Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr7
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: 21614486
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 1093914 characters in sequence are not A, C, G, or T
File 38 of 54
Found at i:15191544 original size:24 final size:24
Alignment explanation
Indices: 15191512--15191593 Score: 103
Period size: 24 Copynumber: 3.5 Consensus size: 24
15191502 GTGACATGAC
15191512 TGTGACACGACAGGGTTTAGAGTT
1 TGTGACACGACAGGGTTTAGAGTT
*
15191536 TGTGACACGATAGGGTTTAGAGTT
1 TGTGACACGACAGGGTTTAGAGTT
* * * * *
15191560 TGTGACACAATAGGG-TGAGAATA
1 TGTGACACGACAGGGTTTAGAGTT
15191583 TGTGACACGAC
1 TGTGACACGAC
15191594 TTAGAAGGAA
Statistics
Matches: 51, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
23 14 0.27
24 37 0.73
ACGTcount: A:0.29, C:0.12, G:0.32, T:0.27
Consensus pattern (24 bp):
TGTGACACGACAGGGTTTAGAGTT
Found at i:15191590 original size:23 final size:23
Alignment explanation
Indices: 15191536--15191635 Score: 69
Period size: 23 Copynumber: 4.3 Consensus size: 23
15191526 GTTTAGAGTT
* * * *
15191536 TGTGACACGATAGGGTTTAGAGTT
1 TGTGACACAATAGGG-TGAGAATA
15191560 TGTGACACAATAGGGTGAGAATA
1 TGTGACACAATAGGGTGAGAATA
* **
15191583 TGTGACACGACTTA-GAAG-GAATA
1 TGTGACAC-A-ATAGGGTGAGAATA
* * *
15191606 TGTGAGACAACATGGTGAGAATA
1 TGTGACACAATAGGGTGAGAATA
15191629 TGTGACA
1 TGTGACA
15191636 GGCCATGCTA
Statistics
Matches: 59, Mismatches: 13, Indels: 9
0.73 0.16 0.11
Matches are distributed among these distances:
21 1 0.02
22 3 0.05
23 36 0.61
24 17 0.29
25 2 0.03
ACGTcount: A:0.35, C:0.10, G:0.30, T:0.25
Consensus pattern (23 bp):
TGTGACACAATAGGGTGAGAATA
Found at i:15191623 original size:46 final size:46
Alignment explanation
Indices: 15191560--15191679 Score: 134
Period size: 46 Copynumber: 2.6 Consensus size: 46
15191550 GTTTAGAGTT
* * *
15191560 TGTGACACAATAGGGTGAGAATATGTGACACGACTTAG-AAGGAATA
1 TGTGACACAACATGGTGAGAATATGTGACACGACAT-GCAAGGAATA
* * * * *
15191606 TGTGAGACAACATGGTGAGAATATGTGACAGGCCATGCTATGAATA
1 TGTGACACAACATGGTGAGAATATGTGACACGACATGCAAGGAATA
* *
15191652 TGTGACACACCATGGTGACAATATGTGA
1 TGTGACACAACATGGTGAGAATATGTGA
15191680 GATGGCATAG
Statistics
Matches: 62, Mismatches: 11, Indels: 2
0.83 0.15 0.03
Matches are distributed among these distances:
45 1 0.02
46 61 0.98
ACGTcount: A:0.36, C:0.13, G:0.28, T:0.23
Consensus pattern (46 bp):
TGTGACACAACATGGTGAGAATATGTGACACGACATGCAAGGAATA
Found at i:15191642 original size:23 final size:23
Alignment explanation
Indices: 15191616--15191703 Score: 83
Period size: 23 Copynumber: 3.9 Consensus size: 23
15191606 TGTGAGACAA
15191616 CATGGTGAGAATATGTGACAGGC
1 CATGGTGAGAATATGTGACAGGC
* **
15191639 CATGCT-ATGAATATGTGACACAC
1 CATGGTGA-GAATATGTGACAGGC
* *
15191662 CATGGTGACAATATGTGAGATGG-
1 CATGGTGAGAATATGTGACA-GGC
*
15191685 CATAGTGAG-ATATGTGACA
1 CATGGTGAGAATATGTGACA
15191704 TGATTGTGAC
Statistics
Matches: 51, Mismatches: 11, Indels: 7
0.74 0.16 0.10
Matches are distributed among these distances:
22 10 0.20
23 40 0.78
24 1 0.02
ACGTcount: A:0.33, C:0.14, G:0.28, T:0.25
Consensus pattern (23 bp):
CATGGTGAGAATATGTGACAGGC
Found at i:15191768 original size:23 final size:23
Alignment explanation
Indices: 15191736--15191786 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
15191726 AGAGCTTGTA
* * *
15191736 ACATGCCATGGTGGGAATGTGTG
1 ACATGCCATGGTGAGAATCTATG
*
15191759 ACATGGCATGGTGAGAATCTATG
1 ACATGCCATGGTGAGAATCTATG
15191782 ACATG
1 ACATG
15191787 ACATTTTGAG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.27, C:0.14, G:0.33, T:0.25
Consensus pattern (23 bp):
ACATGCCATGGTGAGAATCTATG
Found at i:15191836 original size:23 final size:23
Alignment explanation
Indices: 15191803--15191957 Score: 148
Period size: 23 Copynumber: 6.7 Consensus size: 23
15191793 TGAGAAGTTA
* *
15191803 GAGAATGTGTGAGACGGCATGGT
1 GAGAATATGTGACACGGCATGGT
* * *
15191826 AAGAATATGTGACACAGCAAGGTT
1 GAGAATATGTGACACGGCATGG-T
* * * **
15191850 TAGAGTTTGTGACACACCATGGT
1 GAGAATATGTGACACGGCATGGT
*
15191873 GGGAATATGTGACACGGCATGGT
1 GAGAATATGTGACACGGCATGGT
* * **
15191896 GAAAATTTGTGACACGGCATTTT
1 GAGAATATGTGACACGGCATGGT
* *
15191919 GAGAATGTGTGAGACGGCATGGT
1 GAGAATATGTGACACGGCATGGT
15191942 GAGAATATGTGACACG
1 GAGAATATGTGACACG
15191958 ACTATGACAT
Statistics
Matches: 103, Mismatches: 28, Indels: 2
0.77 0.21 0.02
Matches are distributed among these distances:
23 85 0.83
24 18 0.17
ACGTcount: A:0.30, C:0.12, G:0.33, T:0.25
Consensus pattern (23 bp):
GAGAATATGTGACACGGCATGGT
Found at i:15192003 original size:127 final size:125
Alignment explanation
Indices: 15191675--15192083 Score: 383
Period size: 127 Copynumber: 3.2 Consensus size: 125
15191665 GGTGACAATA
* * * * * * * *
15191675 TGTGAGATGGCATAGTGAG-ATATGTGACATGATTGTGACACGGTAGAGTTTAGAGCTTGTAACA
1 TGTGAGACGGCATGGTGAGAATATGTGACACGACTATGACA-GG-AAAGTTTAGAGTTTGTGACA
* * * * * *
15191739 TGCCATGGTGGGAATGTGTGACATGGCATGGTGAGAATCTATGACATGACATTTTGAGAAGTTAG
64 TGCCATGGTGGGAATATGTGACACGGCATGGTGAAAAT-T-TG---TGACA---TG-GCATTTTG
15191804 AGAATG
120 AGAATG
* * **
15191810 TGTGAGACGGCATGGTAAGAATATGTG--AC-AC-A-G-C---AAGGTTTAGAGTTTGTGACACA
1 TGTGAGACGGCATGGTGAGAATATGTGACACGACTATGACAGGAAAGTTTAGAGTTTGTGACATG
*
15191866 CCATGGTGGGAATATGTGACACGGCATGGTGAAAATTTGTGACACGGCATTTTGAGAATG
66 CCATGGTGGGAATATGTGACACGGCATGGTGAAAATTTGTGACATGGCATTTTGAGAATG
15191926 TGTGAGACGGCATGGTGAGAATATGTGACACGACTATGACATGGAAAAGTTTAGAGTTTGTGACA
1 TGTGAGACGGCATGGTGAGAATATGTGACACGACTATGACA-GG-AAAGTTTAGAGTTTGTGACA
* * *
15191991 TGCCATGGTGGGAATCTGTGACACGGCATGGTCAGAAA-TTGTGACATGGCATGTTGA-AATCG
64 TGCCATGGTGGGAATATGTGACACGGCATGGTGA-AAATTTGTGACATGGCATTTTGAGAAT-G
* *
15192053 TGTGAGATGGCATGGTGAGAATCTGTGACAC
1 TGTGAGACGGCATGGTGAGAATATGTGACAC
15192084 AGCATAGTGA
Statistics
Matches: 231, Mismatches: 29, Indels: 36
0.78 0.10 0.12
Matches are distributed among these distances:
116 37 0.16
117 1 0.00
118 2 0.01
119 2 0.01
120 6 0.03
121 1 0.00
122 1 0.00
123 2 0.01
124 1 0.00
125 49 0.21
126 3 0.01
127 96 0.42
128 3 0.01
130 1 0.00
131 1 0.00
133 1 0.00
134 1 0.00
135 16 0.07
136 7 0.03
ACGTcount: A:0.29, C:0.12, G:0.32, T:0.27
Consensus pattern (125 bp):
TGTGAGACGGCATGGTGAGAATATGTGACACGACTATGACAGGAAAGTTTAGAGTTTGTGACATG
CCATGGTGGGAATATGTGACACGGCATGGTGAAAATTTGTGACATGGCATTTTGAGAATG
Found at i:15192036 original size:46 final size:45
Alignment explanation
Indices: 15191983--15192135 Score: 125
Period size: 46 Copynumber: 3.3 Consensus size: 45
15191973 AGTTTAGAGT
*
15191983 TTGTGACATGCCATGGTGGGAATC-TGTGACACGGCATGGTCAGAAA
1 TTGTGACATGCCAT-GTGGAAATCGTGTGACACGGCATGGTCAG-AA
* * * * *
15192029 TTGTGACATGGCATGTTGAAATCGTGTGAGATGGCATGGTGAGAA
1 TTGTGACATGCCATGTGGAAATCGTGTGACACGGCATGGTCAGAA
* * * *
15192074 TCTGTGACACAG-CATAGT-GAGATAGTGTGACACGGCATGG-CTTGAA
1 T-TGTGACA-TGCCAT-GTGGAAATCGTGTGACACGGCATGGTC-AGAA
15192120 TATGTGACATGCCATG
1 T-TGTGACATGCCATG
15192136 ACTTGAATAT
Statistics
Matches: 86, Mismatches: 15, Indels: 13
0.75 0.13 0.11
Matches are distributed among these distances:
45 12 0.14
46 71 0.83
47 3 0.03
ACGTcount: A:0.27, C:0.15, G:0.32, T:0.26
Consensus pattern (45 bp):
TTGTGACATGCCATGTGGAAATCGTGTGACACGGCATGGTCAGAA
Found at i:15192075 original size:69 final size:69
Alignment explanation
Indices: 15191984--15192135 Score: 182
Period size: 69 Copynumber: 2.2 Consensus size: 69
15191974 GTTTAGAGTT
* * * * *
15191984 TGTGACATGCCATGGTGGGAATCTGTGACACGGCATGGTCAGAAATTGTGACATGGCATGTTGAA
1 TGTGACATGCCATGGTGAGAATCTGTGACACAGCATAGTCAGAAAGTGTGACACGGCATGTTGAA
15192049 ATCG
66 ATCG
* * * *
15192053 TGTGAGATGGCATGGTGAGAATCTGTGACACAGCATAGTGAGATAGTGTGACACGGCATGGCTTG
1 TGTGACATGCCATGGTGAGAATCTGTGACACAGCATAGTCAGAAAGTGTGACACGGCAT-G-TTG
*
15192118 -AAT-A
64 AAATCG
15192122 TGTGACATGCCATG
1 TGTGACATGCCATG
15192136 ACTTGAATAT
Statistics
Matches: 69, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
69 62 0.90
70 4 0.06
71 3 0.04
ACGTcount: A:0.27, C:0.15, G:0.32, T:0.26
Consensus pattern (69 bp):
TGTGACATGCCATGGTGAGAATCTGTGACACAGCATAGTCAGAAAGTGTGACACGGCATGTTGAA
ATCG
Found at i:15192088 original size:23 final size:23
Alignment explanation
Indices: 15191984--15192113 Score: 113
Period size: 23 Copynumber: 5.7 Consensus size: 23
15191974 GTTTAGAGTT
* * *
15191984 TGTGACATGCCATGGTGGGAATC
1 TGTGACACGGCATGGTGAGAATC
*
15192007 TGTGACACGGCATGGTCAGAAAT-
1 TGTGACACGGCATGGTGAG-AATC
* *
15192030 TGTGACATGGCATGTTGA-AATC
1 TGTGACACGGCATGGTGAGAATC
* *
15192052 GTGTGAGATGGCATGGTGAGAATC
1 -TGTGACACGGCATGGTGAGAATC
* * *
15192076 TGTGACACAGCATAGTGAG-ATAG
1 TGTGACACGGCATGGTGAGAAT-C
15192099 TGTGACACGGCATGG
1 TGTGACACGGCATGG
15192114 CTTGAATATG
Statistics
Matches: 86, Mismatches: 16, Indels: 10
0.77 0.14 0.09
Matches are distributed among these distances:
21 3 0.03
22 2 0.02
23 74 0.86
24 7 0.08
ACGTcount: A:0.27, C:0.15, G:0.34, T:0.25
Consensus pattern (23 bp):
TGTGACACGGCATGGTGAGAATC
Found at i:15192125 original size:23 final size:23
Alignment explanation
Indices: 15192099--15192165 Score: 98
Period size: 23 Copynumber: 2.9 Consensus size: 23
15192089 AGTGAGATAG
*
15192099 TGTGACACGGCATGGCTTGAATA
1 TGTGACACGCCATGGCTTGAATA
* *
15192122 TGTGACATGCCATGACTTGAATA
1 TGTGACACGCCATGGCTTGAATA
*
15192145 TGTGACACGCCATGGCATGAA
1 TGTGACACGCCATGGCTTGAA
15192166 ATAGAAAAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.28, C:0.19, G:0.27, T:0.25
Consensus pattern (23 bp):
TGTGACACGCCATGGCTTGAATA
Found at i:15192799 original size:31 final size:30
Alignment explanation
Indices: 15192761--15192866 Score: 167
Period size: 31 Copynumber: 3.4 Consensus size: 30
15192751 AACGTTGGCG
15192761 TGTAACAACATTTGACTTGGTATGCATAGC
1 TGTAACAACATTTGACTTGGTATGCATAGC
*
15192791 ATGTAACAAAATTTGACTTGGTATGCATAGC
1 -TGTAACAACATTTGACTTGGTATGCATAGC
*
15192822 GTGTAACAACATTTTACTTGGTATGCATAGTC
1 -TGTAACAACATTTGACTTGGTATGCATAG-C
15192854 TGTAACAACATTT
1 TGTAACAACATTT
15192867 ATTTCTTTCT
Statistics
Matches: 70, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
31 69 0.99
32 1 0.01
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.35
Consensus pattern (30 bp):
TGTAACAACATTTGACTTGGTATGCATAGC
Found at i:15195602 original size:74 final size:73
Alignment explanation
Indices: 15195481--15195754 Score: 261
Period size: 74 Copynumber: 3.7 Consensus size: 73
15195471 CAGATTTGTG
* * ** *
15195481 AGACAGAGA-ATACTTAATCTACCAAGAAGCATGGTTAGTCAACTAAGAGCACACTGCTAGAAAT
