATGCT
1 ACTGCTACTGAAACGGGCTAAGGCCCAGAATGCC
*
18925482 TCTGCTACTGAAA
1 ACTGCTACTGAAA
18925495 GAGGGGCTAA
Statistics
Matches: 39, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
33 4 0.10
34 35 0.90
ACGTcount: A:0.26, C:0.26, G:0.26, T:0.21
Consensus pattern (34 bp):
ACTGCTACTGAAACGGGCTAAGGCCCAGAATGCC
Found at i:18934054 original size:49 final size:50
Alignment explanation
Indices: 18933964--18934204 Score: 290
Period size: 49 Copynumber: 4.9 Consensus size: 50
18933954 AGCTATTGTG
* *
18933964 AGGTCACGTGTGTAGTACTAAGTGTAGGCTACTACGTGTACCAGATAATT
1 AGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT
* * * * *
18934014 -GGTCGCATGGGTAGTACTAAGTGCAGGCTACTATGCGTACCTGATAACTT
1 AGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAA-TT
* * * * **
18934064 CGATCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGATGGTT
1 AGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT
* *
18934114 AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATT
1 AGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT
* * *
18934164 -GGTCGCATGTGTAGTACTAAGTGCAGG-TACTATGCGTACCA
1 AGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCA
18934205 AATAGCTTCG
Statistics
Matches: 161, Mismatches: 28, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
48 11 0.07
49 65 0.40
50 48 0.30
51 37 0.23
ACGTcount: A:0.25, C:0.18, G:0.28, T:0.29
Consensus pattern (50 bp):
AGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT
Found at i:18934101 original size:28 final size:28
Alignment explanation
Indices: 18934069--18934152 Score: 83
Period size: 28 Copynumber: 3.2 Consensus size: 28
18934059 AACTTCGATC
18934069 ACGTGTGTAGTACTAAGTGCAGGCTACT
1 ACGTGTGTAGTACTAAGTGCAGGCTACT
* * *
18934097 ACGTGTATCAG-A-T-GGT-TAGG-T-C-
1 ACGTGTGT-AGTACTAAGTGCAGGCTACT
18934119 ACGTGTGTAGTACTAAGTGCAGGCTACT
1 ACGTGTGTAGTACTAAGTGCAGGCTACT
18934147 ACGTGT
1 ACGTGT
18934153 ACCGGATAAT
Statistics
Matches: 42, Mismatches: 6, Indels: 16
0.66 0.09 0.25
Matches are distributed among these distances:
21 2 0.05
22 8 0.19
23 2 0.05
24 3 0.07
25 6 0.14
26 3 0.07
27 2 0.05
28 14 0.33
29 2 0.05
ACGTcount: A:0.24, C:0.17, G:0.30, T:0.30
Consensus pattern (28 bp):
ACGTGTGTAGTACTAAGTGCAGGCTACT
Found at i:18934226 original size:101 final size:101
Alignment explanation
Indices: 18933967--18934226 Score: 260
Period size: 101 Copynumber: 2.6 Consensus size: 101
18933957 TATTGTGAGG
* * * * ** * *
18933967 TCACGTGTGTAGTACTAAGTGTAGGCTACTACGTGTACCAGATAATT-GGTCGCA-TGGGTAGTA
1 TCACATGTGTAGTACTAAGTGCAGGCTACTACGCGTACCAAATGCTTAGGTC-AAGTGTGTAGTA
* *
18934030 CTAAGTGCAGGCTACTATGCGTACCTGATAACTTCGA
65 CTAAGTGCAGGCTACTACGCGTACCGGATAACTTCGA
* * * * * *
18934067 TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGATGGTTAGGTCACGTGTGTAGTAC
1 TCACATGTGTAGTACTAAGTGCAGGCTACTACGCGTACCAAATGCTTAGGTCAAGTGTGTAGTAC
* *
18934132 TAAGTGCAGGCTACTACGTGTACCGGATAA-TT-GG
66 TAAGTGCAGGCTACTACGCGTACCGGATAACTTCGA
* * *
18934166 TCGCATGTGTAGTACTAAGTGCAGG-TACTATGCGTACCAAATAGCTTCGGCTACAAGTGTG
