Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009612.1 Kokia drynarioides strain JFW-HI SEQ_124328, whole genome shotgun sequence
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: 229655
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Warning! 71 characters in sequence are not A, C, G, or T
Found at i:11097 original size:29 final size:29
Alignment explanation
Indices: 11062--11157 Score: 86
Period size: 29 Copynumber: 3.3 Consensus size: 29
11052 GTCAAAAACA
11062 TAATTTTTAGACATCTGGGGGTAAAATGG
1 TAATTTTTAGACATCTGGGGGTAAAATGG
* ** * * * *
11091 TACTTTTCGGAGAGTTTGGGGTTAAAAAAGG
1 TAATTTTTAGACA-TCTGGGGGT-AAAATGG
* *
11122 -AATTTTTAGACATCCGAGGGTAAAATGG
1 TAATTTTTAGACATCTGGGGGTAAAATGG
11150 TAATTTTT
1 TAATTTTT
11158 TGAAGGTTCA
Statistics
Matches: 48, Mismatches: 16, Indels: 6
0.69 0.23 0.09
Matches are distributed among these distances:
28 6 0.12
29 21 0.44
30 15 0.31
31 6 0.12
ACGTcount: A:0.31, C:0.07, G:0.26, T:0.35
Consensus pattern (29 bp):
TAATTTTTAGACATCTGGGGGTAAAATGG
Found at i:11132 original size:59 final size:59
Alignment explanation
Indices: 11009--11274 Score: 240
Period size: 59 Copynumber: 4.5 Consensus size: 59
10999 AAAACGATAA
* * * * * * * *
11009 TTTT-GACATTCGGGGGCAAAATGATAATTTT-GGAAGGTT-AGATGTCAAAAACATAAT
1 TTTTAGACATCCGAGGGTAAAATGGTAATTTTCGGAAGGTTCAG-GGTTAAAAATAGAAT
* * * **
11066 TTTTAGACATCTGGGGGTAAAATGGTACTTTTCGG-AGAGTTTGGGGTTAAAAA-AGGAAT
1 TTTTAGACATCCGAGGGTAAAATGGTAATTTTCGGAAG-GTTCAGGGTTAAAAATA-GAAT
**
11125 TTTTAGACATCCGAGGGTAAAATGGTAATTTTTTGAAGGTTCAGGGTTAAAAATAGAAT
1 TTTTAGACATCCGAGGGTAAAATGGTAATTTTCGGAAGGTTCAGGGTTAAAAATAGAAT
* ** * *
11184 TTTTAGATATTAGAGTGTAAAATGGTAATTTT-GAAAGGATTCAGGGTTAAAAATAGAAT
1 TTTTAGACATCCGAGGGTAAAATGGTAATTTTCGGAAGG-TTCAGGGTTAAAAATAGAAT
* *
11243 TTTTAGATATTCG-GCGGTAAAATGGTAATTTT
1 TTTTAGACATCCGAG-GGTAAAATGGTAATTTT
11275 TGGGTCAAAA
Statistics
Matches: 176, Mismatches: 24, Indels: 16
0.81 0.11 0.07
Matches are distributed among these distances:
57 4 0.02
58 30 0.17
59 138 0.78
60 4 0.02
ACGTcount: A:0.35, C:0.06, G:0.24, T:0.35
Consensus pattern (59 bp):
TTTTAGACATCCGAGGGTAAAATGGTAATTTTCGGAAGGTTCAGGGTTAAAAATAGAAT
Found at i:11170 original size:29 final size:29
Alignment explanation
Indices: 11138--11277 Score: 69
Period size: 29 Copynumber: 4.8 Consensus size: 29
11128 TAGACATCCG
* *
11138 AGGGTAAAATGGTAATTTTTTGAAGGTTC
1 AGGGTAAAATGGTAATTTTTGGAAAGTTC
* * *
11167 AGGGTTAAAAATAG-AATTTTTAGATA-TT-
1 AGGG-T-AAAATGGTAATTTTTGGAAAGTTC
11195 AGAGTGTAAAATGGTAA-TTTT-GAAAGGATTC
1 AG-G-GTAAAATGGTAATTTTTGGAAA-G-TTC
* * *
11226 AGGGTTAAAAATAG-AATTTTTAGATA-TTC
1 AGGG-T-AAAATGGTAATTTTTGGAAAGTTC
*
11255 GGCGGTAAAATGGTAATTTTTGG
1 AG-GGTAAAATGGTAATTTTTGG
11278 GTCAAAATTG
Statistics
Matches: 85, Mismatches: 11, Indels: 30
0.67 0.09 0.24
Matches are distributed among these distances:
27 3 0.04
28 18 0.21
29 24 0.28
30 19 0.22
31 18 0.21
32 3 0.04
ACGTcount: A:0.36, C:0.03, G:0.24, T:0.36
Consensus pattern (29 bp):
AGGGTAAAATGGTAATTTTTGGAAAGTTC
Found at i:11176 original size:30 final size:30
Alignment explanation
Indices: 11138--11235 Score: 75
Period size: 30 Copynumber: 3.3 Consensus size: 30
11128 TAGACATCCG
11138 AGGG-TAAAATGGTAATTTTTTGAAGGTTC
1 AGGGTTAAAATGGTAATTTTTTGAAGGTTC
* *
11167 AGGGTTAAAAATAG-AATTTTTAGATA--TT-
1 AGGGTT-AAAATGGTAATTTTTTGA-AGGTTC
*
11195 AGAGTGTAAAATGGTAA--TTTTGAAAGGATTC
1 AGGGT-TAAAATGGTAATTTTTTG-AAGG-TTC
11226 AGGGTTAAAA
1 AGGGTTAAAA
11236 ATAGAATTTT
Statistics
Matches: 53, Mismatches: 6, Indels: 19
0.68 0.08 0.24
Matches are distributed among these distances:
27 5 0.09
28 11 0.21
29 9 0.17
30 17 0.32
31 11 0.21
ACGTcount: A:0.39, C:0.02, G:0.24, T:0.35
Consensus pattern (30 bp):
AGGGTTAAAATGGTAATTTTTTGAAGGTTC
Found at i:11244 original size:30 final size:30
Alignment explanation
Indices: 11155--11245 Score: 84
Period size: 28 Copynumber: 3.1 Consensus size: 30
11145 AATGGTAATT
11155 TTTTG-AAGG-TTCAGGGTTAAAAATAGAA
1 TTTTGAAAGGATTCAGGGTTAAAAATAGAA
* * * * *
11183 TTTTTAGA-TATT-AGAGTGT-AAAATGGTAA
1 TTTTGAAAGGATTCAGGGT-TAAAAATAG-AA
11212 TTTTGAAAGGATTCAGGGTTAAAAATAGAA
1 TTTTGAAAGGATTCAGGGTTAAAAATAGAA
11242 TTTT
1 TTTT
11246 TAGATATTCG
Statistics
Matches: 46, Mismatches: 10, Indels: 12
0.68 0.15 0.18
Matches are distributed among these distances:
28 14 0.30
29 12 0.26
30 10 0.22
31 10 0.22
ACGTcount: A:0.38, C:0.02, G:0.22, T:0.37
Consensus pattern (30 bp):
TTTTGAAAGGATTCAGGGTTAAAAATAGAA
Found at i:11323 original size:29 final size:29
Alignment explanation
Indices: 11276--11707 Score: 355
Period size: 29 Copynumber: 14.8 Consensus size: 29
11266 GGTAATTTTT
* *
11276 GGGTCAAAATTGGAATTTTAGAAAGTTCGA
1 GGGT-AAAAATGGAATTTTGGAAAGTTCGA
*
11306 GGGTAAAAATGTAATTTTTGG-AAGTTCGA
1 GGGTAAAAATGGAA-TTTTGGAAAGTTCGA
11335 -GGTCAAAAATGGAATTTTGGAAAGTTCGA
1 GGGT-AAAAATGGAATTTTGGAAAGTTCGA
11364 GGGTAAAATAT--AATTTTTGGAAAGTTC-A
1 GGGTAAAA-ATGGAA-TTTTGGAAAGTTCGA
*
11392 AGGTCAAAAATGGAATTTTGGAAAGTTCGA
1 GGGT-AAAAATGGAATTTTGGAAAGTTCGA
* * *
11422 GGGT-AAAATGTAATTTTTTGAAAGTT-TA
1 GGGTAAAAATGGAA-TTTTGGAAAGTTCGA
* * * *
11450 AGGTCAAAAATGGAATTTTGGAGAGTTTGG
1 GGGT-AAAAATGGAATTTTGGAAAGTTCGA
* *
11480 GGGTAAAAATGTAATTTTTGGAAAGTTTGA
1 GGGTAAAAATGGAA-TTTTGGAAAGTTCGA
* * * * *
11510 GGTTAGAAATGGAATTTTGGAAATTTTGG
1 GGGTAAAAATGGAATTTTGGAAAGTTCGA
** * *
11539 GGGTAAAAATATAATTTTTGGAAAATTTGA
1 GGGTAAAAATGGAA-TTTTGGAAAGTTCGA
* * *
11569 GGTTAAAAATGGAATTTTGGAATGTTCGG
1 GGGTAAAAATGGAATTTTGGAAAGTTCGA
* *
11598 GGGTAAAAACGTAATTCTTGGAAA-TTC--
1 GGGTAAAAATGGAATT-TTGGAAAGTTCGA
** * *
11625 GTTTCAAAAATGGAATTTTGGAAGGTTCAA
1 GGGT-AAAAATGGAATTTTGGAAAGTTCGA
* *
11655 GGGTAAAAATGTAATTTTTGTG-AAGTTAGA
1 GGGTAAAAATGGAA-TTTTG-GAAAGTTCGA
*
11685 GGGAAAAAATGGAATTTTGGAAA
1 GGGTAAAAATGGAATTTTGGAAA
11708 AGTTTAGGGA
Statistics
Matches: 324, Mismatches: 54, Indels: 49
0.76 0.13 0.11
Matches are distributed among these distances:
27 8 0.02
28 43 0.13
29 163 0.50
30 109 0.34
31 1 0.00
ACGTcount: A:0.37, C:0.03, G:0.26, T:0.33
Consensus pattern (29 bp):
GGGTAAAAATGGAATTTTGGAAAGTTCGA
Found at i:11497 original size:59 final size:59
Alignment explanation
Indices: 11277--11707 Score: 509
Period size: 59 Copynumber: 7.4 Consensus size: 59
11267 GTAATTTTTG
* * **
11277 GGTCAAAATTGGAATTTTAGAAAGTTCGAGGGTAAAAATGTAATTTTTGG-AAGTTCGA
1 GGTCAAAAATGGAATTTTGGAAAGTTCGAGGGTAAAAATGTAATTTTTGGAAAGTTTAA
* *
11335 GGTCAAAAATGGAATTTTGGAAAGTTCGAGGGT-AAAATATAATTTTTGGAAAGTTCAA
1 GGTCAAAAATGGAATTTTGGAAAGTTCGAGGGTAAAAATGTAATTTTTGGAAAGTTTAA
*
11393 GGTCAAAAATGGAATTTTGGAAAGTTCGAGGGT-AAAATGTAATTTTTTGAAAGTTTAA
1 GGTCAAAAATGGAATTTTGGAAAGTTCGAGGGTAAAAATGTAATTTTTGGAAAGTTTAA
* * * *
11451 GGTCAAAAATGGAATTTTGGAGAGTTTGGGGGTAAAAATGTAATTTTTGGAAAGTTTGA
1 GGTCAAAAATGGAATTTTGGAAAGTTCGAGGGTAAAAATGTAATTTTTGGAAAGTTTAA
* * * * * * * *
11510 GGTTAGAAATGGAATTTTGGAAATTTTGGGGGTAAAAATATAATTTTTGGAAAATTTGA
1 GGTCAAAAATGGAATTTTGGAAAGTTCGAGGGTAAAAATGTAATTTTTGGAAAGTTTAA
* * * * * *
11569 GGTTAAAAATGGAATTTTGGAATGTTCGGGGGTAAAAACGTAATTCTTGGAAA--TT-C
1 GGTCAAAAATGGAATTTTGGAAAGTTCGAGGGTAAAAATGTAATTTTTGGAAAGTTTAA
* * *
11625 GTTTCAAAAATGGAATTTTGGAAGGTTCAAGGGTAAAAATGTAATTTTTGTG-AAG-TTAGA
1 G-GTCAAAAATGGAATTTTGGAAAGTTCGAGGGTAAAAATGTAATTTTTG-GAAAGTTTA-A
**
11685 GGGAAAAAATGGAATTTTGGAAA
1 GGTCAAAAATGGAATTTTGGAAA
11708 AGTTTAGGGA
Statistics
Matches: 328, Mismatches: 38, Indels: 13
0.87 0.10 0.03
Matches are distributed among these distances:
56 1 0.00
57 60 0.18
58 126 0.38
59 140 0.43
60 1 0.00
ACGTcount: A:0.37, C:0.03, G:0.26, T:0.33
Consensus pattern (59 bp):
GGTCAAAAATGGAATTTTGGAAAGTTCGAGGGTAAAAATGTAATTTTTGGAAAGTTTAA
Found at i:12256 original size:17 final size:16
Alignment explanation
Indices: 12234--12281 Score: 69
Period size: 17 Copynumber: 2.9 Consensus size: 16
12224 ATTTTAAATT
12234 TTTAAATTTAAAATAAA
1 TTTAAATTTAAAAT-AA
12251 TTTAAATTTAAAATAA
1 TTTAAATTTAAAATAA
*
12267 TTGTAAACTTAAAAT
1 TT-TAAATTTAAAAT
12282 CAACTTGGAA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
16 4 0.14
17 25 0.86
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (16 bp):
TTTAAATTTAAAATAA
Found at i:12881 original size:50 final size:49
Alignment explanation
Indices: 12719--13278 Score: 187
Period size: 49 Copynumber: 11.5 Consensus size: 49
12709 TTCGCCGTTA
* *
12719 CGACTTAAA-TTTTCCTTTCATG-CTTCTGAGGTATAAGGTTAGCCATTG
1 CGACTTAAACCTTTCCCTTCATGTCTT-TGAGGTATAAGGTTAGCCATTG
* ** * * * *
12767 CGACCTAAACCTTTCCCCCCTTGTCTTCGCA-GTACT--GGATTCGCCGTTG
1 CGACTTAAACCTTTCCCTTCATGTCTTTG-AGGTA-TAAGG-TTAGCCATTG
* ** *
12816 CGGCTTAAAAATTTCCCTTTCATGTCTTTGAGGTATAAGGTTTGCCATTG
1 CGACTTAAACCTTTCCC-TTCATGTCTTTGAGGTATAAGGTTAGCCATTG
* * * * ***
12866 CGACTTAGACCTTTCCCTTCATATC-TTCATGGTACT--GGATTCGTTGTTG
1 CGACTTAAACCTTTCCCTTCATGTCTTTGA-GGTA-TAAGG-TTAGCCATTG
* * * * * * **
12915 CGGCTTAAATCTTTCTCTTCATATC-TTCATGGTAT-TGGATTCA-CTGTTG
1 CGACTTAAACCTTTCCCTTCATGTCTTTGA-GGTATAAGG-TT-AGCCATTG
* * * * * *
12964 CGGCTTAAATCTTTCCCTTCCTGTC-TTCATGGTACT--GGATTCGCCATTA
1 CGACTTAAACCTTTCCCTTCATGTCTTTGA-GGTA-TAAGG-TTAGCCATTG
** * * * * * *
13013 CGGTTTAAATCTTTCCCTTCATGTCTCTGTGGTATAAGGTTCGTCGTTG
1 CGACTTAAACCTTTCCCTTCATGTCTTTGAGGTATAAGGTTAGCCATTG
* ** * * * *
13062 CAACTTAAACCTTTCCCTTTGTGTCTTCGTGGTACT--GGATTCA-CTATTA
1 CGACTTAAACCTTTCCCTTCATGTCTTTGAGGTA-TAAGG-TT-AGCCATTG
* * * *
13111 CGGCTTAAATCTTTCCCTTCATGTCTCTGAGGTACT-AGGTTCA-CCGTTG
1 CGACTTAAACCTTTCCCTTCATGTCTTTGAGGTA-TAAGGTT-AGCCATTG
* * * *
13160 CGACTTAAACCTTTCCCTTCGTGTCTTCGTGG--T--GGATTCGCCATTG
1 CGACTTAAACCTTTCCCTTCATGTCTTTGAGGTATAAGG-TTAGCCATTG
* * * * *
13206 CGGCTTAAATCTTTCCCTTCATG-CTTCTGAGGTACAAGGTTCGCCGTTG
1 CGACTTAAACCTTTCCCTTCATGTCTT-TGAGGTATAAGGTTAGCCATTG
* *
13255 TGACTTAAACCTTTCCCTCCATGT
1 CGACTTAAACCTTTCCCTTCATGT
13279 TTCGCGGTAC
Statistics
Matches: 388, Mismatches: 93, Indels: 60
0.72 0.17 0.11
Matches are distributed among these distances:
45 5 0.01
46 31 0.08
48 19 0.05
49 284 0.73
50 47 0.12
51 2 0.01
ACGTcount: A:0.17, C:0.25, G:0.19, T:0.39
Consensus pattern (49 bp):
CGACTTAAACCTTTCCCTTCATGTCTTTGAGGTATAAGGTTAGCCATTG
Found at i:12929 original size:49 final size:49
Alignment explanation
Indices: 12798--13278 Score: 360
Period size: 49 Copynumber: 9.9 Consensus size: 49
12788 TGTCTTCGCA
** *
12798 GTACTGGATTCGCCGTTGCGGCTTAAAAATTTCCCTTTCATGTCTTTGA-G
