Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A04
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: 82679320
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 4050000 characters in sequence are not A, C, G, or T
File 193 of 255
Found at i:64180237 original size:32 final size:32
Alignment explanation
Indices: 64180194--64180289 Score: 138
Period size: 32 Copynumber: 3.0 Consensus size: 32
64180184 TCTTTTTTTT
* *
64180194 TTGCCAAGTTTTCTTTCTTGGAGGGGAAGTTA
1 TTGCCATGTTTTCTTTCTTGGAGGGGAAATTA
* *
64180226 TTGCCATGTTTTCTTTCTTAGAAGGGAAATTA
1 TTGCCATGTTTTCTTTCTTGGAGGGGAAATTA
* *
64180258 TTACCATGTTTTCTTTCTTGAAGGGGAAATTA
1 TTGCCATGTTTTCTTTCTTGGAGGGGAAATTA
64180290 GAGTCGTTTG
Statistics
Matches: 56, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 56 1.00
ACGTcount: A:0.23, C:0.12, G:0.22, T:0.43
Consensus pattern (32 bp):
TTGCCATGTTTTCTTTCTTGGAGGGGAAATTA
Found at i:64217450 original size:21 final size:22
Alignment explanation
Indices: 64217415--64217459 Score: 74
Period size: 21 Copynumber: 2.1 Consensus size: 22
64217405 GAAAACAGGG
*
64217415 CACAGCCCGTGTAAGAGGGCAA
1 CACAGCCCATGTAAGAGGGCAA
64217437 CACA-CCCATGTAAGAGGGCAA
1 CACAGCCCATGTAAGAGGGCAA
64217458 CA
1 CA
64217460 TGCCTGTGTA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 18 0.82
22 4 0.18
ACGTcount: A:0.36, C:0.29, G:0.27, T:0.09
Consensus pattern (22 bp):
CACAGCCCATGTAAGAGGGCAA
Found at i:64217469 original size:21 final size:20
Alignment explanation
Indices: 64217411--64217469 Score: 66
Period size: 21 Copynumber: 2.9 Consensus size: 20
64217401 CTTTGAAAAC
64217411 AGGGC-ACAGCCCGTGTAAG
1 AGGGCAACAGCCCGTGTAAG
* *
64217430 AGGGCAACACACCCATGTAAG
1 AGGGCAACA-GCCCGTGTAAG
*
64217451 AGGGCAACATGCCTGTGTA
1 AGGGCAACA-GCCCGTGTA
64217470 GAACTTGAAC
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
19 5 0.16
20 3 0.09
21 24 0.75
ACGTcount: A:0.31, C:0.25, G:0.31, T:0.14
Consensus pattern (20 bp):
AGGGCAACAGCCCGTGTAAG
Found at i:64218650 original size:47 final size:47
Alignment explanation
Indices: 64218581--64218890 Score: 276
Period size: 47 Copynumber: 6.7 Consensus size: 47
64218571 GGTATAATAC
* *
64218581 CGATGCCATGTGCCAAACATGGTCTTACACTGGCTCATCCATCAAGT-
1 CGATGCCATGTCCCAGACATGGTCTTACACTGGCTCAT-CATCAAGTG
* * *
64218628 CGATGCCATGTCTCAGACATGGTCTTACACTGGCACATCTAT-ACGTG
1 CGATGCCATGTCCCAGACATGGTCTTACACTGGCTCATC-ATCAAGTG
* *
64218675 CCGATGCCATGTCCCAGACATGGTCTTACACTGACACATC-TC--GTAG
1 -CGATGCCATGTCCCAGACATGGTCTTACACTGGCTCATCATCAAGT-G
* *
64218721 CTGATG-TATGTCCCAGACAT-GTCTTACACTGGCTTACATC-TCGAG-G
1 C-GATGCCATGTCCCAGACATGGTCTTACACTGGC-T-CATCATCAAGTG
* *
64218767 CCGATG-CATGTCCCAGACAT-GTCTTACACTAGCTC-TCCTCTCAA-TG
1 -CGATGCCATGTCCCAGACATGGTCTTACACTGGCTCAT-C-ATCAAGTG
64218813 CTGATGCCATGTCCCAGACATGGTCTTACACTGGCTC-TCAT-AATGTGG
1 C-GATGCCATGTCCCAGACATGGTCTTACACTGGCTCATCATCAA-GT-G
64218861 CTGATG-CATGTCCCAGACAT-GTCTTACACT
1 C-GATGCCATGTCCCAGACATGGTCTTACACT
64218891 AGCACACAAA
Statistics
Matches: 227, Mismatches: 15, Indels: 43
0.80 0.05 0.15
Matches are distributed among these distances:
43 1 0.00
44 14 0.06
45 20 0.09
46 65 0.29
47 67 0.30
48 60 0.26
ACGTcount: A:0.23, C:0.30, G:0.20, T:0.28
Consensus pattern (47 bp):
CGATGCCATGTCCCAGACATGGTCTTACACTGGCTCATCATCAAGTG
Found at i:64218778 original size:46 final size:46
Alignment explanation
Indices: 64218580--64218890 Score: 271
Period size: 46 Copynumber: 6.7 Consensus size: 46
64218570 GGGTATAATA
* * *
64218580 CCGATGCCATGTGCCAAACATGGTCTTACACTGGCTCATCCATC-AAG
1 CCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCAT-C-TCGAGG
* * * **
64218627 TCGATGCCATGTCTCAGACATGGTCTTACACTGGCACATCTATACGTG
1 CCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCATCTCGA-G-G
* *
64218675 CCGATGCCATGTCCCAGACATGGTCTTACACTGACACATCTCGTA-G
1 CCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCATCTCG-AGG
* *
64218721 CTGATG-TATGTCCCAGACAT-GTCTTACACTGGCTTACATCTCGAGG
1 CCGATGCCATGTCCCAGACATGGTCTTACACTGGC-T-CATCTCGAGG
* * * *
64218767 CCGATG-CATGTCCCAGACAT-GTCTTACACTAGCTCTCCTCTCAATG
1 CCGATGCCATGTCCCAGACATGGTCTTACACT-G-GCTCATCTCGAGG
* * *
64218813 CTGATGCCATGTCCCAGACATGGTCTTACACTGGCTC-TCATAATGTGG
1 CCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCATC-T--CGAGG
*
64218861 CTGATG-CATGTCCCAGACAT-GTCTTACACT
1 CCGATGCCATGTCCCAGACATGGTCTTACACT
64218891 AGCACACAAA
Statistics
Matches: 222, Mismatches: 28, Indels: 29
0.80 0.10 0.10
Matches are distributed among these distances:
44 12 0.05
45 17 0.08
46 70 0.32
47 65 0.29
48 57 0.26
49 1 0.00
ACGTcount: A:0.23, C:0.30, G:0.20, T:0.28
Consensus pattern (46 bp):
CCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCATCTCGAGG
Found at i:64218845 original size:94 final size:95
Alignment explanation
Indices: 64218580--64218893 Score: 316
Period size: 94 Copynumber: 3.4 Consensus size: 95
64218570 GGGTATAATA
* * * * *
64218580 CCGATGCCATGTGCCAAACATGGTCTTACACTGGCTCATCC-ATCAA-G-TCGATGCCATGTCTC
1 CCGATGCCATGTCCCAGACATGGTCTTACACTAGCTC-TCCTCTCAATGCT-GATGCCATGTCCC
*
64218642 AGACATGGTCTTACACTGGC--ACATCTATACGTG
64 AGACATGGTCTTACACTGGCTTACATCT-GA-G-G
* * * * *
64218675 CCGATGCCATGTCCCAGACATGGTCTTACACT-G-ACACATCTC-GTAGCTGATG-TATGTCCCA
1 CCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCCTCTCAAT-GCTGATGCCATGTCCCA
64218736 GACAT-GTCTTACACTGGCTTACATCTCGAGG
65 GACATGGTCTTACACTGGCTTACATCT-GAGG
64218767 CCGATG-CATGTCCCAGACAT-GTCTTACACTAGCTCTCCTCTCAATGCTGATGCCATGTCCCAG
1 CCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCCTCTCAATGCTGATGCCATGTCCCAG
* *
64218830 ACATGGTCTTACACTGGCTCT-CATAATGTGG
66 ACATGGTCTTACACTGGCT-TACAT-CTGAGG
*
64218861 CTGATG-CATGTCCCAGACAT-GTCTTACACTAGC
1 CCGATGCCATGTCCCAGACATGGTCTTACACTAGC
64218894 ACACAAATAA
Statistics
Matches: 187, Mismatches: 19, Indels: 27
0.80 0.08 0.12
Matches are distributed among these distances:
90 10 0.05
91 15 0.08
92 34 0.18
93 30 0.16
94 65 0.35
95 33 0.18
ACGTcount: A:0.23, C:0.30, G:0.20, T:0.27
Consensus pattern (95 bp):
CCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCCTCTCAATGCTGATGCCATGTCCCAG
ACATGGTCTTACACTGGCTTACATCTGAGG
Found at i:64225560 original size:18 final size:19
Alignment explanation
Indices: 64225537--64225575 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
64225527 TACAAATACA
*
64225537 AACATT-ACATAATTATTT
1 AACATTCACATAATAATTT
*
64225555 AACATTCACATCATAATTT
1 AACATTCACATAATAATTT
64225574 AA
1 AA
64225576 TCAAAATACA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.46, C:0.15, G:0.00, T:0.38
Consensus pattern (19 bp):
AACATTCACATAATAATTT
Found at i:64226270 original size:5 final size:5
Alignment explanation
Indices: 64226260--64226287 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
64226250 TTTAGCTATT
64226260 TATAA TATAA TATAA TATAA TATAA TAT
1 TATAA TATAA TATAA TATAA TATAA TAT
64226288 TCTTATTTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (5 bp):
TATAA
Found at i:64226943 original size:20 final size:20
Alignment explanation
Indices: 64226918--64226956 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
64226908 CAATTTGACC
64226918 CACACGGCCAACCACATGGT
1 CACACGGCCAACCACATGGT
64226938 CACACGGCCAACCACATGG
1 CACACGGCCAACCACATGG
64226957 CTGTGTGACC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.31, C:0.41, G:0.21, T:0.08
Consensus pattern (20 bp):
CACACGGCCAACCACATGGT
Found at i:64226981 original size:29 final size:29
Alignment explanation
Indices: 64226949--64227052 Score: 113
Period size: 29 Copynumber: 3.6 Consensus size: 29
64226939 ACACGGCCAA
* *
64226949 CCACATGGCTGTGTGACCCACATGGTTTG
1 CCACATGGCTGTGTGACCCACACGGTCTG
* * *
64226978 CCACA-CGATCATGTGACCCACACGGTCTG
1 CCACATGGCT-GTGTGACCCACACGGTCTG
*
64227007 CCACACT-GTTGTGTGACCCACACGGTCTG
1 CCACA-TGGCTGTGTGACCCACACGGTCTG
*
64227036 CCACACGGCTGTGTGAC
1 CCACATGGCTGTGTGAC
64227053 ATCAACAGAA
Statistics
Matches: 62, Mismatches: 9, Indels: 8
0.78 0.11 0.10
Matches are distributed among these distances:
28 2 0.03
29 58 0.94
30 2 0.03
ACGTcount: A:0.19, C:0.34, G:0.25, T:0.22
Consensus pattern (29 bp):
CCACATGGCTGTGTGACCCACACGGTCTG
Found at i:64232419 original size:12 final size:13
Alignment explanation
Indices: 64232402--64232430 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
64232392 AAGAGGTCTT
64232402 TTTTAATTTTT-A
1 TTTTAATTTTTAA
64232414 TTTTAATTTTTAA
1 TTTTAATTTTTAA
64232427 TTTT
1 TTTT
64232431 TCCTTCGTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.69
13 5 0.31
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (13 bp):
TTTTAATTTTTAA
Found at i:64236272 original size:18 final size:18
Alignment explanation
Indices: 64236249--64236284 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
64236239 GTTTCTTATC
64236249 AAAAAAGGATACTCTTAA
1 AAAAAAGGATACTCTTAA
64236267 AAAAAAGGATACTCTTAA
1 AAAAAAGGATACTCTTAA
64236285 TGTAGGCTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.56, C:0.11, G:0.11, T:0.22
Consensus pattern (18 bp):
AAAAAAGGATACTCTTAA
Found at i:64246046 original size:18 final size:18
Alignment explanation
Indices: 64246005--64246047 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
64245995 TGTGGAGGAT
* *
64246005 AGTCCAAATGTGGCGAGC
1 AGTCCAAATATGGCGAAC
*
64246023 AATCCAAATATGGCGAAC
1 AGTCCAAATATGGCGAAC
64246041 AGTCCAA
1 AGTCCAA
64246048 GAGTGGCGGA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.37, C:0.23, G:0.23, T:0.16
Consensus pattern (18 bp):
AGTCCAAATATGGCGAAC
Found at i:64246779 original size:42 final size:42
Alignment explanation
Indices: 64246716--64246798 Score: 130
Period size: 42 Copynumber: 2.0 Consensus size: 42
64246706 AATCCTAATT
64246716 GGAAAATAGTTCCCTTATTCTAATAAACTACTAAAACATAAG
1 GGAAAATAGTTCCCTTATTCTAATAAACTACTAAAACATAAG
* * * *
64246758 GGAAACTAGTTCCCTTGTTCTAATAAACTAGTAAAAGATAA
1 GGAAAATAGTTCCCTTATTCTAATAAACTACTAAAACATAA
64246799 AATAAAAATA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.43, C:0.16, G:0.12, T:0.29
Consensus pattern (42 bp):
GGAAAATAGTTCCCTTATTCTAATAAACTACTAAAACATAAG
Found at i:64246850 original size:19 final size:18
Alignment explanation
Indices: 64246826--64246869 Score: 79
Period size: 19 Copynumber: 2.4 Consensus size: 18
64246816 AATATGAATA
64246826 AAATTTATCTACCTAAAT
1 AAATTTATCTACCTAAAT
64246844 AAGATTTATCTACCTAAAT
1 AA-ATTTATCTACCTAAAT
64246863 AAATTTA
1 AAATTTA
64246870 AAATATATAC
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
18 7 0.28
19 18 0.72
ACGTcount: A:0.45, C:0.14, G:0.02, T:0.39
Consensus pattern (18 bp):