1 TCACATGTGTAGTACTAAGTGCAGGCTACTACGCGTACCAAAT-GCTTAGG-T-CAAGTGTG
18934227 GAAATGAGAA
Statistics
Matches: 135, Mismatches: 20, Indels: 9
0.82 0.12 0.05
Matches are distributed among these distances:
98 13 0.10
99 29 0.21
100 46 0.34
101 47 0.35
ACGTcount: A:0.25, C:0.18, G:0.27, T:0.29
Consensus pattern (101 bp):
TCACATGTGTAGTACTAAGTGCAGGCTACTACGCGTACCAAATGCTTAGGTCAAGTGTGTAGTAC
TAAGTGCAGGCTACTACGCGTACCGGATAACTTCGA
Found at i:18935617 original size:12 final size:13
Alignment explanation
Indices: 18935600--18935628 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
18935590 TAAGAAACTT
18935600 AAATACCAAT-CA
1 AAATACCAATCCA
18935612 AAATACCAATCCA
1 AAATACCAATCCA
18935625 AAAT
1 AAAT
18935629 GACAATAATC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.59, C:0.24, G:0.00, T:0.17
Consensus pattern (13 bp):
AAATACCAATCCA
Found at i:18938353 original size:41 final size:41
Alignment explanation
Indices: 18938286--18938368 Score: 130
Period size: 41 Copynumber: 2.0 Consensus size: 41
18938276 GTTTTGCGAC
*
18938286 GACTACTACTGAGATCCCTTATGATGTCCTACAATTGATTA
1 GACTACTACTGAGATCCCTTACGATGTCCTACAATTGATTA
* * *
18938327 GACTGCTACTGAGATCTCTTCCGATGTCCTACAATTGATTA
1 GACTACTACTGAGATCCCTTACGATGTCCTACAATTGATTA
18938368 G
1 G
18938369 CACAGTCCTT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 38 1.00
ACGTcount: A:0.27, C:0.23, G:0.17, T:0.34
Consensus pattern (41 bp):
GACTACTACTGAGATCCCTTACGATGTCCTACAATTGATTA
Found at i:18946890 original size:36 final size:36
Alignment explanation
Indices: 18946850--18946930 Score: 137
Period size: 36 Copynumber: 2.2 Consensus size: 36
18946840 GGTGGTTACT
*
18946850 CATGAAGAGACCCAAGGCATAATTTTTTATATAACC
1 CATGAAGAGACCCAAGGCATAATTTTTTATAAAACC
18946886 CATGAAGAGACCCAAGGCATAATTTTTTATAAAACC
1 CATGAAGAGACCCAAGGCATAATTTTTTATAAAACC
18946922 C-TAGAAGAG
1 CAT-GAAGAG
18946931 GTTCAGGTAT
Statistics
Matches: 43, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
35 1 0.02
36 42 0.98
ACGTcount: A:0.41, C:0.19, G:0.16, T:0.25
Consensus pattern (36 bp):
CATGAAGAGACCCAAGGCATAATTTTTTATAAAACC
Found at i:18960153 original size:5 final size:5
Alignment explanation
Indices: 18960143--18960177 Score: 52
Period size: 5 Copynumber: 6.6 Consensus size: 5
18960133 TTTTTACATT
18960143 TTTTA TTTTA TTTTA TTTTA TTTTTA TCTTTA TTT
1 TTTTA TTTTA TTTTA TTTTA -TTTTA T-TTTA TTT
18960178 ATATGTTAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
5 18 0.64
6 10 0.36
ACGTcount: A:0.17, C:0.03, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTTA
Found at i:18967335 original size:45 final size:45
Alignment explanation
Indices: 18967271--18967445 Score: 223
Period size: 45 Copynumber: 4.0 Consensus size: 45
18967261 ATATCGTACA
* * *
18967271 ATACTATTCAGACCTTTGAGCCTAGCAGGTTATAATGCCGGTGAG
1 ATACTATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAG
18967316 ATACTATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAG
1 ATACTATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAG
* * *
18967361 ATACTATTCGGGCCTTCGAGCCTAGCAGGCTATAATGCCAGTGAA