1 AGACAGAGAGA-ACTTAATCAACTAAGAAGCACAGTTAGTCAACTAAGAGCACACTACTAGAAAT
15195545 CTCAATTACA
65 -TCAATTACA
* * * *
15195555 AGACAAAGAGAATTTAATCAACTAAGAAGCACAGTTAGTCAACTAAGAGCTCACTACCAGAAATT
1 AGACAGAGAGAACTTAATCAACTAAGAAGCACAGTTAGTCAACTAAGAGCACACTACTAGAAATT
15195620 GCAAATT-CA
66 -C-AATTACA
* * * * * * **
15195629 AGACAGAGAAAACTTAATCGATTAAGAAACACAGTTATTCAACTCAGAGCTGACTACTAGAAATT
1 AGACAGAGAGAACTTAATCAACTAAGAAGCACAGTTAGTCAACTAAGAGCACACTACTAGAAA--
*
15195694 TTGAATTA-A
64 TTCAATTACA
* *
15195703 AGACAGAGA-AGACTTAATCAA-TAAAGAAGCATAGTTATTCAACTAAGAGCAC
1 AGACAGAGAGA-ACTTAATCAACT-AAGAAGCACAGTTAGTCAACTAAGAGCAC
15195755 TTTGTTTGAA
Statistics
Matches: 166, Mismatches: 26, Indels: 16
0.80 0.12 0.08
Matches are distributed among these distances:
73 3 0.02
74 156 0.94
75 5 0.03
76 2 0.01
ACGTcount: A:0.45, C:0.18, G:0.16, T:0.22
Consensus pattern (73 bp):
AGACAGAGAGAACTTAATCAACTAAGAAGCACAGTTAGTCAACTAAGAGCACACTACTAGAAATT
CAATTACA
Found at i:15204460 original size:43 final size:42
Alignment explanation
Indices: 15204331--15204508 Score: 239
Period size: 42 Copynumber: 4.2 Consensus size: 42
15204321 TTTTGTGTGA
* * * * *
15204331 TGATGATGACCCAACTATGTGCGTGTGAGAGTGCACATGAGC
1 TGATGATGACCTAGCCATGTGCGAGTGGGAGTGCACATGAGC
*
15204373 TGATGATGACCTAGCCATGTGCGTGTGGGAGTGCACATGAGC
1 TGATGATGACCTAGCCATGTGCGAGTGGGAGTGCACATGAGC
15204415 TGATGATGACCTAGCCATGTGCGAGTGGGGAGTGCACATGAGC
1 TGATGATGACCTAGCCATGTGCGAGT-GGGAGTGCACATGAGC
* * * *
15204458 TGATGATGACCTAGCTATGTGCCAGTAGGGAATGTACATGAGC
1 TGATGATGACCTAGCCATGTGCGAGT-GGGAGTGCACATGAGC
*
15204501 TTATGATG
1 TGATGATG
15204509 GCAGGATGGT
Statistics
Matches: 124, Mismatches: 11, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
42 63 0.51
43 61 0.49
ACGTcount: A:0.25, C:0.17, G:0.33, T:0.25
Consensus pattern (42 bp):
TGATGATGACCTAGCCATGTGCGAGTGGGAGTGCACATGAGC
Found at i:15204478 original size:85 final size:85
Alignment explanation
Indices: 15204331--15204508 Score: 241
Period size: 85 Copynumber: 2.1 Consensus size: 85
15204321 TTTTGTGTGA
* * *
15204331 TGATGATGACCCAACTATGTGCGTGTGAGAGTGCACATGAGCTGATGATGACCTAGCCATGTGCG
1 TGATGATGACCCAACCATGTGCGAGTGAGAGTGCACATGAGCTGATGATGACCTAGCCATGTGCC
* *
15204396 TGT-GGGAGTGCACATGAGC
66 AGTAGGGAATGCACATGAGC
* * * *
15204415 TGATGATGACCTAGCCATGTGCGAGTGGGGAGTGCACATGAGCTGATGATGACCTAGCTATGTGC
1 TGATGATGACCCAACCATGTGCGAGT-GAGAGTGCACATGAGCTGATGATGACCTAGCCATGTGC
*
15204480 CAGTAGGGAATGTACATGAGC
65 CAGTAGGGAATGCACATGAGC
*
15204501 TTATGATG
1 TGATGATG
15204509 GCAGGATGGT
Statistics
Matches: 81, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
84 22 0.27
85 38 0.47
86 21 0.26
ACGTcount: A:0.25, C:0.17, G:0.33, T:0.25
Consensus pattern (85 bp):
TGATGATGACCCAACCATGTGCGAGTGAGAGTGCACATGAGCTGATGATGACCTAGCCATGTGCC
AGTAGGGAATGCACATGAGC
Found at i:15205032 original size:19 final size:19
Alignment explanation
Indices: 15205008--15205048 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
15204998 GGAGGTTTGG
15205008 TGAGAAACCCTCGGCCAGT
1 TGAGAAACCCTCGGCCAGT
15205027 TGAGAAACCCTCGGCCAGT
1 TGAGAAACCCTCGGCCAGT
15205046 TGA
1 TGA
15205049 TAATTTGAGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.27, C:0.29, G:0.27, T:0.17
Consensus pattern (19 bp):
TGAGAAACCCTCGGCCAGT
Found at i:15208831 original size:20 final size:20
Alignment explanation
Indices: 15208770--15208832 Score: 101
Period size: 20 Copynumber: 3.2 Consensus size: 20
15208760 TATATACCCA
15208770 TCATCATCATC-TCACCAAC
1 TCATCATCATCATCACCAAC
*
15208789 CCATCATCATCATCACCAAC
1 TCATCATCATCATCACCAAC
*
15208809 TCATCATCATCATCACCAGC
1 TCATCATCATCATCACCAAC
15208829 TCAT
1 TCAT
15208833 GCACACTCCC
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
19 10 0.25
20 30 0.75
ACGTcount: A:0.32, C:0.41, G:0.02, T:0.25
Consensus pattern (20 bp):
TCATCATCATCATCACCAAC
Found at i:15208883 original size:43 final size:43
Alignment explanation
Indices: 15208818--15208983 Score: 183
Period size: 43 Copynumber: 3.9 Consensus size: 43
15208808 CTCATCATCA
* * * * **
15208818 TCATCACCAGCTCATGCACACTCCCTACTCGCGCAT-GGCTAGG
1 TCATCACCAGGTTATGCGCACTCCCTACTCGCACATAATC-AGG
*
15208861 TCATCACCAGGTTATGCGCACTCCCTACTCGCACATAATCGGG
1 TCATCACCAGGTTATGCGCACTCCCTACTCGCACATAATCAGG
* * *
15208904 TCATCATCAGGTTATGAGCACTCCCTACTCGCACATAATCGGG
1 TCATCACCAGGTTATGCGCACTCCCTACTCGCACATAATCAGG
** *
15208947 TCATC-CTCAACTTATGCGTACTCCCTACTCGCACATA
1 TCATCAC-CAGGTTATGCGCACTCCCTACTCGCACATA
15208984 GCCGAGTCAA
Statistics
Matches: 107, Mismatches: 14, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
43 106 0.99
44 1 0.01
ACGTcount: A:0.23, C:0.36, G:0.16, T:0.25
Consensus pattern (43 bp):
TCATCACCAGGTTATGCGCACTCCCTACTCGCACATAATCAGG
Found at i:15211967 original size:28 final size:29
Alignment explanation
Indices: 15211927--15211991 Score: 89
Period size: 28 Copynumber: 2.3 Consensus size: 29
15211917 AGGCAGCTTT
* * *
15211927 AACATTTTTGTCTTAATTTAGAGAAGA-A
1 AACATATTTGTCTCAATTTAGACAAGATA
15211955 AACATATTTGTCTCAATTTAGACAAGATA
1 AACATATTTGTCTCAATTTAGACAAGATA
15211984 AA-ATATTT
1 AACATATTT
15211992 TTTTGTCTTA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
28 30 0.91
29 3 0.09
ACGTcount: A:0.42, C:0.09, G:0.11, T:0.38
Consensus pattern (29 bp):
AACATATTTGTCTCAATTTAGACAAGATA
Found at i:15219706 original size:27 final size:27
Alignment explanation
Indices: 15219676--15219732 Score: 71
Period size: 28 Copynumber: 2.1 Consensus size: 27
15219666 TCGGAGTAAA
*
15219676 AGGGCAAAAT-AGTAATTTTTTCACCCC
1 AGGGC-AAATCAGTAAATTTTTCACCCC
*
15219703 AGGGGCAAATCGGTAAATTTTTCACCCC
1 A-GGGCAAATCAGTAAATTTTTCACCCC
15219731 AG
1 AG
15219733 CACTTGTCAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
27 6 0.23
28 20 0.77
ACGTcount: A:0.32, C:0.23, G:0.19, T:0.26
Consensus pattern (27 bp):
AGGGCAAATCAGTAAATTTTTCACCCC
Found at i:15225195 original size:23 final size:23
Alignment explanation
Indices: 15225169--15225216 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
15225159 TACTAAGTCA
*
15225169 GATAAACATTGGAGCAAAACCAG
1 GATAAACATTGAAGCAAAACCAG
*
15225192 GATAAACGTTGAAGCAAAACCAG
1 GATAAACATTGAAGCAAAACCAG
15225215 GA
1 GA
15225217 GAACCAGGTA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.48, C:0.17, G:0.23, T:0.12
Consensus pattern (23 bp):
GATAAACATTGAAGCAAAACCAG
Found at i:15227106 original size:96 final size:95
Alignment explanation
Indices: 15226942--15227129 Score: 306
Period size: 96 Copynumber: 2.0 Consensus size: 95
15226932 ACTACACCAA
15226942 GCTCTTATCATCTTTGAGATATATGATGAGGGAATGAATTACATTGAAAAACTGTACACTAAAAG
1 GCTCTTATCATCTTTGAGATATATGATGAGGGAATGAATTACATTGAAAAACTGTACACTAAAAG
**
15227007 GTTGTCAAGGAATCCTTTGACTCTCCNTCAT
66 GTTGTCAAAAAATCCTTTGACTCTCC-TCAT
* * *
15227038 GCTCTTATCATCTCTTG-GTTATATGATGAGGGAATGAATTGCATTGATAAACTGTACACTAAAA
1 GCTCTTATCATCT-TTGAGATATATGATGAGGGAATGAATTACATTGAAAAACTGTACACTAAAA
15227102 GGTTGTCAAAAAATCCTTTGACTCTCCT
65 GGTTGTCAAAAAATCCTTTGACTCTCCT
15227130 AACAATTGGG
Statistics
Matches: 86, Mismatches: 5, Indels: 3
0.91 0.05 0.03
Matches are distributed among these distances:
95 1 0.01
96 82 0.95
97 3 0.03
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Consensus pattern (95 bp):
GCTCTTATCATCTTTGAGATATATGATGAGGGAATGAATTACATTGAAAAACTGTACACTAAAAG
GTTGTCAAAAAATCCTTTGACTCTCCTCAT
Found at i:15227845 original size:77 final size:77
Alignment explanation
Indices: 15227715--15227877 Score: 290
Period size: 77 Copynumber: 2.1 Consensus size: 77
15227705 GAGTGGCTGT
* **
15227715 AATTCTTTTACACCAAAGGTGTTCGTGTTTTGTCACCAAAAGGAATCGGTTTGATTATGATATCA
1 AATTCTTTTACACCAAAGGTGTTCGTGTTTTGTAACCAAAAGGAATCCATTTGATTATGATATCA
15227780 CTTGAAAAGGTA
66 CTTGAAAAGGTA
*
15227792 AATTCTTTTACACCAGAGGTGTTCGTGTTTTGTAACCAAAAGGAATCCATTTGATTATGATATCA
1 AATTCTTTTACACCAAAGGTGTTCGTGTTTTGTAACCAAAAGGAATCCATTTGATTATGATATCA
15227857 CTTGAAAAGGTA
66 CTTGAAAAGGTA
15227869 AATTCTTTT
1 AATTCTTTT
15227878 TCTGATTTTA
Statistics
Matches: 82, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
77 82 1.00
ACGTcount: A:0.31, C:0.14, G:0.18, T:0.37
Consensus pattern (77 bp):
AATTCTTTTACACCAAAGGTGTTCGTGTTTTGTAACCAAAAGGAATCCATTTGATTATGATATCA
CTTGAAAAGGTA
Found at i:15239204 original size:11 final size:11
Alignment explanation
Indices: 15239188--15239212 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
15239178 TTCTTATGTG
15239188 ATAAAATAATA
1 ATAAAATAATA
15239199 ATAAAATAATA
1 ATAAAATAATA
15239210 ATA
1 ATA
15239213 TCTTATTGAG
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:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (11 bp):
ATAAAATAATA
Found at i:15239331 original size:19 final size:19
Alignment explanation
Indices: 15239307--15239345 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
15239297 GCGAGAGAAA
15239307 AATTTTAGAATAAAATAAT
1 AATTTTAGAATAAAATAAT
* *
15239326 AATTTTTGGATAAAATAAT
1 AATTTTAGAATAAAATAAT
15239345 A
1 A
15239346 TTAAAATAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.54, C:0.00, G:0.08, T:0.38
Consensus pattern (19 bp):
AATTTTAGAATAAAATAAT
Found at i:15240089 original size:16 final size:16
Alignment explanation
Indices: 15240068--15240099 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
15240058 AAATGCATGA
15240068 AGCCTTATTGGTTTAT
1 AGCCTTATTGGTTTAT
15240084 AGCCTTATTGGTTTAT
1 AGCCTTATTGGTTTAT
15240100 GGGATGGCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.19, C:0.12, G:0.19, T:0.50
Consensus pattern (16 bp):
AGCCTTATTGGTTTAT
Found at i:15242060 original size:25 final size:25
Alignment explanation
Indices: 15242026--15242085 Score: 84
Period size: 25 Copynumber: 2.4 Consensus size: 25
15242016 TTTGTGATAT
* *
15242026 ATATACGTGGCAAGGCCACAGGTTG
1 ATATACGTGGCAAGGCCACAAGTCG
* *
15242051 ATATATGTGGCTAGGCCACAAGTCG
1 ATATACGTGGCAAGGCCACAAGTCG
15242076 ATATACGTGG
1 ATATACGTGG
15242086 TTGTGACCAC
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.28, C:0.18, G:0.30, T:0.23
Consensus pattern (25 bp):
ATATACGTGGCAAGGCCACAAGTCG
Found at i:15246183 original size:74 final size:74
Alignment explanation
Indices: 15246062--15246210 Score: 289
Period size: 74 Copynumber: 2.0 Consensus size: 74
15246052 AAGTATCGAT
15246062 ACATTCTTGAATGCATCAATAATTTTAATGCAGAATATGTTGTTTAATGGAATTTGATGAGAATT
1 ACATTCTTGAATGCATCAATAATTTTAATGCAGAATATGTTGTTTAATGGAATTTGATGAGAATT
15246127 TCAAAGTTA
66 TCAAAGTTA
*
15246136 ACATTCTTGAATGTATCAATAATTTTAATGCAGAATATGTTGTTTAATGGAATTTGATGAGAATT