AAATTTATCTACCTAAAT
Found at i:64255869 original size:18 final size:18
Alignment explanation
Indices: 64255816--64255901 Score: 77
Period size: 18 Copynumber: 4.8 Consensus size: 18
64255806 ACACTCCAAA
* *
64255816 TGTCTGCGATA-TTGGCT
1 TGTCTGCCATATTTGGAT
* *
64255833 TGTCTGCCACT-CTTAGAT
1 TGTCTGCCA-TATTTGGAT
*
64255851 TGTCTACCATATTTGGAT
1 TGTCTGCCATATTTGGAT
* *
64255869 TGTTTGCAATATTTGGAT
1 TGTCTGCCATATTTGGAT
*
64255887 TGTCTGCCACATTTG
1 TGTCTGCCATATTTG
64255902 ATAATTTGCC
Statistics
Matches: 54, Mismatches: 12, Indels: 5
0.76 0.17 0.07
Matches are distributed among these distances:
17 9 0.17
18 45 0.83
ACGTcount: A:0.17, C:0.19, G:0.21, T:0.43
Consensus pattern (18 bp):
TGTCTGCCATATTTGGAT
Found at i:64259771 original size:40 final size:40
Alignment explanation
Indices: 64259718--64259803 Score: 154
Period size: 40 Copynumber: 2.1 Consensus size: 40
64259708 CATTTTATTC
*
64259718 AATTTAGTCCTTATGAACAAAACTAACAATTAAACATTAT
1 AATTTAGTCCTTATGAACAAAACGAACAATTAAACATTAT
*
64259758 AATTTAGTGCTTATGAACAAAACGAACAATTAAACATTAT
1 AATTTAGTCCTTATGAACAAAACGAACAATTAAACATTAT
64259798 AATTTA
1 AATTTA
64259804 ATCCCTTTTT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 44 1.00
ACGTcount: A:0.48, C:0.13, G:0.07, T:0.33
Consensus pattern (40 bp):
AATTTAGTCCTTATGAACAAAACGAACAATTAAACATTAT
Found at i:64267968 original size:21 final size:20
Alignment explanation
Indices: 64267912--64267960 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 20
64267902 TACATCAAAA
*
64267912 TAAAAGAAGGCTAAAGATTCC
1 TAAAAGAA-TCTAAAGATTCC
*
64267933 TAAAAGAATCAAAAGCATTCC
1 TAAAAGAATCTAAAG-ATTCC
64267954 ATAAAAG
1 -TAAAAG
64267961 CATTAAAGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 5 0.21
21 13 0.54
22 6 0.25
ACGTcount: A:0.53, C:0.14, G:0.14, T:0.18
Consensus pattern (20 bp):
TAAAAGAATCTAAAGATTCC
Found at i:64286755 original size:8 final size:8
Alignment explanation
Indices: 64286742--64286771 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
64286732 ACAAATGCCA
64286742 GCTTTTCG
1 GCTTTTCG
64286750 GCTTTTCG
1 GCTTTTCG
*
64286758 ACTTTTCG
1 GCTTTTCG
64286766 GCTTTT
1 GCTTTT
64286772 ACCGATCTAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.03, C:0.23, G:0.20, T:0.53
Consensus pattern (8 bp):
GCTTTTCG
Found at i:64289423 original size:47 final size:46
Alignment explanation
Indices: 64289367--64289461 Score: 154
Period size: 47 Copynumber: 2.0 Consensus size: 46
64289357 AAAATTTTCT
* *
64289367 TTAACTAAGTAACTTATCTGGAAATAATAAGGGCAAATTTAACAAGC
1 TTAACTAAGTAACTTATCCGGAAATAATAAGAGC-AATTTAACAAGC
*
64289414 TTAACTAAGTAACTTATCCGGAAATATTAAGAGCAATTTAACAAGC
1 TTAACTAAGTAACTTATCCGGAAATAATAAGAGCAATTTAACAAGC
64289460 TT
1 TT
64289462 TAAATTCAAC
Statistics
Matches: 45, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
46 14 0.31
47 31 0.69
ACGTcount: A:0.43, C:0.14, G:0.14, T:0.29
Consensus pattern (46 bp):
TTAACTAAGTAACTTATCCGGAAATAATAAGAGCAATTTAACAAGC
Found at i:64293149 original size:29 final size:29
Alignment explanation
Indices: 64293116--64293175 Score: 111
Period size: 29 Copynumber: 2.1 Consensus size: 29
64293106 TAAAGCTTAC
*
64293116 TTTGTTTATTTTTCTATGTTTTATAGTGA
1 TTTGTTTATTTTTCTATGTTCTATAGTGA
64293145 TTTGTTTATTTTTCTATGTTCTATAGTGA
1 TTTGTTTATTTTTCTATGTTCTATAGTGA
64293174 TT
1 TT
64293176 ACAAAACTAG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.17, C:0.05, G:0.13, T:0.65
Consensus pattern (29 bp):
TTTGTTTATTTTTCTATGTTCTATAGTGA
Found at i:64293683 original size:13 final size:13
Alignment explanation
Indices: 64293665--64293689 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
64293655 GGTTTATTTA
64293665 TTAAACTAATTAT
1 TTAAACTAATTAT
64293678 TTAAACTAATTA
1 TTAAACTAATTA
64293690 ACTGATTTAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (13 bp):
TTAAACTAATTAT
Found at i:64296635 original size:6 final size:5
Alignment explanation
Indices: 64296606--64296685 Score: 58
Period size: 5 Copynumber: 15.2 Consensus size: 5
64296596 TATGTCTTTC
*
64296606 AAAAT AAAAT --AAT AAAATT GAAAT GAAAAT AAAAAT AAAAAT AAAAT
1 AAAAT AAAAT AAAAT AAAA-T AAAAT -AAAAT -AAAAT -AAAAT AAAAT
*
64296653 AAAAT AAAAAT AAAACT -AAAT AATAAA AAAAT A
1 AAAAT -AAAAT AAAA-T AAAAT AA-AAT AAAAT A
64296686 GGAGGATTCA
Statistics
Matches: 62, Mismatches: 5, Indels: 16
0.75 0.06 0.19
Matches are distributed among these distances:
3 3 0.05
4 1 0.02
5 29 0.47
6 29 0.47
ACGTcount: A:0.76, C:0.01, G:0.03, T:0.20
Consensus pattern (5 bp):
AAAAT
Found at i:64296658 original size:16 final size:16
Alignment explanation
Indices: 64296616--64296685 Score: 72
Period size: 16 Copynumber: 4.2 Consensus size: 16
64296606 AAAATAAAAT
**
64296616 AATAAAATTGAAATGAA
1 AATAAAATAAAAAT-AA
64296633 AATAAAAATAAAAATAA
1 AAT-AAAATAAAAATAA
64296650 AATAAAATAAAAATAA
1 AATAAAATAAAAATAA
64296666 AACT-AAATAATAAA-AA
1 AA-TAAAATAA-AAATAA
64296682 AATA
1 AATA
64296686 GGAGGATTCA
Statistics
Matches: 47, Mismatches: 2, Indels: 9
0.81 0.03 0.16
Matches are distributed among these distances:
15 1 0.02
16 25 0.53
17 12 0.26
18 9 0.19
ACGTcount: A:0.76, C:0.01, G:0.03, T:0.20
Consensus pattern (16 bp):
AATAAAATAAAAATAA
Found at i:64296685 original size:11 final size:11
Alignment explanation
Indices: 64296606--64296680 Score: 71
Period size: 11 Copynumber: 6.4 Consensus size: 11
64296596 TATGTCTTTC
64296606 AAAATAAAATAAT
1 AAAAT-AAA-AAT
**
64296619 AAAATTGAAAT
1 AAAATAAAAAT
64296630 GAAAATAAAAAT
1 -AAAATAAAAAT
64296642 AAAA-ATAAAAT
1 AAAATA-AAAAT
64296653 AAAATAAAAAT
1 AAAATAAAAAT
64296664 AAAACTAAATAAT
1 AAAA-TAAA-AAT
64296677 AAAA
1 AAAA
64296681 AAATAGGAGG
Statistics
Matches: 53, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
10 1 0.02
11 25 0.47
12 15 0.28
13 12 0.23
ACGTcount: A:0.76, C:0.01, G:0.03, T:0.20
Consensus pattern (11 bp):
AAAATAAAAAT
Found at i:64316079 original size:13 final size:13
Alignment explanation
Indices: 64316061--64316090 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
64316051 AATAAACCAA
64316061 AATATCATCAATG
1 AATATCATCAATG
*
64316074 AATATCATTAATG
1 AATATCATCAATG
64316087 AATA
1 AATA
64316091 CTACCACAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.50, C:0.10, G:0.07, T:0.33
Consensus pattern (13 bp):
AATATCATCAATG
Found at i:64321821 original size:20 final size:21
Alignment explanation
Indices: 64321783--64321821 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
64321773 TTTAAAACAC
64321783 ATTTATTCATAAAAATTCAAT
1 ATTTATTCATAAAAATTCAAT
* *
64321804 ATTT-TTCATCAAATTTCA
1 ATTTATTCATAAAAATTCA
64321822 TAACTTTACA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.41, C:0.13, G:0.00, T:0.46
Consensus pattern (21 bp):
ATTTATTCATAAAAATTCAAT
Found at i:64332555 original size:89 final size:89
Alignment explanation
Indices: 64332452--64332731 Score: 339
Period size: 89 Copynumber: 3.1 Consensus size: 89
64332442 GGCTTTACCA
*
64332452 CATATACATATCTCATACATATTTCACATTAGCCATTCGGATTTACCACACACATATATATTTAT
1 CATATACATATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACACACATATATATTTAT
64332517 CTTGTACATCAATTTCAGCAATAG
66 CTTGTACATCAATTTCAGCAATAG
* * * *
64332541 CATATACATATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCTCATA
1 CATATACATATCTCATACATATTTCACATTAGCCATTCGGCTTTACCAC--ACACATATAT-ATT
* * * ** *
64332606 CATATT-TCACACTAGCCA-TTCAGCTTTACCA
63 TATCTTGT-ACA-T--CAATTTCAGCAATA--G
* *
64332637 CATATACCTATCTCATACATATTTCACATTAGCCATTCAGCTTTACCACACACATATATATTTAT
1 CATATACATATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACACACATATATATTTAT
64332702 CTTGTACATCAATTTCAGCAATAG
66 CTTGTACATCAATTTCAGCAATAG
*
64332726 CTTATA
1 CATATA
64332732 AGCAACTCAA
Statistics
Matches: 156, Mismatches: 24, Indels: 22
0.77 0.12 0.11
Matches are distributed among these distances:
89 52 0.33
90 2 0.01
91 17 0.11
92 10 0.06
93 10 0.06
94 17 0.11
95 2 0.01
96 46 0.29
ACGTcount: A:0.34, C:0.25, G:0.06, T:0.35
Consensus pattern (89 bp):
CATATACATATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACACACATATATATTTAT
CTTGTACATCAATTTCAGCAATAG
Found at i:64332605 original size:48 final size:48
Alignment explanation
Indices: 64332399--64332686 Score: 232
Period size: 48 Copynumber: 6.1 Consensus size: 48
64332389 ACTACCATTC
*
64332399 TACCACATATACATATCTCATACATATTTCACACTAGCCATTCGGCTT
1 TACCACATATACATATCTCATACATATTTCACACTAGCCATTCAGCTT
* * *
64332447 TACCACATATACATATCTCATACATATTTCACATTAGCCATTCGGATT
1 TACCACATATACATATCTCATACATATTTCACACTAGCCATTCAGCTT
* ** * *
64332495 TACCACACACATATATATTTATCTTGTACATCAATTTCAGCAATAG-CATAT-A-C-A
1 T---AC-CACATATACA--TATCTCATACAT--ATTTCA-CACTAGCCAT-TCAGCTT
* * * *
64332549 TATCTC--ATACATAT-T--T-CACA-------CTAGCCATTCGGCTT
1 TACCACATATACATATCTCATACATATTTCACACTAGCCATTCAGCTT
64332584 TACCACATATACATATCTCATACATATTTCACACTAGCCATTCAGCTT
1 TACCACATATACATATCTCATACATATTTCACACTAGCCATTCAGCTT
* *
64332632 TACCACATATACCTATCTCATACATATTTCACATTAGCCATTCAGCTT
1 TACCACATATACATATCTCATACATATTTCACACTAGCCATTCAGCTT
64332680 TACCACA
1 TACCACA
64332687 CACATATATA
Statistics
Matches: 191, Mismatches: 22, Indels: 54
0.72 0.08 0.20
Matches are distributed among these distances:
32 4 0.02
33 3 0.02
34 1 0.01
35 4 0.02
37 8 0.04
38 1 0.01
40 2 0.01
41 3 0.02
42 2 0.01
43 1 0.01
45 1 0.01
46 3 0.02
48 118 0.62
50 2 0.01
51 3 0.02
52 9 0.05
54 11 0.06
56 9 0.05
57 6 0.03
ACGTcount: A:0.33, C:0.27, G:0.06, T:0.34
Consensus pattern (48 bp):
TACCACATATACATATCTCATACATATTTCACACTAGCCATTCAGCTT
Found at i:64332711 original size:185 final size:185
Alignment explanation
Indices: 64332399--64332731 Score: 621
Period size: 185 Copynumber: 1.8 Consensus size: 185
64332389 ACTACCATTC
*
64332399 TACCACATATACATATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACATATC
1 TACCACATATACATATCTCATACATATTTCACACTAGCCATTCAGCTTTACCACATATACATATC
*
64332464 TCATACATATTTCACATTAGCCATTCGGATTTACCACACACATATATATTTATCTTGTACATCAA
66 TCATACATATTTCACATTAGCCATTCAGATTTACCACACACATATATATTTATCTTGTACATCAA
64332529 TTTCAGCAATAGCATATACATATCTCATACATATTTCACACTAGCCATTCGGCTT
131 TTTCAGCAATAGCATATACATATCTCATACATATTTCACACTAGCCATTCGGCTT
*
64332584 TACCACATATACATATCTCATACATATTTCACACTAGCCATTCAGCTTTACCACATATACCTATC
1 TACCACATATACATATCTCATACATATTTCACACTAGCCATTCAGCTTTACCACATATACATATC
*
64332649 TCATACATATTTCACATTAGCCATTCAGCTTTACCACACACATATATATTTATCTTGTACATCAA
66 TCATACATATTTCACATTAGCCATTCAGATTTACCACACACATATATATTTATCTTGTACATCAA
*
64332714 TTTCAGCAATAGCTTATA
131 TTTCAGCAATAGCATATA
64332732 AGCAACTCAA
Statistics