1 ATACTATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAG
* * * *
18967406 ATGA-TA-TC-GGTCTTCGAACCTAGCAGGC-AAAATGCCGGTG
1 AT-ACTATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTG
18967446 GATGAATTCA
Statistics
Matches: 119, Mismatches: 10, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
42 10 0.08
43 18 0.15
44 2 0.02
45 88 0.74
46 1 0.01
ACGTcount: A:0.26, C:0.22, G:0.26, T:0.26
Consensus pattern (45 bp):
ATACTATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAG
Found at i:18978284 original size:35 final size:35
Alignment explanation
Indices: 18978240--18978312 Score: 119
Period size: 35 Copynumber: 2.1 Consensus size: 35
18978230 TCTTTTGCAA
* *
18978240 GTAATTCATTTATAAGGTTATTCTTGATGAGTTTT
1 GTAAGTCATTTAGAAGGTTATTCTTGATGAGTTTT
*
18978275 GTAAGTCATTTAGAAGGTTATTCTTGATGATTTTT
1 GTAAGTCATTTAGAAGGTTATTCTTGATGAGTTTT
18978310 GTA
1 GTA
18978313 TTTTTGGACC
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.26, C:0.05, G:0.19, T:0.49
Consensus pattern (35 bp):
GTAAGTCATTTAGAAGGTTATTCTTGATGAGTTTT
Found at i:18985231 original size:34 final size:34
Alignment explanation
Indices: 18985188--18985258 Score: 133
Period size: 34 Copynumber: 2.1 Consensus size: 34
18985178 CCCAAACAGG
*
18985188 TAAGTACGAATCATGAACCTCGTGTGCCATATCC
1 TAAGTACGAATCATGAACCTCATGTGCCATATCC
18985222 TAAGTACGAATCATGAACCTCATGTGCCATATCC
1 TAAGTACGAATCATGAACCTCATGTGCCATATCC
18985256 TAA
1 TAA
18985259 AGCGATGACG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.32, C:0.25, G:0.15, T:0.27
Consensus pattern (34 bp):
TAAGTACGAATCATGAACCTCATGTGCCATATCC
Found at i:18988753 original size:5 final size:5
Alignment explanation
Indices: 18988728--18988817 Score: 67
Period size: 5 Copynumber: 16.8 Consensus size: 5
18988718 GACTCCTATT
* *
18988728 TTTTT TTTTA TTCTTA TTTTTA TTTTA TTTTA TTTTAA TTTTTC TTTTGA
1 TTTTA TTTTA TT-TTA -TTTTA TTTTA TTTTA TTTT-A -TTTTA TTTT-A
*
18988778 TTCTTA TTTTCA TTTCAA TTTTA --TTA TTTTA TTTTA TTTT
1 TT-TTA TTTT-A TTT-TA TTTTA TTTTA TTTTA TTTTA TTTT
18988818 GAAAGACATA
Statistics
Matches: 70, Mismatches: 5, Indels: 20
0.74 0.05 0.21
Matches are distributed among these distances:
3 3 0.04
5 39 0.56
6 20 0.29
7 8 0.11
ACGTcount: A:0.18, C:0.06, G:0.01, T:0.76
Consensus pattern (5 bp):
TTTTA
Found at i:18988781 original size:40 final size:41
Alignment explanation
Indices: 18988725--18988802 Score: 113
Period size: 40 Copynumber: 1.9 Consensus size: 41
18988715 ATTGACTCCT
* * * *
18988725 ATTTTTTTTTTTATTCTTATTTTTATTT-TATTTTATTTTA
1 ATTTTTCTTTTGATTCTTATTTTCATTTCAATTTTATTTTA
18988765 ATTTTTCTTTTGATTCTTATTTTCATTTCAATTTTATT
1 ATTTTTCTTTTGATTCTTATTTTCATTTCAATTTTATT
18988803 ATTTTATTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
40 25 0.76
41 8 0.24
ACGTcount: A:0.18, C:0.06, G:0.01, T:0.74
Consensus pattern (41 bp):
ATTTTTCTTTTGATTCTTATTTTCATTTCAATTTTATTTTA
Found at i:18988787 original size:12 final size:10
Alignment explanation
Indices: 18988728--18988817 Score: 67
Period size: 12 Copynumber: 8.4 Consensus size: 10