1 GTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCC-TTCATGTC-TTCATG
* * * * * *
12848 GTA-TAAGG-TTTGCCATTGCGACTTAGACCTTTCCCTTCATATCTTCATG
1 GTACT--GGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGTCTTCATG
** * *
12897 GTACTGGATTCGTTGTTGCGGCTTAAATCTTTCTCTTCATATCTTCATG
1 GTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGTCTTCATG
* * * *
12946 GTATTGGATTCACTGTTGCGGCTTAAATCTTTCCCTTCCTGTCTTCATG
1 GTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGTCTTCATG
* * * *
12995 GTACTGGATTCGCCATTACGGTTTAAATCTTTCCCTTCATGTC-TCTGTG
1 GTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGTCTTC-ATG
* ** * ** *
13044 GTA-TAAGG-TTCGTCGTTGCAACTTAAACCTTTCCCTTTGTGTCTTCGTG
1 GTACT--GGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGTCTTCATG
* ** * *
13093 GTACTGGATTCACTATTACGGCTTAAATCTTTCCCTTCATGTCTCTGA-G
1 GTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGTCT-TCATG
* * * * *
13142 GTACTAGG-TTCACCGTTGCGACTTAAACCTTTCCCTTCGTGTCTTCGTG
1 GTACT-GGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGTCTTCATG
*
13191 G---TGGATTCGCCATTGCGGCTTAAATCTTTCCCTTCATG-CTTC-TGAG
1 GTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGTCTTCAT--G
* * * * *
13237 GTACAAGG-TTCGCCGTTGTGACTTAAACCTTTCCCTCCATGT
1 GTAC-TGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGT
13279 TTCGCGGTAC
Statistics
Matches: 339, Mismatches: 70, Indels: 44
0.75 0.15 0.10
Matches are distributed among these distances:
44 1 0.00
45 6 0.02
46 31 0.09
48 11 0.03
49 253 0.75
50 35 0.10
51 2 0.01
ACGTcount: A:0.17, C:0.25, G:0.19, T:0.39
Consensus pattern (49 bp):
GTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGTCTTCATG
Found at i:12991 original size:98 final size:97
Alignment explanation
Indices: 12708--13272 Score: 445
Period size: 98 Copynumber: 5.8 Consensus size: 97
12698 ATGACACTAA
* * * **
12708 ATTCGCCGTTACGACTTAAAT-TTTCCTTTCATG-CTTC-TGAGGTATAAGGTT-AGCCATTGCG
1 ATTCGCCATTACGGCTTAAATCTTTCCCTTCATGTCTTCAT--GGTAT-AGGTTCA-CTGTTGCG
* ** * ***
12769 ACCTAAACCTTTCCCCCCTTGTCTTCGCAGTACTGG
62 ACTTAAACCTTTCCCTTCGTGTCTTCATGGTACTGG
* * ** * ** **
12805 ATTCGCCGTTGCGGCTTAAAAATTTCCCTTTCATGTCTTTGA-GGTATAAGGTTTGCCATTGCGA
1 ATTCGCCATTACGGCTTAAATCTTTCCC-TTCATGTC-TTCATGGTAT-AGGTTCACTGTTGCGA
* * *
12869 CTTAGACCTTTCCCTTCATATCTTCATGGTACTGG
63 CTTAAACCTTTCCCTTCGTGTCTTCATGGTACTGG
*** * * * * *
12904 ATTCGTTGTTGCGGCTTAAATCTTTCTCTTCATATCTTCATGGTATTGGATTCACTGTTGCGGCT
1 ATTCGCCATTACGGCTTAAATCTTTCCCTTCATGTCTTCATGGTATAGG-TTCACTGTTGCGACT
* *
12969 TAAATCTTTCCCTTCCTGTCTTCATGGTACTGG
65 TAAACCTTTCCCTTCGTGTCTTCATGGTACTGG
* * * *
13002 ATTCGCCATTACGGTTTAAATCTTTCCCTTCATGTC-TCTGTGGTATAAGGTTC-GTCGTTGCAA
1 ATTCGCCATTACGGCTTAAATCTTTCCCTTCATGTCTTC-ATGGTAT-AGGTTCACT-GTTGCGA
* *
13065 CTTAAACCTTTCCCTTTGTGTCTTCGTGGTACTGG
63 CTTAAACCTTTCCCTTCGTGTCTTCATGGTACTGG
* * * *
13100 ATTCACTATTACGGCTTAAATCTTTCCCTTCATGTCTCTGA-GGTACTAGGTTCACCGTTGCGAC
1 ATTCGCCATTACGGCTTAAATCTTTCCCTTCATGTCT-TCATGGTA-TAGGTTCACTGTTGCGAC
*
13164 TTAAACCTTTCCCTTCGTGTCTTCGTGG---TGG
64 TTAAACCTTTCCCTTCGTGTCTTCATGGTACTGG
* * * * *
13195 ATTCGCCATTGCGGCTTAAATCTTTCCCTTCATG-CTTC-TGAGGTACAAGGTTCGCCGTTGTGA
1 ATTCGCCATTACGGCTTAAATCTTTCCCTTCATGTCTTCAT--GGTA-TAGGTTCACTGTTGCGA
13258 CTTAAACCTTTCCCT
63 CTTAAACCTTTCCCT
13273 CCATGTTTCG
Statistics
Matches: 386, Mismatches: 64, Indels: 38
0.79 0.13 0.08
Matches are distributed among these distances:
93 1 0.00
94 2 0.01
95 68 0.18
97 26 0.07
98 207 0.54
99 78 0.20
100 2 0.01
101 2 0.01
ACGTcount: A:0.18, C:0.25, G:0.19, T:0.39
Consensus pattern (97 bp):
ATTCGCCATTACGGCTTAAATCTTTCCCTTCATGTCTTCATGGTATAGGTTCACTGTTGCGACTT
AAACCTTTCCCTTCGTGTCTTCATGGTACTGG
Found at i:13192 original size:147 final size:146
Alignment explanation
Indices: 12709--13192 Score: 437
Period size: 147 Copynumber: 3.3 Consensus size: 146
12699 TGACACTAAA
* * * * * * * *
12709 TTCGCCGTTACGACTTAAA-TTTTCCTTTCATG-CTTCTGAGGTATAAGGTTAGCCATTGCGACC
1 TTCGCCATTACGACTTAAACCTTTCCCTTCATGTCTTCTGTGGTATAAGGTTCGTCGTTGCGACT
** ** * * **
12772 TAAACCTTTCCCCCCTTGTCTTCGCAGTACTGGATTCGCCGTTGCGGCTTAAAAATTTCCCTTTC
66 TAAACCTTT-CCCTTTTGTCTTCGTGGTACTGGATTCACTGTTGCGGCTTAAATCTTTCCC-TTC
12837 ATGTCTTTGAGGTA-TAAGG
129 ATGTC-TTGAGGTACT-AGG
* * * * * * *
12856 TTTGCCATTGCGACTTAGACCTTTCCCTTCATATCTTC-ATGGTACT--GGATTCGTTGTTGCGG
1 TTCGCCATTACGACTTAAACCTTTCCCTTCATGTCTTCTGTGGTA-TAAGG-TTCGTCGTTGCGA
* * * * * *
12918 CTTAAATCTTTCTCTTCATATCTTCATGGTATTGGATTCACTGTTGCGGCTTAAATCTTTCCCTT
64 CTTAAACCTTTCCCTT-TTGTCTTCGTGGTACTGGATTCACTGTTGCGGCTTAAATCTTTCCCTT
* *
12983 CCTGTCTTCATGGTACT-GG
128 CATGTCTTGA-GGTACTAGG
** * *
13002 ATTCGCCATTACGGTTTAAATCTTTCCCTTCATGTC-TCTGTGGTATAAGGTTCGTCGTTGCAAC
1 -TTCGCCATTACGACTTAAACCTTTCCCTTCATGTCTTCTGTGGTATAAGGTTCGTCGTTGCGAC
* *
13066 TTAAACCTTTCCCTTTGTGTCTTCGTGGTACTGGATTCACTATTACGGCTTAAATCTTTCCCTTC
65 TTAAACCTTTCCCTTT-TGTCTTCGTGGTACTGGATTCACTGTTGCGGCTTAAATCTTTCCCTTC
13131 ATGTCTCTGAGGTACTAGG
129 ATGTCT-TGAGGTACTAGG
* * * *
13150 TTCACCGTTGCGACTTAAACCTTTCCCTTCGTGTCTTC-GTGGT
1 TTCGCCATTACGACTTAAACCTTTCCCTTCATGTCTTCTGTGGT
13193 GGATTCGCCA
Statistics
Matches: 263, Mismatches: 59, Indels: 30
0.75 0.17 0.09
Matches are distributed among these distances:
146 8 0.03
147 174 0.66
148 76 0.29
149 5 0.02
ACGTcount: A:0.17, C:0.25, G:0.18, T:0.39
Consensus pattern (146 bp):
TTCGCCATTACGACTTAAACCTTTCCCTTCATGTCTTCTGTGGTATAAGGTTCGTCGTTGCGACT
TAAACCTTTCCCTTTTGTCTTCGTGGTACTGGATTCACTGTTGCGGCTTAAATCTTTCCCTTCAT
GTCTTGAGGTACTAGG
Found at i:25107 original size:29 final size:29
Alignment explanation
Indices: 25075--25224 Score: 123
Period size: 30 Copynumber: 5.1 Consensus size: 29
25065 AAAATAGGAT
* *
25075 TTTTAGACATTCAAGGGTAAAATGGTAAA
1 TTTTAGATATTCGAGGGTAAAATGGTAAA
* * * *
25104 TTTTGGAGAGTTTG-GGGTTAAAAATGG-AAT
1 TTTTAGATA-TTCGAGGG-T-AAAATGGTAAA
25134 TTTTAGATATTCGAGGGTAAAATGGTAAA
1 TTTTAGATATTCGAGGGTAAAATGGTAAA
* *
25163 TTTTGGA-AGGTTCG-GGGTTAAAAATGG-AAT
1 TTTTAGATA--TTCGAGGG-T-AAAATGGTAAA
25193 TTTTAGATATTCGAGGGTAAAATGGT-AA
1 TTTTAGATATTCGAGGGTAAAATGGTAAA
25221 TTTT
1 TTTT
25225 GAAAGGATTC
Statistics
Matches: 96, Mismatches: 13, Indels: 25
0.72 0.10 0.19
Matches are distributed among these distances:
28 20 0.21
29 30 0.31
30 31 0.32
31 15 0.16
ACGTcount: A:0.34, C:0.03, G:0.27, T:0.36
Consensus pattern (29 bp):
TTTTAGATATTCGAGGGTAAAATGGTAAA
Found at i:25117 original size:59 final size:58
Alignment explanation
Indices: 25025--25287 Score: 332
Period size: 59 Copynumber: 4.5 Consensus size: 58
25015 AATTTTGGAT
* * * * *
25025 ATTCGGGGGCAAAATGATAATTTTGGAAGGTTTGAGGTTAAAAATAGG-ATTTTTAGAC
1 ATTCGAGGGTAAAATGGTAATTTTGGAAGGTTCGGGGTTAAAAAT-GGAATTTTTAGAC
* * *
25083 ATTCAAGGGTAAAATGGTAAATTTTGG-AGAGTTTGGGGTTAAAAATGGAATTTTTAGAT
1 ATTCGAGGGTAAAATGGT-AATTTTGGAAG-GTTCGGGGTTAAAAATGGAATTTTTAGAC
*
25142 ATTCGAGGGTAAAATGGTAAATTTTGGAAGGTTCGGGGTTAAAAATGGAATTTTTAGAT
1 ATTCGAGGGTAAAATGGT-AATTTTGGAAGGTTCGGGGTTAAAAATGGAATTTTTAGAC
* * * *
25201 ATTCGAGGGTAAAATGGTAATTTTGAAAGGATTCGGGTTTAAAAATAGAAATTTTAGAC
1 ATTCGAGGGTAAAATGGTAATTTTGGAAGG-TTCGGGGTTAAAAATGGAATTTTTAGAC
* *
25260 ATTCGAGGGTAATATGATAATTTTGGAA
1 ATTCGAGGGTAAAATGGTAATTTTGGAA
25288 AATTCAAGGA
Statistics
Matches: 184, Mismatches: 16, Indels: 9
0.88 0.08 0.04
Matches are distributed among these distances:
58 29 0.16
59 153 0.83
60 2 0.01
ACGTcount: A:0.36, C:0.04, G:0.27, T:0.34
Consensus pattern (58 bp):
ATTCGAGGGTAAAATGGTAATTTTGGAAGGTTCGGGGTTAAAAATGGAATTTTTAGAC
Found at i:25126 original size:30 final size:29
Alignment explanation
Indices: 25092--25244 Score: 104
Period size: 30 Copynumber: 5.2 Consensus size: 29
25082 CATTCAAGGG
*
25092 TAAAATGGTAAATTTTGGAGAGTTTGGGGT
1 TAAAATGGTAAATTTTGGA-AGTTCGGGGT
* *
25122 TAAAAATGG-AATTTTTAGATA-TTCGAGGG-
1 T-AAAATGGTAAATTTTGGA-AGTTCG-GGGT
25151 TAAAATGGTAAATTTTGGAAGGTTCGGGGT
1 TAAAATGGTAAATTTTGGAA-GTTCGGGGT
* *
25181 TAAAAATGG-AATTTTTAGATA-TTCGAGGG-
1 T-AAAATGGTAAATTTTGGA-AGTTCG-GGGT
* *
25210 TAAAATGGT-AATTTTGAAAGGATTCGGGTT
1 TAAAATGGTAAATTTTGGAA-G-TTCGGGGT
25240 TAAAA
1 TAAAA
25245 ATAGAAATTT
Statistics
Matches: 97, Mismatches: 12, Indels: 28
0.71 0.09 0.20
Matches are distributed among these distances:
27 1 0.01
28 21 0.22
29 22 0.23
30 38 0.39
31 15 0.15
ACGTcount: A:0.35, C:0.03, G:0.27, T:0.35
Consensus pattern (29 bp):
TAAAATGGTAAATTTTGGAAGTTCGGGGT
Found at i:25351 original size:30 final size:29
Alignment explanation
Indices: 25299--25563 Score: 225
Period size: 30 Copynumber: 8.9 Consensus size: 29
25289 ATTCAAGGAC
***
25299 AAAAATGGAATTTCAAAAAGTTTAGGGGT
1 AAAAATGGAATTTTGGAAAGTTTAGGGGT
* * *
25328 AAAAATGTAATTTTTAGAAAGTTTAGGGTT
1 AAAAATGGAA-TTTTGGAAAGTTTAGGGGT
***
25358 AAAAAATGGAATTTTGGAAAGTTTAGATAT
1 -AAAAATGGAATTTTGGAAAGTTTAGGGGT
* *
25388 AAAAATGTAATTTTTGGAAAGTTT-GAGGT
1 AAAAATGGAA-TTTTGGAAAGTTTAGGGGT
*
25417 GAAAAATGGAATTTTGGAAAGTTTGGGGGT
1 -AAAAATGGAATTTTGGAAAGTTTAGGGGT
* * *
25447 AAGAAATGTAATTTTTTGAAAATTT-GGGGT
1 AA-AAATGGAA-TTTTGGAAAGTTTAGGGGT
* * *
25477 CAAAAATGGAATTTTAGAAGGTTTAAGGGT
1 -AAAAATGGAATTTTGGAAAGTTTAGGGGT
*
25507 AAAAATGTAATTTTTGTG-AAGTTT-GAGGG-
1 AAAAATGGAA-TTTTG-GAAAGTTTAG-GGGT
25536 AAAAATGGAATTTTGGAAAAGTTTAGGG
1 AAAAATGGAATTTTGG-AAAGTTTAGGG
25564 ACCTTCAAGG
Statistics
Matches: 194, Mismatches: 27, Indels: 30
0.77 0.11 0.12
Matches are distributed among these distances:
27 1 0.01
28 5 0.03
29 72 0.37
30 93 0.48
31 23 0.12
ACGTcount: A:0.40, C:0.01, G:0.26, T:0.34
Consensus pattern (29 bp):
AAAAATGGAATTTTGGAAAGTTTAGGGGT
Found at i:25371 original size:60 final size:56
Alignment explanation
Indices: 25299--25563 Score: 287
Period size: 60 Copynumber: 4.5 Consensus size: 56
25289 ATTCAAGGAC
***
25299 AAAAATGGAATTTCAAAAAGTTTAGGGGTAAAAATGTAATTTTTAGAAAGTTTAGGGTT
1 AAAAATGGAATTTTGGAAAGTTTAGGGGTAAAAATGTAATTTTT-GAAAGTTT-GGG-T
***
25358 AAAAAATGGAATTTTGGAAAGTTTAGATATAAAAATGTAATTTTTGGAAAGTTTGAGGT
1 -AAAAATGGAATTTTGGAAAGTTTAGGGGTAAAAATGTAATTTTT-GAAAGTTTG-GGT
* *
25417 GAAAAATGGAATTTTGGAAAGTTTGGGGGTAAGAAATGTAATTTTTTGAAAATTTGGGGT
1 -AAAAATGGAATTTTGGAAAGTTTAGGGGTAA-AAATGTAA-TTTTTGAAAGTTT-GGGT
* * * * *
25477 CAAAAATGGAATTTTAGAAGGTTTAAGGGTAAAAATGTAATTTTTGTGAAGTTTGAGGG
1 -AAAAATGGAATTTTGGAAAGTTTAGGGGTAAAAATGTAATTTTTG-AAAGTTTG-GGT
25536 AAAAATGGAATTTTGGAAAAGTTTAGGG
1 AAAAATGGAATTTTGG-AAAGTTTAGGG
25564 ACCTTCAAGG
Statistics
Matches: 174, Mismatches: 24, Indels: 15