Matches: 143, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
185 143 1.00
ACGTcount: A:0.33, C:0.26, G:0.06, T:0.35
Consensus pattern (185 bp):
TACCACATATACATATCTCATACATATTTCACACTAGCCATTCAGCTTTACCACATATACATATC
TCATACATATTTCACATTAGCCATTCAGATTTACCACACACATATATATTTATCTTGTACATCAA
TTTCAGCAATAGCATATACATATCTCATACATATTTCACACTAGCCATTCGGCTT
Found at i:64335688 original size:44 final size:44
Alignment explanation
Indices: 64335640--64335724 Score: 109
Period size: 44 Copynumber: 1.9 Consensus size: 44
64335630 ATTTTTGATA
*
64335640 TCTGTTCTGCATGTAAGACCATGTCT-ATGACGTTGGCATCGACT
1 TCTGTTCTGCATGTAAGACCATGTCTGA-GACATTGGCATCGACT
* ***
64335684 TCTGTTTTTTGTGTAAGACCATGTCTGAGACATTGGCATCG
1 TCTGTTCTGCATGTAAGACCATGTCTGAGACATTGGCATCG
64335725 TATTTGATTT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
44 34 0.97
45 1 0.03
ACGTcount: A:0.20, C:0.20, G:0.24, T:0.36
Consensus pattern (44 bp):
TCTGTTCTGCATGTAAGACCATGTCTGAGACATTGGCATCGACT
Found at i:64335763 original size:42 final size:43
Alignment explanation
Indices: 64335651--64335797 Score: 126
Period size: 42 Copynumber: 3.4 Consensus size: 43
64335641 CTGTTCTGCA
* * *
64335651 TGTAAGACCATGTCT-ATGAC-GTTGGCATCGACT-TCTGTTTTTTG
1 TGTAAGACCATGTCTGA-GACAG-TGGCATCGA-TATTTG-ATTTCG
*
64335695 TGTAAGACCATGTCTGAGACATTGGCATCG-TATTTGATTTCG
1 TGTAAGACCATGTCTGAGACAGTGGCATCGATATTTGATTTCG
* * * *
64335737 TGTAAGACCCA-GTCTGGGACAGTGGCATCGATGTTTGATTACA
1 TGTAAGA-CCATGTCTGAGACAGTGGCATCGATATTTGATTTCG
*
64335780 TGTATGACCATGTC-GAGA
1 TGTAAGACCATGTCTGAGA
64335798 ACGTCGACAT
Statistics
Matches: 86, Mismatches: 11, Indels: 14
0.77 0.10 0.13
Matches are distributed among these distances:
42 35 0.41
43 24 0.28
44 26 0.30
45 1 0.01
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (43 bp):
TGTAAGACCATGTCTGAGACAGTGGCATCGATATTTGATTTCG
Found at i:64337643 original size:4 final size:4
Alignment explanation
Indices: 64337634--64337666 Score: 66
Period size: 4 Copynumber: 8.2 Consensus size: 4
64337624 AGCAAACGTG
64337634 AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA A
1 AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA A
64337667 TAGAAAAGGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (4 bp):
AGAA
Found at i:64338482 original size:47 final size:46
Alignment explanation
Indices: 64338431--64338542 Score: 136
Period size: 47 Copynumber: 2.4 Consensus size: 46
64338421 GACATTGAGT
*
64338431 CGATG-AGACACTATGTGCCGACTACTATTAAAGTTCCGGATTTGTTC
1 CGATGAAG-CACTATGTGCCGA-TAATATTAAAGTTCCGGATTTGTTC
* * * * *
64338478 CGATGAAGTACTTTGTGTACTATAATGTTAAAGTTCCGGATTTGTTC
1 CGATGAAGCACTATGTG-CCGATAATATTAAAGTTCCGGATTTGTTC
64338525 CGATGAAGCACTATGTGC
1 CGATGAAGCACTATGTGC
64338543 TTATCCCGGA
Statistics
Matches: 54, Mismatches: 9, Indels: 5
0.79 0.13 0.07
Matches are distributed among these distances:
47 50 0.93
48 4 0.07
ACGTcount: A:0.26, C:0.18, G:0.22, T:0.34
Consensus pattern (46 bp):
CGATGAAGCACTATGTGCCGATAATATTAAAGTTCCGGATTTGTTC
Found at i:64344888 original size:4 final size:4
Alignment explanation
Indices: 64344879--64344907 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
64344869 AGCAAACGTG
64344879 AGAA AGAA AGAA AGAA AGAA AGAA AGAA A
1 AGAA AGAA AGAA AGAA AGAA AGAA AGAA A
64344908 TAGAAAAGGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (4 bp):
AGAA
Found at i:64352680 original size:18 final size:18
Alignment explanation
Indices: 64352659--64352693 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
64352649 TCCAAAAGAA
64352659 ATTTTTAATTTTATTTGC
1 ATTTTTAATTTTATTTGC
64352677 ATTTTTAATTTTATTTG
1 ATTTTTAATTTTATTTG
64352694 TTTATGCTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.23, C:0.03, G:0.06, T:0.69
Consensus pattern (18 bp):
ATTTTTAATTTTATTTGC
Found at i:64354915 original size:17 final size:17
Alignment explanation
Indices: 64354895--64354930 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
64354885 TGATTATGAT
64354895 ATGGTTCTGGTATATAA
1 ATGGTTCTGGTATATAA
64354912 ATGGTTCTGGTATATAA
1 ATGGTTCTGGTATATAA
64354929 AT
1 AT
64354931 TATGAGGCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.31, C:0.06, G:0.22, T:0.42
Consensus pattern (17 bp):
ATGGTTCTGGTATATAA
Found at i:64356071 original size:21 final size:24
Alignment explanation
Indices: 64356045--64356091 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 24
64356035 TTACTCCAAG
64356045 GAAGCCG-ATT-A-ATCCATCTCA
1 GAAGCCGAATTCACATCCATCTCA
64356066 GAAGCCGAATTCATCATCCATCTCA
1 GAAGCCGAATTCA-CATCCATCTCA
64356091 G
1 G
64356092 GAGTTTTGGG
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
21 7 0.32
22 3 0.14
23 1 0.05
25 11 0.50
ACGTcount: A:0.32, C:0.30, G:0.15, T:0.23
Consensus pattern (24 bp):
GAAGCCGAATTCACATCCATCTCA
Found at i:64357468 original size:31 final size:31
Alignment explanation
Indices: 64357430--64357493 Score: 119
Period size: 31 Copynumber: 2.1 Consensus size: 31
64357420 TCCCAACGTT
*
64357430 CACTTAGCGAACTTCTTGGAACTATGCGATA
1 CACTTAGCGAACTTCTAGGAACTATGCGATA
64357461 CACTTAGCGAACTTCTAGGAACTATGCGATA
1 CACTTAGCGAACTTCTAGGAACTATGCGATA
64357492 CA
1 CA
64357494 TTTAAAATTA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.31, C:0.23, G:0.19, T:0.27
Consensus pattern (31 bp):
CACTTAGCGAACTTCTAGGAACTATGCGATA
Found at i:64359477 original size:17 final size:18
Alignment explanation
Indices: 64359445--64359483 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
64359435 TGAATGGCAA
64359445 ACACATAAACCGAAAAC-
1 ACACATAAACCGAAAACT
64359462 ACACGATAAACC-AAAACT
1 ACAC-ATAAACCGAAAACT
64359480 ACAC
1 ACAC
64359484 CAGAACAAGC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 9 0.45
18 11 0.55
ACGTcount: A:0.56, C:0.31, G:0.05, T:0.08
Consensus pattern (18 bp):
ACACATAAACCGAAAACT
Found at i:64373442 original size:27 final size:26
Alignment explanation
Indices: 64373412--64373483 Score: 90
Period size: 27 Copynumber: 2.7 Consensus size: 26
64373402 CAACAAGACG
*
64373412 TTAAACATGGGATAGTCTATTGGGACA
1 TTAAACA-GGGATAGTCTAATGGGACA
*
64373439 TTAAATAGGGTATAGTCTAATGGGACA
1 TTAAACAGGG-ATAGTCTAATGGGACA
*
64373466 TTAAACACAGGATAGTCT
1 TTAAACA-GGGATAGTCT
64373484 GATAAGATGT
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
26 3 0.08
27 34 0.87
28 2 0.05
ACGTcount: A:0.36, C:0.11, G:0.24, T:0.29
Consensus pattern (26 bp):
TTAAACAGGGATAGTCTAATGGGACA
Found at i:64386226 original size:45 final size:45
Alignment explanation
Indices: 64386142--64386227 Score: 109
Period size: 45 Copynumber: 1.9 Consensus size: 45
64386132 TATATGCCTA
* * *
64386142 AAATGAGTAAAACCATAATTGAAAGATGCTATGGCATCATGATAT
1 AAATGAGTAAAACCATAACTGAAAGATGCTAAGACATCATGATAT
* ** *
64386187 AAATGAGTAAGACCATGGCTGAAAGATGCTAAGATATCATG
1 AAATGAGTAAAACCATAACTGAAAGATGCTAAGACATCATG
64386228 TGAAAGCATG
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
45 34 1.00
ACGTcount: A:0.43, C:0.12, G:0.21, T:0.24
Consensus pattern (45 bp):
AAATGAGTAAAACCATAACTGAAAGATGCTAAGACATCATGATAT
Found at i:64386438 original size:27 final size:27
Alignment explanation
Indices: 64386364--64386454 Score: 85
Period size: 27 Copynumber: 3.4 Consensus size: 27
64386354 ACGACATCAT
64386364 AGATAGTCCGATGGGACGTTAAACACG
1 AGATAGTCCGATGGGACGTTAAACACG
** *** * *
64386391 AGATAGTTTGACAAGAAGTTAAACATG
1 AGATAGTCCGATGGGACGTTAAACACG
*
64386418 -GCATAGTCCGATGGGACGTTAAACACA
1 AG-ATAGTCCGATGGGACGTTAAACACG
*
64386445 AGGTAGTCCG
1 AGATAGTCCG
64386455 TCAGGAAAGT
Statistics
Matches: 46, Mismatches: 16, Indels: 4
0.70 0.24 0.06
Matches are distributed among these distances:
26 1 0.02
27 44 0.96
28 1 0.02
ACGTcount: A:0.35, C:0.16, G:0.27, T:0.21
Consensus pattern (27 bp):
AGATAGTCCGATGGGACGTTAAACACG
Found at i:64389264 original size:26 final size:25
Alignment explanation
Indices: 64389197--64389269 Score: 92
Period size: 26 Copynumber: 2.8 Consensus size: 25
64389187 TCCCATCCCT
*
64389197 ATTTTACCCTAGCAAAATTTTGATG
1 ATTTTACCCTAGTAAAATTTTGATG
* *
64389222 ATTTTACCATTGATAAAATTTTGATG
1 ATTTTACCCTAG-TAAAATTTTGATG
*
64389248 ATTTTGGCCCTAGTAAAATTTT
1 ATTTT-ACCCTAGTAAAATTTT
64389270 AAAAAAATAT
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
25 10 0.25
26 26 0.65
27 4 0.10
ACGTcount: A:0.32, C:0.12, G:0.12, T:0.44
Consensus pattern (25 bp):
ATTTTACCCTAGTAAAATTTTGATG
Found at i:64396447 original size:31 final size:31
Alignment explanation
Indices: 64396412--64396523 Score: 136
Period size: 31 Copynumber: 3.6 Consensus size: 31
64396402 TACATGGTAC
64396412 AAATATGCAATTATGAATGATTACAGAGTAT
1 AAATATGCAATTATGAATGATTACAGAGTAT
* * *
64396443 AAATATGCAGTTATGAATGATTATAGGGTAT
1 AAATATGCAATTATGAATGATTACAGAGTAT
* * * *
64396474 AAATATACAATTATAAATGATTGCAGTGTAT
1 AAATATGCAATTATGAATGATTACAGAGTAT
*
64396505 GAAA-ATGCAAATATGAATG
1 -AAATATGCAATTATGAATG
64396524 GTTGATGGCC
Statistics
Matches: 68, Mismatches: 12, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
31 65 0.96
32 3 0.04
ACGTcount: A:0.45, C:0.05, G:0.18, T:0.32
Consensus pattern (31 bp):
AAATATGCAATTATGAATGATTACAGAGTAT
Found at i:64396485 original size:62 final size:62
Alignment explanation
Indices: 64396407--64396523 Score: 155
Period size: 62 Copynumber: 1.9 Consensus size: 62
64396397 GATAGTACAT
* * **
64396407 GGTACAAATATGCAATTATGAATGATTACAGAGTAT-AAATATGCAGTTATGAATGATTATAG
1 GGTACAAATATACAATTATAAATGATTACAGAGTATGAAA-ATGCAAATATGAATGATTATAG
* * *
64396469 GGTATAAATATACAATTATAAATGATTGCAGTGTATGAAAATGCAAATATGAATG
1 GGTACAAATATACAATTATAAATGATTACAGAGTATGAAAATGCAAATATGAATG
64396524 GTTGATGGCC
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
62 44 0.94
63 3 0.06
ACGTcount: A:0.44, C:0.06, G:0.19, T:0.32
Consensus pattern (62 bp):
GGTACAAATATACAATTATAAATGATTACAGAGTATGAAAATGCAAATATGAATGATTATAG
Found at i:64397307 original size:105 final size:105
Alignment explanation
Indices: 64397120--64397328 Score: 364
Period size: 105 Copynumber: 2.0 Consensus size: 105
64397110 AGCTAGATCA
* *
64397120 TTGCGGACATCATACTATCATCGAAACAGTACAATTATGTTCATTTTGAATCCTAATATTGTGGC
1 TTGCAGACATCATACTATCATCGAAACAGTACAATTATATTCATTTTGAATCCTAATATTGTGGC
*
64397185 CTGTATATAGGGTCTTTATTATAGAAATGATCATCCCTAC
66 CCGTATATAGGGTCTTTATTATAGAAATGATCATCCCTAC
*
64397225 TTGCAGACATCATACTATCATCGAAACAGTACAATTATATTCATTTTGAGTCCTAATATTGTGGC
1 TTGCAGACATCATACTATCATCGAAACAGTACAATTATATTCATTTTGAATCCTAATATTGTGGC
* *
64397290 CCGTATATAGGGTCTTTATTATGGAAATGATTATCCCTA
66 CCGTATATAGGGTCTTTATTATAGAAATGATCATCCCTA
64397329 TTTGTGAGTG
Statistics
Matches: 98, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
105 98 1.00