1 ACATTCTTGAATGCATCAATAATTTTAATGCAGAATATGTTGTTTAATGGAATTTGATGAGAATT
15246201 TCAAAGTTA
66 TCAAAGTTA
15246210 A
1 A
15246211 AGGATTCTCA
Statistics
Matches: 74, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
74 74 1.00
ACGTcount: A:0.37, C:0.07, G:0.16, T:0.40
Consensus pattern (74 bp):
ACATTCTTGAATGCATCAATAATTTTAATGCAGAATATGTTGTTTAATGGAATTTGATGAGAATT
TCAAAGTTA
Found at i:15247739 original size:55 final size:55
Alignment explanation
Indices: 15247595--15247747 Score: 159
Period size: 55 Copynumber: 2.8 Consensus size: 55
15247585 CAGTCCTCAG
* * * *
15247595 CTCATGTGCCTTCCCACACCGTACATAGCTGGATAT-AGTCCA-CCACCAGTCATCAG
1 CTCATGTGCATTCCCACACCGCACATAGCTGGA-ATCA--CCACCCACCAGTCAACAA
* * * * *
15247651 CTCATGTGGACTCTCACACCGCACA-CGATTGGAATCACCACCCACCAGTCAACAA
1 CTCATGTGCATTCCCACACCGCACATAG-CTGGAATCACCACCCACCAGTCAACAA
*
15247706 CTCATGTGCATTCCCACACCGCACATAGCTGGAATCATCACC
1 CTCATGTGCATTCCCACACCGCACATAGCTGGAATCACCACC
15247748 GTCATTACCA
Statistics
Matches: 78, Mismatches: 15, Indels: 9
0.76 0.15 0.09
Matches are distributed among these distances:
54 3 0.04
55 49 0.63
56 26 0.33
ACGTcount: A:0.27, C:0.37, G:0.15, T:0.20
Consensus pattern (55 bp):
CTCATGTGCATTCCCACACCGCACATAGCTGGAATCACCACCCACCAGTCAACAA
Found at i:15250700 original size:60 final size:59
Alignment explanation
Indices: 15250588--15250701 Score: 165
Period size: 60 Copynumber: 1.9 Consensus size: 59
15250578 CAAAAAGTTT
* * * * *
15250588 TTCGCTGCAGCAAAATTTCTACCCAAAAACAGAATGTTTCTCGCTGTAGCGAGATTGAA
1 TTCGCTGCAGCAAAATTGCAACCCAAAAACAGAAAGTTTCTAGCTGCAGCGAGATTGAA
*
15250647 TTCGCTGCAGCGAAATTGCAACCCAGAAAACAGAAAGTTTCTAGCTGCAGCGAGA
1 TTCGCTGCAGCAAAATTGCAACCCA-AAAACAGAAAGTTTCTAGCTGCAGCGAGA
15250702 AGCTACAGTG
Statistics
Matches: 48, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
59 22 0.46
60 26 0.54
ACGTcount: A:0.33, C:0.23, G:0.21, T:0.23
Consensus pattern (59 bp):
TTCGCTGCAGCAAAATTGCAACCCAAAAACAGAAAGTTTCTAGCTGCAGCGAGATTGAA
Found at i:15252010 original size:19 final size:20
Alignment explanation
Indices: 15251976--15252013 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
15251966 GAAGAAGACC
15251976 AGCTGCTGGAAAATTCAAGA
1 AGCTGCTGGAAAATTCAAGA
15251996 AGCTGCTGG-AAATTCAAG
1 AGCTGCTGGAAAATTCAAG
15252014 GTATTTATGG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.37, C:0.16, G:0.26, T:0.21
Consensus pattern (20 bp):
AGCTGCTGGAAAATTCAAGA
Found at i:15257775 original size:39 final size:35
Alignment explanation
Indices: 15257594--15257800 Score: 190
Period size: 35 Copynumber: 5.9 Consensus size: 35
15257584 GTCCAATAAC
* ** *
15257594 TTAATTAAGCCCAACAATTTAATTAAACAATTTTAA
1 TTAATTAGGCCCAATGACTTAATTAAACAA-TTTAA
* * *
15257630 TCT-ACTAGGCCTAATGACTTAATTAAACAAATTCAA
1 T-TAATTAGGCCCAATGACTTAATTAAAC-AATTTAA
* * **** *
15257666 TCAATTAGGCCCAATAACTTAATTGTTTAATGTAA
1 TTAATTAGGCCCAATGACTTAATTAAACAATTTAA
15257701 TTAATTAGGCCCAATGACTTAATTAAACAATTTAA
1 TTAATTAGGCCCAATGACTTAATTAAACAATTTAA
**
15257736 TTAATTAGGCCCAATGA-TTCAATTAAACAATTTGG
1 TTAATTAGGCCCAATGACTT-AATTAAACAATTTAA
*
15257771 TTAATTAGGCAC-A--ACTTAATTAAACAATTT
1 TTAATTAGGCCCAATGACTTAATTAAACAATTT
15257801 TAATCAAGTG
Statistics
Matches: 139, Mismatches: 27, Indels: 14
0.77 0.15 0.08
Matches are distributed among these distances:
32 14 0.10
33 2 0.01
34 3 0.02
35 74 0.53
36 43 0.31
37 3 0.02
ACGTcount: A:0.42, C:0.15, G:0.09, T:0.35
Consensus pattern (35 bp):
TTAATTAGGCCCAATGACTTAATTAAACAATTTAA
Found at i:15261507 original size:39 final size:39
Alignment explanation
Indices: 15261414--15261593 Score: 158
Period size: 39 Copynumber: 4.7 Consensus size: 39
15261404 GATGGTGCCA
* * * *
15261414 GTAGTGTGCAGTGTGAGAGAGCACACGTTGATGATATAT
1 GTAGTGTGCGGTGTGGGAGAGCACATGATGATGATATAT
*
15261453 GCCA-TGTGCGGTGTGGGAGAGCACATGATGATGATATAT
1 G-TAGTGTGCGGTGTGGGAGAGCACATGATGATGATATAT
* * * * * *
15261492 GTCGTGTGCGGTGTGGAAGTGCACATGACGGTGATA-GT
1 GTAGTGTGCGGTGTGGGAGAGCACATGATGATGATATAT
*
15261530 G-AG-GTGCGGTGTGGGA-ATGCACCTGATGATGATAT-T
1 GTAGTGTGCGGTGTGGGAGA-GCACATGATGATGATATAT
* *
15261566 GTAATGTGCAGTGTGGGA-ATGCACATGA
1 GTAGTGTGCGGTGTGGGAGA-GCACATGA
15261594 GTCGGGGGAG
Statistics
Matches: 114, Mismatches: 21, Indels: 13
0.77 0.14 0.09
Matches are distributed among these distances:
36 27 0.24
37 2 0.02
38 23 0.20
39 61 0.54
40 1 0.01
ACGTcount: A:0.24, C:0.12, G:0.37, T:0.27
Consensus pattern (39 bp):
GTAGTGTGCGGTGTGGGAGAGCACATGATGATGATATAT
Found at i:15261551 original size:36 final size:37
Alignment explanation
Indices: 15261458--15261593 Score: 118
Period size: 38 Copynumber: 3.6 Consensus size: 37
15261448 TATATGCCAT
* *
15261458 GTGCGGTGTGGGAGA-GCACATGATGATGATATATGT-CG
1 GTGCGGTGTGGGA-ATGCACATGACGATG--ATATGTAAG
* *
15261496 TGTGCGGTGT-GGAAGTGCACATGACGGTGATA-GTGAG
1 -GTGCGGTGTGGGAA-TGCACATGACGATGATATGTAAG
* * *
15261533 GTGCGGTGTGGGAATGCACCTGATGATGATATTGTAAT
1 GTGCGGTGTGGGAATGCACATGACGATGATA-TGTAAG
*
15261571 GTGCAGTGTGGGAATGCACATGA
1 GTGCGGTGTGGGAATGCACATGA
15261594 GTCGGGGGAG
Statistics
Matches: 81, Mismatches: 10, Indels: 13
0.78 0.10 0.12
Matches are distributed among these distances:
36 25 0.31
37 9 0.11
38 27 0.33
39 20 0.25
ACGTcount: A:0.24, C:0.11, G:0.39, T:0.26
Consensus pattern (37 bp):
GTGCGGTGTGGGAATGCACATGACGATGATATGTAAG
Found at i:15265878 original size:15 final size:17
Alignment explanation
Indices: 15265838--15265880 Score: 54
Period size: 15 Copynumber: 2.6 Consensus size: 17
15265828 TTAGTTTCTA
15265838 TTAATTAATTTAGTGTT
1 TTAATTAATTTAGTGTT
**
15265855 TGCATTAATTTA-T-TT
1 TTAATTAATTTAGTGTT
15265870 TTAATTAATTT
1 TTAATTAATTT
15265881 TCTAAAACAA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
15 11 0.50
16 1 0.05
17 10 0.45
ACGTcount: A:0.30, C:0.02, G:0.07, T:0.60
Consensus pattern (17 bp):
TTAATTAATTTAGTGTT
Found at i:15269792 original size:15 final size:15
Alignment explanation
Indices: 15269774--15269818 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
15269764 TTTTATTTTC
*
15269774 TGTTAATTGATTTAA
1 TGTTAATTAATTTAA
15269789 TGTTTACATTAATTTAA
1 TG-TTA-ATTAATTTAA
*
15269806 TTTTAATTAATTT
1 TGTTAATTAATTT
15269819 TCTAAAACAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
15 10 0.38
16 6 0.23
17 10 0.38
ACGTcount: A:0.33, C:0.02, G:0.07, T:0.58
Consensus pattern (15 bp):
TGTTAATTAATTTAA
Found at i:15273366 original size:23 final size:22
Alignment explanation
Indices: 15273334--15273388 Score: 56
Period size: 22 Copynumber: 2.4 Consensus size: 22
15273324 TTTGGAGGGA
*
15273334 TTTTGGTGCTGAAAATTCAAGGT
1 TTTTGCTGCT-AAAATTCAAGGT
* *
15273357 TTTTGCTGCTAAATTTTAAGGT
1 TTTTGCTGCTAAAATTCAAGGT
15273379 TATGTTGCTG
1 T-T-TTGCTG
15273389 GAAATTTTTG
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
22 11 0.41
23 10 0.37
24 6 0.22
ACGTcount: A:0.22, C:0.09, G:0.24, T:0.45
Consensus pattern (22 bp):
TTTTGCTGCTAAAATTCAAGGT
Found at i:15273377 original size:22 final size:22
Alignment explanation
Indices: 15273334--15273396 Score: 56
Period size: 23 Copynumber: 2.8 Consensus size: 22
15273324 TTTGGAGGGA
* * *
15273334 TTTTGGTGCTGAAAATTCAAGGT
1 TTTTGCTGCT-AAATTTTAAGGT
15273357 TTTTGCTGCTAAATTTTAAGGT
1 TTTTGCTGCTAAATTTTAAGGT
*
15273379 TATGTTGCTG-GAAATTTT
1 T-T-TTGCTGCTAAATTTT
15273397 TGGAGATTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
22 11 0.32
23 17 0.50
24 6 0.18
ACGTcount: A:0.24, C:0.08, G:0.22, T:0.46
Consensus pattern (22 bp):
TTTTGCTGCTAAATTTTAAGGT
Found at i:15282738 original size:122 final size:122
Alignment explanation
Indices: 15282543--15282789 Score: 451
Period size: 122 Copynumber: 2.0 Consensus size: 122
15282533 AATGTATGGA
* *
15282543 AAGGTGTGAGAATGCACTAGTTTGACTATTTATAAAAGTTCGAACTTGGATGGTTATCAATGGCT
1 AAGGTGTGAGAAGGCACTAGTTTGACTATTTATAAAAGTTCGAACTTGGATGGTCATCAATGGCT
15282608 GGTGAGTAACCAAACAATGTGTAAGCAAATGAACAAAGGGAGTTACGATTGGTAGGT
66 GGTGAGTAACCAAACAATGTGTAAGCAAATGAACAAAGGGAGTTACGATTGGTAGGT
15282665 AAGGTGTGA-AAGGGCACTAGTTTGACTATTTATAAAAGTTCGAACTTGGATGGTCATCAATGGC
1 AAGGTGTGAGAA-GGCACTAGTTTGACTATTTATAAAAGTTCGAACTTGGATGGTCATCAATGGC
*
15282729 TGGTGAGTAACCAAACAATGTGTAAGTAAATGAACAAAGGGAGTTACGATTGGTAGGT
65 TGGTGAGTAACCAAACAATGTGTAAGCAAATGAACAAAGGGAGTTACGATTGGTAGGT
15282787 AAG
1 AAG
15282790 AGTGGAACTC
Statistics
Matches: 121, Mismatches: 3, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
121 2 0.02
122 119 0.98
ACGTcount: A:0.35, C:0.11, G:0.28, T:0.27
Consensus pattern (122 bp):
AAGGTGTGAGAAGGCACTAGTTTGACTATTTATAAAAGTTCGAACTTGGATGGTCATCAATGGCT
GGTGAGTAACCAAACAATGTGTAAGCAAATGAACAAAGGGAGTTACGATTGGTAGGT
Found at i:15285490 original size:24 final size:25
Alignment explanation
Indices: 15285450--15285496 Score: 62
Period size: 24 Copynumber: 1.9 Consensus size: 25
15285440 TTTGTACAAG
15285450 AAAATTGGATAGCTTTG-TGCTGCC
1 AAAATTGGATAGCTTTGTTGCTGCC
*
15285474 AAAATTGAGA-AGTTTTGTTGCTG
1 AAAATTG-GATAGCTTTGTTGCTG
15285497 GAAATTTGAG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 13 0.65
25 7 0.35
ACGTcount: A:0.28, C:0.11, G:0.26, T:0.36
Consensus pattern (25 bp):
AAAATTGGATAGCTTTGTTGCTGCC
Found at i:15285619 original size:22 final size:22
Alignment explanation
Indices: 15285591--15285640 Score: 82
Period size: 22 Copynumber: 2.3 Consensus size: 22
15285581 TTGAGAGGAA
*
15285591 GTGAAGAGAGAAAGCCACGGTG
1 GTGAAGACAGAAAGCCACGGTG
*
15285613 GTGAAGACAGGAAGCCACGGTG
1 GTGAAGACAGAAAGCCACGGTG
15285635 GTGAAG
1 GTGAAG
15285641 GGAGTGACGG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.34, C:0.14, G:0.42, T:0.10
Consensus pattern (22 bp):
GTGAAGACAGAAAGCCACGGTG
Found at i:15285695 original size:25 final size:23
Alignment explanation
Indices: 15285653--15285698 Score: 65
Period size: 25 Copynumber: 1.9 Consensus size: 23
15285643 AGTGACGGGC
15285653 TGGAAAGAAAAAAAAAAGAAACG
1 TGGAAAGAAAAAAAAAAGAAACG
*
15285676 TGGAAGAGAGAAAAAGAAAGAAA
1 TGGAA-AGA-AAAAAAAAAGAAA
15285699 AAGAAAAGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 5 0.25
24 3 0.15
25 12 0.60
ACGTcount: A:0.67, C:0.02, G:0.26, T:0.04
Consensus pattern (23 bp):
TGGAAAGAAAAAAAAAAGAAACG
Found at i:15285705 original size:16 final size:17
Alignment explanation
Indices: 15285684--15285721 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
15285674 CGTGGAAGAG
15285684 AGAAAAAG-AAAGAAAA
1 AGAAAAAGAAAAGAAAA
*
15285700 AG-AAAAGAAAAGAAAT
1 AGAAAAAGAAAAGAAAA
15285716 AGAAAA
1 AGAAAA
15285722 TAAGTGGGCA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
15 5 0.26