18988718 GACTCCTATT
*
18988728 TTTTTTTTTA
1 TTTTATTTTA
18988738 TTCTTATTTTTA
1 TT-TTA-TTTTA
18988750 TTTTATTTTA
1 TTTTATTTTA
*
18988760 TTTTAATTTTTC
1 TTTT-A-TTTTA
18988772 TTTTGATTCTTA
1 TTTT-ATT-TTA
*
18988784 TTTTCATTTCAA
1 TTTT-ATTT-TA
18988796 TTTTA--TTA
1 TTTTATTTTA
18988804 TTTTATTTTA
1 TTTTATTTTA
18988814 TTTT
1 TTTT
18988818 GAAAGACATA
Statistics
Matches: 65, Mismatches: 7, Indels: 16
0.74 0.08 0.18
Matches are distributed among these distances:
8 6 0.09
9 1 0.02
10 18 0.28
11 10 0.15
12 30 0.46
ACGTcount: A:0.18, C:0.06, G:0.01, T:0.76
Consensus pattern (10 bp):
TTTTATTTTA
Found at i:19003543 original size:6 final size:6
Alignment explanation
Indices: 19003532--19003566 Score: 52
Period size: 6 Copynumber: 5.5 Consensus size: 6
19003522 TAATTTCTCT
19003532 TTTTTC TTTTTC TTTTCTCC TTTTTC TTTTTC TTT
1 TTTTTC TTTTTC TTTT-T-C TTTTTC TTTTTC TTT
19003567 CTATTTCGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
6 20 0.74
7 2 0.07
8 5 0.19
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (6 bp):
TTTTTC
Found at i:19003550 original size:20 final size:20
Alignment explanation
Indices: 19003525--19003566 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
19003515 CAAATCCTAA
*
19003525 TTTCTCTTTTTTCTTTTTCT
1 TTTCTCCTTTTTCTTTTTCT
19003545 TTTCTCCTTTTTCTTTTTCT
1 TTTCTCCTTTTTCTTTTTCT
19003565 TT
1 TT
19003567 CTATTTCGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (20 bp):
TTTCTCCTTTTTCTTTTTCT
Found at i:19005555 original size:18 final size:18
Alignment explanation
Indices: 19005534--19005575 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
19005524 AATCAGTAAC
19005534 TCAGTAACAGTCAAATAT
1 TCAGTAACAGTCAAATAT
* *
19005552 TCAGTAGCAGTCAATTAT
1 TCAGTAACAGTCAAATAT
19005570 TCAGTA
1 TCAGTA
19005576 CCTTTATTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.38, C:0.17, G:0.14, T:0.31
Consensus pattern (18 bp):
TCAGTAACAGTCAAATAT
Found at i:19006924 original size:20 final size:22
Alignment explanation
Indices: 19006874--19006930 Score: 75
Period size: 22 Copynumber: 2.7 Consensus size: 22
19006864 TCCCCTATTC
*
19006874 TTCTCTGTTTCATTTGCTTTGT
1 TTCTCTTTTTCATTTGCTTTGT
19006896 TTCTCTTTTTCATTT-CTTT-T
1 TTCTCTTTTTCATTTGCTTTGT
19006916 GTT-TCTTTTTCATTT
1 -TTCTCTTTTTCATTT
19006931 ATTATTTATT
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
20 13 0.39
21 6 0.18
22 14 0.42
ACGTcount: A:0.05, C:0.18, G:0.07, T:0.70
Consensus pattern (22 bp):
TTCTCTTTTTCATTTGCTTTGT
Found at i:19007065 original size:4 final size:4
Alignment explanation
Indices: 19007052--19007095 Score: 61
Period size: 4 Copynumber: 10.2 Consensus size: 4
19007042 ATTTGTCACA
19007052 ATTT ATTTT ATTT ATTT ATTTT ATTT ATTT ATTT AATTT ATTT A
1 ATTT A-TTT ATTT ATTT A-TTT ATTT ATTT ATTT -ATTT ATTT A
19007096 ATTAATATAA
Statistics
Matches: 37, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
4 25 0.68
5 12 0.32
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (4 bp):
ATTT
Found at i:19007070 original size:13 final size:13
Alignment explanation