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (105 bp):
TTGCAGACATCATACTATCATCGAAACAGTACAATTATATTCATTTTGAATCCTAATATTGTGGC
CCGTATATAGGGTCTTTATTATAGAAATGATCATCCCTAC
Found at i:64398748 original size:13 final size:13
Alignment explanation
Indices: 64398730--64398756 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
64398720 GCTTGGCAGG
64398730 GACACGCCCGTGT
1 GACACGCCCGTGT
64398743 GACACGCCCGTGT
1 GACACGCCCGTGT
64398756 G
1 G
64398757 CGATTACTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.15, C:0.37, G:0.33, T:0.15
Consensus pattern (13 bp):
GACACGCCCGTGT
Found at i:64407833 original size:20 final size:20
Alignment explanation
Indices: 64407806--64407847 Score: 50
Period size: 21 Copynumber: 2.1 Consensus size: 20
64407796 TAAATTTTAA
*
64407806 ATTTAACCCTTA-AAAATGC
1 ATTTAACCCTCATAAAATGC
*
64407825 ATTTCAACCGTCATAAAATGC
1 ATTT-AACCCTCATAAAATGC
64407846 AT
1 AT
64407848 ACCTTAATTC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
19 4 0.21
20 6 0.32
21 9 0.47
ACGTcount: A:0.40, C:0.21, G:0.07, T:0.31
Consensus pattern (20 bp):
ATTTAACCCTCATAAAATGC
Found at i:64409750 original size:18 final size:18
Alignment explanation
Indices: 64409727--64409763 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
64409717 CTTGTTTTTG
64409727 TAAGCTGAAATACTCATA
1 TAAGCTGAAATACTCATA
64409745 TAAGCTGAAATACTCATA
1 TAAGCTGAAATACTCATA
64409763 T
1 T
64409764 TCAATAACTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.43, C:0.16, G:0.11, T:0.30
Consensus pattern (18 bp):
TAAGCTGAAATACTCATA
Found at i:64428619 original size:48 final size:47
Alignment explanation
Indices: 64428462--64428646 Score: 148
Period size: 48 Copynumber: 3.9 Consensus size: 47
64428452 TAGGGATATG
*
64428462 TGTGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGTATCAATA
1 TGTGATCCCATGTAAGACCATGTCT-GGACATGGCATTGGCATCAATA
* * * * * *
64428510 TGAGA-CATCGTGTAAGACCATAG-CTGGGC-T---ATCGGCTTCAATA
1 TGTGATC-CCATGTAAGACCAT-GTCTGGACATGGCATTGGCATCAATA
* * * *
64428553 TGCATGATCCAATATAAGACCATGTCTGGAACATGGTATTGGCATCGATA
1 TG--TGATCCCATGTAAGACCATGTCTGG-ACATGGCATTGGCATCAATA
* *
64428603 TGTGATCCCATGTAAGACCATATCTAGGATATGGCATTGGCATC
1 TGTGATCCCATGTAAGACCATGTCT-GGACATGGCATTGGCATC
64428647 CTACTATGTG
Statistics
Matches: 104, Mismatches: 21, Indels: 24
0.70 0.14 0.16
Matches are distributed among these distances:
43 12 0.12
44 1 0.01
45 16 0.15
46 3 0.03
47 5 0.05
48 52 0.50
49 3 0.03
50 12 0.12
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.28
Consensus pattern (47 bp):
TGTGATCCCATGTAAGACCATGTCTGGACATGGCATTGGCATCAATA
Found at i:64465818 original size:27 final size:27
Alignment explanation
Indices: 64465788--64465965 Score: 160
Period size: 27 Copynumber: 6.6 Consensus size: 27
64465778 ATATTGAGCC
* *
64465788 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
* * *
64465815 CGCACACTTAGTGCCACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
*
64465842 CGCACACTTAGTGCTACATAGTCAGACT
1 CGCACACTTAGTGCTACATAATCA-ACT
** ** *
64465870 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
* **
64465897 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAATCAACT
* * * *
64465924 CGCACACTGAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
*
64465951 CGCACCCTTAGTGCT
1 CGCACACTTAGTGCT
64465966 GTACAATTTA
Statistics
Matches: 124, Mismatches: 24, Indels: 6
0.81 0.16 0.04
Matches are distributed among these distances:
27 100 0.81
28 24 0.19
ACGTcount: A:0.29, C:0.29, G:0.16, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:64465927 original size:82 final size:81
Alignment explanation
Indices: 64465809--64465964 Score: 206
Period size: 82 Copynumber: 1.9 Consensus size: 81
64465799 TGCTATATAA
* * * *
64465809 TCAACTCGCACACTTAGTGCCACGTAATCAAATCGCACACTTAGTGCTACATAGTCAGACTCGCA
1 TCAACTCGCACACTTAGTGCCACATAATCAAATCGCACACTGAGTGCAACATAGTCA-AATCGCA
64465874 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
64465891 TCAATTCGCACACTTAGTG-CATCATATTCATTTCGCACACTGAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCCA-CATAATCAAATCGCACACTGAGTGCAACATAGTCAAATCGCA
*
64465955 CCCTTAGTGC
65 CACTTAGTGC
64465965 TGTACAATTT
Statistics
Matches: 64, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
81 17 0.27
82 47 0.73
ACGTcount: A:0.28, C:0.29, G:0.17, T:0.26
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCCACATAATCAAATCGCACACTGAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:64473808 original size:27 final size:27
Alignment explanation
Indices: 64473778--64473955 Score: 160
Period size: 27 Copynumber: 6.6 Consensus size: 27
64473768 ATATTGAGCC
* *
64473778 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
* * *
64473805 CGCACACTTAGTGCCACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
*
64473832 CGCACACTTAGTGCTACATAGTCAGACT
1 CGCACACTTAGTGCTACATAATCA-ACT
** ** *
64473860 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
* **
64473887 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAATCAACT
* * * *
64473914 CGCACACTGAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
*
64473941 CGCACCCTTAGTGCT
1 CGCACACTTAGTGCT
64473956 GTACAATTTA
Statistics
Matches: 124, Mismatches: 24, Indels: 6
0.81 0.16 0.04
Matches are distributed among these distances:
27 100 0.81
28 24 0.19
ACGTcount: A:0.29, C:0.29, G:0.16, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:64473917 original size:82 final size:81
Alignment explanation
Indices: 64473799--64473954 Score: 206
Period size: 82 Copynumber: 1.9 Consensus size: 81
64473789 TGCTATATAA
* * * *
64473799 TCAACTCGCACACTTAGTGCCACGTAATCAAATCGCACACTTAGTGCTACATAGTCAGACTCGCA
1 TCAACTCGCACACTTAGTGCCACATAATCAAATCGCACACTGAGTGCAACATAGTCA-AATCGCA
64473864 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
64473881 TCAATTCGCACACTTAGTG-CATCATATTCATTTCGCACACTGAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCCA-CATAATCAAATCGCACACTGAGTGCAACATAGTCAAATCGCA
*
64473945 CCCTTAGTGC
65 CACTTAGTGC
64473955 TGTACAATTT
Statistics
Matches: 64, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
81 17 0.27
82 47 0.73
ACGTcount: A:0.28, C:0.29, G:0.17, T:0.26
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCCACATAATCAAATCGCACACTGAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:64475798 original size:22 final size:24
Alignment explanation
Indices: 64475773--64475834 Score: 65
Period size: 22 Copynumber: 2.6 Consensus size: 24
64475763 TTAGACTTTA
64475773 TGTATTGAATGCTTG-TTAAA-AT
1 TGTATTGAATGCTTGTTTAAAGAT
* * *
64475795 TGTATTAAATTCTTGTTTAAAGGT
1 TGTATTGAATGCTTGTTTAAAGAT
*
64475819 TGGATTGAATGGCTTG
1 TGTATTGAAT-GCTTG
64475835 ATTGGTATAT
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
22 13 0.42
23 5 0.16
24 9 0.29
25 4 0.13
ACGTcount: A:0.27, C:0.05, G:0.23, T:0.45
Consensus pattern (24 bp):
TGTATTGAATGCTTGTTTAAAGAT
Found at i:64481518 original size:29 final size:31
Alignment explanation
Indices: 64481448--64481512 Score: 103
Period size: 32 Copynumber: 2.1 Consensus size: 31
64481438 CACTTTTATT
* *
64481448 CTCTTAAAAATTTATAATTCAATTATTATATC
1 CTCTTAAAATTTTATAATTCAATTATTACA-C
64481480 CTCTTAAAATTTTATAATTCAATTATTACAC
1 CTCTTAAAATTTTATAATTCAATTATTACAC
64481511 CT
1 CT
64481513 TAAAATAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
31 3 0.10
32 28 0.90
ACGTcount: A:0.38, C:0.15, G:0.00, T:0.46
Consensus pattern (31 bp):
CTCTTAAAATTTTATAATTCAATTATTACAC
Found at i:64489864 original size:17 final size:18
Alignment explanation
Indices: 64489839--64489900 Score: 67
Period size: 18 Copynumber: 3.6 Consensus size: 18
64489829 TTTTTAATAT
*
64489839 TATTAAATAAA-CATTTA
1 TATTTAATAAATCATTTA
*
64489856 TATTTAATAAATTATTTA
1 TATTTAATAAATCATTTA
64489874 T-TTTAATTAAATCATTTA
1 TATTTAA-TAAATCATTTA
*
64489892 -ATATAATAA
1 TATTTAATAA
64489901 TATTATTAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
17 18 0.47
18 20 0.53
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (18 bp):
TATTTAATAAATCATTTA
Found at i:64489872 original size:18 final size:18
Alignment explanation
Indices: 64489851--64489907 Score: 64
Period size: 18 Copynumber: 3.2 Consensus size: 18
64489841 TTAAATAAAC
64489851 ATTTATATTTAATAAATT
1 ATTTATATTTAATAAATT
*
64489869 ATTTAT-TTTAATTAAATC
1 ATTTATATTTAA-TAAATT
*
64489887 ATTTA-ATATAATAATATT
1 ATTTATATTTAATAA-ATT
64489905 ATT
1 ATT
64489908 AATAATTTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
17 8 0.24
18 25 0.76
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (18 bp):
ATTTATATTTAATAAATT
Found at i:64489916 original size:39 final size:37
Alignment explanation
Indices: 64489827--64489916 Score: 96
Period size: 35 Copynumber: 2.4 Consensus size: 37
64489817 CAAATATTGT
* *
64489827 AATTTTTAATATTATTAAATAAACATTTATATTTAATA
1 AATTATTAATATT-TTAAATAAACATTTATATATAATA
*
64489865 AATTATT--TATTTTAATTAAATCATTTA-ATATAATA
1 AATTATTAATATTTTAAATAAA-CATTTATATATAATA
64489900 ATATTATTAATAATTTT
1 A-ATTATTAAT-ATTTT
64489917 TAAAATTAAT
Statistics
Matches: 44, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
35 16 0.36
36 16 0.36
38 7 0.16
39 5 0.11
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (37 bp):
AATTATTAATATTTTAAATAAACATTTATATATAATA
Found at i:64489926 original size:16 final size:17
Alignment explanation
Indices: 64489905--64489940 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
64489895 TAATAATATT
64489905 ATTAATAATT-TTTAAA
1 ATTAATAATTATTTAAA
*
64489921 ATTAATAATTATTTTAA
1 ATTAATAATTATTTAAA
64489938 ATT
1 ATT
64489941 TTAAATAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 10 0.56
17 8 0.44
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
ATTAATAATTATTTAAA
Found at i:64489944 original size:19 final size:18
Alignment explanation
Indices: 64489906--64489964 Score: 59
Period size: 20 Copynumber: 3.2 Consensus size: 18
64489896 AATAATATTA
*
64489906 TTAATAAT-TTTTAAA-A
1 TTAATAATATTTTAAATT
64489922 TTAATAATTATTTTAAATT
1 TTAATAA-TATTTTAAATT
64489941 TTAAATAATATTCTTAATATT
1 TT-AATAATATT-TTAA-ATT
64489962 TTA
1 TTA
64489965 TATTAGCATT
Statistics
Matches: 36, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
16 7 0.19
17 1 0.03
18 7 0.19
19 6 0.17
20 10 0.28
21 5 0.14
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (18 bp):
TTAATAATATTTTAAATT
Found at i:64491017 original size:19 final size:21
Alignment explanation
Indices: 64490985--64491030 Score: 78
Period size: 19 Copynumber: 2.3 Consensus size: 21
64490975 AAAAATATTA
64490985 AATAAATGATTAAATTTAATT