0.82 0.11 0.07
Matches are distributed among these distances:
58 22 0.13
59 53 0.30
60 93 0.53
61 6 0.03
ACGTcount: A:0.40, C:0.01, G:0.26, T:0.34
Consensus pattern (56 bp):
AAAAATGGAATTTTGGAAAGTTTAGGGGTAAAAATGTAATTTTTGAAAGTTTGGGT
Found at i:25438 original size:119 final size:118
Alignment explanation
Indices: 25299--25563 Score: 356
Period size: 119 Copynumber: 2.2 Consensus size: 118
25289 ATTCAAGGAC
*** * *
25299 AAAAATGGAATTTCAAAAAGTTTAGGGGTAA-AAATGTAATTTTTAGAAAGTTTAGGGTTAAAAA
1 AAAAATGGAATTTTGGAAAGTTTAGGGGTAAGAAATGTAATTTTTAGAAAATTT-GGGGTAAAAA
* *
25363 ATGGAATTTTGGAAAGTTT-AGATATAAAAATGTAATTTTTG-GAAAGTTTGAGGTG
65 ATGGAATTTTAGAAAGTTTAAG-GATAAAAATGTAATTTTTGTG-AAGTTTGAGG-G
* * *
25418 AAAAATGGAATTTTGGAAAGTTTGGGGGTAAGAAATGTAATTTTTTGAAAATTTGGGGTCAAAAA
1 AAAAATGGAATTTTGGAAAGTTTAGGGGTAAGAAATGTAATTTTTAGAAAATTTGGGGTAAAAAA
* *
25483 TGGAATTTTAGAAGGTTTAAGGGTAAAAATGTAATTTTTGTGAAGTTTGAGGG
66 TGGAATTTTAGAAAGTTTAAGGATAAAAATGTAATTTTTGTGAAGTTTGAGGG
25536 AAAAATGGAATTTTGGAAAAGTTTAGGG
1 AAAAATGGAATTTTGG-AAAGTTTAGGG
25564 ACCTTCAAGG
Statistics
Matches: 129, Mismatches: 13, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
118 17 0.13
119 89 0.69
120 23 0.18
ACGTcount: A:0.40, C:0.01, G:0.26, T:0.34
Consensus pattern (118 bp):
AAAAATGGAATTTTGGAAAGTTTAGGGGTAAGAAATGTAATTTTTAGAAAATTTGGGGTAAAAAA
TGGAATTTTAGAAAGTTTAAGGATAAAAATGTAATTTTTGTGAAGTTTGAGGG
Found at i:26709 original size:19 final size:19
Alignment explanation
Indices: 26685--26727 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
26675 AATTTTTTAT
*
26685 TTAATATTAATATTAATTA
1 TTAATATTAATAATAATTA
* *
26704 TTAATATTATTAATATTTA
1 TTAATATTAATAATAATTA
26723 TTAAT
1 TTAAT
26728 GCTATTTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
TTAATATTAATAATAATTA
Found at i:26714 original size:9 final size:9
Alignment explanation
Indices: 26685--26790 Score: 56
Period size: 9 Copynumber: 11.3 Consensus size: 9
26675 AATTTTTTAT
26685 TTAATATTA
1 TTAATATTA
* *
26694 ATATTAATTA
1 TTAAT-ATTA
26704 TTAATATTA
1 TTAATATTA
26713 TTAATATTTA
1 TTAATA-TTA
26723 TTAATGCTATTTA
1 TTAA---TA-TTA
*
26736 TTACT-TCTA
1 TTAATAT-TA
*
26745 TT--TGTTA
1 TTAATATTA
*
26752 TTAACATTA
1 TTAATATTA
*
26761 TTATTATTA
1 TTAATATTA
*
26770 TTATTATTA
1 TTAATATTA
*
26779 TTATTATTA
1 TTAATATTA
26788 TTA
1 TTA
26791 TTATATATTT
Statistics
Matches: 79, Mismatches: 9, Indels: 18
0.75 0.08 0.17
Matches are distributed among these distances:
7 5 0.06
8 2 0.03
9 48 0.61
10 15 0.19
13 9 0.11
ACGTcount: A:0.36, C:0.04, G:0.02, T:0.58
Consensus pattern (9 bp):
TTAATATTA
Found at i:26765 original size:3 final size:3
Alignment explanation
Indices: 26757--26804 Score: 78
Period size: 3 Copynumber: 15.3 Consensus size: 3
26747 TGTTATTAAC
26757 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATAT ATTT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T A-TT ATT
26804 A
1 A
26805 CCATATTTAT
Statistics
Matches: 43, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
3 38 0.88
4 4 0.09
5 1 0.02
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:27475 original size:15 final size:15
Alignment explanation
Indices: 27455--27527 Score: 76
Period size: 17 Copynumber: 4.6 Consensus size: 15
27445 TTAGAACAAT
*
27455 ATTTAAAATTTTTAA
1 ATTTAAAATATTTAA
27470 ATTTAAAATAAATTTAA
1 ATTTAAAAT--ATTTAA
27487 ATTTAATAA-ATTTAA
1 ATTTAA-AATATTTAA
27502 ATTTAAAATAATTGTAA
1 ATTTAAAAT-ATT-TAA
*
27519 ACTTAAAAT
1 ATTTAAAAT
27528 CAATTTGGAA
Statistics
Matches: 50, Mismatches: 2, Indels: 10
0.81 0.03 0.16
Matches are distributed among these distances:
14 2 0.04
15 21 0.42
16 3 0.06
17 22 0.44
18 2 0.04
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.44
Consensus pattern (15 bp):
ATTTAAAATATTTAA
Found at i:27476 original size:6 final size:6
Alignment explanation
Indices: 27465--27508 Score: 51
Period size: 6 Copynumber: 8.0 Consensus size: 6
27455 ATTTAAAATT
*
27465 TTTAAA TTTAAA -ATAAA TTTAAA TTT-AA --TAAA TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
27509 ATAATTGTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
3 1 0.03
4 2 0.06
5 6 0.19
6 23 0.72
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (6 bp):
TTTAAA
Found at i:27487 original size:17 final size:17
Alignment explanation
Indices: 27465--27533 Score: 90
Period size: 17 Copynumber: 4.2 Consensus size: 17
27455 ATTTAAAATT
27465 TTTAAATTTAAAATAAA
1 TTTAAATTTAAAATAAA
27482 TTTAAATTT--AATAAA
1 TTTAAATTTAAAATAAA
27497 TTTAAATTTAAAAT-AA
1 TTTAAATTTAAAATAAA
* *
27513 TTGTAAACTTAAAATCAA
1 TT-TAAATTTAAAATAAA
27531 TTT
1 TTT
27534 GGAATGCAAA
Statistics
Matches: 47, Mismatches: 1, Indels: 8
0.84 0.02 0.14
Matches are distributed among these distances:
15 15 0.32
16 4 0.09
17 24 0.51
18 4 0.09
ACGTcount: A:0.52, C:0.03, G:0.01, T:0.43
Consensus pattern (17 bp):
TTTAAATTTAAAATAAA
Found at i:27491 original size:32 final size:32
Alignment explanation
Indices: 27455--27527 Score: 96
Period size: 32 Copynumber: 2.3 Consensus size: 32
27445 TTAGAACAAT
*
27455 ATTTAAAATTTTTAAATTTAAAATAAATT-TAA
1 ATTTAAAATATTTAAATTTAAAAT-AATTGTAA
27487 ATTTAATAA-ATTTAAATTTAAAATAATTGTAA
1 ATTTAA-AATATTTAAATTTAAAATAATTGTAA
*
27519 ACTTAAAAT
1 ATTTAAAAT
27528 CAATTTGGAA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
31 6 0.17
32 28 0.78
33 2 0.06
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.44
Consensus pattern (32 bp):
ATTTAAAATATTTAAATTTAAAATAATTGTAA
Found at i:27752 original size:26 final size:25
Alignment explanation
Indices: 27716--27770 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 25
27706 TTCCTTTTTT
* * *
27716 TTTTTTCTTTTCATTTTTAGATTAGG
1 TTTTCTCTTTTC-TTTTTAGAATAGA
27742 TTTTCTCTTTTCTTTTTAGAATAGA
1 TTTTCTCTTTTCTTTTTAGAATAGA
27767 TTTT
1 TTTT
27771 AACTTTGCTG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
25 15 0.58
26 11 0.42
ACGTcount: A:0.16, C:0.09, G:0.09, T:0.65
Consensus pattern (25 bp):
TTTTCTCTTTTCTTTTTAGAATAGA
Found at i:27758 original size:37 final size:38
Alignment explanation
Indices: 27684--27758 Score: 89
Period size: 37 Copynumber: 2.0 Consensus size: 38
27674 CTTTCTTTAG
* * *
27684 TTTTCATAGTTTTAGGTTAGCTTTCCTTTTTTTTTTTTC
1 TTTTCATA-TTTTAGATTAGCTTTCCTCTTTTCTTTTTC
* *
27723 TTTTCAT-TTTTAGATTAGGTTTTCTCTTTTCTTTTT
1 TTTTCATATTTTAGATTAGCTTTCCTCTTTTCTTTTT
27759 AGAATAGATT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
37 24 0.77
39 7 0.23
ACGTcount: A:0.11, C:0.12, G:0.09, T:0.68
Consensus pattern (38 bp):
TTTTCATATTTTAGATTAGCTTTCCTCTTTTCTTTTTC
Found at i:27776 original size:25 final size:25
Alignment explanation
Indices: 27722--27785 Score: 65
Period size: 25 Copynumber: 2.5 Consensus size: 25
27712 TTTTTTTTTT
* * **
27722 CTTTTCATTTTTAGATTAGGTTTTCT
1 CTTTTC-TTTTTAGAATAGATTTTAA
27748 CTTTTCTTTTTAGAATAGATTTTAA
1 CTTTTCTTTTTAGAATAGATTTTAA
*
27773 CTTTGCTGTTTTA
1 CTTTTCT-TTTTA
27786 TTTCTTCCTT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
25 21 0.66
26 11 0.34
ACGTcount: A:0.19, C:0.11, G:0.11, T:0.59
Consensus pattern (25 bp):
CTTTTCTTTTTAGAATAGATTTTAA
Found at i:27921 original size:2 final size:2
Alignment explanation
Indices: 27914--27938 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
27904 GTGCTTGATA
27914 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 A
27939 AATTTGATTA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:38165 original size:12 final size:12
Alignment explanation
Indices: 38148--38177 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
38138 ATGACACACT
38148 GCCGTGTGATAG
1 GCCGTGTGATAG
*
38160 GCCGTGTGGTAG
1 GCCGTGTGATAG
38172 GCCGTG
1 GCCGTG
38178 CAACTCATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.10, C:0.20, G:0.47, T:0.23
Consensus pattern (12 bp):
GCCGTGTGATAG
Found at i:41214 original size:23 final size:23
Alignment explanation
Indices: 41187--41234 Score: 87
Period size: 23 Copynumber: 2.1 Consensus size: 23
41177 TAAGTAGTAT
41187 AAATATTTTCAACTAAATAATAA
1 AAATATTTTCAACTAAATAATAA
*
41210 AAATATTTTCAATTAAATAATAA
1 AAATATTTTCAACTAAATAATAA
41233 AA
1 AA
41235 TTTGAATTGA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.35
Consensus pattern (23 bp):
AAATATTTTCAACTAAATAATAA
Found at i:50911 original size:29 final size:29
Alignment explanation
Indices: 50869--50929 Score: 113
Period size: 29 Copynumber: 2.1 Consensus size: 29
50859 ATATAGGAAA
*
50869 GATAGAGAAAGTACCGGCTAATGCATCTG
1 GATAAAGAAAGTACCGGCTAATGCATCTG
50898 GATAAAGAAAGTACCGGCTAATGCATCTG
1 GATAAAGAAAGTACCGGCTAATGCATCTG
50927 GAT
1 GAT
50930 CCAGCTGCAC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.36, C:0.16, G:0.26, T:0.21
Consensus pattern (29 bp):
GATAAAGAAAGTACCGGCTAATGCATCTG
Found at i:52893 original size:30 final size:29
Alignment explanation
Indices: 52852--53314 Score: 256
Period size: 29 Copynumber: 15.7 Consensus size: 29
52842 CTCGAGGGTG
* * *
52852 AAATGGTAATTTTGGGAAAATTCGAGGTTAA
1 AAATGG-AATTTTTGG-AAGTTCAAGGTTAA
* *
52883 AAATGGAATTTTTGGAAGTTCAAGGCTAT
1 AAATGGAATTTTTGGAAGTTCAAGGTTAA
*
52912 AAATGAAATTTTTGGAAGTTTCAAGGTTAA
1 AAATGGAATTTTTGGAAG-TTCAAGGTTAA
* *
52942 AAATGGGATTTTTGGAAGTT--AGCGAGTAA
1 AAATGGAATTTTTGGAAGTTCAAG-G-TTAA
* * ***
52971 AAATGGAATTTTTGAAATTTTTTGGGTTAA
1 AAATGGAATTTTTGGAA-GTTCAAGGTTAA
* * *** *
53001 AATTGG-ATTTTTGGAAATTTGGGGGTAA
1 AAATGGAATTTTTGGAAGTTCAAGGTTAA
* ** *
53029 AAAT-GAGATTTTTGGATGTTCGGGGGTAA
1 AAATGGA-ATTTTTGGAAGTTCAAGGTTAA
* * * *
53058 AAATGGATTTTTTGGAAGTTTTAGGGTCAA
1 AAATGGAATTTTTGGAAG-TTCAAGGTTAA
*** *
53088 AAATAGG-ATTTTTGGAAGTTTGGGGGTAA
1 AAAT-GGAATTTTTGGAAGTTCAAGGTTAA
* *** *
53117 AAATTGAATTTTTGGAAGTTTTGGGGTCAA
1 AAATGGAATTTTTGGAAG-TTCAAGGTTAA
* ** *
53147 AAATGGGATTTTTGGAAGTTCGGGGGTAA
1 AAATGGAATTTTTGGAAGTTCAAGGTTAA
* * **
53176 AAATGGAAATTTTGGAACTT-TTGGTGTCAA
1 AAATGGAATTTTTGGAAGTTCAAGGT-T-AA
* ** *
53206 AAATGGGATTTTTGGAAGTTCGGGGGTAA
1 AAATGGAATTTTTGGAAGTTCAAGGTTAA
*
53235 AAATGGAATTTTTGGAAGTTTC-AGGATAAA
1 AAATGGAATTTTTGGAAG-TTCAAGG-TTAA
* ** *
53265 AAATGGGATTTTTGGAAGTTCGGGGGTAA
1 AAATGGAATTTTTGGAAGTTCAAGGTTAA
*
53294 AAATGGAGTTTTTGGATAGTT
1 AAATGGAATTTTTGGA-AGTT
53315 TAGGGACCTT
Statistics
Matches: 347, Mismatches: 65, Indels: 41
0.77 0.14 0.09
Matches are distributed among these distances:
27 3 0.01
28 16 0.05
29 177 0.51
30 139 0.40
31 11 0.03
32 1 0.00