Indices: 19007052--19007095 Score: 79
Period size: 13 Copynumber: 3.4 Consensus size: 13
19007042 ATTTGTCACA
19007052 ATTTATTTTATTT
1 ATTTATTTTATTT
19007065 ATTTATTTTATTT
1 ATTTATTTTATTT
*
19007078 ATTTATTTAATTT
1 ATTTATTTTATTT
19007091 ATTTA
1 ATTTA
19007096 ATTAATATAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
13 30 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (13 bp):
ATTTATTTTATTT
Found at i:19007095 original size:9 final size:9
Alignment explanation
Indices: 19007051--19007098 Score: 71
Period size: 9 Copynumber: 5.4 Consensus size: 9
19007041 CATTTGTCAC
19007051 AATTTATTT
1 AATTTATTT
*
19007060 TATTTATTT
1 AATTTATTT
*
19007069 ATTTTATTT
1 AATTTATTT
19007078 -ATTTATTT
1 AATTTATTT
19007086 AATTTATTT
1 AATTTATTT
19007095 AATT
1 AATT
19007099 AATATAAAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
8 7 0.21
9 27 0.79
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (9 bp):
AATTTATTT
Found at i:19007100 original size:13 final size:13
Alignment explanation
Indices: 19007052--19007101 Score: 73
Period size: 13 Copynumber: 3.8 Consensus size: 13
19007042 ATTTGTCACA
*
19007052 ATTTATTTTATTT
1 ATTTATTTAATTT
*
19007065 ATTTATTTTATTT
1 ATTTATTTAATTT
19007078 ATTTATTTAATTT
1 ATTTATTTAATTT
*
19007091 ATTTAATTAAT
1 ATTTATTTAAT
19007102 ATAAAATAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 35 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (13 bp):
ATTTATTTAATTT
Found at i:19007118 original size:11 final size:11
Alignment explanation
Indices: 19007098--19007134 Score: 67
Period size: 11 Copynumber: 3.5 Consensus size: 11
19007088 TTTATTTAAT
19007098 TAAT-ATAAAA
1 TAATAATAAAA
19007108 TAATAATAAAA
1 TAATAATAAAA
19007119 TAATAATAAAA
1 TAATAATAAAA
19007130 TAATA
1 TAATA
19007135 TTTACTTAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 4 0.15
11 22 0.85
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (11 bp):
TAATAATAAAA
Found at i:19014698 original size:57 final size:57
Alignment explanation
Indices: 19014615--19014731 Score: 162
Period size: 57 Copynumber: 2.1 Consensus size: 57
19014605 GAAATGGTGT
* * *
19014615 AAATAGAGAATTGGAAACATTGGGAAATGATTATAGTTTTCTCCAAAATGAAAATGA
1 AAATAGAGAAATGGAAACATTGGGAAATGAATACAGTTTTCTCCAAAATGAAAATGA
* * * * *
19014672 AAATGGAGAAATGGAATCATTTGGAAATGAATGCGGTTTTCTCCAAAATGAAAATGA
1 AAATAGAGAAATGGAAACATTGGGAAATGAATACAGTTTTCTCCAAAATGAAAATGA
19014729 AAA
1 AAA
19014732 ATACCTGAAA
Statistics
Matches: 52, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
57 52 1.00
ACGTcount: A:0.45, C:0.08, G:0.21, T:0.26
Consensus pattern (57 bp):
AAATAGAGAAATGGAAACATTGGGAAATGAATACAGTTTTCTCCAAAATGAAAATGA
Found at i:19015228 original size:28 final size:28
Alignment explanation
Indices: 19015188--19015244 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
19015178 GGGTAATACT
19015188 TGTTCTCTCGATATGATTCTATTTTATC
1 TGTTCTCTCGATATGATTCTATTTTATC
19015216 TGTTCTCTCGATATGATTCTATTTTATC
1 TGTTCTCTCGATATGATTCTATTTTATC
19015244 T
1 T
19015245 CATGGTAACC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.18, C:0.18, G:0.11, T:0.54