1 AATAAATGATTAAATTTAATT
64491006 AATAAAT-A-TAAATTTAATT
1 AATAAATGATTAAATTTAATT
64491025 AATAAA
1 AATAAA
64491031 AAAATATAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
19 17 0.68
20 1 0.04
21 7 0.28
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (21 bp):
AATAAATGATTAAATTTAATT
Found at i:64496399 original size:33 final size:35
Alignment explanation
Indices: 64496333--64496407 Score: 127
Period size: 33 Copynumber: 2.2 Consensus size: 35
64496323 CGTGAAATTT
64496333 TAAAATATTTATTTTAGATATAAAATTATGATGTA
1 TAAAATATTTATTTTAGATATAAAATTATGATGTA
*
64496368 TAAAATATTTATTTTA-A-ATAATATTATGATGTA
1 TAAAATATTTATTTTAGATATAAAATTATGATGTA
64496401 TAAAATA
1 TAAAATA
64496408 AGAGAGGAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
33 22 0.56
34 1 0.03
35 16 0.41
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.45
Consensus pattern (35 bp):
TAAAATATTTATTTTAGATATAAAATTATGATGTA
Found at i:64496926 original size:28 final size:29
Alignment explanation
Indices: 64496881--64496941 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 29
64496871 AATTTAGGGT
64496881 TTAAGGTTTAAGA-ATTTTAAAAAATAAA
1 TTAAGGTTTAAGATATTTTAAAAAATAAA
* * *
64496909 TTAAGGTTT-AGATTTTTTTGAAAAATTAA
1 TTAAGGTTTAAGA-TATTTTAAAAAATAAA
64496938 TTAA
1 TTAA
64496942 ATTAGGTTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
27 3 0.11
28 9 0.32
29 16 0.57
ACGTcount: A:0.46, C:0.00, G:0.11, T:0.43
Consensus pattern (29 bp):
TTAAGGTTTAAGATATTTTAAAAAATAAA
Found at i:64496944 original size:34 final size:33
Alignment explanation
Indices: 64496905--64497036 Score: 133
Period size: 34 Copynumber: 3.9 Consensus size: 33
64496895 TTTTAAAAAA
* *
64496905 TAAATTAAGGTTTAGATTTTTTTGAAAAATTAAT
1 TAAATTAAGGTTTA-ATGTTTTTAAAAAATTAAT
* **
64496939 TAAATT-AGGTTTAAAGGGTTTAAATAAATTAAT
1 TAAATTAAGGTTTAATGTTTTTAAA-AAATTAAT
*
64496972 TAAATTAGGGTTTAGA-GTTTTTAAGAAAATTAAT
1 TAAATTAAGGTTTA-ATGTTTTTAA-AAAATTAAT
* *
64497006 TAAATTAGGGTTTAATTTTTTTAAAATAATT
1 TAAATTAAGGTTTAATGTTTTTAAAA-AATT
64497037 TTTTTGTTTA
Statistics
Matches: 83, Mismatches: 9, Indels: 12
0.80 0.09 0.12
Matches are distributed among these distances:
32 6 0.07
33 24 0.29
34 51 0.61
35 2 0.02
ACGTcount: A:0.42, C:0.00, G:0.14, T:0.45
Consensus pattern (33 bp):
TAAATTAAGGTTTAATGTTTTTAAAAAATTAAT
Found at i:64497349 original size:124 final size:123
Alignment explanation
Indices: 64497124--64497364 Score: 288
Period size: 124 Copynumber: 1.9 Consensus size: 123
64497114 GAAAAATTAA
* * * * * *
64497124 TTTTGAGAAGACGGTTCTGAAAAGATAATGTCAAAAACGCTTCAAACAAAATGCACTGTTAGCAA
1 TTTTGAGAAAACGGTTCTGAAAAAATAATGTAAAAAACCCTTCAAACAAAATGCACTATCAGCAA
* * *
64497189 AATTACTGAAAAAAGCTTTCACATGGATGCTCTTTTTTTACAGTAGTTCCTAAATTTTT
66 AATTACTGAAAAAAGC-TTCACATGGACGCTATTTTTCTACAGTAGTTCCTAAATTTTT
* * * **
64497248 TTTTGAGAAAACGGTTTTGAAAAAATAGTGTAAAAAACCCTTCAAGCAGGATGCACTATCAGCAA
1 TTTTGAGAAAACGGTTCTGAAAAAATAATGTAAAAAACCCTTCAAACAAAATGCACTATCAGCAA
* *
64497313 AATT-CATGAAAAAAGC-TCCCATGTGAACGCTATTTTTCTATAGTAGTTCCTA
66 AATTAC-TGAAAAAAGCTTCACATG-G-ACGCTATTTTTCTACAGTAGTTCCTA
64497365 TTTGACCTTA
Statistics
Matches: 98, Mismatches: 16, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
122 6 0.06
123 2 0.02
124 90 0.92
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.31
Consensus pattern (123 bp):
TTTTGAGAAAACGGTTCTGAAAAAATAATGTAAAAAACCCTTCAAACAAAATGCACTATCAGCAA
AATTACTGAAAAAAGCTTCACATGGACGCTATTTTTCTACAGTAGTTCCTAAATTTTT
Found at i:64500462 original size:24 final size:23
Alignment explanation
Indices: 64500406--64500462 Score: 71
Period size: 25 Copynumber: 2.3 Consensus size: 23
64500396 AAGAACTTCT
64500406 ATTTTATTAAAAATATAAAAATA
1 ATTTTATTAAAAATATAAAAATA
64500429 ATTTGCTATT-AAAATATTAAAAATA
1 ATTT--TATTAAAAATA-TAAAAATA
64500454 ACTTTTATT
1 A-TTTTATT
64500463 TTATTAAGTG
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
23 4 0.13
24 10 0.33
25 13 0.43
26 3 0.10
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.44
Consensus pattern (23 bp):
ATTTTATTAAAAATATAAAAATA
Found at i:64500937 original size:17 final size:18
Alignment explanation
Indices: 64500905--64500947 Score: 70
Period size: 17 Copynumber: 2.4 Consensus size: 18
64500895 GACTGGGAAA
*
64500905 AGGAAACATATAAGGGCT
1 AGGATACATATAAGGGCT
64500923 AGGATACAT-TAAGGGCT
1 AGGATACATATAAGGGCT
64500940 AGGATACA
1 AGGATACA
64500948 CACCTCGCAT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 16 0.67
18 8 0.33
ACGTcount: A:0.42, C:0.12, G:0.28, T:0.19
Consensus pattern (18 bp):
AGGATACATATAAGGGCT
Found at i:64507161 original size:10 final size:10
Alignment explanation
Indices: 64507134--64507193 Score: 70
Period size: 10 Copynumber: 6.0 Consensus size: 10
64507124 TGAAATTCTA
64507134 AAAGATAAAT
1 AAAGATAAAT
*
64507144 ACAA-ATAATT
1 A-AAGATAAAT
*
64507154 AAAGATAATT
1 AAAGATAAAT
64507164 AAAGATAAAT
1 AAAGATAAAT
64507174 AAAGATAAAT
1 AAAGATAAAT
64507184 GAAA-ATAAAT
1 -AAAGATAAAT
64507194 CCTAAAATTA
Statistics
Matches: 45, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
9 2 0.04
10 38 0.84
11 5 0.11
ACGTcount: A:0.67, C:0.02, G:0.08, T:0.23
Consensus pattern (10 bp):
AAAGATAAAT
Found at i:64510162 original size:49 final size:49
Alignment explanation
Indices: 64510097--64510609 Score: 775
Period size: 47 Copynumber: 10.9 Consensus size: 49
64510087 TAGTATGGCG
*
64510097 TAATGGCTGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCC
1 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCC
*
64510146 TAATAGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAA-G-C
1 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCC
64510193 TAAT-G-CGATGTGATG-AT-TG-AAGTG----TATATGTGATAAGGCC
1 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCC
64510233 TAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCC
1 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCC
64510280 TAAT-GCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCC
1 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCC
64510328 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGG-C
1 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCC
*
64510376 TAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGATAAGACC
1 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCC
64510423 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCC
1 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCC
64510472 TAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCC
1 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCC
* *
64510519 TAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGACAGGGCC
1 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCC
* * * * *
64510566 GAGTGGCCAACGTGATGGATGTGAAAGTGTATA-A-ATGTGATAAG
1 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAG
64510610 TCCCGAAGGG
Statistics
Matches: 434, Mismatches: 13, Indels: 36
0.90 0.03 0.07
Matches are distributed among these distances:
38 12 0.03
39 1 0.00
40 5 0.01
41 1 0.00
42 15 0.03
43 4 0.01
44 4 0.01
45 15 0.03
46 40 0.09
47 150 0.35
48 54 0.12
49 133 0.31
ACGTcount: A:0.33, C:0.08, G:0.29, T:0.30
Consensus pattern (49 bp):
TAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCC
Found at i:64510322 original size:95 final size:95
Alignment explanation
Indices: 64510097--64510609 Score: 773
Period size: 95 Copynumber: 5.5 Consensus size: 95
64510087 TAGTATGGCG
* *
64510097 TAATGGCTGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATAGCCGATGTGAT
1 TAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGAT
64510162 GAATGTGAAAGTGTATATATATGTGATAA-G-C
64 GAATGTGAAAGTG-ATATATATGTGATAAGGCC
64510193 TAAT-G-CGATGTGATG-AT-TG-AAGTG--TATATGTGATAAGGCCTAATGGCCGATGTGATGA
1 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
64510251 ATGTGAAAGTG-TATATATGTGATAAGGCC
66 ATGTGAAAGTGATATATATGTGATAAGGCC
64510280 TAAT-GCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGAT
1 TAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGAT
64510344 GAATGTGAAAGTGTATATATATGTGATAAGG-C
64 GAATGTGAAAGTG-ATATATATGTGATAAGGCC
*
64510376 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGACCTAATGGCCGATGTGATGA
1 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
64510441 ATGTGAAAGTGTATATATATGTGATAAGGCC
66 ATGTGAAAGTG-ATATATATGTGATAAGGCC
64510472 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
1 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
* *
64510537 ATGTGAAAGTG-TATATATGTGACAGGGCC
66 ATGTGAAAGTGATATATATGTGATAAGGCC
* * * * * *
64510566 GAGTGGCCAACGTGATGGATGTGAAAGTGTATAAATGTGATAAG
1 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAG
64510610 TCCCGAAGGG
Statistics
Matches: 391, Mismatches: 12, Indels: 30
0.90 0.03 0.07
Matches are distributed among these distances:
85 14 0.04
86 1 0.00
87 50 0.13
88 10 0.03
89 2 0.01
90 2 0.01
91 10 0.03
92 2 0.01
93 2 0.01
94 63 0.16
95 110 0.28
96 85 0.22
97 40 0.10
ACGTcount: A:0.33, C:0.08, G:0.29, T:0.30
Consensus pattern (95 bp):
TAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
ATGTGAAAGTGATATATATGTGATAAGGCC
Found at i:64510402 original size:143 final size:143
Alignment explanation
Indices: 64510097--64510609 Score: 809
Period size: 143 Copynumber: 3.7 Consensus size: 143
64510087 TAGTATGGCG
* *
64510097 TAATGGCTGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATAGCCGATGTGAT
1 TAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGAT
64510162 GAATGTGAAAGTGTATATATATGTGATAA-G-CTAAT-G-CGATGTGATG-AT-TG-AAGTG--T
64 GAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTAT
64510218 ATATGTGATAAGGCC
129 ATATGTGATAAGGCC
64510233 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAAT-GCCGATGTGATGA
1 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
64510297 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATAT
66 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TAT
64510362 ATATGTGATAAGG-C
129 ATATGTGATAAGGCC
*
64510376 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGACCTAATGGCCGATGTGATGA
1 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
64510441 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATAT
66 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATAT
64510506 ATGTGATAAGGCC
131 ATGTGATAAGGCC
* * * * * * *
64510519 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGACAGGGCCGAGTGGCCAACGTGATGG
1 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
64510584 ATGTGAAAGTGTATA-A-ATGTGATAAG
66 ATGTGAAAGTGTATATATATGTGATAAG
64510610 TCCCGAAGGG
Statistics