ACGTcount: A:0.32, C:0.03, G:0.29, T:0.36
Consensus pattern (29 bp):
AAATGGAATTTTTGGAAGTTCAAGGTTAA
Found at i:52975 original size:59 final size:57
Alignment explanation
Indices: 52880--53319 Score: 420
Period size: 59 Copynumber: 7.5 Consensus size: 57
52870 AATTCGAGGT
* * ** ** *
52880 TAAAAATGGAATTTTTGGAAGTTCAAGG-CTATAAATGAAATTTTTGGAAGTTTCAAGGT
1 TAAAAATGGAATTTTTGGAAGTT-AGGGTC-AAAAATGGGATTTTTGGAAG-TTCGGGGG
* * * * ** *
52939 TAAAAATGGGATTTTTGGAAGTTAGCGAGT-AAAAATGGAATTTTTGAAATTTTTTGGGT
1 TAAAAATGGAATTTTTGGAAGTTAG-G-GTCAAAAATGGGATTTTTGGAA-GTTCGGGGG
* * * * *
52998 TAAAATTGG-ATTTTTGGAAATTTGGGGGT-AAAAATGAGATTTTTGGATGTTCGGGGG
1 TAAAAATGGAATTTTTGG-AAGTT-AGGGTCAAAAATGGGATTTTTGGAAGTTCGGGGG
* * *
53055 TAAAAATGGATTTTTTGGAAGTTTTAGGGTCAAAAATAGGATTTTTGGAAGTTTGGGGG
1 TAAAAATGGAATTTTTGGAAG--TTAGGGTCAAAAATGGGATTTTTGGAAGTTCGGGGG
* *
53114 TAAAAATTGAATTTTTGGAAGTTTTGGGGTCAAAAATGGGATTTTTGGAAGTTCGGGGG
1 TAAAAATGGAATTTTTGGAAG--TTAGGGTCAAAAATGGGATTTTTGGAAGTTCGGGGG
* * *
53173 TAAAAATGGAAATTTTGGAACTTTTGGTGTCAAAAATGGGATTTTTGGAAGTTCGGGGG
1 TAAAAATGGAATTTTTGGAA-GTTAGG-GTCAAAAATGGGATTTTTGGAAGTTCGGGGG
* *
53232 TAAAAATGGAATTTTTGGAAGTTTCAGGATAAAAAATGGGATTTTTGGAAGTTCGGGGG
1 TAAAAATGGAATTTTTGGAAG-TT-AGGGTCAAAAATGGGATTTTTGGAAGTTCGGGGG
*
53291 TAAAAATGGAGTTTTTGGATAGTTTAGGG
1 TAAAAATGGAATTTTTGGA-AG-TTAGGG
53320 ACCTTCAGGG
Statistics
Matches: 322, Mismatches: 44, Indels: 30
0.81 0.11 0.08
Matches are distributed among these distances:
57 15 0.05
58 41 0.13
59 257 0.80
60 9 0.03
ACGTcount: A:0.32, C:0.03, G:0.29, T:0.36
Consensus pattern (57 bp):
TAAAAATGGAATTTTTGGAAGTTAGGGTCAAAAATGGGATTTTTGGAAGTTCGGGGG
Found at i:53174 original size:118 final size:115
Alignment explanation
Indices: 52880--53318 Score: 472
Period size: 118 Copynumber: 3.7 Consensus size: 115
52870 AATTCGAGGT
* * * * ** ** *
52880 TAAAAATGGAATTTTTGGAAG-TTCAAGGCTATAAATGAAATTTTTGGAAGTTTCAAGGTTAAAA
1 TAAAAATTGAATTTTTGGAAGTTTC-GGGGTAAAAATGGGATTTTTGGAAG-TTCGGGGGTAAAA
* * **
52944 ATGGGATTTTTGGAAG-TTAGCGAGT-AAAAATGGAATTTTTGAAATTTTTTGGG
64 AT-GGATTTTTGGAAGTTTAG-GAGTCAAAAATGG-ATTTTTGGAAGTTTGGGGG
* * * * * *
52997 TTAAAATTGGATTTTTGGAAATTTGGGGGTAAAAATGAGATTTTTGGATGTTCGGGGGTAAAAAT
1 TAAAAATTGAATTTTTGGAAGTTTCGGGGTAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAAAT
53062 GGATTTTTTGGAAGTTTTAGG-GTCAAAAATAGGATTTTTGGAAGTTTGGGGG
66 GGA-TTTTTGGAAG-TTTAGGAGTCAAAAAT-GGATTTTTGGAAGTTTGGGGG
*
53114 TAAAAATTGAATTTTTGGAAGTTTTGGGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAAA
1 TAAAAATTGAATTTTTGGAAGTTTCGGGGT-AAAAATGGGATTTTTGGAAGTTCGGGGGTAAAAA
* * * * *
53179 TGGAAATTTTGGAACTTTTGGTGTCAAAAATGGGATTTTTGGAAGTTCGGGGG
65 TGG-ATTTTTGGAAGTTTAGGAGTCAAAAAT-GGATTTTTGGAAGTTTGGGGG
* * *
53232 TAAAAATGGAATTTTTGGAAGTTTCAGGATAAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAAA
1 TAAAAATTGAATTTTTGGAAGTTTCGGGGT-AAAAATGGGATTTTTGGAAGTTCGGGGGTAAAAA
53297 TGGAGTTTTTGGATAGTTTAGG
65 TGGA-TTTTTGGA-AGTTTAGG
53319 GACCTTCAGG
Statistics
Matches: 275, Mismatches: 36, Indels: 20
0.83 0.11 0.06
Matches are distributed among these distances:
115 3 0.01
116 24 0.09
117 91 0.33
118 150 0.55
119 7 0.03
ACGTcount: A:0.32, C:0.03, G:0.29, T:0.36
Consensus pattern (115 bp):
TAAAAATTGAATTTTTGGAAGTTTCGGGGTAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAAAT
GGATTTTTGGAAGTTTAGGAGTCAAAAATGGATTTTTGGAAGTTTGGGGG
Found at i:54012 original size:78 final size:79
Alignment explanation
Indices: 53914--54073 Score: 209
Period size: 79 Copynumber: 2.0 Consensus size: 79
53904 GCCCGTCGCG
*
53914 GGTCCGTAGCCACGCGCCGTTGTGCG-CTTCCGCCA-AGGC-AACGTCCGACCGTCCACACGCCC
1 GGTCCGTAGCCACGCACCGTTGTGCGTC-TCCGCCATA-GCAAACGTCCGACCGTCCACACGCCC
53976 CACATCTCCAGTCACC
64 CACATCTCCAGTCACC
* * ** *
53992 GGTCCGTAGCCACGCACCGTTGTGCGTCTCCGCCATAGCAAACGTCCGATCGTCCCCGTGCCCCG
1 GGTCCGTAGCCACGCACCGTTGTGCGTCTCCGCCATAGCAAACGTCCGACCGTCCACACGCCCCA
**
54057 CATCTCTGGTCACC
66 CATCTCCAGTCACC
54071 GGT
1 GGT
54074 AAGTTCAAAG
Statistics
Matches: 71, Mismatches: 8, Indels: 5
0.85 0.10 0.06
Matches are distributed among these distances:
78 34 0.48
79 37 0.52
ACGTcount: A:0.15, C:0.42, G:0.24, T:0.18
Consensus pattern (79 bp):
GGTCCGTAGCCACGCACCGTTGTGCGTCTCCGCCATAGCAAACGTCCGACCGTCCACACGCCCCA
CATCTCCAGTCACC
Found at i:55101 original size:6 final size:6
Alignment explanation
Indices: 55092--55169 Score: 60
Period size: 6 Copynumber: 13.5 Consensus size: 6
55082 TGAACTTTAT
* * *
55092 TTTAAA TTTATAA --TAAT TTTAAA TTTGAAA -ATAAA TTTAAA CTTAAA
1 TTTAAA TTTA-AA TTTAAA TTTAAA TTT-AAA TTTAAA TTTAAA TTTAAA
55139 TTTAGAA --TAAA TTTAAA TTT-AA TTTAAA TTT
1 TTTA-AA TTTAAA TTTAAA TTTAAA TTTAAA TTT
55170 TTAACAAATT
Statistics
Matches: 57, Mismatches: 6, Indels: 18
0.70 0.07 0.22
Matches are distributed among these distances:
4 3 0.05
5 12 0.21
6 35 0.61
7 7 0.12
ACGTcount: A:0.49, C:0.01, G:0.03, T:0.47
Consensus pattern (6 bp):
TTTAAA
Found at i:55130 original size:18 final size:17
Alignment explanation
Indices: 55092--55200 Score: 80
Period size: 17 Copynumber: 6.4 Consensus size: 17
55082 TGAACTTTAT
* *
55092 TTTAAATTTATAATAAT
1 TTTAAATTTAAAATAAA
55109 TTTAAATTTGAAAATAAA
1 TTTAAATTT-AAAATAAA
* *
55127 TTTAAACTTAAATTTAGAA
1 TTTAAATTTAAA-ATA-AA
* *
55146 --TAAATTTAAATTTAA
1 TTTAAATTTAAAATAAA
** *
55161 TTTAAATTTTTAACAAA
1 TTTAAATTTAAAATAAA
55178 TTT-AATCTTAAAATAAA
1 TTTAAAT-TTAAAATAAA
55195 TTTAAA
1 TTTAAA
55201 GGGGAGTTTG
Statistics
Matches: 71, Mismatches: 14, Indels: 13
0.72 0.14 0.13
Matches are distributed among these distances:
15 2 0.03
16 5 0.07
17 44 0.62
18 18 0.25
19 2 0.03
ACGTcount: A:0.50, C:0.03, G:0.02, T:0.45
Consensus pattern (17 bp):
TTTAAATTTAAAATAAA
Found at i:55151 original size:23 final size:22
Alignment explanation
Indices: 55110--55166 Score: 78
Period size: 23 Copynumber: 2.5 Consensus size: 22
55100 TATAATAATT
55110 TTAAATTTGAAAATAAATTTAAA
1 TTAAATTT-AAAATAAATTTAAA
*
55133 CTTAAATTTAGAATAAATTTAAA
1 -TTAAATTTAAAATAAATTTAAA
*
55156 TTTAATTTAAA
1 TTAAATTTAAA
55167 TTTTTAACAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
22 9 0.30
23 13 0.43
24 8 0.27
ACGTcount: A:0.53, C:0.02, G:0.04, T:0.42
Consensus pattern (22 bp):
TTAAATTTAAAATAAATTTAAA
Found at i:55169 original size:11 final size:11
Alignment explanation
Indices: 55110--55168 Score: 66
Period size: 11 Copynumber: 5.2 Consensus size: 11
55100 TATAATAATT
55110 TTAAATTTGAAA
1 TTAAATTT-AAA
*
55122 ATAAATTTAAA
1 TTAAATTTAAA
55133 CTTAAATTTAGAA
1 -TTAAATTTA-AA
55146 -TAAATTTAAA
1 TTAAATTTAAA
*
55156 TTTAATTTAAA
1 TTAAATTTAAA
55167 TT
1 TT
55169 TTTAACAAAT
Statistics
Matches: 41, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
10 2 0.05
11 22 0.54
12 15 0.37
13 2 0.05
ACGTcount: A:0.51, C:0.02, G:0.03, T:0.44
Consensus pattern (11 bp):
TTAAATTTAAA
Found at i:56017 original size:218 final size:218
Alignment explanation
Indices: 55686--56174 Score: 888
Period size: 218 Copynumber: 2.2 Consensus size: 218
55676 GGGTTCGAAG
* *
55686 ATCGGGCGTGAGTTTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACTATGTCATTTG
1 ATCGAGCGTGAGTTTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACTACGTCATTTG
* *
55751 TTTCAATTCACTTCTCTGTATCTCATCAGGAAAACGAATTTGGTCCACTTCTCCGTACCTTATCA
66 TTTCAATTCACTTCTCTGTATCTCATCAGGAAAACGAATTTAGTCCACTTCTCCATACCTTATCA
* *
55816 GGGAGATGGTCAGGAAGCTGACCGTTTTATTACTTCGACTTGCTTCTCAATATCTTATCAGGAAG
131 GGGAGATGGTCAGGAAGCTGACCATTTTATTACTTCGACTTGCTTCTCAATATCTCATCAGGAAG
55881 CTGGGATTTGAAGATTTGCTCAT
196 CTGGGATTTGAAGATTTGCTCAT
55904 ATCGAGCGTGAGTTTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACTACGTCATTTG
1 ATCGAGCGTGAGTTTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACTACGTCATTTG
* *
55969 TTTCAATTCACTTCTCTGTATCTCATCAGGAAGACGAATTTAGTCCACTTTTCCATACCTTATCA
66 TTTCAATTCACTTCTCTGTATCTCATCAGGAAAACGAATTTAGTCCACTTCTCCATACCTTATCA
* *
56034 GGGAGATGGTCAGGAAGCTGACCATTTTATTACTTCGACTTGCTTCTCAGTATCTCATTAGGAAG
131 GGGAGATGGTCAGGAAGCTGACCATTTTATTACTTCGACTTGCTTCTCAATATCTCATCAGGAAG
56099 CTGGGATTTGAAGATTTGCTCAT
196 CTGGGATTTGAAGATTTGCTCAT
56122 ATCGAGCGTGAGTTTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGA
1 ATCGAGCGTGAGTTTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGA
56175 TCGTTTTATT
Statistics
Matches: 261, Mismatches: 10, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
218 261 1.00
ACGTcount: A:0.23, C:0.20, G:0.21, T:0.36
Consensus pattern (218 bp):
ATCGAGCGTGAGTTTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACTACGTCATTTG
TTTCAATTCACTTCTCTGTATCTCATCAGGAAAACGAATTTAGTCCACTTCTCCATACCTTATCA
GGGAGATGGTCAGGAAGCTGACCATTTTATTACTTCGACTTGCTTCTCAATATCTCATCAGGAAG
CTGGGATTTGAAGATTTGCTCAT
Found at i:56256 original size:120 final size:120
Alignment explanation
Indices: 56043--56296 Score: 454
Period size: 120 Copynumber: 2.1 Consensus size: 120
56033 AGGGAGATGG
* * * *
56043 TCAGGAAGCTGACCATTTTATTACTTCGACTTGCTTCTCAGTATCTCATTAGGAAGCTGGGATTT
1 TCAGGAAGATGACCATTTTATTACTTCGACTTGCTTCTCAGTATCTCATCAGGAAACTGGGATTC
56108 GAAGATTTGCTCATATCGAGCGTGAGTTTGATTTGGTCTTCTTCTCAGTATCTCA
66 GAAGATTTGCTCATATCGAGCGTGAGTTTGATTTGGTCTTCTTCTCAGTATCTCA
* *
56163 TCAGGAAGATGATCGTTTTATTACTTCGACTTGCTTCTCAGTATCTCATCAGGAAACTGGGATTC
1 TCAGGAAGATGACCATTTTATTACTTCGACTTGCTTCTCAGTATCTCATCAGGAAACTGGGATTC
56228 GAAGATTTGCTCATATCGAGCGTGAGTTTGATTTGGTCTTCTTCTCAGTATCTCA
66 GAAGATTTGCTCATATCGAGCGTGAGTTTGATTTGGTCTTCTTCTCAGTATCTCA
56283 TCAGGAAGATGACC
1 TCAGGAAGATGACC
56297 GTGTCGTTTT
Statistics
Matches: 127, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
120 127 1.00
ACGTcount: A:0.23, C:0.19, G:0.21, T:0.37
Consensus pattern (120 bp):
TCAGGAAGATGACCATTTTATTACTTCGACTTGCTTCTCAGTATCTCATCAGGAAACTGGGATTC
GAAGATTTGCTCATATCGAGCGTGAGTTTGATTTGGTCTTCTTCTCAGTATCTCA
Found at i:57637 original size:17 final size:17
Alignment explanation
Indices: 57615--57662 Score: 69
Period size: 18 Copynumber: 2.8 Consensus size: 17
57605 TTTGAACTTT
*
57615 ATTTTAAATTTATAATA
1 ATTTTAAATTTAAAATA
57632 ATTTTAAATTTGAAAATA
1 ATTTTAAATTT-AAAATA
*
57650 AATTTAAATTTAA
1 ATTTTAAATTTAA
57663 TTTAAATTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
17 13 0.46
18 15 0.54
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (17 bp):
ATTTTAAATTTAAAATA
Found at i:57670 original size:46 final size:45
Alignment explanation
Indices: 57612--57702 Score: 121