Consensus pattern (28 bp):
TGTTCTCTCGATATGATTCTATTTTATC
Found at i:19018142 original size:27 final size:27
Alignment explanation
Indices: 19018102--19018213 Score: 111
Period size: 27 Copynumber: 4.1 Consensus size: 27
19018092 AGGAAGCGTC
* *
19018102 CTGGTGGCTATGCCACAATTATTTGAT
1 CTGGTGGCTCTGCCACAATTATCTGAT
*
19018129 CTGGTGGCTCTGCCACATATT-TCTGTT
1 CTGGTGGCTCTGCCACA-ATTATCTGAT
*
19018156 CTGGTGGCTCTGCCACGATTATCTGTAT
1 CTGGTGGCTCTGCCACAATTATCTG-AT
* * ** *
19018184 CTAGTGACTCTATCAC-ATTATCTGTT
1 CTGGTGGCTCTGCCACAATTATCTGAT
19018210 CTGG
1 CTGG
19018214 CAGCCATGCT
Statistics
Matches: 71, Mismatches: 11, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
26 7 0.10
27 48 0.68
28 16 0.23
ACGTcount: A:0.17, C:0.23, G:0.21, T:0.38
Consensus pattern (27 bp):
CTGGTGGCTCTGCCACAATTATCTGAT
Found at i:19018208 original size:54 final size:54
Alignment explanation
Indices: 19018102--19018213 Score: 136
Period size: 54 Copynumber: 2.1 Consensus size: 54
19018092 AGGAAGCGTC
* * * * *
19018102 CTGGTGGCTATGCCACAATTATTTGATCTGGTGGCTCTGCCACATATTTCTGTT
1 CTGGTGGCTATGCCACAATTATCTGATCTAGTGACTCTACCACATATATCTGTT
* * *
19018156 CTGGTGGCTCTGCCACGATTATCTGTATCTAGTGACTCTATCACAT-TATCTGTT
1 CTGGTGGCTATGCCACAATTATCTG-ATCTAGTGACTCTACCACATATATCTGTT
19018210 CTGG
1 CTGG
19018214 CAGCCATGCT
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
54 33 0.67
55 16 0.33
ACGTcount: A:0.17, C:0.23, G:0.21, T:0.38
Consensus pattern (54 bp):
CTGGTGGCTATGCCACAATTATCTGATCTAGTGACTCTACCACATATATCTGTT
Found at i:19021967 original size:68 final size:67
Alignment explanation
Indices: 19021857--19021992 Score: 245
Period size: 68 Copynumber: 2.0 Consensus size: 67
19021847 TGTTAAGGGA
* *
19021857 GAAGGAACTTTATGCGAAGTTCAGCAGGTGTGAATTTTGGTTGAGGGAGGTAACTTTCTTAGGAC
1 GAAGGAACTTTATGCGAAGTTCAGCAGGTGTGAATTTTGGTTGAGGGAGGTAACTTTCCTAGAAC
19021922 AT
66 AT
19021924 GNAAGGAACTTTATGCGAAGTTCAGCAGGTGTGAATTTTGGTTGAGGGAGGTAACTTTCCTAGAA
1 G-AAGGAACTTTATGCGAAGTTCAGCAGGTGTGAATTTTGGTTGAGGGAGGTAACTTTCCTAGAA
19021989 CAT
65 CAT
19021992 G
1 G
19021993 TGCTCTCTGC
Statistics
Matches: 66, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
67 1 0.02
68 65 0.98
ACGTcount: A:0.27, C:0.11, G:0.31, T:0.30
Consensus pattern (67 bp):
GAAGGAACTTTATGCGAAGTTCAGCAGGTGTGAATTTTGGTTGAGGGAGGTAACTTTCCTAGAAC
AT
Found at i:19022689 original size:22 final size:24
Alignment explanation
Indices: 19022664--19022712 Score: 66
Period size: 22 Copynumber: 2.1 Consensus size: 24
19022654 TTTCTGATCA
19022664 CTTTTCCTCTCC-TT-TTATTTTT
1 CTTTTCCTCTCCATTGTTATTTTT
*
19022686 CTTTTTCTCTCCATTTGTTATTTTT
1 CTTTTCCTCTCCA-TTGTTATTTTT
19022711 CT
1 CT
19022713 CTTCTTCTGT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
22 11 0.48
24 2 0.09
25 10 0.43
ACGTcount: A:0.06, C:0.24, G:0.02, T:0.67
Consensus pattern (24 bp):
CTTTTCCTCTCCATTGTTATTTTT
Found at i:19023991 original size:27 final size:27
Alignment explanation
Indices: 19023951--19024055 Score: 115
Period size: 27 Copynumber: 3.9 Consensus size: 27