16 11 0.58
17 3 0.16
ACGTcount: A:0.79, C:0.00, G:0.18, T:0.03
Consensus pattern (17 bp):
AGAAAAAGAAAAGAAAA
Found at i:15285761 original size:31 final size:32
Alignment explanation
Indices: 15285718--15285778 Score: 81
Period size: 31 Copynumber: 1.9 Consensus size: 32
15285708 AAAGAAATAG
*
15285718 AAAATAAGTGGGCATGGCCC-AATAGGAAACA
1 AAAATAAGTGGGCATAGCCCAAATAGGAAACA
*
15285749 AAAATGAA-TGGGCTTAGCCCAAATAGGAAA
1 AAAAT-AAGTGGGCATAGCCCAAATAGGAAA
15285779 AATAGAAAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
31 15 0.58
32 11 0.42
ACGTcount: A:0.46, C:0.15, G:0.25, T:0.15
Consensus pattern (32 bp):
AAAATAAGTGGGCATAGCCCAAATAGGAAACA
Found at i:15289225 original size:22 final size:22
Alignment explanation
Indices: 15289197--15289251 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
15289187 TTCAGTAACT
**
15289197 TTCTCGCTACAGTGAAAATACA
1 TTCTCGCTACAGCAAAAATACA
*
15289219 TTCTCGCTGCAGCAAAAATACA
1 TTCTCGCTACAGCAAAAATACA
*
15289241 TTATCGCTACA
1 TTCTCGCTACA
15289252 ACAAGATTCA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.35, C:0.25, G:0.13, T:0.27
Consensus pattern (22 bp):
TTCTCGCTACAGCAAAAATACA
Found at i:15289694 original size:42 final size:42
Alignment explanation
Indices: 15289569--15289724 Score: 186
Period size: 42 Copynumber: 3.7 Consensus size: 42
15289559 TAGCTCATGT
* **
15289569 GCACTCCCTACTCACAAATAGCTAGGTCAGCATCGGCTTATGC
1 GCACT-CCTACTCACACATAGCCGGGTCAGCATCGGCTTATGC
* * **
15289612 GCACTCTCTACTCGCACATAGCCGGGTCAACATCAACTTATGC
1 GCACTC-CTACTCACACATAGCCGGGTCAGCATCGGCTTATGC
* * * *
15289655 TCACTCCCACTCTCACATAGTCGGGTCAGCATCGGCTTATGC
1 GCACTCCTACTCACACATAGCCGGGTCAGCATCGGCTTATGC
*
15289697 GCACTTCTACTCACACATAGCCGGGTCA
1 GCACTCCTACTCACACATAGCCGGGTCA
15289725 ATATCATCAC
Statistics
Matches: 93, Mismatches: 19, Indels: 3
0.81 0.17 0.03
Matches are distributed among these distances:
42 54 0.58
43 39 0.42
ACGTcount: A:0.24, C:0.35, G:0.18, T:0.24
Consensus pattern (42 bp):
GCACTCCTACTCACACATAGCCGGGTCAGCATCGGCTTATGC
Found at i:15291252 original size:22 final size:21
Alignment explanation
Indices: 15291212--15291252 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
15291202 TTAGAGGTAC
* *
15291212 TCTAGCTAATCTTGTAAAGGT
1 TCTAGCTAACCTTGAAAAGGT
15291233 TCTAGCTTAACCTTGAAAAG
1 TCTAGC-TAACCTTGAAAAG
15291253 TTAATGTAGG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 6 0.35
22 11 0.65
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Consensus pattern (21 bp):
TCTAGCTAACCTTGAAAAGGT
Found at i:15295343 original size:39 final size:40
Alignment explanation
Indices: 15295289--15295368 Score: 117
Period size: 40 Copynumber: 2.0 Consensus size: 40
15295279 CACTGTAGCA
* * *
15295289 AAATTGTAACCCAG-AAACAGAATGTTTCTCGCTGCAGCG
1 AAATTGCAACCCAGAAAACAAAAAGTTTCTCGCTGCAGCG
*
15295328 AAATTGCAATCCAGAAAACAAAAAGTTTCTCGCTGCAGCG
1 AAATTGCAACCCAGAAAACAAAAAGTTTCTCGCTGCAGCG
15295368 A
1 A
15295369 GAATGCATTT
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
39 12 0.33
40 24 0.67
ACGTcount: A:0.38, C:0.23, G:0.19, T:0.21
Consensus pattern (40 bp):
AAATTGCAACCCAGAAAACAAAAAGTTTCTCGCTGCAGCG
Found at i:15295731 original size:2 final size:2
Alignment explanation
Indices: 15295689--15295723 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
15295679 ACATACTTAC
15295689 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
15295724 CTTATATACC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:15295825 original size:43 final size:43
Alignment explanation
Indices: 15295775--15295887 Score: 140
Period size: 43 Copynumber: 2.6 Consensus size: 43
15295765 CATCAACAGC
* **
15295775 TCATGCGCACTCCTTACTCGCACAT-GGCTGGGTCATCAC-CGGG
1 TCATGCGCACTCCCTACTCGCACATAATC-GGGTCATC-CTCGGG
*
15295818 TTATGCGCACTCCCTACTCGCACATAATCGGGTCATCCTCGGG
1 TCATGCGCACTCCCTACTCGCACATAATCGGGTCATCCTCGGG
* *
15295861 TCATGCGCACTCCCTACGCACACATAA
1 TCATGCGCACTCCCTACTCGCACATAA
15295888 CCGAGTCCAT
Statistics
Matches: 61, Mismatches: 7, Indels: 4
0.85 0.10 0.06
Matches are distributed among these distances:
42 1 0.02
43 59 0.97
44 1 0.02
ACGTcount: A:0.20, C:0.36, G:0.20, T:0.23
Consensus pattern (43 bp):
TCATGCGCACTCCCTACTCGCACATAATCGGGTCATCCTCGGG
Found at i:15300654 original size:19 final size:19
Alignment explanation
Indices: 15300632--15300670 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
15300622 AATAAGAAGC
15300632 TGCTAGAAATTCAAAAAGT
1 TGCTAGAAATTCAAAAAGT
*
15300651 TGCTAGAAATTCAAGAAGT
1 TGCTAGAAATTCAAAAAGT
15300670 T
1 T
15300671 ACTGGAAGGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.44, C:0.10, G:0.18, T:0.28
Consensus pattern (19 bp):
TGCTAGAAATTCAAAAAGT
Found at i:15308382 original size:19 final size:18
Alignment explanation
Indices: 15308345--15308383 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
15308335 ATTTACTTTG
* *
15308345 TTTTTGTTTTATTTTCAT
1 TTTTTCTTTTATTTGCAT
15308363 TTTTTCTTTTATCTTGCAT
1 TTTTTCTTTTAT-TTGCAT
15308382 TT
1 TT
15308384 GTCTACACTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.10, C:0.10, G:0.05, T:0.74
Consensus pattern (18 bp):
TTTTTCTTTTATTTGCAT
Found at i:15323749 original size:26 final size:26
Alignment explanation
Indices: 15323689--15323750 Score: 97
Period size: 26 Copynumber: 2.4 Consensus size: 26
15323679 ACCATATACC
*
15323689 CATCATCAACATGCACACCATCCCAT
1 CATCATCATCATGCACACCATCCCAT
*
15323715 CATCATCATCATGCACATCATCCCAT
1 CATCATCATCATGCACACCATCCCAT
*
15323741 TATCATCATC
1 CATCATCATC
15323751 TCATATGCAA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.32, C:0.39, G:0.03, T:0.26
Consensus pattern (26 bp):
CATCATCATCATGCACACCATCCCAT
Found at i:15324043 original size:42 final size:42
Alignment explanation
Indices: 15323985--15324107 Score: 210
Period size: 42 Copynumber: 2.9 Consensus size: 42
15323975 ATGGGGGCAA
* *
15323985 CAACGGCTTATGTGCACTCCCACTCACACATAGCCGGGTCAG
1 CAACGGCTTATGTGCACTCCTACTCGCACATAGCCGGGTCAG
* *
15324027 CAACGGCTTATATGCACTCCTACTCGCACATAGTCGGGTCAG
1 CAACGGCTTATGTGCACTCCTACTCGCACATAGCCGGGTCAG
15324069 CAACGGCTTATGTGCACTCCTACTCGCACATAGCCGGGT
1 CAACGGCTTATGTGCACTCCTACTCGCACATAGCCGGGT
15324108 TCAAATCAAC
Statistics
Matches: 75, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 75 1.00
ACGTcount: A:0.23, C:0.33, G:0.22, T:0.22
Consensus pattern (42 bp):
CAACGGCTTATGTGCACTCCTACTCGCACATAGCCGGGTCAG
Found at i:15332146 original size:28 final size:28
Alignment explanation
Indices: 15332115--15332191 Score: 118
Period size: 28 Copynumber: 2.8 Consensus size: 28
15332105 TTTTCGAGGG
15332115 TAGGGGCAAAATAGTCATTTTGCCAACC
1 TAGGGGCAAAATAGTCATTTTGCCAACC
*
15332143 TAGGGGCAAAATAGTCATTTTGCCACCC
1 TAGGGGCAAAATAGTCATTTTGCCAACC
* * *
15332171 CAGGGGCAAAATGGTAATTTT
1 TAGGGGCAAAATAGTCATTTT
15332192 ACACACCCAA
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 45 1.00
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.26
Consensus pattern (28 bp):
TAGGGGCAAAATAGTCATTTTGCCAACC
Found at i:15332200 original size:28 final size:27
Alignment explanation
Indices: 15332116--15332200 Score: 107
Period size: 28 Copynumber: 3.0 Consensus size: 27
15332106 TTTCGAGGGT
*
15332116 AGGGGCAAAATAGTCATTTTGCCAACCT
1 AGGGGCAAAATAGTCATTTTGCC-ACCC
15332144 AGGGGCAAAATAGTCATTTTGCCACCCC
1 AGGGGCAAAATAGTCATTTTGCCA-CCC
* * *
15332172 AGGGGCAAAATGGTAATTTTACACACCC
1 AGGGGCAAAATAGTCATTTTGC-CACCC
15332200 A
1 A
15332201 ACACTTGTCA
Statistics
Matches: 51, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
27 1 0.02
28 48 0.94
29 2 0.04
ACGTcount: A:0.33, C:0.24, G:0.21, T:0.22
Consensus pattern (27 bp):
AGGGGCAAAATAGTCATTTTGCCACCC
Found at i:15337772 original size:13 final size:15
Alignment explanation
Indices: 15337741--15337773 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
15337731 TAAACCACTT
15337741 TATAT-TTCTGCATA
1 TATATATTCTGCATA
*
15337755 TATATATTCTGAATA
1 TATATATTCTGCATA
15337770 TATA
1 TATA
15337774 GTGACATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 5 0.29
15 12 0.71
ACGTcount: A:0.36, C:0.09, G:0.06, T:0.48
Consensus pattern (15 bp):
TATATATTCTGCATA
Found at i:15347496 original size:54 final size:54
Alignment explanation
Indices: 15347414--15347530 Score: 225
Period size: 54 Copynumber: 2.2 Consensus size: 54
15347404 TGTGCTCATC
*
15347414 ACCTCTTCGTCTTCCTTAACTATAACTATGTCCATGACCTTGACCTCGACCTTG
1 ACCTCTTCCTCTTCCTTAACTATAACTATGTCCATGACCTTGACCTCGACCTTG
15347468 ACCTCTTCCTCTTCCTTAACTATAACTATGTCCATGACCTTGACCTCGACCTTG
1 ACCTCTTCCTCTTCCTTAACTATAACTATGTCCATGACCTTGACCTCGACCTTG
15347522 ACCTCTTCC
1 ACCTCTTCC
15347531 ACATCCTTGA
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 62 1.00
ACGTcount: A:0.20, C:0.36, G:0.09, T:0.35
Consensus pattern (54 bp):
ACCTCTTCCTCTTCCTTAACTATAACTATGTCCATGACCTTGACCTCGACCTTG
Found at i:15354644 original size:22 final size:22
Alignment explanation
Indices: 15354619--15354686 Score: 54
Period size: 22 Copynumber: 3.2 Consensus size: 22
15354609 TTCTTCTTAC
15354619 TAAGCACATTCTCATGCCATTA
1 TAAGCACATTCTCATGCCATTA
* * **
15354641 TAAGGTATAAAC-CAT--C-TTA
1 TAA-GCACATTCTCATGCCATTA
15354660 CTAAGCACATTCTCATGCCATTA
1 -TAAGCACATTCTCATGCCATTA
15354683 TAAG
1 TAAG
15354687 GTATAAACCA
Statistics
Matches: 32, Mismatches: 8, Indels: 12
0.62 0.15 0.23
Matches are distributed among these distances:
19 7 0.22
20 7 0.22
22 11 0.34
23 7 0.22
ACGTcount: A:0.35, C:0.24, G:0.10, T:0.31
Consensus pattern (22 bp):
TAAGCACATTCTCATGCCATTA
Found at i:15354672 original size:42 final size:42
Alignment explanation
Indices: 15354613--15354697 Score: 170
Period size: 42 Copynumber: 2.0 Consensus size: 42
15354603 GCTCAATTCT
15354613 TCTTACTAAGCACATTCTCATGCCATTATAAGGTATAAACCA
1 TCTTACTAAGCACATTCTCATGCCATTATAAGGTATAAACCA
15354655 TCTTACTAAGCACATTCTCATGCCATTATAAGGTATAAACCA
1 TCTTACTAAGCACATTCTCATGCCATTATAAGGTATAAACCA
15354697 T
1 T
15354698 AAACATTACT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.35, C:0.24, G:0.09, T:0.32
Consensus pattern (42 bp):
TCTTACTAAGCACATTCTCATGCCATTATAAGGTATAAACCA
Found at i:15354840 original size:31 final size:31
Alignment explanation
Indices: 15354804--15354873 Score: 79
Period size: 31 Copynumber: 2.3 Consensus size: 31
15354794 ACCCCCATCA
*
15354804 ACCTTGGGCTAGCAATGTACATCCCCATTGC
1 ACCTTGGGCTAGCAACGTACATCCCCATTGC
* * * *
15354835 ACCTTGGGTTGGCAACGTATATCCCTATTGC
1 ACCTTGGGCTAGCAACGTACATCCCCATTGC
*
15354866 -CATTGGGC
1 ACCTTGGGC
15354874 ATTTTTTGAT
Statistics