Period size: 46 Copynumber: 2.0 Consensus size: 45
57602 GTATTTGAAC
* * *
57612 TTTATTTTAAATTTATAATAATTTTAAAT-TTGAAAATAAATTTAAA
1 TTTAATTTAAATTTATAACAAATTT-AATCTT-AAAATAAATTTAAA
*
57658 TTTAATTTAAATTTTTAACAAATTTAATCTTAAAATAAATTTAAA
1 TTTAATTTAAATTTATAACAAATTTAATCTTAAAATAAATTTAAA
57703 GGGGAGTTTG
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
45 17 0.43
46 23 0.57
ACGTcount: A:0.48, C:0.02, G:0.01, T:0.48
Consensus pattern (45 bp):
TTTAATTTAAATTTATAACAAATTTAATCTTAAAATAAATTTAAA
Found at i:58346 original size:2 final size:2
Alignment explanation
Indices: 58339--58363 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
58329 AAATTCATTC
58339 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 A
58364 AGTTGTAATT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:62009 original size:141 final size:138
Alignment explanation
Indices: 61723--62010 Score: 308
Period size: 141 Copynumber: 2.0 Consensus size: 138
61713 CATTTTTTTA
* ** *
61723 TTTTTAATTAATATTTTTGACACATTAGCTTTTTTGGTTAGATGGTTAGATAATTGTGATATCAT
1 TTTTTAATTAATATTTATGACACATTAGCTCATTTGGTTAGATGGCTAGATAATTGTGATATCAT
* * *
61788 CCTTAAGGCCCAAGTTCAATTCCTCTTATAAGTATTTAAATATGCATTTTTTTTATTTCATGTTA
66 CCTTAAGACCCAAGTTCAATTCCTCTTATAAGCATTTAAATATGCATTTTTTTTATTTAATGTTA
61853 TTTAAAGCTTT
131 TTTAAAG---T
* *
61864 TTTTTAATTAATATTTATGACCCATTAGCTCATTTGGTTAGATGGCTATATAATTGTGATATCAT
1 TTTTTAATTAATATTTATGACACATTAGCTCATTTGGTTAGATGGCTAGATAATTGTGATATCAT
* *** * ** * * *
61929 TCTTGAGATCGAATTTAAGTTTAATTTTTCTTATACGCATTTTAATATGTA-TTTTTTTATTTAA
66 CCTT-A-A--G-ACCCAAGTTCAATTCCTCTTATAAGCATTTAAATATGCATTTTTTTTATTTAA
* *
61993 TGTTGTTTTAAGT
126 TGTTATTTAAAGT
62006 TTTTT
1 TTTTT
62011 TAAATAAATG
Statistics
Matches: 121, Mismatches: 21, Indels: 9
0.80 0.14 0.06
Matches are distributed among these distances:
141 62 0.51
142 7 0.06
143 1 0.01
145 23 0.19
146 28 0.23
ACGTcount: A:0.27, C:0.10, G:0.12, T:0.51
Consensus pattern (138 bp):
TTTTTAATTAATATTTATGACACATTAGCTCATTTGGTTAGATGGCTAGATAATTGTGATATCAT
CCTTAAGACCCAAGTTCAATTCCTCTTATAAGCATTTAAATATGCATTTTTTTTATTTAATGTTA
TTTAAAGT
Found at i:63068 original size:2 final size:2
Alignment explanation
Indices: 63061--63088 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
63051 ATTAGTCGTC
63061 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
63089 ATTACCTGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:69529 original size:21 final size:20
Alignment explanation
Indices: 69479--69533 Score: 67
Period size: 20 Copynumber: 2.7 Consensus size: 20
69469 GCTTGTACGG
**
69479 GTTTGCACTTTGGTGCCTCT
1 GTTTGCACTACGGTGCCTCT
69499 GTTTGCACTACGGTGCCTCT
1 GTTTGCACTACGGTGCCTCT
69519 -TTATAGCACTACGGT
1 GTT-T-GCACTACGGT
69534 TCCCTTTGGT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
19 2 0.06
20 19 0.61
21 10 0.32
ACGTcount: A:0.13, C:0.25, G:0.24, T:0.38
Consensus pattern (20 bp):
GTTTGCACTACGGTGCCTCT
Found at i:71343 original size:57 final size:57
Alignment explanation
Indices: 71255--71369 Score: 230
Period size: 57 Copynumber: 2.0 Consensus size: 57
71245 GAGACCATAA
71255 CCCTCACTAAGAAGTGTAGTGCAATTATTTATAGAAAGAGTTGAAGGATCCAAAGAG
1 CCCTCACTAAGAAGTGTAGTGCAATTATTTATAGAAAGAGTTGAAGGATCCAAAGAG
71312 CCCTCACTAAGAAGTGTAGTGCAATTATTTATAGAAAGAGTTGAAGGATCCAAAGAG
1 CCCTCACTAAGAAGTGTAGTGCAATTATTTATAGAAAGAGTTGAAGGATCCAAAGAG
71369 C
1 C
71370 TTTATCATAA
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 58 1.00
ACGTcount: A:0.38, C:0.15, G:0.23, T:0.24
Consensus pattern (57 bp):
CCCTCACTAAGAAGTGTAGTGCAATTATTTATAGAAAGAGTTGAAGGATCCAAAGAG
Found at i:73375 original size:23 final size:23
Alignment explanation
Indices: 73349--73393 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
73339 AATAAAAAAA
*
73349 TAATATTTTTT-TTCAATTTAGTT
1 TAAT-TTTTTTGTTAAATTTAGTT
73372 TAATTTTTTTGTTAAATTTAGT
1 TAATTTTTTTGTTAAATTTAGT
73394 AATTACATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 6 0.30
23 14 0.70
ACGTcount: A:0.27, C:0.02, G:0.07, T:0.64
Consensus pattern (23 bp):
TAATTTTTTTGTTAAATTTAGTT
Found at i:83530 original size:32 final size:32
Alignment explanation
Indices: 83489--83549 Score: 122
Period size: 32 Copynumber: 1.9 Consensus size: 32
83479 CACTATCTCG
83489 ATCGCATCTCCACATTCTAAGGACTTAATCAA
1 ATCGCATCTCCACATTCTAAGGACTTAATCAA
83521 ATCGCATCTCCACATTCTAAGGACTTAAT
1 ATCGCATCTCCACATTCTAAGGACTTAAT
83550 TGATTCACAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.33, C:0.28, G:0.10, T:0.30
Consensus pattern (32 bp):
ATCGCATCTCCACATTCTAAGGACTTAATCAA
Found at i:86528 original size:21 final size:21
Alignment explanation
Indices: 86478--86538 Score: 68
Period size: 21 Copynumber: 2.9 Consensus size: 21
86468 ACAACATGTG
* * *
86478 AAAGTGTTCGCATAACATCTA
1 AAAGAGTTTGCATAACATATA
*
86499 AAAGAGTTTGCATAGCATATA
1 AAAGAGTTTGCATAACATATA
*
86520 AAAGAGTTTTCATATACAT
1 AAAGAGTTTGCATA-ACAT
86539 GTAACTAGCT
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
21 30 0.91
22 3 0.09
ACGTcount: A:0.41, C:0.13, G:0.15, T:0.31
Consensus pattern (21 bp):
AAAGAGTTTGCATAACATATA
Found at i:91256 original size:21 final size:21
Alignment explanation
Indices: 91227--91275 Score: 89
Period size: 21 Copynumber: 2.3 Consensus size: 21
91217 TGACTTCTTC
*
91227 GTCGTGACATACAGGGGCTAT
1 GTCGCGACATACAGGGGCTAT
91248 GTCGCGACATACAGGGGCTAT
1 GTCGCGACATACAGGGGCTAT
91269 GTCGCGA
1 GTCGCGA
91276 TAACGCTTGT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.22, C:0.22, G:0.35, T:0.20
Consensus pattern (21 bp):
GTCGCGACATACAGGGGCTAT
Found at i:91533 original size:13 final size:14
Alignment explanation
Indices: 91515--91548 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
91505 TTGCTTAGGC
91515 TTTAGTTTTCAA-T
1 TTTAGTTTTCAATT
*
91528 TTTAGTTTTTAATT
1 TTTAGTTTTCAATT
91542 TTTAGTT
1 TTTAGTT
91549 GTTAAACGAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 11 0.58
14 8 0.42
ACGTcount: A:0.21, C:0.03, G:0.09, T:0.68
Consensus pattern (14 bp):
TTTAGTTTTCAATT
Found at i:91544 original size:14 final size:13
Alignment explanation
Indices: 91515--91553 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
91505 TTGCTTAGGC
*
91515 TTTAGTTTTCAAT
1 TTTAGTTTTTAAT
91528 TTTAGTTTTTAATT
1 TTTAGTTTTTAA-T
*
91542 TTTAGTTGTTAA
1 TTTAGTTTTTAA
91554 ACGAGATTGT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 11 0.48
14 12 0.52
ACGTcount: A:0.23, C:0.03, G:0.10, T:0.64
Consensus pattern (13 bp):
TTTAGTTTTTAAT
Found at i:92122 original size:17 final size:17
Alignment explanation
Indices: 92093--92125 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
92083 AAACGTTTCC
92093 TTTACTTTCTATTTTAG
1 TTTACTTTCTATTTTAG
92110 TTTACCTTT-TATTTTA
1 TTTA-CTTTCTATTTTA
92126 TGCTTTAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.18, C:0.12, G:0.03, T:0.67
Consensus pattern (17 bp):
TTTACTTTCTATTTTAG
Found at i:101175 original size:54 final size:54
Alignment explanation
Indices: 101112--101221 Score: 202
Period size: 54 Copynumber: 2.0 Consensus size: 54
101102 CCATCATCCT
*
101112 TTAACACAAAACATGCAAAATAACCATTCTCTTACACAACCAACCTTAACCGAA
1 TTAACACAAAACATGCAAAATAACCATTCTCTAACACAACCAACCTTAACCGAA
*
101166 TTAACACAAAACATGCAAAATAACCATTCTCTAACACAACCAACCTTAATCGAA
1 TTAACACAAAACATGCAAAATAACCATTCTCTAACACAACCAACCTTAACCGAA
101220 TT
1 TT
101222 TTCTAGGTTG
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
54 54 1.00
ACGTcount: A:0.46, C:0.28, G:0.04, T:0.22
Consensus pattern (54 bp):
TTAACACAAAACATGCAAAATAACCATTCTCTAACACAACCAACCTTAACCGAA
Found at i:108125 original size:17 final size:17
Alignment explanation
Indices: 108103--108141 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
108093 GGGTAAAGTT
*
108103 TTGGAATTGATTAAATA
1 TTGGAATTGAATAAATA
* *
108120 TTGGAATTTAATCAATA
1 TTGGAATTGAATAAATA
108137 TTGGA
1 TTGGA
108142 TAATTATTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.38, C:0.03, G:0.18, T:0.41
Consensus pattern (17 bp):
TTGGAATTGAATAAATA
Found at i:108890 original size:43 final size:43
Alignment explanation
Indices: 108814--108992 Score: 161
Period size: 43 Copynumber: 4.1 Consensus size: 43
108804 TTAATGTCAT
* *
108814 TGAGAGGAACACTATTTCTTAAATATTGTAAGTATGTGACTGAA
1 TGAGAGGAACACTATTTCCT-AATATTGAAAGTATGTGACTGAA
* * * **
108858 TGAGAGGAACATTGTTTCCTAATATTGAAAGTATGTGATCAGTTT
1 TGAGAGGAACACTATTTCCTAATATTGAAAGTATGTGA-CTG-AA
* *
108903 TGTGA--AACACTATTTCCTAATATTGAAACTATGTGA-TCGAA
1 TGAGAGGAACACTATTTCCTAATATTGAAAGTATGTGACT-GAA
* * *
108944 TGA-ATGGAACACTGTTTCCTAATATTGATAA-TATGTGATTGAT
1 TGAGA-GGAACACTATTTCCTAATATTGA-AAGTATGTGACTGAA
108987 TGAGAG
1 TGAGAG
108993 CATGTTGAAA
Statistics
Matches: 109, Mismatches: 17, Indels: 19
0.75 0.12 0.13
Matches are distributed among these distances:
40 1 0.01
41 2 0.02
42 1 0.01
43 78 0.72
44 23 0.21
45 4 0.04
ACGTcount: A:0.34, C:0.10, G:0.20, T:0.36
Consensus pattern (43 bp):
TGAGAGGAACACTATTTCCTAATATTGAAAGTATGTGACTGAA
Found at i:108945 original size:86 final size:87
Alignment explanation
Indices: 108821--108982 Score: 233
Period size: 86 Copynumber: 1.9 Consensus size: 87
108811 CATTGAGAGG
* * * *
108821 AACACTATTTCTTAAATATTGTAAGTATGTGACTGAATGAGA-GGAACATTGTTTCCTAATATTG
1 AACACTATTTCCTAAATATTGAAACTATGTGACTGAATGA-ATGGAACACTGTTTCCTAATATTG
108885 A-AAGTATGTGATCAGTTTTGTGA
65 ATAA-TATGTGATCAGTTTTGTGA
108908 AACACTATTTCCT-AATATTGAAACTATGTGA-TCGAATGAATGGAACACTGTTTCCTAATATTG
1 AACACTATTTCCTAAATATTGAAACTATGTGACT-GAATGAATGGAACACTGTTTCCTAATATTG
108971 ATAATATGTGAT
65 ATAATATGTGAT
108983 TGATTGAGAG
Statistics
Matches: 68, Mismatches: 4, Indels: 7
0.86 0.05 0.09
Matches are distributed among these distances:
85 2 0.03
86 52 0.76
87 14 0.21
ACGTcount: A:0.35, C:0.11, G:0.17, T:0.37
Consensus pattern (87 bp):
AACACTATTTCCTAAATATTGAAACTATGTGACTGAATGAATGGAACACTGTTTCCTAATATTGA
TAATATGTGATCAGTTTTGTGA
Found at i:113236 original size:21 final size:22
Alignment explanation
Indices: 113212--113257 Score: 53
Period size: 20 Copynumber: 2.2 Consensus size: 22
113202 TAGTTTAATT
*
113212 TTTTTAGTTTT-TTATT-ATTTA
1 TTTTTA-TTTTATAATTAATTTA
113233 -TTTTATTTTATAATTAATTTA
1 TTTTTATTTTATAATTAATTTA
113254 TTTT
1 TTTT
113258 ATTAATATGT
Statistics
Matches: 21, Mismatches: 1, Indels: 5
0.78 0.04 0.19
Matches are distributed among these distances:
19 4 0.19
20 9 0.43
21 5 0.24
22 3 0.14
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.74