Matches: 354, Mismatches: 10, Indels: 21
0.92 0.03 0.05
Matches are distributed among these distances:
133 40 0.11
134 23 0.06
135 5 0.01
136 29 0.08
137 10 0.03
138 2 0.01
139 2 0.01
140 5 0.01
141 10 0.03
142 17 0.05
143 124 0.35
144 87 0.25
ACGTcount: A:0.33, C:0.08, G:0.29, T:0.30
Consensus pattern (143 bp):
TAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATAT
ATGTGATAAGGCC
Found at i:64511602 original size:19 final size:19
Alignment explanation
Indices: 64511578--64511614 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
64511568 TAATATGTCT
64511578 TTTTTTCTTTC-CTTTTTTC
1 TTTTTT-TTTCTCTTTTTTC
64511597 TTTTTTTTTCTCTTTTTT
1 TTTTTTTTTCTCTTTTTT
64511615 AATAGAATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (19 bp):
TTTTTTTTTCTCTTTTTTC
Found at i:64511811 original size:96 final size:97
Alignment explanation
Indices: 64511637--64511818 Score: 267
Period size: 96 Copynumber: 1.9 Consensus size: 97
64511627 ATTTAATTTA
* * * * *
64511637 TTTATTTTTACTTAGGAATATATTAAACCTTTTGACACGAAGAGAGATGACAGCTAAGCACCCCA
1 TTTATTTTTACTTAAGAACATATCAAACCTTTTGACACAAAGAGAGATGACAGCCAAGCACCCCA
64511702 CCCCAATTACTCAGCCCAACATACTCCTAATT
66 CCCCAATTACTCAGCCCAACATACTCCTAATT
* *
64511734 TTTATTTTT-CTTAAGAACATATCGAACCTTTTGACACAAAGAGAGATGACAGCCAAGCACCTCA
1 TTTATTTTTACTTAAGAACATATCAAACCTTTTGACACAAAGAGAGATGACAGCCAAGCACCCCA
** *
64511798 CCCCGGTTGCTCAGCCCAACA
66 CCCCAATTACTCAGCCCAACA
64511819 CATTCTTAAA
Statistics
Matches: 75, Mismatches: 10, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
96 66 0.88
97 9 0.12
ACGTcount: A:0.33, C:0.27, G:0.13, T:0.27
Consensus pattern (97 bp):
TTTATTTTTACTTAAGAACATATCAAACCTTTTGACACAAAGAGAGATGACAGCCAAGCACCCCA
CCCCAATTACTCAGCCCAACATACTCCTAATT
Found at i:64512636 original size:15 final size:15
Alignment explanation
Indices: 64512616--64512663 Score: 62
Period size: 15 Copynumber: 3.1 Consensus size: 15
64512606 TTAATATCTG
*
64512616 AAAATAATAAATAAT
1 AAAATAATAAATAAA
64512631 AAAATAATAAGATAAA
1 AAAATAATAA-ATAAA
64512647 ATAAATAA-AAATAAA
1 A-AAATAATAAATAAA
64512662 AA
1 AA
64512664 TTTGTTGCCT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
14 1 0.03
15 16 0.53
16 7 0.23
17 6 0.20
ACGTcount: A:0.77, C:0.00, G:0.02, T:0.21
Consensus pattern (15 bp):
AAAATAATAAATAAA
Found at i:64516333 original size:10 final size:9
Alignment explanation
Indices: 64516318--64516371 Score: 56
Period size: 10 Copynumber: 5.7 Consensus size: 9
64516308 ATTCTAAAAG
64516318 ATAAATACAA
1 ATAAATA-AA
64516328 ATAAATAAA
1 ATAAATAAA
*
64516337 GATAATTAAA
1 -ATAAATAAA
64516347 GATAAATAAA
1 -ATAAATAAA
64516357 A-AAATGAAA
1 ATAAAT-AAA
64516366 ATAAAT
1 ATAAAT
64516372 CCTAAAATTA
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
8 4 0.10
9 7 0.18
10 28 0.72
ACGTcount: A:0.70, C:0.02, G:0.06, T:0.22
Consensus pattern (9 bp):
ATAAATAAA
Found at i:64520055 original size:39 final size:39
Alignment explanation
Indices: 64520001--64520079 Score: 158
Period size: 39 Copynumber: 2.0 Consensus size: 39
64519991 AAATCAATAA
64520001 ACCAATCAGAAAGATTAACTTGCTTCAGGGTTTGTAACT
1 ACCAATCAGAAAGATTAACTTGCTTCAGGGTTTGTAACT
64520040 ACCAATCAGAAAGATTAACTTGCTTCAGGGTTTGTAACT
1 ACCAATCAGAAAGATTAACTTGCTTCAGGGTTTGTAACT
64520079 A
1 A
64520080 ACTTTGGATT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30
Consensus pattern (39 bp):
ACCAATCAGAAAGATTAACTTGCTTCAGGGTTTGTAACT
Found at i:64522344 original size:25 final size:25
Alignment explanation
Indices: 64522316--64522365 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
64522306 ACATGACAAA
64522316 TGATAACACAAAACAATACCACATG
1 TGATAACACAAAACAATACCACATG
*
64522341 TGATAACACAATACAATACCACATG
1 TGATAACACAAAACAATACCACATG
64522366 ACATGCTGTG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.50, C:0.24, G:0.08, T:0.18
Consensus pattern (25 bp):
TGATAACACAAAACAATACCACATG
Found at i:64527815 original size:41 final size:41
Alignment explanation
Indices: 64527770--64527851 Score: 110
Period size: 41 Copynumber: 2.0 Consensus size: 41
64527760 GCCAGGCTCG
* *
64527770 AAGCCTGATATAACGCATCAACACAAAGCCTACTAGGCACA
1 AAGCCTGATATAACACACCAACACAAAGCCTACTAGGCACA
** * *
64527811 AAGCCTGATATAACACACCGGCACGAAGCCTGCTAGGCACA
1 AAGCCTGATATAACACACCAACACAAAGCCTACTAGGCACA
64527852 TAGCTCGTAT
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.38, C:0.30, G:0.18, T:0.13
Consensus pattern (41 bp):
AAGCCTGATATAACACACCAACACAAAGCCTACTAGGCACA
Found at i:64527913 original size:38 final size:38
Alignment explanation
Indices: 64527791--64527938 Score: 129
Period size: 38 Copynumber: 3.8 Consensus size: 38
64527781 AACGCATCAA
* *
64527791 CACAAAGCCT-ACTAGGCACAAAGCCTGATATAACACACCGG
1 CACAAAGCCTGA-TAGGCACAAAGCCCGA-AT-A-TCACCGG
* * * * * * *
64527832 CACGAAGCCTGCTAGGCACATAGCTCGTATATTACCAG
1 CACAAAGCCTGATAGGCACAAAGCCCGAATATCACCGG
* *
64527870 CACAAAGCCTGATAGGCACAGAGCCCAAATATCACCGG
1 CACAAAGCCTGATAGGCACAAAGCCCGAATATCACCGG
*
64527908 TACAAAGCCT-ACTAGGCACAAAGCCCGAATA
1 CACAAAGCCTGA-TAGGCACAAAGCCCGAATA
64527939 ACGTTACGTT
Statistics
Matches: 85, Mismatches: 20, Indels: 7
0.76 0.18 0.06
Matches are distributed among these distances:
37 1 0.01
38 60 0.71
39 1 0.01
40 2 0.02
41 21 0.25
ACGTcount: A:0.36, C:0.30, G:0.19, T:0.14
Consensus pattern (38 bp):
CACAAAGCCTGATAGGCACAAAGCCCGAATATCACCGG
Found at i:64539462 original size:40 final size:40
Alignment explanation
Indices: 64539397--64539491 Score: 115
Period size: 40 Copynumber: 2.4 Consensus size: 40
64539387 ACCAACTCCG
* * *
64539397 TCCAACCCAACACACC--ATGTGGGGATAAAATTGACCCA
1 TCCAACCCTACACACCAAATATGGGGATAAAATCGACCCA
* *
64539435 -CCTATCCCTGCACACCAAATATGGGGATAAAATCGACCCA
1 TCC-AACCCTACACACCAAATATGGGGATAAAATCGACCCA
64539475 TCCAACCCTACACACCA
1 TCCAACCCTACACACCA
64539492 TAAAGTACTG
Statistics
Matches: 46, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
37 2 0.04
38 10 0.22
40 32 0.70
41 2 0.04
ACGTcount: A:0.36, C:0.36, G:0.13, T:0.16
Consensus pattern (40 bp):
TCCAACCCTACACACCAAATATGGGGATAAAATCGACCCA
Found at i:64544020 original size:38 final size:38
Alignment explanation
Indices: 64543964--64544067 Score: 122
Period size: 38 Copynumber: 2.8 Consensus size: 38
64543954 AGCCTAATAT
* *
64543964 AATA-CACTGGCATGAAGCCTGCTAGGCACATAGC-CTG
1 AATATCACTGGCATAAAGCCTGCTAGGCACAAAGCTC-G
*
64544001 AATATCACTGGCATAAAGCCTGCTAGGCGCAAAGCTCG
1 AATATCACTGGCATAAAGCCTGCTAGGCACAAAGCTCG
** * *
64544039 AATATCACCAGCACAAAGCCTACTAGGCA
1 AATATCACTGGCATAAAGCCTGCTAGGCA
64544068 TAGAGCCCGA
Statistics
Matches: 57, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
37 4 0.07
38 52 0.91
39 1 0.02
ACGTcount: A:0.34, C:0.28, G:0.21, T:0.17
Consensus pattern (38 bp):
AATATCACTGGCATAAAGCCTGCTAGGCACAAAGCTCG
Found at i:64544079 original size:38 final size:38
Alignment explanation
Indices: 64543978--64544080 Score: 116
Period size: 38 Copynumber: 2.7 Consensus size: 38
64543968 CACTGGCATG
* * ** *
64543978 AAGCCTGCTAGGCACATAGCCTGAATATCACTGGCATA
1 AAGCCTGCTAGGCACAAAGCCCGAATATCACCAGCACA
* *
64544016 AAGCCTGCTAGGCGCAAAGCTCGAATATCACCAGCACA
1 AAGCCTGCTAGGCACAAAGCCCGAATATCACCAGCACA
* * *
64544054 AAGCCTACTAGGCATAGAGCCCGAATA
1 AAGCCTGCTAGGCACAAAGCCCGAATA
64544081 ACATTACGTT
Statistics
Matches: 53, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
38 53 1.00
ACGTcount: A:0.34, C:0.28, G:0.21, T:0.17
Consensus pattern (38 bp):
AAGCCTGCTAGGCACAAAGCCCGAATATCACCAGCACA
Found at i:64545449 original size:3 final size:3
Alignment explanation
Indices: 64545434--64545485 Score: 77
Period size: 3 Copynumber: 17.3 Consensus size: 3
64545424 CAGAATGACA
* * *
64545434 TTG TTG ATG TTG TTG TTG TTG TTG TTG TTT TTG TTG TTG TTG GTG TTG
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG
64545482 TTG T
1 TTG T
64545486 GATTTTTCAT
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.02, C:0.00, G:0.33, T:0.65
Consensus pattern (3 bp):
TTG
Found at i:64548268 original size:25 final size:25
Alignment explanation
Indices: 64548240--64548290 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
64548230 TATGTTTGGG
*
64548240 TACGTTTTGGATTAACTTACTTTGA
1 TACGTTTTAGATTAACTTACTTTGA
64548265 TACGTTTTAGATTAACTTACTTTGA
1 TACGTTTTAGATTAACTTACTTTGA
64548290 T
1 T
64548291 TTTATCCTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.25, C:0.12, G:0.14, T:0.49
Consensus pattern (25 bp):
TACGTTTTAGATTAACTTACTTTGA
Found at i:64548286 original size:68 final size:68
Alignment explanation
Indices: 64548197--64548333 Score: 256
Period size: 68 Copynumber: 2.0 Consensus size: 68
64548187 GCTTTTTGGG
*
64548197 TACGTTTTGGATTAACTTACTTTGATTTTACCCTATGTTTGGGTACGTTTTGGATTAACTTACTT
1 TACGTTTTAGATTAACTTACTTTGATTTTACCCTATGTTTGGGTACGTTTTGGATTAACTTACTT
64548262 TGA
66 TGA
*
64548265 TACGTTTTAGATTAACTTACTTTGATTTTATCCTATGTTTGGGTACGTTTTGGATTAACTTACTT
1 TACGTTTTAGATTAACTTACTTTGATTTTACCCTATGTTTGGGTACGTTTTGGATTAACTTACTT
64548330 TGA
66 TGA
64548333 T
1 T
64548334 TTTATCCTAT
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
68 67 1.00
ACGTcount: A:0.21, C:0.12, G:0.17, T:0.50
Consensus pattern (68 bp):
TACGTTTTAGATTAACTTACTTTGATTTTACCCTATGTTTGGGTACGTTTTGGATTAACTTACTT
TGA
Found at i:64548313 original size:43 final size:43
Alignment explanation
Indices: 64548265--64548353 Score: 160
Period size: 43 Copynumber: 2.1 Consensus size: 43
64548255 CTTACTTTGA
*
64548265 TACGTTTTAGATTAACTTACTTTGATTTTATCCTATGTTTGGG
1 TACGTTTTAGATTAACTTACTTTGATTTTATCCTATGTTAGGG
*
64548308 TACGTTTTGGATTAACTTACTTTGATTTTATCCTATGTTAGGG
1 TACGTTTTAGATTAACTTACTTTGATTTTATCCTATGTTAGGG
64548351 TAC
1 TAC
64548354 TTCTGTTGGA
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.21, C:0.12, G:0.17, T:0.49
Consensus pattern (43 bp):
TACGTTTTAGATTAACTTACTTTGATTTTATCCTATGTTAGGG
Found at i:64549664 original size:27 final size:27
Alignment explanation
Indices: 64549614--64549940 Score: 284
Period size: 27 Copynumber: 12.1 Consensus size: 27
64549604 GGTCGTTATT
* * * *
64549614 TGACCGTAATACCCGTGTAAGGTAAAA
1 TGACCGTAATGCCCCTATAGGGTAAAA
*
64549641 TGACCATAATGCCCCTGA-AGGGTAAAA
1 TGACCGTAATGCCCCT-ATAGGGTAAAA
* * * *
64549668 TGACCATAATACCCTTGTAGGGTAAAA
1 TGACCGTAATGCCCCTATAGGGTAAAA
* * *
64549695 TGATCGTAATACCCCTATAGGCTAAAA
1 TGACCGTAATGCCCCTATAGGGTAAAA
* * *
64549722 TGGCCCTAATACCCCTATAGGGTAAAA
1 TGACCGTAATGCCCCTATAGGGTAAAA
* *
64549749 TGACTGTAATGCCCCTATAGGGTTAAA
1 TGACCGTAATGCCCCTATAGGGTAAAA
* * *
64549776 TGACCGTAATAG-CCCTTTATGATAAAA
1 TGACCGTAAT-GCCCCTATAGGGTAAAA
*
64549803 TGACCGTAATGCCCCTATAGGGTTAAA
1 TGACCGTAATGCCCCTATAGGGTAAAA