19023941 AGGAAACGTC
*
19023951 CTGGTGGCTATGCCACAATTATCTGAT
1 CTGGTGGCTCTGCCACAATTATCTGAT
*
19023978 CTGGTGGCTCTGCCACATATT-TCTGTT
1 CTGGTGGCTCTGCCACA-ATTATCTGAT
* *
19024005 CTGGTGGCTCTGCCACGATTATCTGTGT
1 CTGGTGGCTCTGCCACAATTATCTG-AT
* * *
19024033 CTAGTGACTCTGTCAC-ATTATCT
1 CTGGTGGCTCTGCCACAATTATCT
19024056 ATTCTGGCAG
Statistics
Matches: 68, Mismatches: 7, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
26 3 0.04
27 48 0.71
28 17 0.25
ACGTcount: A:0.16, C:0.25, G:0.22, T:0.37
Consensus pattern (27 bp):
CTGGTGGCTCTGCCACAATTATCTGAT
Found at i:19024061 original size:54 final size:54
Alignment explanation
Indices: 19023951--19024062 Score: 136
Period size: 54 Copynumber: 2.1 Consensus size: 54
19023941 AGGAAACGTC
* * * *
19023951 CTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATTTCTGTT
1 CTGGTGGCTATGCCACAATTATCTGATCTAGTGACTCTGCCACATATATCTATT
* * * *
19024005 CTGGTGGCTCTGCCACGATTATCTGTGTCTAGTGACTCTGTCACAT-TATCTATT
1 CTGGTGGCTATGCCACAATTATCTG-ATCTAGTGACTCTGCCACATATATCTATT
19024059 CTGG
1 CTGG
19024063 CAGCCATGCT
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
54 33 0.67
55 16 0.33
ACGTcount: A:0.16, C:0.24, G:0.22, T:0.38
Consensus pattern (54 bp):
CTGGTGGCTATGCCACAATTATCTGATCTAGTGACTCTGCCACATATATCTATT
Found at i:19025961 original size:20 final size:22
Alignment explanation
Indices: 19025936--19025976 Score: 59
Period size: 20 Copynumber: 1.9 Consensus size: 22
19025926 GTGACATTTT
19025936 CTTTTT-TCTTTT-TCACTCGA
1 CTTTTTCTCTTTTCTCACTCGA
19025956 CTTTTTCCTCTTTTCTCACTC
1 CTTTTT-CTCTTTTCTCACTC
19025977 ACAATGATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 6 0.33
22 6 0.33
23 6 0.33
ACGTcount: A:0.07, C:0.32, G:0.02, T:0.59
Consensus pattern (22 bp):
CTTTTTCTCTTTTCTCACTCGA
Found at i:19027695 original size:24 final size:24
Alignment explanation
Indices: 19027668--19027713 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
19027658 TAAGCTCCAT
* *
19027668 CGAGCTGGAAACAGTATGCTCTGA
1 CGAGCTGGAAACAATAAGCTCTGA
* *
19027692 CGAGTTGGGAACAATAAGCTCT
1 CGAGCTGGAAACAATAAGCTCT
19027714 TATGAGCTAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.30, C:0.20, G:0.28, T:0.22
Consensus pattern (24 bp):
CGAGCTGGAAACAATAAGCTCTGA
Found at i:19027907 original size:17 final size:19
Alignment explanation
Indices: 19027876--19027921 Score: 60
Period size: 17 Copynumber: 2.5 Consensus size: 19
19027866 ATAAGGCATT
19027876 TTTATTTCAAGTACAT-CA
1 TTTATTTCAAGTACATACA
*
19027894 TTTA-TTCAATTACATACA
1 TTTATTTCAAGTACATACA
*
19027912 TTCATTTCAA
1 TTTATTTCAA
19027922 ATCATTACAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 10 0.42
18 9 0.38
19 5 0.21
ACGTcount: A:0.35, C:0.17, G:0.02, T:0.46
Consensus pattern (19 bp):
TTTATTTCAAGTACATACA
Found at i:19034094 original size:24 final size:24
Alignment explanation
Indices: 19034059--19034117 Score: 91
Period size: 24 Copynumber: 2.5 Consensus size: 24
19034049 TAAGCTGATG
*
19034059 AACAGTAAGCTCTATCGAGCTAGA
1 AACAGTAAGCTCTAACGAGCTAGA
* *