Consensus pattern (22 bp):
TTTTTATTTTATAATTAATTTA
Found at i:113241 original size:17 final size:17
Alignment explanation
Indices: 113221--113263 Score: 61
Period size: 16 Copynumber: 2.6 Consensus size: 17
113211 TTTTTTAGTT
* *
113221 TTTTATTATTTATTTTA
1 TTTTATTAATTAATTTA
113238 TTTTA-TAATTAATTTA
1 TTTTATTAATTAATTTA
113254 TTTTATTAAT
1 TTTTATTAAT
113264 ATGTTTAGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 14 0.61
17 9 0.39
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (17 bp):
TTTTATTAATTAATTTA
Found at i:116724 original size:23 final size:23
Alignment explanation
Indices: 116698--116741 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
116688 ATTCATTTAA
116698 TTTA-TTTTTAATATTTAGTTTTC
1 TTTACTTTTTAAT-TTTAGTTTTC
*
116721 TTTACTTTTTAATTTTGGTTT
1 TTTACTTTTTAATTTTAGTTT
116742 ATGACCCGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 11 0.58
24 8 0.42
ACGTcount: A:0.18, C:0.05, G:0.07, T:0.70
Consensus pattern (23 bp):
TTTACTTTTTAATTTTAGTTTTC
Found at i:121312 original size:20 final size:21
Alignment explanation
Indices: 121287--121325 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
121277 GCATTTTTAG
*
121287 CATTTT-TAACTTAGTAATTT
1 CATTTTCTAACTCAGTAATTT
121307 CATTTTCTAACTCAGTAAT
1 CATTTTCTAACTCAGTAAT
121326 GCTAGGTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.31, C:0.15, G:0.05, T:0.49
Consensus pattern (21 bp):
CATTTTCTAACTCAGTAATTT
Found at i:124175 original size:12 final size:13
Alignment explanation
Indices: 124155--124207 Score: 56
Period size: 12 Copynumber: 4.1 Consensus size: 13
124145 GAGACTGATG
124155 AGGAGAAAGAAGA
1 AGGAGAAAGAAGA
124168 AGGA-AAAGAAGA
1 AGGAGAAAGAAGA
* *
124180 AGAATGAGAAGAGGA
1 AGGA-GA-AAGAAGA
124195 AGG-GAAAGAAGA
1 AGGAGAAAGAAGA
124207 A
1 A
124208 AAAAAGGAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
12 18 0.55
13 6 0.18
14 1 0.03
15 8 0.24
ACGTcount: A:0.60, C:0.00, G:0.38, T:0.02
Consensus pattern (13 bp):
AGGAGAAAGAAGA
Found at i:124533 original size:3 final size:3
Alignment explanation
Indices: 124527--124552 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
124517 GGAGGAATGC
124527 AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AA
124553 AACCCATGCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:125530 original size:20 final size:21
Alignment explanation
Indices: 125505--125544 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
125495 TGCATTTTTA
*
125505 GCATTTT-TAACTTAGTAATT
1 GCATTTTCTAACTCAGTAATT
125525 GCATTTTCTAACTCAGTAAT
1 GCATTTTCTAACTCAGTAAT
125545 GCTAGGTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.30, C:0.15, G:0.10, T:0.45
Consensus pattern (21 bp):
GCATTTTCTAACTCAGTAATT
Found at i:130732 original size:9 final size:9
Alignment explanation
Indices: 130714--130743 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
130704 GTGTGCAGAG
*
130714 CTTCTTCTC
1 CTTCTCCTC
130723 CTTCTCCTC
1 CTTCTCCTC
130732 CTTCTCCTC
1 CTTCTCCTC
130741 CTT
1 CTT
130744 GGGACACTGC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (9 bp):
CTTCTCCTC
Found at i:136897 original size:20 final size:19
Alignment explanation
Indices: 136874--136942 Score: 61
Period size: 20 Copynumber: 3.5 Consensus size: 19
136864 AATACAAGAT
136874 AATTCAAAATAATTTTCAAA
1 AATTCAAAATAATTTT-AAA
*
136894 AATTTAAAATAA-TTTATAA
1 AATTCAAAATAATTTTA-AA
* *
136913 ATTTCAAAAT-ATTCATAAAA
1 AATTCAAAATAATT--TTAAA
136933 AATTCAAAAT
1 AATTCAAAAT
136943 TTATATTTAA
Statistics
Matches: 40, Mismatches: 5, Indels: 8
0.75 0.09 0.15
Matches are distributed among these distances:
18 2 0.05
19 14 0.35
20 22 0.55
21 2 0.05
ACGTcount: A:0.57, C:0.07, G:0.00, T:0.36
Consensus pattern (19 bp):
AATTCAAAATAATTTTAAA
Found at i:136923 original size:19 final size:21
Alignment explanation
Indices: 136876--136923 Score: 66
Period size: 19 Copynumber: 2.4 Consensus size: 21
136866 TACAAGATAA
136876 TTCAAAATAATTTTCAAAAAT
1 TTCAAAATAATTTTCAAAAAT
*
136897 TT-AAAATAA-TTT-ATAAAT
1 TTCAAAATAATTTTCAAAAAT
136915 TTCAAAATA
1 TTCAAAATA
136924 TTCATAAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
18 7 0.28
19 9 0.36
20 7 0.28
21 2 0.08
ACGTcount: A:0.54, C:0.06, G:0.00, T:0.40
Consensus pattern (21 bp):
TTCAAAATAATTTTCAAAAAT
Found at i:136930 original size:18 final size:18
Alignment explanation
Indices: 136874--136931 Score: 55
Period size: 18 Copynumber: 3.1 Consensus size: 18
136864 AATACAAGAT
* *
136874 AATTCAAAATAATTTTCAAA
1 AATTTAAAATAA--TTCATA
*
136894 AATTTAAAATAATTTATA
1 AATTTAAAATAATTCATA
136912 AATTTCAAAAT-ATTCATA
1 AATTT-AAAATAATTCATA
136930 AA
1 AA
136932 AAATTCAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
18 17 0.52
19 5 0.15
20 11 0.33
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.38
Consensus pattern (18 bp):
AATTTAAAATAATTCATA
Found at i:137556 original size:14 final size:15
Alignment explanation
Indices: 137527--137563 Score: 58
Period size: 14 Copynumber: 2.5 Consensus size: 15
137517 AATCTTAAAA
137527 AATATTATATTTTTTT
1 AATATT-TATTTTTTT
137543 AATATTTA-TTTTTT
1 AATATTTATTTTTTT
137557 AATATTT
1 AATATTT
137564 TATTATACTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 13 0.62
15 2 0.10
16 6 0.29
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (15 bp):
AATATTTATTTTTTT
Found at i:138077 original size:20 final size:20
Alignment explanation
Indices: 138054--138146 Score: 52
Period size: 22 Copynumber: 4.5 Consensus size: 20
138044 CTAAGATTTT
138054 ATAAAATTAAAAAATATATA
1 ATAAAATTAAAAAATATATA
*
138074 ATAAATATATAAAATAATTATTTTA
1 ATAAA-AT-TAAAA-AA-TA-TATA
*
138099 A-AAAA-T-AAAAATATATT
1 ATAAAATTAAAAAATATATA
*
138116 ATAAATCATTATAAAATAT-T-
1 ATAAA--ATTAAAAAATATATA
138136 ATGAAAATTAA
1 AT-AAAATTAA
138147 CTATAAATTA
Statistics
Matches: 57, Mismatches: 5, Indels: 23
0.67 0.06 0.27
Matches are distributed among these distances:
17 3 0.05
18 5 0.09
19 6 0.11
20 11 0.19
21 8 0.14
22 12 0.21
23 3 0.05
24 5 0.09
25 4 0.07
ACGTcount: A:0.62, C:0.01, G:0.01, T:0.35
Consensus pattern (20 bp):
ATAAAATTAAAAAATATATA
Found at i:138111 original size:42 final size:45
Alignment explanation
Indices: 138049--138137 Score: 123
Period size: 42 Copynumber: 2.0 Consensus size: 45
138039 ATGTTCTAAG
*
138049 ATTTTATAAAATTAAAAAATATATAATAAAT-A-TATAAAATAATT
1 ATTTTATAAAAATAAAAAATATATAATAAATCATTATAAAAT-ATT
*
138093 ATTTTA-AAAAAT-AAAAATATATTATAAATCATTATAAAATATT
1 ATTTTATAAAAATAAAAAATATATAATAAATCATTATAAAATATT
138136 AT
1 AT
138138 GAAAATTAAC
Statistics
Matches: 41, Mismatches: 2, Indels: 5
0.85 0.04 0.10
Matches are distributed among these distances:
42 16 0.39
43 11 0.27
44 14 0.34
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (45 bp):
ATTTTATAAAAATAAAAAATATATAATAAATCATTATAAAATATT
Found at i:138520 original size:16 final size:18
Alignment explanation
Indices: 138488--138523 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
138478 TGTAATATAT
138488 TATATTATATTATATTTA
1 TATATTATATTATATTTA
138506 TATATTAT-TTA-ATTTA
1 TATATTATATTATATTTA
138522 TA
1 TA
138524 ACACAAAAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 7 0.39
17 3 0.17
18 8 0.44
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (18 bp):
TATATTATATTATATTTA
Found at i:142360 original size:20 final size:20
Alignment explanation
Indices: 142331--142391 Score: 68
Period size: 20 Copynumber: 2.9 Consensus size: 20
142321 GAAACAACAA
142331 CAAAACAGTAACAAAACATC
1 CAAAACAGTAACAAAACATC
* *
142351 CAAAATAGTACCAAAACATCAC
1 CAAAACAGTAACAAAACAT--C
*
142373 CAAAAACAGTACCAAAACA
1 C-AAAACAGTAACAAAACA
142392 GCACCAAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
20 17 0.49
22 2 0.06
23 16 0.46
ACGTcount: A:0.59, C:0.26, G:0.05, T:0.10
Consensus pattern (20 bp):
CAAAACAGTAACAAAACATC
Found at i:142364 original size:11 final size:11
Alignment explanation
Indices: 142331--142425 Score: 88
Period size: 11 Copynumber: 8.6 Consensus size: 11
142321 GAAACAACAA
*
142331 CAAAACAGTAA
1 CAAAACAGTAC
142342 CAAAACA-T-C
1 CAAAACAGTAC
*
142351 CAAAATAGTAC
1 CAAAACAGTAC
142362 CAAAACA-TCAC
1 CAAAACAGT-AC
142373 CAAAAACAGTAC
1 C-AAAACAGTAC
*
142385 CAAAACAGCAC
1 CAAAACAGTAC
*
142396 CAAAAACAGTAT
1 C-AAAACAGTAC
* *
142408 CAAATCAGCAC
1 CAAAACAGTAC
142419 CAAAACA
1 CAAAACA
142426 ACATGCAAAA
Statistics
Matches: 68, Mismatches: 10, Indels: 12
0.76 0.11 0.13
Matches are distributed among these distances:
9 6 0.09
10 3 0.04
11 40 0.59
12 18 0.26
13 1 0.01
ACGTcount: A:0.57, C:0.27, G:0.06, T:0.09
Consensus pattern (11 bp):
CAAAACAGTAC
Found at i:142383 original size:23 final size:23
Alignment explanation
Indices: 142332--142423 Score: 109
Period size: 23 Copynumber: 4.1 Consensus size: 23
142322 AAACAACAAC
* *
142332 AAAACAGTAACAAAACA--TCC-
1 AAAACAGTACCAAAACAGCACCA
* *
142352 AAAATAGTACCAAAACATCACCA
1 AAAACAGTACCAAAACAGCACCA
142375 AAAACAGTACCAAAACAGCACCA
1 AAAACAGTACCAAAACAGCACCA
* *
142398 AAAACAGTATCAAATCAGCACCA
1 AAAACAGTACCAAAACAGCACCA
142421 AAA
1 AAA
142424 CAACATGCAA
Statistics
Matches: 62, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
20 15 0.24
22 2 0.03
23 45 0.73
ACGTcount: A:0.58, C:0.26, G:0.07, T:0.10
Consensus pattern (23 bp):
AAAACAGTACCAAAACAGCACCA
Found at i:142404 original size:12 final size:12
Alignment explanation
Indices: 142363--142423 Score: 63
Period size: 12 Copynumber: 5.2 Consensus size: 12
142353 AAATAGTACC
*
142363 AAAACATCACCA
1 AAAACAGCACCA
*
142375 AAAACAGTACC-
1 AAAACAGCACCA
142386 AAAACAGCACCA
1 AAAACAGCACCA
* *
142398 AAAACAGTATC-
1 AAAACAGCACCA
*
142409 AAATCAGCACCA
1 AAAACAGCACCA
142421 AAA
1 AAA
142424 CAACATGCAA
Statistics
Matches: 39, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
11 18 0.46
12 21 0.54
ACGTcount: A:0.57, C:0.28, G:0.07, T:0.08
Consensus pattern (12 bp):
AAAACAGCACCA
Found at i:142434 original size:23 final size:23
Alignment explanation
Indices: 142362--142435 Score: 69
Period size: 23 Copynumber: 3.2 Consensus size: 23
142352 AAAATAGTAC
* ** *
142362 CAAAACATCACCAAAAACAGTAC
1 CAAAACAGCACCAAAAACAACAT
**
142385 CAAAACAGCACCAAAAACAGTAT
1 CAAAACAGCACCAAAAACAACAT
*
142408 CAAATCAGCACC-AAAACAACAT
1 CAAAACAGCACCAAAAACAACAT
142430 GCAAAA
1 -CAAAA
142436 TGTAATCAAC
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
22 8 0.18
23 36 0.82