Matches: 32, Mismatches: 7, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
30 6 0.19
31 26 0.81
ACGTcount: A:0.20, C:0.29, G:0.23, T:0.29
Consensus pattern (31 bp):
ACCTTGGGCTAGCAACGTACATCCCCATTGC
Found at i:15355265 original size:136 final size:135
Alignment explanation
Indices: 15354991--15355326 Score: 380
Period size: 136 Copynumber: 2.5 Consensus size: 135
15354981 CCTTCACATA
* * *
15354991 CATACTTACTTATCTCATAAGGTATATGCAATTTACATCATATACATAATCTCATGGCATT-T-A
1 CATACTTAATCATCTCATATGGTATATGCAATTTACATCATATACATAATCTCATGGCATTATCA
* * * * *
15355054 TGCTTGCTCAATCATCTCATGGAGTATATGGAACATTCATCATATACATATTCTCATAGTATTAA
66 TGCATACTCAATCACCTCATGGAGTATATGGAACATTCATCATATACACATCCTCATAGTATTAA
15355119 TCATG
131 TCATG
* * * *
15355124 CATACTTAATCATCTCATGTGGTATATGGAATATACATCATATACATATTCTCATGGCATTAATC
1 CATACTTAATCATCTCATATGGTATATGCAATTTACATCATATACATAATCTCATGGCATT-ATC
* * * *
15355189 ATGCATATTTAATCGCCTCATATG-GTATAT-GAA-ATTTACATCATATACACCATCCT-ATAGT
65 ATGCATACTCAATCACCTCAT-GGAGTATATGGAACA-TT-CATCATATACA-CATCCTCATAGT
15355250 A-TACATCATG
126 ATTA-ATCATG
* * * *
15355260 CATACTTGATCATCTCATATGGCATATGCAATTTACATTATATACATAATCTTATGGCATTTATC
1 CATACTTAATCATCTCATATGGTATATGCAATTTACATCATATACATAATCTCATGGCA-TTATC
15355325 AT
65 AT
15355327 ACCAACATGT
Statistics
Matches: 170, Mismatches: 24, Indels: 15
0.81 0.11 0.07
Matches are distributed among these distances:
133 54 0.32
134 1 0.01
135 8 0.05
136 100 0.59
137 7 0.04
ACGTcount: A:0.34, C:0.19, G:0.10, T:0.38
Consensus pattern (135 bp):
CATACTTAATCATCTCATATGGTATATGCAATTTACATCATATACATAATCTCATGGCATTATCA
TGCATACTCAATCACCTCATGGAGTATATGGAACATTCATCATATACACATCCTCATAGTATTAA
TCATG
Found at i:15355326 original size:68 final size:68
Alignment explanation
Indices: 15354991--15355326 Score: 326
Period size: 68 Copynumber: 5.0 Consensus size: 68
15354981 CCTTCACATA
* * *
15354991 CATACTTACTTATCTCATAAGGTATATGCAATTTACATCATATACATAATCTCATGGCATT--T-
1 CATACTTAATCATCTCATATGGTATATGCAATTTACATCATATACATAATCTCATGGCATTAATC
15355053 ATG
66 ATG
* * * * * * * * *
15355056 CTTGCTCAATCATCTCAT-GGAGTATATGGAACATT-CATCATATACATATTCTCATAGTATTAA
1 CATACTTAATCATCTCATATG-GTATATGCAA-TTTACATCATATACATAATCTCATGGCATTAA
15355119 TCATG
64 TCATG
* * * *
15355124 CATACTTAATCATCTCATGTGGTATATGGAATATACATCATATACATATTCTCATGGCATTAATC
1 CATACTTAATCATCTCATATGGTATATGCAATTTACATCATATACATAATCTCATGGCATTAATC
15355189 ATG
66 ATG
* ** * ** * *
15355192 CATATTTAATCGCCTCATATGGTATATGAAATTTACATCATATACACCATC-CTATAGTA-TACA
1 CATACTTAATCATCTCATATGGTATATGCAATTTACATCATATACATAATCTC-ATGGCATTA-A
15355255 TCATG
64 TCATG
* * * * *
15355260 CATACTTGATCATCTCATATGGCATATGCAATTTACATTATATACATAATCTTATGGCATTTATC
1 CATACTTAATCATCTCATATGGTATATGCAATTTACATCATATACATAATCTCATGGCATTAATC
15355325 AT
66 AT
15355327 ACCAACATGT
Statistics
Matches: 217, Mismatches: 43, Indels: 19
0.78 0.15 0.07
Matches are distributed among these distances:
64 1 0.00
65 45 0.21
66 2 0.01
67 5 0.02
68 162 0.75
69 2 0.01
ACGTcount: A:0.34, C:0.19, G:0.10, T:0.38
Consensus pattern (68 bp):
CATACTTAATCATCTCATATGGTATATGCAATTTACATCATATACATAATCTCATGGCATTAATC
ATG
Found at i:15358108 original size:54 final size:54
Alignment explanation
Indices: 15358024--15358183 Score: 232
Period size: 54 Copynumber: 3.0 Consensus size: 54
15358014 AGCAATCATT
*
15358024 CCATCTCACCCAGCTCATGTGCATCCCACCACATCAGGCACATAGCCAAACATC
1 CCATCTCACCCAGCTCATGTGCATCCCACCACATCAGGCACATAGCCGAACATC
* * * *
15358078 CTATCTCACCTAGCTCATGTGCATCCCACCACATC-GTGCAAATAGTCGAACATC
1 CCATCTCACCCAGCTCATGTGCATCCCACCACATCAG-GCACATAGCCGAACATC
* * *
15358132 CCATCTCACCCAGCTCATGTGTATCTCACCACATCATGCACATAGCCGAACA
1 CCATCTCACCCAGCTCATGTGCATCCCACCACATCAGGCACATAGCCGAACA
15358184 GTATCACCAT
Statistics
Matches: 92, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
53 1 0.01
54 91 0.99
ACGTcount: A:0.29, C:0.39, G:0.12, T:0.21
Consensus pattern (54 bp):
CCATCTCACCCAGCTCATGTGCATCCCACCACATCAGGCACATAGCCGAACATC
Found at i:15358301 original size:2 final size:2
Alignment explanation
Indices: 15358289--15358323 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
15358279 TATGAAATAG
*
15358289 TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
15358324 CAACATCATA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:15364386 original size:2 final size:2
Alignment explanation
Indices: 15364374--15364456 Score: 112
Period size: 2 Copynumber: 41.0 Consensus size: 2
15364364 CTATCAATAC
* * * * *
15364374 AT AT CAT AT AT AT AT TT AG AT AT AT AT AT AT TT AG AT AT AT AG
1 AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
15364417 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
15364457 CAACATAACA
Statistics
Matches: 70, Mismatches: 10, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
2 68 0.97
3 2 0.03
ACGTcount: A:0.47, C:0.01, G:0.04, T:0.48
Consensus pattern (2 bp):
AT
Found at i:15385263 original size:33 final size:32
Alignment explanation
Indices: 15385221--15385335 Score: 104
Period size: 33 Copynumber: 3.4 Consensus size: 32
15385211 GAAATGAGCT
15385221 TTTTATGGGATCAAGCGAAACCTTCACAATGCA
1 TTTTATGGGATCAAGCGAAACCTTCACAATG-A
* * * *
15385254 TTTTATGGGATGAAGCAAAACCTTTACAATGG
1 TTTTATGGGATCAAGCGAAACCTTCACAATGA
* * * *
15385286 TTTTCACGAGATGAAGCGAAACCTTTCAACAATGGT
1 TTTT-ATGGGATCAAGCGAAACC-TTC-ACAAT-GA
*
15385322 TTTTATGGGCTCAA
1 TTTTATGGGATCAA
15385336 CCACAAACCC
Statistics
Matches: 65, Mismatches: 13, Indels: 6
0.77 0.15 0.07
Matches are distributed among these distances:
32 4 0.06
33 43 0.66
34 2 0.03
35 11 0.17
36 5 0.08
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.30
Consensus pattern (32 bp):
TTTTATGGGATCAAGCGAAACCTTCACAATGA
Found at i:15386860 original size:21 final size:20
Alignment explanation
Indices: 15386814--15386866 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
15386804 TCATGAAGAC
* *
15386814 ATGAAGCCATAGTGACCCTG
1 ATGAAGCCATAGTAACCCTA
*
15386834 ATGAAGCCATAGTCAACCTTA
1 ATGAAGCCATAGT-AACCCTA
15386855 ATGAAG-CATAGT
1 ATGAAGCCATAGT
15386867 TGACCCAAAG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 19 0.66
21 10 0.34
ACGTcount: A:0.36, C:0.21, G:0.21, T:0.23
Consensus pattern (20 bp):
ATGAAGCCATAGTAACCCTA
Found at i:15390002 original size:35 final size:34
Alignment explanation
Indices: 15389897--15390002 Score: 131
Period size: 35 Copynumber: 3.1 Consensus size: 34
15389887 GGAAGTGTGG
*
15389897 ATGATGATATTGCTTGTGCGAGTAAGAAGTGCAC
1 ATGATGATATTGCTTGTGCGAGTAAGGAGTGCAC
* ** *
15389931 ACGATGATATTGAAATGTGCGAGTAGGGAGTGCAC
1 ATGATGATATTG-CTTGTGCGAGTAAGGAGTGCAC
* *
15389966 ATGATGATATTGCCTTGTGCGTGTACGGAGTGCAC
1 ATGATGATATTG-CTTGTGCGAGTAAGGAGTGCAC
15390001 AT
1 AT
15390003 TGGCTAAGTG
Statistics
Matches: 60, Mismatches: 11, Indels: 1
0.83 0.15 0.01
Matches are distributed among these distances:
34 11 0.18
35 49 0.82
ACGTcount: A:0.27, C:0.13, G:0.31, T:0.28
Consensus pattern (34 bp):
ATGATGATATTGCTTGTGCGAGTAAGGAGTGCAC
Found at i:15396275 original size:91 final size:92
Alignment explanation
Indices: 15396165--15396332 Score: 268
Period size: 91 Copynumber: 1.8 Consensus size: 92
15396155 TTGTACTTGT
*
15396165 AAGGAAATGTCCTTTTTTCAAACAATGTAATGGCT-CGTGGTAGAATAATTGTAAAATCTCATAA
1 AAGGAAATGTCCTTATTTCAAACAATGTAATGGCTAC-TGGTAGAATAATTGTAAAATCTCATAA
15396229 ACTCTTTAGAGGGAAAGACCCTTTAGGA
65 ACTCTTTAGAGGGAAAGACCCTTTAGGA
* * *
15396257 AAGG-AATGTCCTTATTTCAAGCATTGTAATGGCTACTGGTAGAATAATTGTAAAATCTCGTAAA
1 AAGGAAATGTCCTTATTTCAAACAATGTAATGGCTACTGGTAGAATAATTGTAAAATCTCATAAA
*
15396321 CTCTTTATAGGG
66 CTCTTTAGAGGG
15396333 GGTGAGCAGT
Statistics
Matches: 70, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
91 65 0.93
92 5 0.07
ACGTcount: A:0.35, C:0.14, G:0.20, T:0.32
Consensus pattern (92 bp):
AAGGAAATGTCCTTATTTCAAACAATGTAATGGCTACTGGTAGAATAATTGTAAAATCTCATAAA
CTCTTTAGAGGGAAAGACCCTTTAGGA
Found at i:15405038 original size:25 final size:25
Alignment explanation
Indices: 15405010--15405069 Score: 84
Period size: 25 Copynumber: 2.4 Consensus size: 25
15405000 GTGGTCACAA
* * *
15405010 CCACATATATCAACTTGTGGCCTTG
1 CCACGTATAACAACCTGTGGCCTTG
*
15405035 CCACGTATAACAACCTGTGGCTTTG
1 CCACGTATAACAACCTGTGGCCTTG
15405060 CCACGTATAA
1 CCACGTATAA
15405070 TCACAGACCA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.27, C:0.28, G:0.17, T:0.28
Consensus pattern (25 bp):
CCACGTATAACAACCTGTGGCCTTG
Found at i:15410188 original size:2 final size:2
Alignment explanation
Indices: 15410173--15410217 Score: 63
Period size: 2 Copynumber: 22.0 Consensus size: 2
15410163 CAAACATCTC
* *
15410173 TA TA TA GTA AA TA TA TA TA TA TA TA TA TA TA TA TA TA TA CA TA
1 TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
15410216 TA
1 TA
15410218 AGCATACACC
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
2 36 0.95
3 2 0.05
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.44
Consensus pattern (2 bp):
TA
Found at i:15410298 original size:54 final size:54
Alignment explanation
Indices: 15410223--15410494 Score: 357
Period size: 54 Copynumber: 5.0 Consensus size: 54
15410213 ATATAAGCAT
* * * * *
15410223 ACACCACCTTCTCACCAAGCTCATGTGTATCCCCCCACATCGTGCATATAGCCGG
1 ACACC-CCATCTCACCCAGCTCATGTGCATCCCCCCACATCGTGCACATAGCCAG
* * *
15410278 ACACCCCGTCTCACCCAGCTCATGTGCATCCCCCCACATTGTGCACATAGCTAG
1 ACACCCCATCTCACCCAGCTCATGTGCATCCCCCCACATCGTGCACATAGCCAG
* * * *
15410332 ACATCCCAT-TGCACCCAACTCATGTGCATCCCCTCACATCGTGCACATAGCCGG
1 ACACCCCATCT-CACCCAGCTCATGTGCATCCCCCCACATCGTGCACATAGCCAG
* * *
15410386 ACATCCCATCTCACCCAGCTCATGTGCATCCTCCCACATTGTGCACATAGCCAG
1 ACACCCCATCTCACCCAGCTCATGTGCATCCCCCCACATCGTGCACATAGCCAG
* * *
15410440 ACACCCCGTCTCACCCAACTCATGTGCATCCCCCCACATCGTGCAAATAGCCAG
1 ACACCCCATCTCACCCAGCTCATGTGCATCCCCCCACATCGTGCACATAGCCAG
15410494 A
1 A
15410495 GTCATCGTGT
Statistics
Matches: 190, Mismatches: 25, Indels: 5
0.86 0.11 0.02
Matches are distributed among these distances:
53 1 0.01
54 183 0.96
55 6 0.03
ACGTcount: A:0.24, C:0.42, G:0.14, T:0.20
Consensus pattern (54 bp):
ACACCCCATCTCACCCAGCTCATGTGCATCCCCCCACATCGTGCACATAGCCAG
Found at i:15410431 original size:108 final size:108
Alignment explanation
Indices: 15410223--15410491 Score: 398
Period size: 108 Copynumber: 2.5 Consensus size: 108
15410213 ATATAAGCAT
* * * *
15410223 ACACCACCTTCTCA-CCAAGCTCATGTGTATCCCCCCACATCGTGCATATAGCCGGACACCCCGT
1 ACACC-CCATCTCACCCAA-CTCATGTGCATCCCCCCACATCGTGCAAATAGCCGGACACCCCAT
*
15410287 CTCACCCAGCTCATGTGCATCCCCCCACATTGTGCACATAGCTAG