* *
64549830 TGACCGTAATAG-CCCTGTAGGATAAAA
1 TGACCGTAAT-GCCCCTATAGGGTAAAA
* * * *
64549857 TAACCGTAATACCCCCATAAGGT-AAA
1 TGACCGTAATGCCCCTATAGGGTAAAA
* * *
64549883 TGACCGTAATTCCCTTCTAGGGTAAAA
1 TGACCGTAATGCCCCTATAGGGTAAAA
* * * * *
64549910 TGATCGTGATACCCCTATATGGCAAAA
1 TGACCGTAATGCCCCTATAGGGTAAAA
64549937 TGAC
1 TGAC
64549941 GAGTAGCCCT
Statistics
Matches: 239, Mismatches: 54, Indels: 14
0.78 0.18 0.05
Matches are distributed among these distances:
26 21 0.09
27 216 0.90
28 2 0.01
ACGTcount: A:0.35, C:0.21, G:0.19, T:0.25
Consensus pattern (27 bp):
TGACCGTAATGCCCCTATAGGGTAAAA
Found at i:64549696 original size:54 final size:54
Alignment explanation
Indices: 64549614--64549940 Score: 347
Period size: 54 Copynumber: 6.1 Consensus size: 54
64549604 GGTCGTTATT
* * *
64549614 TGACCGTAATACCCGTGTAAGGTAAAATGACCATAATGCCCCTGA-AGGGTAAAA
1 TGACCGTAATACCCTTGTAGGGTAAAATGACCGTAATGCCCCT-ATAGGGTAAAA
* * * *
64549668 TGACCATAATACCCTTGTAGGGTAAAATGATCGTAATACCCCTATAGGCTAAAA
1 TGACCGTAATACCCTTGTAGGGTAAAATGACCGTAATGCCCCTATAGGGTAAAA
* * * * * *
64549722 TGGCCCTAATACCCCTATAGGGTAAAATGACTGTAATGCCCCTATAGGGTTAAA
1 TGACCGTAATACCCTTGTAGGGTAAAATGACCGTAATGCCCCTATAGGGTAAAA
* * *
64549776 TGACCGTAATAGCCCTT-TATGATAAAATGACCGTAATGCCCCTATAGGGTTAAA
1 TGACCGTAATA-CCCTTGTAGGGTAAAATGACCGTAATGCCCCTATAGGGTAAAA
* * * * *
64549830 TGACCGTAATAGCCC-TGTAGGATAAAATAACCGTAATACCCCCATAAGGT-AAA
1 TGACCGTAATA-CCCTTGTAGGGTAAAATGACCGTAATGCCCCTATAGGGTAAAA
* * * * * * *
64549883 TGACCGTAATTCCCTTCTAGGGTAAAATGATCGTGATACCCCTATATGGCAAAA
1 TGACCGTAATACCCTTGTAGGGTAAAATGACCGTAATGCCCCTATAGGGTAAAA
64549937 TGAC
1 TGAC
64549941 GAGTAGCCCT
Statistics
Matches: 232, Mismatches: 36, Indels: 10
0.83 0.13 0.04
Matches are distributed among these distances:
52 3 0.01
53 42 0.18
54 183 0.79
55 4 0.02
ACGTcount: A:0.35, C:0.21, G:0.19, T:0.25
Consensus pattern (54 bp):
TGACCGTAATACCCTTGTAGGGTAAAATGACCGTAATGCCCCTATAGGGTAAAA
Found at i:64549770 original size:81 final size:81
Alignment explanation
Indices: 64549614--64549940 Score: 345
Period size: 81 Copynumber: 4.0 Consensus size: 81
64549604 GGTCGTTATT
* * * *
64549614 TGACCGTAATACCCGTGTAAGGTAAAATGACCATAATGCCCCTGA-AGGGTAAAATGACCATAAT
1 TGACCGTAATACCCCTATAAGGTAAAATGACCGTAATGCCCCT-ATAGGGTAAAATGACCGTAAT
* *
64549678 ACCCTTGTAGGGTAAAA
65 ACCCCTATAGGGTAAAA
* * * * *
64549695 TGATCGTAATACCCCTAT-AGGCTAAAATGGCCCTAATACCCCTATAGGGTAAAATGACTGTAAT
1 TGACCGTAATACCCCTATAAGG-TAAAATGACCGTAATGCCCCTATAGGGTAAAATGACCGTAAT
* *
64549759 GCCCCTATAGGGTTAAA
65 ACCCCTATAGGGTAAAA
* * * * *
64549776 TGACCGTAATAGCCCTTTATGATAAAATGACCGTAATGCCCCTATAGGGTTAAATGACCGTAATA
1 TGACCGTAATACCCCTATAAGGTAAAATGACCGTAATGCCCCTATAGGGTAAAATGACCGTAATA
* * *
64549841 GCCCTGTAGGATAAAA
66 CCCCTATAGGGTAAAA
* * * * * * *
64549857 TAACCGTAATACCCCCATAAGGT-AAATGACCGTAATTCCCTTCTAGGGTAAAATGATCGTGATA
1 TGACCGTAATACCCCTATAAGGTAAAATGACCGTAATGCCCCTATAGGGTAAAATGACCGTAATA
* *
64549921 CCCCTATATGGCAAAA
66 CCCCTATAGGGTAAAA
64549937 TGAC
1 TGAC
64549941 GAGTAGCCCT
Statistics
Matches: 198, Mismatches: 45, Indels: 7
0.79 0.18 0.03
Matches are distributed among these distances:
80 53 0.27
81 144 0.73
82 1 0.01
ACGTcount: A:0.35, C:0.21, G:0.19, T:0.25
Consensus pattern (81 bp):
TGACCGTAATACCCCTATAAGGTAAAATGACCGTAATGCCCCTATAGGGTAAAATGACCGTAATA
CCCCTATAGGGTAAAA
Found at i:64550121 original size:27 final size:25
Alignment explanation
Indices: 64550077--64550156 Score: 79
Period size: 27 Copynumber: 3.0 Consensus size: 25
64550067 ATGGAGGAAG
* * *
64550077 TACTGTACAGGTGACTATGTCACAT
1 TACTGTACTGGTGGCTATGCCACAT
64550102 TCACTGTTACTGGTGGCTATGCCACAAT
1 T-ACTG-TACTGGTGGCTATGCCAC-AT
* *
64550130 TACTGATACTGGTGGCTTTGGCACAT
1 TACTG-TACTGGTGGCTATGCCACAT
64550156 T
1 T
64550157 TGCTGTTTCT
Statistics
Matches: 46, Mismatches: 6, Indels: 5
0.81 0.11 0.09
Matches are distributed among these distances:
25 1 0.02
26 7 0.15
27 35 0.76
28 3 0.07
ACGTcount: A:0.23, C:0.21, G:0.23, T:0.34
Consensus pattern (25 bp):
TACTGTACTGGTGGCTATGCCACAT
Found at i:64550168 original size:27 final size:27
Alignment explanation
Indices: 64550077--64550146 Score: 81
Period size: 27 Copynumber: 2.6 Consensus size: 27
64550067 ATGGAGGAAG
* * *
64550077 TACTG-TACAGGTGACTATGTCAC-AT
1 TACTGTTACTGGTGGCTATGCCACAAT
64550102 TCACTGTTACTGGTGGCTATGCCACAAT
1 T-ACTGTTACTGGTGGCTATGCCACAAT
*
64550130 TACTGATACTGGTGGCT
1 TACTGTTACTGGTGGCT
64550147 TTGGCACATT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
25 1 0.03
26 4 0.11
27 30 0.79
28 3 0.08
ACGTcount: A:0.23, C:0.21, G:0.23, T:0.33
Consensus pattern (27 bp):
TACTGTTACTGGTGGCTATGCCACAAT
Found at i:64550381 original size:33 final size:33
Alignment explanation
Indices: 64550344--64550409 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 33
64550334 GCTTAGGCCC
* * *
64550344 ATACTGTTACTGTATAGGGCTAAGGCCCAGACT
1 ATACTGATACTGAATAGCGCTAAGGCCCAGACT
* *
64550377 ATACTGATACTGAATAGCGCTCAGGCCTAGACT
1 ATACTGATACTGAATAGCGCTAAGGCCCAGACT
64550410 GTTACCGATC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.29, C:0.23, G:0.23, T:0.26
Consensus pattern (33 bp):
ATACTGATACTGAATAGCGCTAAGGCCCAGACT
Found at i:64553630 original size:21 final size:21
Alignment explanation
Indices: 64553606--64553646 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
64553596 ATTTGTGATT
*
64553606 TTTTTGAATTAT-TTTTTTATG
1 TTTTT-AATTATATTATTTATG
64553627 TTTTTAATTATATTATTTAT
1 TTTTTAATTATATTATTTAT
64553647 AATTATATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.24, C:0.00, G:0.05, T:0.71
Consensus pattern (21 bp):
TTTTTAATTATATTATTTATG
Found at i:64561715 original size:30 final size:30
Alignment explanation
Indices: 64561679--64561738 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
64561669 TTCCTGAGCC
*
64561679 TAGGGGCAAAAGTGTAATTATGCAAAAGTT
1 TAGGGGCAAAAATGTAATTATGCAAAAGTT
* *
64561709 TAGGGGCAAAAATGTAATTTTGCCAAAGTT
1 TAGGGGCAAAAATGTAATTATGCAAAAGTT
64561739 CGTATTAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.38, C:0.08, G:0.25, T:0.28
Consensus pattern (30 bp):
TAGGGGCAAAAATGTAATTATGCAAAAGTT
Found at i:64569165 original size:30 final size:30
Alignment explanation
Indices: 64569129--64569188 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
64569119 TTCCCGAGCC
*
64569129 TAGGGGCAAAAGTGTAATTATGCAAAAGTT
1 TAGGGGCAAAAATGTAATTATGCAAAAGTT
* *
64569159 TAGGGGCAAAAATGTAATTTTGCCAAAGTT
1 TAGGGGCAAAAATGTAATTATGCAAAAGTT
64569189 CGTATTAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.38, C:0.08, G:0.25, T:0.28
Consensus pattern (30 bp):
TAGGGGCAAAAATGTAATTATGCAAAAGTT
Found at i:64571873 original size:14 final size:14
Alignment explanation
Indices: 64571854--64571898 Score: 58
Period size: 14 Copynumber: 3.4 Consensus size: 14
64571844 CTAATTTTTA
*
64571854 CAAGTTGTAATTTG
1 CAAGTTGTAATATG
*
64571868 CAAGTTG--ATCTG
1 CAAGTTGTAATATG
64571880 CAAGTTGTAATATG
1 CAAGTTGTAATATG
64571894 CAAGT
1 CAAGT
64571899 GGTGCAAGTA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
12 11 0.41
14 16 0.59
ACGTcount: A:0.31, C:0.11, G:0.22, T:0.36
Consensus pattern (14 bp):
CAAGTTGTAATATG
Found at i:64576496 original size:14 final size:13
Alignment explanation
Indices: 64576477--64576520 Score: 54
Period size: 14 Copynumber: 3.3 Consensus size: 13
64576467 CTAATTTTTA
64576477 CAAGTTGTAATTTG
1 CAAGTTG-AATTTG
64576491 CAAGTTG-ATTTG
1 CAAGTTGAATTTG
*
64576503 CAAGTTGCAATATG
1 CAAGTTG-AATTTG
64576517 CAAG
1 CAAG
64576521 CGGTGCAAGT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
12 12 0.44
14 15 0.56
ACGTcount: A:0.32, C:0.11, G:0.23, T:0.34
Consensus pattern (13 bp):
CAAGTTGAATTTG
Found at i:64579106 original size:12 final size:12
Alignment explanation
Indices: 64579091--64579127 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
64579081 TTTAATTTGA
64579091 ATTTAGATTTAG
1 ATTTAGATTTAG
64579103 ATTTAGATTTAG
1 ATTTAGATTTAG
*
64579115 ATTT-GAATTAG
1 ATTTAGATTTAG
64579126 AT
1 AT
64579128 AATTTGTGTA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 8 0.33
12 16 0.67
ACGTcount: A:0.35, C:0.00, G:0.16, T:0.49
Consensus pattern (12 bp):
ATTTAGATTTAG
Found at i:64579112 original size:18 final size:17
Alignment explanation
Indices: 64579091--64579127 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
64579081 TTTAATTTGA
*
64579091 ATTTAGATTTAGATTTAG
1 ATTTAGATTT-GAATTAG
64579109 ATTTAGATTTGAATTAG
1 ATTTAGATTTGAATTAG
64579126 AT
1 AT
64579128 AATTTGTGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 8 0.44
18 10 0.56
ACGTcount: A:0.35, C:0.00, G:0.16, T:0.49
Consensus pattern (17 bp):
ATTTAGATTTGAATTAG
Found at i:64580032 original size:16 final size:15
Alignment explanation
Indices: 64580007--64580060 Score: 56
Period size: 16 Copynumber: 3.5 Consensus size: 15
64579997 TAAAATCACA
*
64580007 AAATAAAATATAAAT
1 AAATTAAATATAAAT
* *
64580022 GAAATTCAATAATAAAA
1 -AAATTAAAT-ATAAAT
64580039 AAATTAAAT-TAAAT
1 AAATTAAATATAAAT
64580053 AAATTAAA
1 AAATTAAA
64580061 ACCACATTAA
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
14 12 0.38
16 15 0.47
17 5 0.16
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.28
Consensus pattern (15 bp):
AAATTAAATATAAAT
Found at i:64580032 original size:21 final size:20
Alignment explanation
Indices: 64580007--64580055 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
64579997 TAAAATCACA
*
64580007 AAATAAAATATAAATGAAATT
1 AAATAAAA-AAAAATGAAATT
* *
64580028 CAATAATAAAAAAATTAAATT
1 AAATAA-AAAAAAATGAAATT
64580049 AAATAAA
1 AAATAAA
64580056 TTAAAACCAC
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
20 1 0.04
21 20 0.87
22 2 0.09
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.27
Consensus pattern (20 bp):
AAATAAAAAAAAATGAAATT
Found at i:64584252 original size:21 final size:21
Alignment explanation
Indices: 64584206--64584252 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
64584196 TTTCGTTTCT
*
64584206 CTTTTAGGTTTCAAATTTCGG
1 CTTTTAGGTTTCAAATTTCGA
* * *
64584227 GTTTTAGGTTTCAAGTTTTGA
1 CTTTTAGGTTTCAAATTTCGA
64584248 CTTTT
1 CTTTT
64584253 GATTTTTGGA
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.17, C:0.11, G:0.19, T:0.53
Consensus pattern (21 bp):
CTTTTAGGTTTCAAATTTCGA
Found at i:64584390 original size:20 final size:20
Alignment explanation
Indices: 64584354--64584398 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
64584344 ACAGTGCATT
*
64584354 AAATATCCTAATGTGAGGGA
1 AAATATCCTAATATGAGGGA
64584374 AAATATCCT-ATCATGAGGGA
1 AAATATCCTAAT-ATGAGGGA
*
64584394 TAATA