ACGTcount: A:0.57, C:0.28, G:0.07, T:0.08
Consensus pattern (23 bp):
CAAAACAGCACCAAAAACAACAT
Found at i:149661 original size:46 final size:46
Alignment explanation
Indices: 149609--149705 Score: 131
Period size: 46 Copynumber: 2.1 Consensus size: 46
149599 CTATTTTTTA
* *
149609 TGCAAGTCATTTTTTCTGCATACATATTCTTTACCTACATTATTGG
1 TGCAAGTCATTTTGTCTACATACATATTCTTTACCTACATTATTGG
* * * * *
149655 TGCAAGTTATTTTGTCTACATGCGTATTCTTTGCCTACATTATTTG
1 TGCAAGTCATTTTGTCTACATACATATTCTTTACCTACATTATTGG
149701 TGCAA
1 TGCAA
149706 ATAACGTTTT
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
46 44 1.00
ACGTcount: A:0.23, C:0.19, G:0.13, T:0.45
Consensus pattern (46 bp):
TGCAAGTCATTTTGTCTACATACATATTCTTTACCTACATTATTGG
Found at i:159606 original size:17 final size:17
Alignment explanation
Indices: 159584--159622 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
159574 CTCCACTTTG
* * *
159584 ACAAGAATTCTCTACGA
1 ACAAGAACTCTCAACAA
159601 ACAAGAACTCTCAACAA
1 ACAAGAACTCTCAACAA
159618 ACAAG
1 ACAAG
159623 TTCTCCACCT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.49, C:0.26, G:0.10, T:0.15
Consensus pattern (17 bp):
ACAAGAACTCTCAACAA
Found at i:166148 original size:31 final size:31
Alignment explanation
Indices: 166113--166172 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
166103 AAGAGGAAGG
166113 TATTTATACAATTTGATATCTGAATTTGACA
1 TATTTATACAATTTGATATCTGAATTTGACA
* ** * *
166144 TATTTTTTTATTTTGATATTTGAATTTGA
1 TATTTATACAATTTGATATCTGAATTTGA
166173 TCATTTTTTT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.30, C:0.05, G:0.10, T:0.55
Consensus pattern (31 bp):
TATTTATACAATTTGATATCTGAATTTGACA
Found at i:166181 original size:30 final size:30
Alignment explanation
Indices: 166122--166200 Score: 97
Period size: 30 Copynumber: 2.6 Consensus size: 30
166112 GTATTTATAC
166122 AATTTGATATCTGAATTTGACATATTTTTTT
1 AATTTGATATCTGAATTTGACA-ATTTTTTT
* *
166153 ATTTTGATATTTGAATTTGATC-ATTTTTTT
1 AATTTGATATCTGAATTTGA-CAATTTTTTT
* *
166183 AATTTGACATCTAAATTT
1 AATTTGATATCTGAATTT
166201 ATTTGTACCT
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
30 22 0.54
31 18 0.44
32 1 0.02
ACGTcount: A:0.29, C:0.06, G:0.09, T:0.56
Consensus pattern (30 bp):
AATTTGATATCTGAATTTGACAATTTTTTT
Found at i:166181 original size:31 final size:31
Alignment explanation
Indices: 166124--166200 Score: 95
Period size: 31 Copynumber: 2.5 Consensus size: 31
166114 ATTTATACAA
*
166124 TTTGATATCTGAATTTGACATATTTTTTTAT
1 TTTGATATCTGAATTTGACATATTTTTTAAT
*
166155 TTTGATATTTGAATTTGATCAT-TTTTTTAA-
1 TTTGATATCTGAATTTGA-CATATTTTTTAAT
* *
166185 TTTGACATCTAAATTT
1 TTTGATATCTGAATTT
166201 ATTTGTACCT
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
30 13 0.32
31 24 0.60
32 3 0.08
ACGTcount: A:0.27, C:0.06, G:0.09, T:0.57
Consensus pattern (31 bp):
TTTGATATCTGAATTTGACATATTTTTTAAT
Found at i:167522 original size:23 final size:22
Alignment explanation
Indices: 167492--167536 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 22
167482 TTCATATTCA
167492 TGTTCATTT-ATTTATATTTTAAT
1 TGTTCATTTAATTT-T-TTTTAAT
167515 TGTTCATTTAATTTTTTTTAAT
1 TGTTCATTTAATTTTTTTTAAT
167537 ATCATATTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 7 0.33
23 10 0.48
24 4 0.19
ACGTcount: A:0.24, C:0.04, G:0.04, T:0.67
Consensus pattern (22 bp):
TGTTCATTTAATTTTTTTTAAT
Found at i:169533 original size:16 final size:18
Alignment explanation
Indices: 169507--169540 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
169497 TTAAATTAGA
169507 TAAATTAATTTT-TCAAT
1 TAAATTAATTTTCTCAAT
169524 TAAA-TAATTTTCTCAAT
1 TAAATTAATTTTCTCAAT
169541 CCAATTCTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.41, C:0.09, G:0.00, T:0.50
Consensus pattern (18 bp):
TAAATTAATTTTCTCAAT
Found at i:171680 original size:80 final size:81
Alignment explanation
Indices: 171570--171737 Score: 275
Period size: 80 Copynumber: 2.1 Consensus size: 81
171560 GTCAGAAAAT
* * *
171570 TTTTATAGGGGGTCGAAGTTAAATTGTAATTTTTATGATAGTAAAAGTGTAATTTTTAAAAGATT
1 TTTT-TAGGGGCTCGAAGTTAAATTATAATTTTTATGATAGTAAAAGTGCAATTTTTAAAAGATT
171635 AAATTAAAAATTTATCA
65 AAATTAAAAATTTATCA
*
171652 TTTTTAGGGGCT-GAAGTTAAATTATAATTTTTATGATAGTAAAAGTGCAATTTTTAAAGGATTA
1 TTTTTAGGGGCTCGAAGTTAAATTATAATTTTTATGATAGTAAAAGTGCAATTTTTAAAAGATTA
*
171716 AATTAAAATTTTATCA
66 AATTAAAAATTTATCA
171732 TTTTTA
1 TTTTTA
171738 AGGAAGGCCA
Statistics
Matches: 81, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
80 70 0.86
81 7 0.09
82 4 0.05
ACGTcount: A:0.39, C:0.03, G:0.15, T:0.43
Consensus pattern (81 bp):
TTTTTAGGGGCTCGAAGTTAAATTATAATTTTTATGATAGTAAAAGTGCAATTTTTAAAAGATTA
AATTAAAAATTTATCA
Found at i:172938 original size:19 final size:19
Alignment explanation
Indices: 172923--172971 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
172913 CTAATTAGGG
172923 GATATTATTTTAATTAAGA
1 GATATTATTTTAATTAAGA
*
172942 GATATTATTCTAATTAAGA
1 GATATTATTTTAATTAAGA
172961 GATATTATTTT
1 GATATTATTTT
172972 CTTAGTAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.39, C:0.02, G:0.10, T:0.49
Consensus pattern (19 bp):
GATATTATTTTAATTAAGA
Found at i:172966 original size:16 final size:18
Alignment explanation
Indices: 172910--172969 Score: 66
Period size: 19 Copynumber: 3.2 Consensus size: 18
172900 ATTTTTAGAG
* *
172910 ATTCTAATTAGGGGATATT
1 ATTCTAATTAAGAGA-ATT
*
172929 ATTTTAATTAAGAGATATT
1 ATTCTAATTAAGAGA-ATT
172948 ATTCTAATTAAGAGATATT
1 ATTCTAATTAAGAGA-ATT
172967 ATT
1 ATT
172970 TTCTTAGTAA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 37 1.00
ACGTcount: A:0.38, C:0.03, G:0.13, T:0.45
Consensus pattern (18 bp):
ATTCTAATTAAGAGAATT
Found at i:175501 original size:21 final size:22
Alignment explanation
Indices: 175470--175511 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
175460 ATTCACATGT
175470 TTTCTTACTCATGATTCTTTTG
1 TTTCTTACTCATGATTCTTTTG
**
175492 TTTC-TACTCATTTTTCTTTT
1 TTTCTTACTCATGATTCTTTT
175512 CTTTTTGATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.12, C:0.19, G:0.05, T:0.64
Consensus pattern (22 bp):
TTTCTTACTCATGATTCTTTTG
Found at i:185767 original size:30 final size:30
Alignment explanation
Indices: 185731--185806 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
185721 TTACGTTAGC
*
185731 AAGACACCCCCCACATTTTAAAGTGGTTGT
1 AAGACACCCCCCACATTTCAAAGTGGTTGT
* *
185761 AAGACACCCCTCACATTTCCAAGTGGTTGT
1 AAGACACCCCCCACATTTCAAAGTGGTTGT
* * *
185791 AGGACACTCCCTACAT
1 AAGACACCCCCCACAT
185807 GTTCTATGAT
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.29, C:0.30, G:0.16, T:0.25
Consensus pattern (30 bp):
AAGACACCCCCCACATTTCAAAGTGGTTGT
Found at i:187672 original size:15 final size:15
Alignment explanation
Indices: 187635--187675 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
187625 TTTTCTTTGA
187635 TTTCACAATTTGAAGC
1 TTTCACAATTT-AAGC
187651 --T-ACAATTTAAGC
1 TTTCACAATTTAAGC
187663 TTTCACAATTTAA
1 TTTCACAATTTAA
187676 AGCCACAACT
Statistics
Matches: 22, Mismatches: 0, Indels: 7
0.76 0.00 0.24
Matches are distributed among these distances:
12 4 0.18
13 7 0.32
14 2 0.09
15 9 0.41
ACGTcount: A:0.37, C:0.17, G:0.07, T:0.39
Consensus pattern (15 bp):
TTTCACAATTTAAGC
Found at i:188277 original size:52 final size:47
Alignment explanation
Indices: 188220--188338 Score: 107
Period size: 54 Copynumber: 2.4 Consensus size: 47
188210 ATATAAGATC
*
188220 TCTATAAAATAATATAAACAAATAATTTTTGTTTATGTAAAAACATACCAGA
1 TCTATAAAATAATATAAACAAAT-ATTTTT-TTTATATAAAAA-AT--CAGA
*
188272 TCTATACAAAATCAA-ATTAAATAAATATTTTTTTTATATAAAAAATCAGA
1 TCTAT--AAAAT-AATA-TAAACAAATATTTTTTTTATATAAAAAATCAGA
* *
188322 TCTGTAAAAAAAT-TAAA
1 TCTATAAAATAATATAAA
188339 TAGTAGGATC
Statistics
Matches: 58, Mismatches: 4, Indels: 16
0.74 0.05 0.21
Matches are distributed among these distances:
46 4 0.07
47 2 0.03
48 4 0.07
50 8 0.14
52 7 0.12
53 11 0.19
54 12 0.21
55 10 0.17
ACGTcount: A:0.52, C:0.08, G:0.04, T:0.35
Consensus pattern (47 bp):
TCTATAAAATAATATAAACAAATATTTTTTTTATATAAAAAATCAGA
Found at i:189676 original size:26 final size:26
Alignment explanation
Indices: 189644--189731 Score: 79
Period size: 26 Copynumber: 3.4 Consensus size: 26
189634 ATTACTTGGG
*
189644 AAGCCTTTGTGGTTAATCTTCTGGAA
1 AAGCCTTTGTGGTTAATCTTCTGAAA
* * ** * *
189670 AAGCCTTCGCGACTACTCTTGTGAAA
1 AAGCCTTTGTGGTTAATCTTCTGAAA
* *
189696 AAGCCTTTGTAGTTAATCTTGTGAAA
1 AAGCCTTTGTGGTTAATCTTCTGAAA
*
189722 AA-CCATTGTG
1 AAGCCTTTGTG
189732 ACATGTTATC
Statistics
Matches: 47, Mismatches: 15, Indels: 1
0.75 0.24 0.02
Matches are distributed among these distances:
25 6 0.13
26 41 0.87
ACGTcount: A:0.27, C:0.18, G:0.20, T:0.34
Consensus pattern (26 bp):
AAGCCTTTGTGGTTAATCTTCTGAAA
Found at i:190472 original size:13 final size:13
Alignment explanation
Indices: 190454--190479 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
190444 TCTGCCTTCT
190454 TTGTCGCTACATA
1 TTGTCGCTACATA
190467 TTGTCGCTACATA
1 TTGTCGCTACATA
190480 GCATGTGTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.23, G:0.15, T:0.38
Consensus pattern (13 bp):
TTGTCGCTACATA
Found at i:190552 original size:40 final size:39
Alignment explanation
Indices: 190499--190586 Score: 113
Period size: 40 Copynumber: 2.2 Consensus size: 39
190489 TGTTACAAAA
* * * * *
190499 AAACCCCTATGTCGTAACATAGAATGTTTATGTTGTGAC
1 AAACCCCTTTGTCGCAACACAGAATGTTTATGTCGCGAC
*
190538 AAACCACCTTTGTCGCAACACAGCATGTTTATGTCGCGAC
1 AAACC-CCTTTGTCGCAACACAGAATGTTTATGTCGCGAC
190578 AAACCCCTT
1 AAACCCCTT
190587 AAGATGTCTA
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
39 9 0.21
40 33 0.79
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.28
Consensus pattern (39 bp):
AAACCCCTTTGTCGCAACACAGAATGTTTATGTCGCGAC
Found at i:196368 original size:3 final size:3
Alignment explanation
Indices: 196356--196450 Score: 50
Period size: 3 Copynumber: 31.0 Consensus size: 3
196346 TTTTTTTTGG
* * *
196356 TTA TTAA TTA TTA ATA CTTA TTA TTA TTA -CA GTTA TTA ATA TTA TTA
1 TTA TT-A TTA TTA TTA -TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA
* * * * * **
196403 ATG TTA CTA GTA TTA -TA TTTA TTA TTA TTA ATA TTA AAA TTA TTA
1 TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA
196448 TTA
1 TTA
196451 ATGATAGTTA
Statistics
Matches: 67, Mismatches: 19, Indels: 12
0.68 0.19 0.12
Matches are distributed among these distances:
2 3 0.04
3 56 0.84