64 CTCACCCAGCTCATGTGCATCCCCCCACATTGTGCACATAGCCAG
* * * *
15410332 ACATCCCAT-TGCACCCAACTCATGTGCATCCCCTCACATCGTGCACATAGCCGGACATCCCATC
1 ACACCCCATCT-CACCCAACTCATGTGCATCCCCCCACATCGTGCAAATAGCCGGACACCCCATC
*
15410396 TCACCCAGCTCATGTGCATCCTCCCACATTGTGCACATAGCCAG
65 TCACCCAGCTCATGTGCATCCCCCCACATTGTGCACATAGCCAG
*
15410440 ACACCCCGTCTCACCCAACTCATGTGCATCCCCCCACATCGTGCAAATAGCC
1 ACACCCCATCTCACCCAACTCATGTGCATCCCCCCACATCGTGCAAATAGCC
15410492 AGAGTCATCG
Statistics
Matches: 144, Mismatches: 13, Indels: 7
0.88 0.08 0.04
Matches are distributed among these distances:
107 1 0.01
108 134 0.93
109 9 0.06
ACGTcount: A:0.24, C:0.42, G:0.14, T:0.20
Consensus pattern (108 bp):
ACACCCCATCTCACCCAACTCATGTGCATCCCCCCACATCGTGCAAATAGCCGGACACCCCATCT
CACCCAGCTCATGTGCATCCCCCCACATTGTGCACATAGCCAG
Found at i:15414899 original size:2 final size:2
Alignment explanation
Indices: 15414894--15414918 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
15414884 CATATATGTG
15414894 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
15414919 TCTACACAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:15418506 original size:20 final size:20
Alignment explanation
Indices: 15418465--15418521 Score: 71
Period size: 20 Copynumber: 2.9 Consensus size: 20
15418455 TCAAGTTGCT
*
15418465 ATCTATCAATAGATGTGCCC
1 ATCTATCAATAGATCTGCCC
15418485 ATCTATCAATAGATCTAG-CC
1 ATCTATCAATAGATCT-GCCC
**
15418505 ATCTATGGATAGATCTG
1 ATCTATCAATAGATCTG
15418522 GACATCAATC
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
19 1 0.03
20 31 0.94
21 1 0.03
ACGTcount: A:0.32, C:0.21, G:0.16, T:0.32
Consensus pattern (20 bp):
ATCTATCAATAGATCTGCCC
Found at i:15420774 original size:14 final size:14
Alignment explanation
Indices: 15420755--15420783 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
15420745 CTTACTCGTG
15420755 ATGCATCAAAATAA
1 ATGCATCAAAATAA
15420769 ATGCATCAAAATAA
1 ATGCATCAAAATAA
15420783 A
1 A
15420784 CTGTATAACC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.59, C:0.14, G:0.07, T:0.21
Consensus pattern (14 bp):
ATGCATCAAAATAA
Found at i:15422903 original size:48 final size:48
Alignment explanation
Indices: 15422814--15422906 Score: 132
Period size: 48 Copynumber: 1.9 Consensus size: 48
15422804 TCTACGAACA
* * *** *
15422814 AAACATACATATCTCACATCATATTATTGTCTGGAATCATCCACGGAT
1 AAACATACATATCTCACAACATATCATTGTCCAAAACCATCCACGGAT
15422862 AAACATACATATCTCACAACATATCATTGTCCAAAACCATCCACG
1 AAACATACATATCTCACAACATATCATTGTCCAAAACCATCCACG
15422907 AATGGAACAT
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
48 39 1.00
ACGTcount: A:0.39, C:0.27, G:0.08, T:0.27
Consensus pattern (48 bp):
AAACATACATATCTCACAACATATCATTGTCCAAAACCATCCACGGAT
Found at i:15424227 original size:29 final size:27
Alignment explanation
Indices: 15424171--15424229 Score: 73
Period size: 29 Copynumber: 2.1 Consensus size: 27
15424161 GGCCAATGCT
**
15424171 ATTATTTACCCTAAATTCTCTTTGCAG
1 ATTATTTACCCTAAATTCTCTTCACAG
*
15424198 ATTATTTACCCCTAAAATTTTCTTCACAG
1 ATTATTTA-CCCT-AAATTCTCTTCACAG
15424227 ATT
1 ATT
15424230 CAATCTTACA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
27 8 0.30
28 4 0.15
29 15 0.56
ACGTcount: A:0.29, C:0.22, G:0.05, T:0.44
Consensus pattern (27 bp):
ATTATTTACCCTAAATTCTCTTCACAG
Found at i:15426581 original size:123 final size:123
Alignment explanation
Indices: 15426362--15426608 Score: 440
Period size: 123 Copynumber: 2.0 Consensus size: 123
15426352 TTCAAGGACT
* *
15426362 TAATTAAAAGAGTTTAACTAAGTAATGGGCCCAATATTATAATGTGTTATAATATTCAGGGCTTA
1 TAATTAAAAGAGTTTAACTAAGTAATGAGCACAATATTATAATGTGTTATAATATTCAGGGCTTA
*
15426427 ATTGCAAAATTGAAGTTATTCTAACCTAACTATATAAGTCATTTTTTAACTATTTTCC
66 ATTGCAAAATTGAAGTTATTCTAACCTAACTATATAAGTCATCTTTTAACTATTTTCC
* *
15426485 TAATTAAAAGAGTTTAACTAAGTAATGAGCATAATATTATAATGTGTTATAATATTGAGGGCTTA
1 TAATTAAAAGAGTTTAACTAAGTAATGAGCACAATATTATAATGTGTTATAATATTCAGGGCTTA
*
15426550 ATTGCAAAATTGAAGTTATTTTAACCTAACTATATAAGTCATCTTTTAACTATTTTCC
66 ATTGCAAAATTGAAGTTATTCTAACCTAACTATATAAGTCATCTTTTAACTATTTTCC
15426608 T
1 T
15426609 TATAAGAGTT
Statistics
Matches: 118, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
123 118 1.00
ACGTcount: A:0.37, C:0.11, G:0.12, T:0.40
Consensus pattern (123 bp):
TAATTAAAAGAGTTTAACTAAGTAATGAGCACAATATTATAATGTGTTATAATATTCAGGGCTTA
ATTGCAAAATTGAAGTTATTCTAACCTAACTATATAAGTCATCTTTTAACTATTTTCC
Found at i:15429185 original size:33 final size:33
Alignment explanation
Indices: 15429142--15429205 Score: 103
Period size: 33 Copynumber: 1.9 Consensus size: 33
15429132 AATTTATTTA
*
15429142 TATAATTTTCATATGAA-TTTTTTCTATCTAAGT
1 TATAACTTTCATATGAATTTTTTTC-ATCTAAGT
15429175 TATAACTTTCATATGAATTTTTTTCATCTAA
1 TATAACTTTCATATGAATTTTTTTCATCTAA
15429206 ATTGTTTTAT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
33 22 0.76
34 7 0.24
ACGTcount: A:0.31, C:0.11, G:0.05, T:0.53
Consensus pattern (33 bp):
TATAACTTTCATATGAATTTTTTTCATCTAAGT
Found at i:15468430 original size:12 final size:12
Alignment explanation
Indices: 15468413--15468445 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
15468403 AATTGTTGCT
*
15468413 TTGTTCCCTTCC
1 TTGTTCACTTCC
15468425 TTGTTCACTTCC
1 TTGTTCACTTCC
15468437 TTGTTCACT
1 TTGTTCACT
15468446 CACTAGGTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.06, C:0.33, G:0.09, T:0.52
Consensus pattern (12 bp):
TTGTTCACTTCC
Found at i:15473489 original size:36 final size:36
Alignment explanation
Indices: 15473437--15473656 Score: 197
Period size: 36 Copynumber: 5.9 Consensus size: 36
15473427 AAATACAACC
* *
15473437 GTGCGTGTGCGGTGTGGGAGTGCACATGACGGTAATG
1 GTGCG-GTGCGGTGTGGGAGTGCACATGATGATAATG
* * * *
15473474 GTGCGGTGCGATGTGGGAGTGCACCTGATAATATTTGCGG
1 GTGCGGTGCGGTGTGGGAGTGCACATGATGATA-AT---G
*
15473514 TGTGCAGTGTGCGGTGTGGGAGTGCACATGACGATAATG
1 -GTGC-G-GTGCGGTGTGGGAGTGCACATGATGATAATG
* * * * *
15473553 GTGCAGTGCGGTGTGGGAGTGCACTTGATAATATTT
1 GTGCGGTGCGGTGTGGGAGTGCACATGATGATAATG
** * *
15473589 GTGATGTGCGGTGTGGGAGTGCACATGATGGTGATG
1 GTGCGGTGCGGTGTGGGAGTGCACATGATGATAATG
** *
15473625 GTGAAGTGCGGTGTGGGAGTGCACCTGATGAT
1 GTGCGGTGCGGTGTGGGAGTGCACATGATGAT
15473657 GATATTGTAA
Statistics
Matches: 148, Mismatches: 28, Indels: 15
0.77 0.15 0.08
Matches are distributed among these distances:
36 106 0.72
37 6 0.04
38 4 0.03
39 1 0.01
40 1 0.01
41 4 0.03
42 2 0.01
43 24 0.16
ACGTcount: A:0.18, C:0.12, G:0.42, T:0.27
Consensus pattern (36 bp):
GTGCGGTGCGGTGTGGGAGTGCACATGATGATAATG
Found at i:15473626 original size:72 final size:72
Alignment explanation
Indices: 15473442--15473690 Score: 309
Period size: 79 Copynumber: 3.3 Consensus size: 72
15473432 CAACCGTGCG
* *
15473442 TGTGCGGTGTGGGAGTGCACATGACGGTAATGGTGCGGTGCGATGTGGGAGTGCACCTGATAATA
1 TGTGCGGTGTGGGAGTGCACATGACGGTAATGGTGCAGTGCGGTGTGGGAGTGCACCTGATAATA
15473507 TTTGCGGTGTGCA
66 -TT----TGTG-A
* *
15473520 GTGTGCGGTGTGGGAGTGCACATGACGATAATGGTGCAGTGCGGTGTGGGAGTGCACTTGATAAT
1 -TGTGCGGTGTGGGAGTGCACATGACGGTAATGGTGCAGTGCGGTGTGGGAGTGCACCTGATAAT
15473585 ATTTGTGA
65 ATTTGTGA
* * * *
15473593 TGTGCGGTGTGGGAGTGCACATGATGGTGATGGTGAAGTGCGGTGTGGGAGTGCACCTGATGATG
1 TGTGCGGTGTGGGAGTGCACATGACGGTAATGGTGCAGTGCGGTGTGGGAGTGCACCTGATAAT-
*
15473658 ATATTGTAA
65 AT-TTGTGA
** *
15473667 TGTGCAATGTGAGAGTGCACATGA
1 TGTGCGGTGTGGGAGTGCACATGA
15473691 TGACCTAGCT
Statistics
Matches: 154, Mismatches: 14, Indels: 9
0.87 0.08 0.05
Matches are distributed among these distances:
72 58 0.38
73 3 0.02
74 30 0.19
78 2 0.01
79 61 0.40
ACGTcount: A:0.20, C:0.12, G:0.40, T:0.28
Consensus pattern (72 bp):
TGTGCGGTGTGGGAGTGCACATGACGGTAATGGTGCAGTGCGGTGTGGGAGTGCACCTGATAATA
TTTGTGA
Found at i:15477890 original size:5 final size:5
Alignment explanation
Indices: 15477865--15477922 Score: 68
Period size: 5 Copynumber: 11.8 Consensus size: 5
15477855 CTAAAAATTA
*
15477865 AAAAT -AAAT AATAAT AAAAT ATAAT AATAAT AAAAT -AAAT AAAAT AAAAT
1 AAAAT AAAAT AA-AAT AAAAT AAAAT AA-AAT AAAAT AAAAT AAAAT AAAAT
15477915 AAAA- AAAA
1 AAAAT AAAA
15477923 AAAGAAAAGG
Statistics
Matches: 47, Mismatches: 2, Indels: 9
0.81 0.03 0.16
Matches are distributed among these distances:
4 12 0.26
5 25 0.53
6 10 0.21
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (5 bp):
AAAAT
Found at i:15477890 original size:16 final size:15
Alignment explanation
Indices: 15477865--15477917 Score: 90
Period size: 16 Copynumber: 3.5 Consensus size: 15
15477855 CTAAAAATTA
15477865 AAAATAAATAATAAT
1 AAAATAAATAATAAT
15477880 AAAATATAATAATAAT
1 AAAATA-AATAATAAT
15477896 AAAATAAATAA-AAT
1 AAAATAAATAATAAT
15477910 AAAATAAA
1 AAAATAAA
15477918 AAAAAAAAGA
Statistics
Matches: 37, Mismatches: 0, Indels: 3
0.93 0.00 0.08
Matches are distributed among these distances:
14 11 0.30
15 11 0.30
16 15 0.41
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (15 bp):
AAAATAAATAATAAT
Found at i:15479644 original size:15 final size:15
Alignment explanation
Indices: 15479624--15479652 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
15479614 GAATGAATTA
15479624 CACTGAAAGGTTGAT
1 CACTGAAAGGTTGAT
15479639 CACTGAAAGGTTGA
1 CACTGAAAGGTTGA
15479653 GTCAAACCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.34, C:0.14, G:0.28, T:0.24
Consensus pattern (15 bp):
CACTGAAAGGTTGAT
Found at i:15480105 original size:36 final size:35
Alignment explanation
Indices: 15479941--15480160 Score: 223
Period size: 35 Copynumber: 6.3 Consensus size: 35
15479931 CACTTGATTA
* *
15479941 AAATTGTTTAATTAAG---TTGTGCCTAATTAACT
1 AAATTGTTTAATTAAGTCATTGGGCCTAATTAATT
15479973 AAATTGTTTAATTGAA-TCATTGGGCCTAATTAATT
1 AAATTGTTTAATT-AAGTCATTGGGCCTAATTAATT
* * *
15480008 AAATTATTTAATTAAGTAATTGGGCTTAATTAATT
1 AAATTGTTTAATTAAGTCATTGGGCCTAATTAATT
*** * *
15480043 AAATTAAATAATTAAGTTATTGGGCCTAATTGATT
1 AAATTGTTTAATTAAGTCATTGGGCCTAATTAATT
* * *
15480078 AAATTTGTTTAATTAAGTCATTAGGCCTAGTTGATT
1 AAA-TTGTTTAATTAAGTCATTGGGCCTAATTAATT
* ** * *
15480114 AAAATTGTTTAATTAAATTGTTGTGCTTAATTAATT
1 -AAATTGTTTAATTAAGTCATTGGGCCTAATTAATT
15480150 AAATTGTTTAA
1 AAATTGTTTAA
15480161 CAAAGGATTC
Statistics
Matches: 157, Mismatches: 24, Indels: 11
0.82 0.12 0.06
Matches are distributed among these distances:
32 13 0.08
33 2 0.01
34 2 0.01
35 87 0.55
36 50 0.32
37 3 0.02
ACGTcount: A:0.36, C:0.06, G:0.13, T:0.45
Consensus pattern (35 bp):
AAATTGTTTAATTAAGTCATTGGGCCTAATTAATT
Found at i:15485342 original size:35 final size:34
Alignment explanation