1 AAATA
64584399 AACATTACAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 2 0.09
20 20 0.91
ACGTcount: A:0.42, C:0.11, G:0.20, T:0.27
Consensus pattern (20 bp):
AAATATCCTAATATGAGGGA
Found at i:64589631 original size:43 final size:42
Alignment explanation
Indices: 64589532--64589636 Score: 111
Period size: 43 Copynumber: 2.5 Consensus size: 42
64589522 AGGGTTACTA
* * * *
64589532 AGATTACATGTAAGACCATATCTGGGATATGACATCGATATG
1 AGATTTCATGTAAGACCATAGCTAGGATATGACATCGATACG
* * * * * *
64589574 AGACTTCGTATAAGACTATAGCTAGGTTATTGGCATCGATACG
1 AGATTTCATGTAAGACCATAGCTAGGATA-TGACATCGATACG
64589617 AGATTTCATGTAAGACCATA
1 AGATTTCATGTAAGACCATA
64589637 TTTGGGATAT
Statistics
Matches: 48, Mismatches: 14, Indels: 1
0.76 0.22 0.02
Matches are distributed among these distances:
42 21 0.44
43 27 0.56
ACGTcount: A:0.34, C:0.15, G:0.21, T:0.30
Consensus pattern (42 bp):
AGATTTCATGTAAGACCATAGCTAGGATATGACATCGATACG
Found at i:64600236 original size:15 final size:16
Alignment explanation
Indices: 64600207--64600236 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
64600197 CAAACATGCT
64600207 TTAACACATTATCAAA
1 TTAACACATTATCAAA
64600223 TTAACACA-TATCAA
1 TTAACACATTATCAA
64600237 CAAGGCACCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.50, C:0.20, G:0.00, T:0.30
Consensus pattern (16 bp):
TTAACACATTATCAAA
Found at i:64611024 original size:79 final size:81
Alignment explanation
Indices: 64610888--64611072 Score: 227
Period size: 79 Copynumber: 2.3 Consensus size: 81
64610878 TTGAATGATG
* *
64610888 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACGATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACGAAATCCGGACTAAGATCCGAAGGCAAT
64610952 TGTGCGAGATACTA-A
66 TGTGCGAGATACTATA
* * * **
64610967 TTCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACGAAATCCGGACTAAGAT-CCGAAGGCA
*
64611029 ATTGTGCGAGTTACTATA
64 ATTGTGCGAGATACTATA
* *
64611047 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
64611073 AATGAGTAGC
Statistics
Matches: 91, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
78 1 0.01
79 57 0.63
80 33 0.36
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACGAAATCCGGACTAAGATCCGAAGGCAAT
TGTGCGAGATACTATA
Found at i:64611086 original size:40 final size:40
Alignment explanation
Indices: 64610889--64611072 Score: 207
Period size: 40 Copynumber: 4.6 Consensus size: 40
64610879 TGAATGATGT
* * * *
64610889 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACGATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAA
* * *
64610929 CCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTA-ATT
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATA-A
64610969 CCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTA-AA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
* *
64611007 TCCGGGTTAAGTCCCGAAGGCAATTGTGCGAGTTACTATAA
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
64611048 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
64611073 AATGAGTAGC
Statistics
Matches: 124, Mismatches: 13, Indels: 14
0.82 0.09 0.09
Matches are distributed among these distances:
39 35 0.28
40 79 0.64
41 10 0.08
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.24
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
Found at i:64611094 original size:79 final size:79
Alignment explanation
Indices: 64610941--64611105 Score: 192
Period size: 79 Copynumber: 2.1 Consensus size: 79
64610931 GGACTAAGAT
* * **
64610941 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCAATTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
*
64611006 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
* * *
64611020 CCGAAGGCAATTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAATGAG-TAGC
1 CCGAAGGCAATTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTTA-C
* *
64611083 TATATCC-GGTTAAATT
63 TAAATCCGGGTTAAATC
64611099 CCGAAGG
1 CCGAAGG
64611106 TACGTGATTT
Statistics
Matches: 73, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
78 2 0.03
79 47 0.64
80 24 0.33
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.25
Consensus pattern (79 bp):
CCGAAGGCAATTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
ATCCGGGTTAAATC
Found at i:64618222 original size:54 final size:55
Alignment explanation
Indices: 64618127--64618253 Score: 179
Period size: 54 Copynumber: 2.3 Consensus size: 55
64618117 TGAGACATAG
* *
64618127 CCGTGGTCGAACCTGCTAAAACAACACGGGCGTGCGACACGCCCGTGTGGAAG-AA
1 CCGTGGTCGAACCTGTTAAAACAACACGGGCGTGCGACACGCCCGTGT-CAAGCAA
* *
64618182 CCGTGGGT-GAACCTGTTAAAA-AGCACGGGCGTGCGACACGCCCGTGTCTAGCAA
1 CCGT-GGTCGAACCTGTTAAAACAACACGGGCGTGCGACACGCCCGTGTCAAGCAA
64618236 CCGTGGTCGAACCTGTTA
1 CCGTGGTCGAACCTGTTA
64618254 GATTGACACG
Statistics
Matches: 65, Mismatches: 4, Indels: 7
0.86 0.05 0.09
Matches are distributed among these distances:
53 5 0.08
54 41 0.63
55 16 0.25
56 3 0.05
ACGTcount: A:0.24, C:0.28, G:0.31, T:0.17
Consensus pattern (55 bp):
CCGTGGTCGAACCTGTTAAAACAACACGGGCGTGCGACACGCCCGTGTCAAGCAA
Found at i:64637383 original size:18 final size:18
Alignment explanation
Indices: 64637362--64637398 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
64637352 GAATGAGGCC
64637362 TAAGGGAGAGCTAACGTA
1 TAAGGGAGAGCTAACGTA
64637380 TAAGGGAGAGCTAACGTA
1 TAAGGGAGAGCTAACGTA
64637398 T
1 T
64637399 CTTATGAGTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.38, C:0.11, G:0.32, T:0.19
Consensus pattern (18 bp):
TAAGGGAGAGCTAACGTA
Found at i:64639305 original size:15 final size:16
Alignment explanation
Indices: 64639273--64639309 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
64639263 TAGTTTGCAT
64639273 ATTTAGGATAATTTGC
1 ATTTAGGATAATTTGC
*
64639289 ATTTGGGATAA-TTGC
1 ATTTAGGATAATTTGC
64639304 ATTTAG
1 ATTTAG
64639310 TTTAATATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
15 9 0.47
16 10 0.53
ACGTcount: A:0.30, C:0.05, G:0.22, T:0.43
Consensus pattern (16 bp):
ATTTAGGATAATTTGC
Found at i:64643160 original size:19 final size:20
Alignment explanation
Indices: 64643136--64643173 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
64643126 GGTACCACCA
64643136 AAACAT-ATATCA-CATCTTT
1 AAACATCAT-TCATCATCTTT
64643155 AAACATCATTCATCATCTT
1 AAACATCATTCATCATCTT
64643174 ACCACCTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.39, C:0.24, G:0.00, T:0.37
Consensus pattern (20 bp):
AAACATCATTCATCATCTTT
Found at i:64643469 original size:46 final size:46
Alignment explanation
Indices: 64643402--64643572 Score: 191
Period size: 46 Copynumber: 3.7 Consensus size: 46
64643392 CGCCCCTAAG
* * *
64643402 TGAACTCGGACTCAACTCAACGAGCTCGGGTGTTCGCATCCATAAA
1 TGAACTCGGACTCAACTCAACGAGTTCGGATGTTAGCATCCATAAA
* * * * **
64643448 TGAACTCGAACTCAACTCAACGAGTTCGGATGCCTAG-TTACATCTCA
1 TGAACTCGGACTCAACTCAACGAGTTCGGATG-TTAGCATCCAT-AAA
* ** * *
64643495 CGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCATAAG
1 TGAACTCGGACTCAACTCAACGAGTTCGGATGTTAGCATCCATAAA
64643541 TGAACTCGGACTCAACTCAACGAGTTCGGATG
1 TGAACTCGGACTCAACTCAACGAGTTCGGATG
64643573 CTCAACCATC
Statistics
Matches: 99, Mismatches: 23, Indels: 6
0.77 0.18 0.05
Matches are distributed among these distances:
46 64 0.65
47 35 0.35
ACGTcount: A:0.29, C:0.27, G:0.20, T:0.23
Consensus pattern (46 bp):
TGAACTCGGACTCAACTCAACGAGTTCGGATGTTAGCATCCATAAA
Found at i:64643513 original size:93 final size:93
Alignment explanation
Indices: 64643403--64643573 Score: 279
Period size: 93 Copynumber: 1.8 Consensus size: 93
64643393 GCCCCTAAGT
***
64643403 GAACTCGGACTCAACTCAACGAGCTCGGGTGTTCGCATCCATAAATGAACTCGAACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAATGAACTCGAACTCAACTCAA
64643468 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
* * * *
64643496 GAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAATGAACTCGAACTCAACTCAA
64643561 CGAGTTCGGATGC
66 CGAGTTCGGATGC
64643574 TCAACCATCC
Statistics
Matches: 71, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
93 71 1.00
ACGTcount: A:0.29, C:0.28, G:0.20, T:0.22
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAATGAACTCGAACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:64651230 original size:45 final size:45
Alignment explanation
Indices: 64651148--64651233 Score: 111
Period size: 45 Copynumber: 1.9 Consensus size: 45
64651138 TACTAATATA
* * *
64651148 TCAGCTCGAAAGAGCTTACTGTTTAGCTTATTGGAGCTTACCGTT
1 TCAGCTCGAAAGAGCTTACAGTTCAGCTTATTAGAGCTTACCGTT
* *
64651193 TCAGCTCGTATGAGCTTACAGTTCAGCTTGA-TAGAGCTTAC
1 TCAGCTCGAAAGAGCTTACAGTTCAGCTT-ATTAGAGCTTAC
64651234 TGTTCATCAG
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
45 34 0.97
46 1 0.03
ACGTcount: A:0.23, C:0.21, G:0.22, T:0.34
Consensus pattern (45 bp):
TCAGCTCGAAAGAGCTTACAGTTCAGCTTATTAGAGCTTACCGTT
Found at i:64651238 original size:22 final size:22
Alignment explanation
Indices: 64651148--64651239 Score: 80
Period size: 22 Copynumber: 4.1 Consensus size: 22
64651138 TACTAATATA
*
64651148 TCAGCTCGAAAGAGCTTACTGT
1 TCAGCTCGATAGAGCTTACTGT
* * * *
64651170 TTAGCT-TATTGGAGCTTACCGTT
1 TCAGCTCGA-TAGAGCTTACTG-T
*
64651193 TCAGCTCG-TATGAGCTTACAGT
1 TCAGCTCGATA-GAGCTTACTGT
*
64651215 TCAGCTTGATAGAGCTTACTGT
1 TCAGCTCGATAGAGCTTACTGT
64651237 TCA
1 TCA
64651240 TCAGCTTAGA
Statistics
Matches: 54, Mismatches: 11, Indels: 10
0.72 0.15 0.13
Matches are distributed among these distances:
21 1 0.02
22 36 0.67
23 17 0.31
ACGTcount: A:0.23, C:0.21, G:0.22, T:0.35
Consensus pattern (22 bp):
TCAGCTCGATAGAGCTTACTGT
Found at i:64665434 original size:31 final size:32
Alignment explanation
Indices: 64665396--64665457 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 32
64665386 CTTCGCTGCA
* *
64665396 ATCTGGTGGCTTCGCCAC-ATATATATATCTG
1 ATCTGGTGGCCTAGCCACAATATATATATCTG
*
64665427 ATCTGGTGGCCTAGCCACAATATCTATATCT
1 ATCTGGTGGCCTAGCCACAATATATATATCT
64665458 AGTGACTTCG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
31 16 0.59
32 11 0.41
ACGTcount: A:0.24, C:0.24, G:0.18, T:0.34
Consensus pattern (32 bp):
ATCTGGTGGCCTAGCCACAATATATATATCTG
Found at i:64670132 original size:25 final size:25
Alignment explanation
Indices: 64670103--64670152 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
64670093 GGAGAAATGG
64670103 AATCATTTAGAAATGAATTTAGGTT
1 AATCATTTAGAAATGAATTTAGGTT
*
64670128 AATCATTTGGAAATGAATTTAGGTT
1 AATCATTTAGAAATGAATTTAGGTT
64670153 TTCAAAAATG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.38, C:0.04, G:0.18, T:0.40
Consensus pattern (25 bp):
AATCATTTAGAAATGAATTTAGGTT
Done.