19034083 AATAGTAAGCTCTAACGAGCTGGA
1 AACAGTAAGCTCTAACGAGCTAGA
19034107 AACAGTAAGCT
1 AACAGTAAGCT
19034118 TTGATGAGCT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.39, C:0.19, G:0.22, T:0.20
Consensus pattern (24 bp):
AACAGTAAGCTCTAACGAGCTAGA
Found at i:19034126 original size:24 final size:23
Alignment explanation
Indices: 19034059--19034128 Score: 77
Period size: 24 Copynumber: 2.9 Consensus size: 23
19034049 TAAGCTGATG
*
19034059 AACAGTAAGCTCTATCGAGCTAGA
1 AACAGTAAGCTCTAT-GAGCTGGA
* *
19034083 AATAGTAAGCTCTAACGAGCTGGA
1 AACAGTAAGCTCT-ATGAGCTGGA
*
19034107 AACAGTAAGCTTTGATGAGCTG
1 AACAGTAAGCTCT-ATGAGCTG
19034129 ATATATTGGT
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
24 37 0.97
25 1 0.03
ACGTcount: A:0.36, C:0.17, G:0.24, T:0.23
Consensus pattern (23 bp):
AACAGTAAGCTCTATGAGCTGGA
Found at i:19051616 original size:17 final size:19
Alignment explanation
Indices: 19051574--19051617 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
19051564 ACGAAATTTT
*
19051574 AATTAGTATTATGAGATAA
1 AATTATTATTATGAGATAA
*
19051593 AATTATTATTATTAGA-AA
1 AATTATTATTATGAGATAA
19051611 AA-TATTA
1 AATTATTA
19051618 CTGCATGTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 5 0.22
18 4 0.17
19 14 0.61
ACGTcount: A:0.50, C:0.00, G:0.09, T:0.41
Consensus pattern (19 bp):
AATTATTATTATGAGATAA
Found at i:19053380 original size:8 final size:8
Alignment explanation
Indices: 19053367--19053398 Score: 55
Period size: 8 Copynumber: 4.0 Consensus size: 8
19053357 CTAGATCGGC
*
19053367 AAAAGCGG
1 AAAAGCCG
19053375 AAAAGCCG
1 AAAAGCCG
19053383 AAAAGCCG
1 AAAAGCCG
19053391 AAAAGCCG
1 AAAAGCCG
19053399 GCATTTGTGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.50, C:0.22, G:0.28, T:0.00
Consensus pattern (8 bp):
AAAAGCCG
Found at i:19054149 original size:60 final size:60
Alignment explanation
Indices: 19054022--19054163 Score: 146
Period size: 60 Copynumber: 2.4 Consensus size: 60
19054012 CCCAACTATG
* * * *
19054022 TTGATATGGGCAAGGCCCAATATATCTCGACTTGTAATAGGGCTATGGCCCAGATTGATA
1 TTGATATGGGCTAGGCCCAATATATCTCGACTTGTAATAGGGCTATCGCCCAAATTAATA
* * *
19054082 CTAATATGGGCTAGGCCCAATATA-CTCTGA-TACTGTAA-GGGGCTATCGCCCAAATTAATA
1 TTGATATGGGCTAGGCCCAATATATCTC-GACT--TGTAATAGGGCTATCGCCCAAATTAATA
* *
19054142 TTGATATGAGCTAAGGCTCAAT
1 TTGATATGGGCT-AGGCCCAAT
19054164 TAACACTAAA
Statistics
Matches: 67, Mismatches: 11, Indels: 7
0.79 0.13 0.08
Matches are distributed among these distances:
59 4 0.06
60 50 0.75
61 13 0.19
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.28
Consensus pattern (60 bp):
TTGATATGGGCTAGGCCCAATATATCTCGACTTGTAATAGGGCTATCGCCCAAATTAATA
Found at i:19056197 original size:10 final size:11
Alignment explanation
Indices: 19056169--19056195 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
19056159 AAGATTGGCA
19056169 TAAAAATTGGG
1 TAAAAATTGGG
19056180 TAAAAATTGGG
1 TAAAAATTGGG
19056191 TAAAA
1 TAAAA
19056196 TTTATGAAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.52, C:0.00, G:0.22, T:0.26
Consensus pattern (11 bp):
TAAAAATTGGG
Done.