Indices: 15485303--15485444 Score: 123
Period size: 32 Copynumber: 4.2 Consensus size: 34
15485293 GATCCCTGGT
* *
15485303 AAAAACTATTATTGTAGGTTGTGGTTGAGCCTTTG
1 AAAAACCACTATTG-AGGTTGTGGTTGAGCCTTTG
* **
15485338 AAAAACCACT-TTG-GGTTTTGGTTGAGCCCATG
1 AAAAACCACTATTGAGGTTGTGGTTGAGCCTTTG
*
15485370 AAAAACCACTA-TGAAAGGTTGTGGTTAAGCCTTTG
1 AAAAACCACTATTG--AGGTTGTGGTTGAGCCTTTG
* * * **
15485405 AAAAACCACT-TTG-GGTTTTGTTTGATCCCGTG
1 AAAAACCACTATTGAGGTTGTGGTTGAGCCTTTG
15485437 AAAAACCA
1 AAAAACCA
15485445 TTGCTAAAGG
Statistics
Matches: 87, Mismatches: 15, Indels: 13
0.76 0.13 0.11
Matches are distributed among these distances:
32 49 0.56
34 3 0.03
35 35 0.40
ACGTcount: A:0.30, C:0.15, G:0.23, T:0.32
Consensus pattern (34 bp):
AAAAACCACTATTGAGGTTGTGGTTGAGCCTTTG
Found at i:15485361 original size:32 final size:32
Alignment explanation
Indices: 15485319--15485444 Score: 135
Period size: 32 Copynumber: 3.8 Consensus size: 32
15485309 TATTATTGTA
*
15485319 GGTTGTGGTTGAGCCTTTGAAAAACCACTTTG
1 GGTTGTGGTTGAGCCCTTGAAAAACCACTTTG
* * *
15485351 GGTTTTGGTTGAGCCCATGAAAAACCACTATG
1 GGTTGTGGTTGAGCCCTTGAAAAACCACTTTG
* *
15485383 AAAGGTTGTGGTTAAGCCTTTGAAAAACCACTTTG
1 ---GGTTGTGGTTGAGCCCTTGAAAAACCACTTTG
* * * *
15485418 GGTTTTGTTTGATCCCGTGAAAAACCA
1 GGTTGTGGTTGAGCCCTTGAAAAACCA
15485445 TTGCTAAAGG
Statistics
Matches: 76, Mismatches: 15, Indels: 6
0.78 0.15 0.06
Matches are distributed among these distances:
32 49 0.64
35 27 0.36
ACGTcount: A:0.27, C:0.17, G:0.25, T:0.32
Consensus pattern (32 bp):
GGTTGTGGTTGAGCCCTTGAAAAACCACTTTG
Found at i:15485468 original size:67 final size:67
Alignment explanation
Indices: 15485318--15485444 Score: 218
Period size: 67 Copynumber: 1.9 Consensus size: 67
15485308 CTATTATTGT
15485318 AGGTTGTGGTTGAGCCTTTGAAAAACCACTTTGGGTTTTGGTTGAGCCCATGAAAAACCACTATG
1 AGGTTGTGGTTGAGCCTTTGAAAAACCACTTTGGGTTTTGGTTGAGCCCATGAAAAACCACTATG
15485383 AA
66 AA
* * * *
15485385 AGGTTGTGGTTAAGCCTTTGAAAAACCACTTTGGGTTTTGTTTGATCCCGTGAAAAACCA
1 AGGTTGTGGTTGAGCCTTTGAAAAACCACTTTGGGTTTTGGTTGAGCCCATGAAAAACCA
15485445 TTGCTAAAGG
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
67 56 1.00
ACGTcount: A:0.28, C:0.17, G:0.24, T:0.31
Consensus pattern (67 bp):
AGGTTGTGGTTGAGCCTTTGAAAAACCACTTTGGGTTTTGGTTGAGCCCATGAAAAACCACTATG
AA
Found at i:15497083 original size:23 final size:22
Alignment explanation
Indices: 15497028--15497089 Score: 61
Period size: 23 Copynumber: 2.7 Consensus size: 22
15497018 CAAATGTGAA
*
15497028 AATAATCAAAAAATAAAAGTAT
1 AATAATCAAAAAATAAAAATAT
* *
15497050 AACATAGCAAAAAATAAAAATAT
1 AATA-ATCAAAAAATAAAAATAT
*
15497073 ATTTAATCAAAGAAATA
1 A-ATAATCAAA-AAATA
15497090 GTTAAAACCC
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
22 3 0.10
23 22 0.71
24 6 0.19
ACGTcount: A:0.66, C:0.06, G:0.05, T:0.23
Consensus pattern (22 bp):
AATAATCAAAAAATAAAAATAT
Found at i:15502035 original size:23 final size:22
Alignment explanation
Indices: 15502007--15502077 Score: 72
Period size: 23 Copynumber: 3.1 Consensus size: 22
15501997 TTTTAAATAT
15502007 ATTTTATTTATAATTAATCATTA
1 ATTTTATTTATAATTAAT-ATTA
* *
15502030 ATTTTATTCT-TAACTGAATTTTA
1 ATTTTATT-TATAA-TTAATATTA
*
15502053 ATTTTATTAATAATTAATAATTA
1 ATTTTATTTATAATTAAT-ATTA
15502076 AT
1 AT
15502078 CAATCAAATT
Statistics
Matches: 39, Mismatches: 5, Indels: 8
0.75 0.10 0.15
Matches are distributed among these distances:
22 4 0.10
23 30 0.77
24 5 0.13
ACGTcount: A:0.39, C:0.04, G:0.01, T:0.55
Consensus pattern (22 bp):
ATTTTATTTATAATTAATATTA
Found at i:15509006 original size:34 final size:34
Alignment explanation
Indices: 15508962--15509042 Score: 99
Period size: 34 Copynumber: 2.4 Consensus size: 34
15508952 TAATCTTTAG
* ** *
15508962 AATGCATTTTCAAATGATCAAGTACAACCTTCAT
1 AATGCCTTTTCAAAAAATCAAGTACAACCTTCAC
* * *
15508996 AATGCCTTTTCAAAAAATTAAGTGCAACTTTCAC
1 AATGCCTTTTCAAAAAATCAAGTACAACCTTCAC
15509030 AATGCCTTTTCAA
1 AATGCCTTTTCAA
15509043 GCGTTGTGCG
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
34 40 1.00
ACGTcount: A:0.37, C:0.21, G:0.09, T:0.33
Consensus pattern (34 bp):
AATGCCTTTTCAAAAAATCAAGTACAACCTTCAC
Found at i:15516494 original size:63 final size:63
Alignment explanation
Indices: 15516420--15516541 Score: 151
Period size: 63 Copynumber: 1.9 Consensus size: 63
15516410 TGAGTTGTCA
* * *
15516420 GTTCTTCATAAAGTCT-TAAACTTTCTATCTT-T-GAAGAATCGATTCTCCTTTTTTGAGATTTT
1 GTTCTTAATAAAG-CTGGAAACTTTCTAT-TTCTAG-AGAATCGATTCTCCTTTCTTGAGATTTT
15516482 G
63 G
* *
15516483 GTTCTTAATAAAGCTGGGAACTTTCTATTTCTAGAGAATCGATTCTTCTTTCTTGAGAT
1 GTTCTTAATAAAGCTGGAAACTTTCTATTTCTAGAGAATCGATTCTCCTTTCTTGAGAT
15516542 GTCAGTTTTT
Statistics
Matches: 51, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
62 4 0.08
63 46 0.90
64 1 0.02
ACGTcount: A:0.25, C:0.16, G:0.15, T:0.45
Consensus pattern (63 bp):
GTTCTTAATAAAGCTGGAAACTTTCTATTTCTAGAGAATCGATTCTCCTTTCTTGAGATTTTG
Found at i:15521341 original size:60 final size:62
Alignment explanation
Indices: 15521238--15521408 Score: 170
Period size: 61 Copynumber: 2.8 Consensus size: 62
15521228 AATAGACAGT
* * * *
15521238 TTCTCACTGCAGTGAGATTCAAGCTGCCAAAATAGAAAGTTTCTCGCTGAAGC-AAAATTCA
1 TTCTCGCTGCAGCGAGATTCAAGCTGACAAAAAAGAAAGTTTCTCGCTGAAGCGAAAATTCA
* * * *
15521299 TTCTCGCTGCAGCGATATTCATG-TGACAAAAAAGAAAGTTTCTCGCTGTAGCGAGAATTCA
1 TTCTCGCTGCAGCGAGATTCAAGCTGACAAAAAAGAAAGTTTCTCGCTGAAGCGAAAATTCA
* * * * * *
15521360 ATCTTGCTTCAGCGAG-TTGCAGGCAG-CAAAAACAGAATGTTTCTCGCTG
1 TTCTCGCTGCAGCGAGATT-CAAGCTGACAAAAA-AGAAAGTTTCTCGCTG
15521409 CAGCAAGAGC
Statistics
Matches: 91, Mismatches: 15, Indels: 7
0.81 0.13 0.06
Matches are distributed among these distances:
60 28 0.31
61 47 0.52
62 16 0.18
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.27
Consensus pattern (62 bp):
TTCTCGCTGCAGCGAGATTCAAGCTGACAAAAAAGAAAGTTTCTCGCTGAAGCGAAAATTCA
Found at i:15524593 original size:18 final size:18
Alignment explanation
Indices: 15524553--15524593 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
15524543 AGAAGATAAT
* *
15524553 CAATTTAAAGCTTGATGC
1 CAATTTAAAGCTAGATAC
*
15524571 AAATTTAAAGCTAGATAC
1 CAATTTAAAGCTAGATAC
15524589 CAATT
1 CAATT
15524594 AAGAAATCTT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.41, C:0.15, G:0.12, T:0.32
Consensus pattern (18 bp):
CAATTTAAAGCTAGATAC
Found at i:15532097 original size:21 final size:20
Alignment explanation
Indices: 15532059--15532097 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
15532049 ATGCTGAATG
* *
15532059 ATTGATAATTCTTGATGAAA
1 ATTGATAATGCTTAATGAAA
15532079 ATTGATGAATGCTTAATGA
1 ATTGAT-AATGCTTAATGA
15532098 TACTAGATGA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 6 0.38
21 10 0.62
ACGTcount: A:0.38, C:0.05, G:0.18, T:0.38
Consensus pattern (20 bp):
ATTGATAATGCTTAATGAAA
Found at i:15533892 original size:20 final size:20
Alignment explanation
Indices: 15533848--15533892 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
15533838 GATCAAGAAT
* *
15533848 CAAGCAATATGAAGAAAAAA
1 CAAGCAAAAAGAAGAAAAAA
* *
15533868 AAAGCAAAAAGAAGAAAAAC
1 CAAGCAAAAAGAAGAAAAAA
15533888 CAAGC
1 CAAGC
15533893 TATAGCAAGC
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.67, C:0.13, G:0.16, T:0.04
Consensus pattern (20 bp):
CAAGCAAAAAGAAGAAAAAA
Found at i:15539603 original size:19 final size:20
Alignment explanation
Indices: 15539581--15539621 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
15539571 ACAAAAGGAA
15539581 ATTTTTA-GAATAAAATAAT
1 ATTTTTATGAATAAAATAAT
*
15539600 A-TTTTATTAATAAAATAAT
1 ATTTTTATGAATAAAATAAT
15539619 ATT
1 ATT
15539622 AAAATATTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
18 5 0.26
19 13 0.68
20 1 0.05
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.46
Consensus pattern (20 bp):
ATTTTTATGAATAAAATAAT
Found at i:15554448 original size:27 final size:29
Alignment explanation
Indices: 15554399--15554453 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 29
15554389 CGAGGAAAAA
* *
15554399 GGCAAAATAGTCATTTTGCCACC-CCAAG
1 GGCAAAATAGTAATTTTGACACCACCAAG
*
15554427 GGCAAAATTGTAATTTT-ACACCACCAA
1 GGCAAAATAGTAATTTTGACACCACCAA
15554454 CACTTGTCCA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
27 4 0.17
28 19 0.83
ACGTcount: A:0.36, C:0.25, G:0.15, T:0.24
Consensus pattern (29 bp):
GGCAAAATAGTAATTTTGACACCACCAAG
Found at i:15562334 original size:22 final size:21
Alignment explanation
Indices: 15562290--15562334 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 21
15562280 ACCAAAACAA
* *
15562290 AATGTTTCTGGCTGCAGCGAG
1 AATGTTTCTCGCTGCAGAGAG
*
15562311 AATGCTTTCTCGCTGCAGATAG
1 AATG-TTTCTCGCTGCAGAGAG
15562333 AA
1 AA
15562335 GTAGGGCACC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 4 0.20
22 16 0.80
ACGTcount: A:0.24, C:0.20, G:0.27, T:0.29
Consensus pattern (21 bp):
AATGTTTCTCGCTGCAGAGAG
Found at i:15562723 original size:84 final size:84
Alignment explanation
Indices: 15562582--15562749 Score: 232
Period size: 84 Copynumber: 2.0 Consensus size: 84
15562572 CAGCTTATAT
* * * * * *
15562582 GCAACGGCTTATGCGTACTCTTACTCGCACATAGTCAGGTCAGCAATGGTTTATGCGCACTCCCA
1 GCAACGACTTATGCGCACTCCTACTCGCACATAGCCAGGTCAGCAATAGCTTATGCGCACTCCCA
*
15562647 CTCGCACATAGCTGGGTCA
66 CTCGCACATAGCCGGGTCA
15562666 GCAACGACTTATGCGCACTCCTACTCGCACATAGCC-GAGTCAGC-ATCAGCTTATGCGCACTCC
1 GCAACGACTTATGCGCACTCCTACTCGCACATAGCCAG-GTCAGCAAT-AGCTTATGCGCACTCC
*
15562729 TACTCGCACATAGCCGGGTCA
64 CACTCGCACATAGCCGGGTCA
15562750 ATATCATCAT
Statistics
Matches: 74, Mismatches: 8, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
83 3 0.04
84 71 0.96
ACGTcount: A:0.23, C:0.33, G:0.21, T:0.23
Consensus pattern (84 bp):
GCAACGACTTATGCGCACTCCTACTCGCACATAGCCAGGTCAGCAATAGCTTATGCGCACTCCCA
CTCGCACATAGCCGGGTCA
Found at i:15562743 original size:42 final size:41
Alignment explanation
Indices: 15562588--15562749 Score: 191
Period size: 42 Copynumber: 3.9 Consensus size: 41
15562578 ATATGCAACG
* * * *
15562588 GCTTATGCGTACTCTTACTCGCACATAGTC-AGGTCAGCAATG
1 GCTTATGCGCACTCCTACTCGCACATAGCCGA-GTCAGC-ATC
* * * * *
15562630 GTTTATGCGCACTCCCACTCGCACATAGCTGGGTCAGCAAC
1 GCTTATGCGCACTCCTACTCGCACATAGCCGAGTCAGCATC
15562671 GACTTATGCGCACTCCTACTCGCACATAGCCGAGTCAGCATC
1 G-CTTATGCGCACTCCTACTCGCACATAGCCGAGTCAGCATC
*
15562713 AGCTTATGCGCACTCCTACTCGCACATAGCCGGGTCA
1 -GCTTATGCGCACTCCTACTCGCACATAGCCGAGTCA
15562750 ATATCATCAT
Statistics
Matches: 102, Mismatches: 15, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
41 2 0.02
42 99 0.97
43 1 0.01
ACGTcount: A:0.23, C:0.33, G:0.21, T:0.23
Consensus pattern (41 bp):
GCTTATGCGCACTCCTACTCGCACATAGCCGAGTCAGCATC
Found at i:15569674 original size:42 final size:42
Alignment explanation
Indices: 15569627--15569752 Score: 180
Period size: 42 Copynumber: 3.0 Consensus size: 42
15569617 CAGCTCATAT
* * *
15569627 GCAACGGCTTATGCGCACTCCCAGTCGCACATAGCCGGGTCA
1 GCAACGGCTTATGCGCACTCCTACTCACACATAGCCGGGTCA
* * *
15569669 GCAACGACTTATGCGCACTCCTACTCACACATAGTCGAGTCA
1 GCAACGGCTTATGCGCACTCCTACTCACACATAGCCGGGTCA
* *
15569711 GCATCAGCTTATGCGCACTCCTACTCACACATAGCCGGGTCA
1 GCAACGGCTTATGCGCACTCCTACTCACACATAGCCGGGTCA
15569753 ATATCATCAT
Statistics
Matches: 73, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 73 1.00
ACGTcount: A:0.25, C:0.35, G:0.21, T:0.20
Consensus pattern (42 bp):
GCAACGGCTTATGCGCACTCCTACTCACACATAGCCGGGTCA
Found at i:15569800 original size:2 final size:2
Alignment explanation
Indices: 15569788--15569839 Score: 86
Period size: 2 Copynumber: 26.0 Consensus size: 2
15569778 CATGTACAAC
*
15569788 AT AT AT TT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
15569830 AT AT GT AT AT
1 AT AT AT AT AT
15569840 CAACATAATG
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (2 bp):
AT
Found at i:15571471 original size:28 final size:28
Alignment explanation
Indices: 15571440--15571504 Score: 94
Period size: 28 Copynumber: 2.3 Consensus size: 28
15571430 TTGAGGATAA
15571440 GGGCAAAATAATCATTTTGCCACCCTAG
1 GGGCAAAATAATCATTTTGCCACCCTAG
** * *
15571468 GGGCAGCATAGTCATTTTGCCACCTTAG
1 GGGCAAAATAATCATTTTGCCACCCTAG
15571496 GGGCAAAAT
1 GGGCAAAAT
15571505 TGTAATTTTA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.29, C:0.23, G:0.23, T:0.25
Consensus pattern (28 bp):
GGGCAAAATAATCATTTTGCCACCCTAG
Found at i:15571512 original size:28 final size:28
Alignment explanation
Indices: 15571440--15571513 Score: 85
Period size: 28 Copynumber: 2.6 Consensus size: 28
15571430 TTGAGGATAA
* *
15571440 GGGCAAAATAATCATTTTGCCACCCTAG
1 GGGCAAAATAGTAATTTTGCCACCCTAG
** * *
15571468 GGGCAGCATAGTCATTTTGCCACCTTAG
1 GGGCAAAATAGTAATTTTGCCACCCTAG
*
15571496 GGGCAAAATTGTAATTTT
1 GGGCAAAATAGTAATTTT
15571514 ACACCACCCA
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 38 1.00
ACGTcount: A:0.28, C:0.20, G:0.22, T:0.30
Consensus pattern (28 bp):
GGGCAAAATAGTAATTTTGCCACCCTAG
Found at i:15580094 original size:48 final size:48
Alignment explanation
Indices: 15579959--15580101 Score: 214
Period size: 49 Copynumber: 2.9 Consensus size: 48
15579949 TTGACCTGGT
**
15579959 TATGTGCGAGTAGGGAGTGCGCATAAGCCGATGATGATGATGACCGGGC
1 TATGTGCGAGTA-GGAGTGCGCATAAGCCGATGATGATGATGACCCAGC
* * *
15580008 TATGTGTGGGTAAGGAGTGCGCATAAGCCGATGGTGATGATGACCCAGC
1 TATGTGCGAGT-AGGAGTGCGCATAAGCCGATGATGATGATGACCCAGC
*
15580057 TATGTGCGAGTAGGAGTGTGCATAAGCCGATGATGATGATGACCC
1 TATGTGCGAGTAGGAGTGCGCATAAGCCGATGATGATGATGACCC
15580102 CGACTATGAT
Statistics
Matches: 84, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
48 32 0.38
49 51 0.61
50 1 0.01
ACGTcount: A:0.25, C:0.16, G:0.36, T:0.22
Consensus pattern (48 bp):
TATGTGCGAGTAGGAGTGCGCATAAGCCGATGATGATGATGACCCAGC
Found at i:15582168 original size:28 final size:27
Alignment explanation
Indices: 15582072--15582168 Score: 115
Period size: 28 Copynumber: 3.5 Consensus size: 27
15582062 AGGTTGTGTA
15582072 TGAACCTTGAAAAGCTAATGGTTATGCT
1 TGAACCTTGAAAAGC-AATGGTTATGCT
*
15582100 TGATA-CATGAAAAGGCAATGGTTATGCT
1 TGA-ACCTTGAAAA-GCAATGGTTATGCT
**
15582128 TGATTCTTGAAAAGACAATGGTTATGCT
1 TGAACCTTGAAAAG-CAATGGTTATGCT
*
15582156 TGAACCTTTAAAA
1 TGAACCTTGAAAA
15582169 AGCACTATAT
Statistics
Matches: 59, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
27 1 0.02
28 55 0.93
29 3 0.05
ACGTcount: A:0.35, C:0.12, G:0.21, T:0.32
Consensus pattern (27 bp):
TGAACCTTGAAAAGCAATGGTTATGCT
Found at i:15586320 original size:21 final size:20
Alignment explanation
Indices: 15586295--15586354 Score: 70
Period size: 20 Copynumber: 3.0 Consensus size: 20
15586285 AGACGTCTAA
*
15586295 AATAATTATTTGAAATGAAAT
1 AATAATTATTTG-AATAAAAT
* *
15586316 TATAATTGTTTGAATAAAAT
1 AATAATTATTTGAATAAAAT
15586336 AATAA-TATTT-AATAAAAT
1 AATAATTATTTGAATAAAAT
15586354 A
1 A
15586355 TTTTATTTTT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
18 9 0.26
19 4 0.12
20 11 0.32
21 10 0.29
ACGTcount: A:0.53, C:0.00, G:0.07, T:0.40
Consensus pattern (20 bp):
AATAATTATTTGAATAAAAT
Found at i:15588277 original size:11 final size:11
Alignment explanation
Indices: 15588250--15588293 Score: 51
Period size: 11 Copynumber: 4.3 Consensus size: 11
15588240 CCTAGGGTTC
15588250 TTGTTCTT-C-
1 TTGTTCTTCCT
15588259 TT-TTCTTCCT
1 TTGTTCTTCCT
15588269 TTGTTCTTCCTT
1 TTGTTCTTCC-T
15588281 TTGTT-TTCCT
1 TTGTTCTTCCT
15588291 TTG
1 TTG
15588294 GCAGGCCATA
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
8 5 0.16
9 3 0.10
10 6 0.19
11 11 0.35
12 6 0.19
ACGTcount: A:0.00, C:0.23, G:0.09, T:0.68
Consensus pattern (11 bp):
TTGTTCTTCCT
Found at i:15596214 original size:2 final size:2
Alignment explanation
Indices: 15596207--15596245 Score: 62
Period size: 2 Copynumber: 19.5 Consensus size: 2
15596197 AATCACATAC
15596207 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T CAT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT A
15596246 AATTGTTTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 1 0.03
2 33 0.94
3 1 0.03
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:15598287 original size:25 final size:25
Alignment explanation
Indices: 15598258--15598308 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
15598248 AAATAGAATG
* * *
15598258 CTTTGTATTTCTTTGAGGTGTGTTA
1 CTTTGTATTTCTCTAAAGTGTGTTA
15598283 CTTTGTATTTCTCTAAAGTGTGTTA
1 CTTTGTATTTCTCTAAAGTGTGTTA
15598308 C
1 C
15598309 AAATTAGGGG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.16, C:0.12, G:0.20, T:0.53
Consensus pattern (25 bp):
CTTTGTATTTCTCTAAAGTGTGTTA
Found at i:15615677 original size:20 final size:20
Alignment explanation
Indices: 15615652--15615697 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
15615642 CTTCTAAACC
15615652 TCAAATCATACTCCAACAAG
1 TCAAATCATACTCCAACAAG
* *
15615672 TCAAATTATACTCCAATAAG
1 TCAAATCATACTCCAACAAG
15615692 TCAAAT
1 TCAAAT
15615698 GGGCCAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.46, C:0.24, G:0.04, T:0.26
Consensus pattern (20 bp):
TCAAATCATACTCCAACAAG
Found at i:15629396 original size:37 final size:37
Alignment explanation
Indices: 15629289--15629399 Score: 123
Period size: 37 Copynumber: 3.0 Consensus size: 37
15629279 CCTCAGCTCT
* * * * *
15629289 TGTGCACTCCCTACACGGACAAGGCAATACCACCATA
1 TGTGCACTCCCTACTCGCACAAGTCAATATCATCATA
** * *
15629326 TGTGCACTCCCTACTCGCACATTTCAATGTCATCATG
1 TGTGCACTCCCTACTCGCACAAGTCAATATCATCATA
* *
15629363 TGTGCACTCCCTACTCGCACACGTCATTATCATCATA
1 TGTGCACTCCCTACTCGCACAAGTCAATATCATCATA
15629400 CAACATTATT
Statistics
Matches: 60, Mismatches: 14, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
37 60 1.00
ACGTcount: A:0.26, C:0.34, G:0.14, T:0.26
Consensus pattern (37 bp):
TGTGCACTCCCTACTCGCACAAGTCAATATCATCATA
Found at i:15630233 original size:29 final size:30
Alignment explanation
Indices: 15630191--15630249 Score: 95
Period size: 29 Copynumber: 2.0 Consensus size: 30
15630181 AAGCAAGCTT
15630191 CCACGGGGGGTG-AAAACAT-GGAAAGGAA
1 CCACGGGGGGTGAAAAACATGGGAAAGGAA
15630219 NCCACGGGGGGTGAAAAACATGGGAAAGGAA
1 -CCACGGGGGGTGAAAAACATGGGAAAGGAA
15630250 GAAGAAGAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
29 12 0.43
30 7 0.25
31 9 0.32
ACGTcount: A:0.39, C:0.14, G:0.39, T:0.07
Consensus pattern (30 bp):
CCACGGGGGGTGAAAAACATGGGAAAGGAA
Found at i:15631671 original size:74 final size:74
Alignment explanation
Indices: 15631477--15631671 Score: 241
Period size: 74 Copynumber: 2.6 Consensus size: 74
15631467 TTCAAATATA
* * *
15631477 GTGCTCTTAGTTGAC-AACTATGCTTTTTAATCGATTAAGTCTTCTCTGTCTTGAAATTGAAATC
1 GTGCTCTTAGTTGACTAACTATGCTTATTAGTCGATTAAGTCTTCTTTGTCTTGAAATTGAAATC
15631541 TCTGGCAGT
66 TCTGGCAGT
* * * *
15631550 GAGCTCTTAGTTGACTAACTGTGCTTATTAGTCGATTAAGT-TCTCTTTGTCTTGTAATTGAGAT
1 GTGCTCTTAGTTGACTAACTATGCTTATTAGTCGATTAAGTCT-TCTTTGTCTTGAAATTGAAAT
* *
15631614 TTCTGGTAGT
65 CTCTGGCAGT
* * * * *
15631624 GTGCTCTTAGTTGACTAACCATACTTCTTGGTCGACTAAGTCTTCTTT
1 GTGCTCTTAGTTGACTAACTATGCTTATTAGTCGATTAAGTCTTCTTT
15631672 ATCTCACAAT
Statistics
Matches: 103, Mismatches: 16, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
73 15 0.15
74 87 0.84
75 1 0.01
ACGTcount: A:0.21, C:0.17, G:0.19, T:0.43
Consensus pattern (74 bp):
GTGCTCTTAGTTGACTAACTATGCTTATTAGTCGATTAAGTCTTCTTTGTCTTGAAATTGAAATC
TCTGGCAGT
Found at i:15633327 original size:36 final size:36
Alignment explanation
Indices: 15633285--15633416 Score: 142
Period size: 36 Copynumber: 3.7 Consensus size: 36
15633275 TCAACTCAGC
* *
15633285 TCATGTGCACTCCCACACCACACATAGC-TAATATCC
1 TCATGTGCACTCCCACACCGCACATAGCAT-ATATCA
* *
15633321 TTATGTGCACTCCCACACCGCACATGGCATATATCA
1 TCATGTGCACTCCCACACCGCACATAGCATATATCA
* * * * *
15633357 TCATGTGCACTCCTACACCGCACACCACCAT-CATCG
1 TCATGTGCACTCCCACACCGCACA-TAGCATATATCA
*
15633393 TCATGTCCACTCCCACACCGCACA
1 TCATGTGCACTCCCACACCGCACA
15633417 CGCACAGTTA
Statistics
Matches: 81, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
36 77 0.95
37 4 0.05
ACGTcount: A:0.27, C:0.41, G:0.11, T:0.21
Consensus pattern (36 bp):
TCATGTGCACTCCCACACCGCACATAGCATATATCA
Found at i:15638151 original size:36 final size:36
Alignment explanation
Indices: 15638104--15638281 Score: 178
Period size: 39 Copynumber: 4.7 Consensus size: 36
15638094 ATAATCGTGT
* *
15638104 GTGTGCGGTGTGGGAGTGCACATGACGGTGATGGTG
1 GTGTGCGGTGTGGGAGTGCACATGATGGTGATTGTG
* *
15638140 GTGTGCGGTGTGGGAGTGCACATGATGATGATATTTG
1 GTGTGCGGTGTGGGAGTGCACATGATGGTGAT-TGTG
* *
15638177 CCATTTGCGGTGTGGGAGTGCACATGATGG-GATTGTG
1 --GTGTGCGGTGTGGGAGTGCACATGATGGTGATTGTG
* *
15638214 GTGTGCGGTGTGGGAGTGCACACGATGATGATGATATATG
1 GTGTGCGGTGTGGGAGTG--CAC-ATGATGGTGAT-TGTG
* *
15638254 CCATGTGAGGTGTGGGAGTGCACATGAT
1 --GTGTGCGGTGTGGGAGTGCACATGAT
15638282 ATTTTCCATG
Statistics
Matches: 118, Mismatches: 14, Indels: 17
0.79 0.09 0.11
Matches are distributed among these distances:
35 16 0.14
36 30 0.25
37 8 0.07
38 9 0.08
39 33 0.28
40 6 0.05
42 16 0.14
ACGTcount: A:0.19, C:0.11, G:0.42, T:0.28
Consensus pattern (36 bp):
GTGTGCGGTGTGGGAGTGCACATGATGGTGATTGTG
Done.