4 8 0.12
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.55
Consensus pattern (3 bp):
TTA
Found at i:197217 original size:10 final size:11
Alignment explanation
Indices: 197202--197230 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
197192 TTTAAGAATA
197202 AATTTAAACC-
1 AATTTAAACCT
197212 AATTTAAACCT
1 AATTTAAACCT
197223 AATTTAAA
1 AATTTAAA
197231 ATAAAAAGCT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 10 0.56
11 8 0.44
ACGTcount: A:0.52, C:0.14, G:0.00, T:0.34
Consensus pattern (11 bp):
AATTTAAACCT
Found at i:197761 original size:49 final size:47
Alignment explanation
Indices: 197637--198308 Score: 346
Period size: 49 Copynumber: 13.7 Consensus size: 47
197627 TGGGGTATAA
* * *
197637 GGTTCGCCATTGCGACTTAAATCCTTCCCCTT-ATGTCTTCGTGGTACT
1 GGTTCGCCGTTACGACTTAAAT-CTTTCCCTTCATGTCTT-GTGGTACT
* * * *
197685 GGATCTGCCGTTGC-AGCTTAGATCTTTCCCTTCATGTCTCTGTGGTACAA
1 GGTTC-GCCGTTACGA-CTTAAATCTTTCCCTTCATGTCT-TGTGGTAC-T
* * * * *
197735 GGTTCGCCATTACGACTTAAACCTTTCCTTTTATGTCTTCATGGTACT
1 GGTTCGCCGTTACGACTTAAATCTTTCCCTTCATGTCTT-GTGGTACT
* * * * * *
197783 GGATCCGCCGTTGCGGCTTAGATCTTTCCCTTTTATATCTTCGTGGTACT
1 GG-TTCGCCGTTACGACTTAAATCTTTCCC-TTCATGTCTT-GTGGTACT
* * * * * * *
197833 GGATCTGTCGTTGCGACTTAGATCTTTCCCTTTATGTTTTTGTGGTATT
1 GGTTC-GCCGTTACGACTTAAATCTTTCCCTTCATG-TCTTGTGGTACT
* * * *
197882 GGATTCGCCGTTGCGGCTTAAATCTTTCCCTTTTATGTCTTTGCGGTACT
1 GG-TTCGCCGTTACGACTTAAATCTTTCCC-TTCATGTC-TTGTGGTACT
* *
197932 GGATTCGCCGTTACGGCTTAGATCTTTCCCTTCATGTCTTCGTGGTACT
1 GG-TTCGCCGTTACGACTTAAATCTTTCCCTTCATGTCTT-GTGGTACT
** * * *
197981 GGATTCATCGTTACGGCTTAAATCTTTCCCTTCAAGTCTTCGTGGTTCT
1 GG-TTCGCCGTTACGACTTAAATCTTTCCCTTCATGTCTT-GTGGTACT
* * *
198030 GGATTCGCTGTTAC-AGCTTAAATATTTCCCTTCAAGTCTTCGTGGTACT
1 GG-TTCGCCGTTACGA-CTTAAATCTTTCCCTTCATGTCTT-GTGGTACT
* * * * **
198079 AGATTCACCGTTACGGCTGAAATCTTTCCCTTCAAATCTT-TGCAGTACT
1 -GGTTCGCCGTTACGACTTAAATCTTTCCCTTCATGTCTTGTG--GTACT
* * * * * * * * *
198128 AGATCTGCCGTTACGGTCTTAGATCTTTCCCATCGTGTTTCTATGGTACAA
1 GGTTC-GCCGTTAC-GACTTAAATCTTTCCCTTCATGTCT-TGTGGTAC-T
* * * ** *
198179 GGTTCGCCATTGCGACTTAAA-CTTTTCCCTTTAAATCTATGCGGTACT
1 GGTTCGCCGTTACGACTTAAATC-TTTCCCTTCATGTCT-TGTGGTACT
* * * * * * * * *
198227 GGATCTACCATTACGGTCTTAGATCTTTCCCGTCGTGTTTCTGTGGTACAA
1 GGTTC-GCCGTTAC-GACTTAAATCTTTCCCTTCATGTCT-TGTGGTAC-T
* * *
198278 GGTTCGCCATTGCGACTTAAACCTTTCCCTT
1 GGTTCGCCGTTACGACTTAAATCTTTCCCTT
198309 TAAATCTTTG
Statistics
Matches: 485, Mismatches: 109, Indels: 59
0.74 0.17 0.09
Matches are distributed among these distances:
47 2 0.00
48 25 0.05
49 297 0.61
50 150 0.31
51 9 0.02
52 2 0.00
ACGTcount: A:0.17, C:0.25, G:0.19, T:0.39
Consensus pattern (47 bp):
GGTTCGCCGTTACGACTTAAATCTTTCCCTTCATGTCTTGTGGTACT
Found at i:197885 original size:99 final size:98
Alignment explanation
Indices: 197649--198158 Score: 456
Period size: 99 Copynumber: 5.2 Consensus size: 98
197639 TTCGCCATTG
* * * * *
197649 CGACTTAAATCCTTCCCCTTATGTCTTCGTGGTACTGGATCTGCCGTTGCAGCTTAGATCTTTCC
1 CGACTTAAATCTTTCCCTTTATGTCTTCGTGGTACTGGATCCGCCGTTGCGGCTTAAATCTTTCC
* * * *
197714 CTTCATGTC-TCTGTGGTACAAGGTTC-GCCATTA
66 CTTCATATCTTC-GTGGTAC-TGGATCTGCCGTTA
* * * *
197747 CGACTTAAACCTTTCCTTTTATGTCTTCATGGTACTGGATCCGCCGTTGCGGCTTAGATCTTTCC
1 CGACTTAAATCTTTCCCTTTATGTCTTCGTGGTACTGGATCCGCCGTTGCGGCTTAAATCTTTCC
* * *
197812 CTTTTATATCTTCGTGGTACTGGATCTGTCGTTG
66 C-TTCATATCTTCGTGGTACTGGATCTGCCGTTA
* * * * *
197846 CGACTTAGATCTTTCCCTTTATGTTTTTGTGGTATTGGATTCGCCGTTGCGGCTTAAATCTTTCC
1 CGACTTAAATCTTTCCCTTTATGTCTTCGTGGTACTGGATCCGCCGTTGCGGCTTAAATCTTTCC
* * * *
197911 CTTTTATGTCTTTGCGGTACTGGAT-TCGCCGTTA
66 C-TTCATATCTTCGTGGTACTGGATCT-GCCGTTA
* * * * ** *
197945 CGGCTTAGATCTTTCCCTTCATGTCTTCGTGGTACTGGATTCATCGTTACGGCTTAAATCTTTCC
1 CGACTTAAATCTTTCCCTTTATGTCTTCGTGGTACTGGATCCGCCGTTGCGGCTTAAATCTTTCC
* *
198010 CTTCA-AGTCTTCGTGGTTCTGGAT-TCGCTGTTA
66 CTTCATA-TCTTCGTGGTACTGGATCT-GCCGTTA
* * * * * * * *
198043 C-AGCTTAAATATTTCCCTTCAAGTCTTCGTGGTACTAGATTCACCGTTACGGCTGAAATCTTTC
1 CGA-CTTAAATCTTTCCCTTTATGTCTTCGTGGTACTGGATCCGCCGTTGCGGCTTAAATCTTTC
* * ** *
198107 CCTTCAAATCTTTGCAGTACTAGATCTGCCGTTA
65 CCTTCATATCTTCGTGGTACTGGATCTGCCGTTA
* *
198141 CGGTCTTAGATCTTTCCC
1 C-GACTTAAATCTTTCCC
198159 ATCGTGTTTC
Statistics
Matches: 344, Mismatches: 58, Indels: 19
0.82 0.14 0.05
Matches are distributed among these distances:
98 170 0.49
99 172 0.50
100 2 0.01
ACGTcount: A:0.16, C:0.25, G:0.19, T:0.40
Consensus pattern (98 bp):
CGACTTAAATCTTTCCCTTTATGTCTTCGTGGTACTGGATCCGCCGTTGCGGCTTAAATCTTTCC
CTTCATATCTTCGTGGTACTGGATCTGCCGTTA
Found at i:197972 original size:148 final size:147
Alignment explanation
Indices: 197664--198308 Score: 533
Period size: 148 Copynumber: 4.4 Consensus size: 147
197654 TAAATCCTTC
197664 CCCTT-ATGTCTTCGTGGTACTGGATCTGCCGTTGC-AGCTTAGATCTTTCCCTTCATGTCTCTG
1 CCCTTCATGTCTTCGTGGTACTGGATCTGCCGTTGCGA-CTTAGATCTTTCCCTTCATGTCTCTG
* * * ** * *
197727 TGGTACAAGGTTCGCCATTACGACTTAAACCTTTCCTTTTATGTCTTCATGGTACTGGATCCGCC
65 TGGTACAAGGTTCGCCATTACGACTTAAATCTTTCCCTTTAAGTCTTCGCGGTACTGGATTCACC
*
197792 GTTGCGGCTTAGATCTTT
130 GTTACGGCTTAGATCTTT
* * * * * *
197810 CCCTTTTATATCTTCGTGGTACTGGATCTGTCGTTGCGACTTAGATCTTTCCCTTTATGTTTTTG
1 CCC-TTCATGTCTTCGTGGTACTGGATCTGCCGTTGCGACTTAGATCTTTCCCTTCATGTCTCTG
** * * * * * *
197875 TGGTA-TTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTTTATGTCTTTGCGGTACTGGATTCG
65 TGGTACAAGG-TTCGCCATTACGACTTAAATCTTTCCC-TTTAAGTCTTCGCGGTACTGGATTCA
197939 CCGTTACGGCTTAGATCTTT
128 CCGTTACGGCTTAGATCTTT
* * * *
197959 CCCTTCATGTCTTCGTGGTACTGGAT-T-CATCGTTACGGCTTAAATCTTTCCCTTCAAGTCT-T
1 CCCTTCATGTCTTCGTGGTACTGGATCTGC--CGTTGCGACTTAGATCTTTCCCTTCATGTCTCT
* * ** * * * *
198021 CGTGGTTC-TGGATTCGCTGTTAC-AGCTTAAATATTTCCCTTCAAGTCTTCGTGGTACTAGATT
64 -GTGGTACAAGG-TTCGCCATTACGA-CTTAAATCTTTCCCTTTAAGTCTTCGCGGTACTGGATT
* *
198084 CACCGTTACGGCTGAAATCTTT
126 CACCGTTACGGCTTAGATCTTT
** * ** * * * * * * *
198106 CCCTTCAAATCTTTGCAGTACTAGATCTGCCGTTACGGTCTTAGATCTTTCCCATCGTGTTTCTA
1 CCCTTCATGTCTTCGTGGTACTGGATCTGCCGTTGC-GACTTAGATCTTTCCCTTCATGTCTCTG
* *
198171 TGGTACAAGGTTCGCCATTGCGACTTAAA-CTTTTCCCTTTAAATCTAT-GCGGTACTGGA-TCT
65 TGGTACAAGGTTCGCCATTACGACTTAAATC-TTTCCCTTTAAGTCT-TCGCGGTACTGGATTC-
*
198233 ACCATTACGGTCTTAGATCTTT
127 ACCGTTACGG-CTTAGATCTTT
* * * * * * *
198255 CCCGTCGTGT-TTCTGTGGTACAAGGTTC-GCCATTGCGACTTAAACCTTTCCCTT
1 CCCTTCATGTCTTC-GTGGTAC-TGGATCTGCCGTTGCGACTTAGATCTTTCCCTT
198309 TAAATCTTTG
Statistics
Matches: 396, Mismatches: 81, Indels: 42
0.76 0.16 0.08
Matches are distributed among these distances:
146 3 0.01
147 72 0.18
148 241 0.61
149 77 0.19
150 3 0.01
ACGTcount: A:0.17, C:0.25, G:0.19, T:0.39
Consensus pattern (147 bp):
CCCTTCATGTCTTCGTGGTACTGGATCTGCCGTTGCGACTTAGATCTTTCCCTTCATGTCTCTGT
GGTACAAGGTTCGCCATTACGACTTAAATCTTTCCCTTTAAGTCTTCGCGGTACTGGATTCACCG
TTACGGCTTAGATCTTT
Found at i:198232 original size:99 final size:99
Alignment explanation
Indices: 198102--198371 Score: 425
Period size: 99 Copynumber: 2.7 Consensus size: 99
198092 CGGCTGAAAT
* * * * *
198102 CTTTCCCTTCAAATCTTTGCAGTACTAGATCTGCCGTTACGGTCTTAGATCTTTCCCATCGTGTT
1 CTTTCCCTTTAAATCTTTGCGGTACTGGATCTACCGTTACGGTCTTAGATCTTTCCCGTCGTGTT
198167 TCTATGGTACAAGGTTCGCCATTGCGACTTAAAC
66 TCTATGGTACAAGGTTCGCCATTGCGACTTAAAC
* * *
198201 TTTTCCCTTTAAATCTATGCGGTACTGGATCTACCATTACGGTCTTAGATCTTTCCCGTCGTGTT
1 CTTTCCCTTTAAATCTTTGCGGTACTGGATCTACCGTTACGGTCTTAGATCTTTCCCGTCGTGTT
*
198266 TCTGTGGTACAAGGTTCGCCATTGCGACTTAAAC
66 TCTATGGTACAAGGTTCGCCATTGCGACTTAAAC
* * *
198300 CTTTCCCTTTAAATCTTTGCGATACTGGATCTACCGTTGCGTTCTTAGATCTTTCCCGTCGTGTT
1 CTTTCCCTTTAAATCTTTGCGGTACTGGATCTACCGTTACGGTCTTAGATCTTTCCCGTCGTGTT
198365 TC-ATGGT
66 TCTATGGT
198372 GCCGAAACCT
Statistics
Matches: 155, Mismatches: 16, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
98 4 0.03
99 151 0.97
ACGTcount: A:0.18, C:0.25, G:0.18, T:0.39
Consensus pattern (99 bp):
CTTTCCCTTTAAATCTTTGCGGTACTGGATCTACCGTTACGGTCTTAGATCTTTCCCGTCGTGTT
TCTATGGTACAAGGTTCGCCATTGCGACTTAAAC
Found at i:198288 original size:50 final size:50
Alignment explanation
Indices: 198138--198288 Score: 119
Period size: 50 Copynumber: 3.0 Consensus size: 50
198128 AGATCTGCCG
*
198138 TTACGGTCTTAGATCTTTCCCATCGTGTTTCTATGGTACAAGGTTCGCCA
1 TTACGGTCTTAGATCTTTCCCATCGTGTTTCTGTGGTACAAGGTTCGCCA
* * * * **** * * * * * *
198188 TTGC-GACTTA-AACTTTTCCCTTTAAATCTATGCGGTAC-TGGATCTACCA
1 TTACGGTCTTAGATC-TTTCCCATCGTGTTTCTGTGGTACAAGGTTC-GCCA
*
198237 TTACGGTCTTAGATCTTTCCCGTCGTGTTTCTGTGGTACAAGGTTCGCCA
1 TTACGGTCTTAGATCTTTCCCATCGTGTTTCTGTGGTACAAGGTTCGCCA
198287 TT
1 TT
198289 GCGACTTAAA
Statistics
Matches: 67, Mismatches: 29, Indels: 10
0.63 0.27 0.09
Matches are distributed among these distances:
48 6 0.09
49 26 0.39
50 29 0.43
51 6 0.09
ACGTcount: A:0.19, C:0.24, G:0.19, T:0.38
Consensus pattern (50 bp):
TTACGGTCTTAGATCTTTCCCATCGTGTTTCTGTGGTACAAGGTTCGCCA
Found at i:207233 original size:131 final size:131
Alignment explanation
Indices: 206999--207262 Score: 528
Period size: 131 Copynumber: 2.0 Consensus size: 131
206989 TCTTCGAGTT
206999 TTTCTATCATTTTTTCCATCTCTGCATTCTTCCTCTCAAAATCTTGTTTAATTATTTCTAGTTCA
1 TTTCTATCATTTTTTCCATCTCTGCATTCTTCCTCTCAAAATCTTGTTTAATTATTTCTAGTTCA
207064 GTCGGGACAACCTGCAAGTGTTCTTCAATTGGGCGAACAATATCCAGGTTTGGCACAGGAATGTT
66 GTCGGGACAACCTGCAAGTGTTCTTCAATTGGGCGAACAATATCCAGGTTTGGCACAGGAATGTT
207129 G
131 G
207130 TTTCTATCATTTTTTCCATCTCTGCATTCTTCCTCTCAAAATCTTGTTTAATTATTTCTAGTTCA
1 TTTCTATCATTTTTTCCATCTCTGCATTCTTCCTCTCAAAATCTTGTTTAATTATTTCTAGTTCA
207195 GTCGGGACAACCTGCAAGTGTTCTTCAATTGGGCGAACAATATCCAGGTTTGGCACAGGAATGTT
66 GTCGGGACAACCTGCAAGTGTTCTTCAATTGGGCGAACAATATCCAGGTTTGGCACAGGAATGTT
207260 G
131 G
207261 TT
1 TT
207263 GTTGATCCTT
Statistics
Matches: 133, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
131 133 1.00
ACGTcount: A:0.23, C:0.21, G:0.17, T:0.39
Consensus pattern (131 bp):
TTTCTATCATTTTTTCCATCTCTGCATTCTTCCTCTCAAAATCTTGTTTAATTATTTCTAGTTCA
GTCGGGACAACCTGCAAGTGTTCTTCAATTGGGCGAACAATATCCAGGTTTGGCACAGGAATGTT
G
Found at i:210202 original size:59 final size:59
Alignment explanation
Indices: 210103--210328 Score: 228
Period size: 59 Copynumber: 3.8 Consensus size: 59
210093 CATCAGTGGC
*
210103 AAATGGTAATTTTGGGAAAGTTTCGAGGGT-AAAATGGTAATTTTTGGAAAAATTTAGGTCAA
1 AAATGG-AATTTT-GGAAAGTTTAG-GGGTAAAAAT-GTAATTTTTGGAAAAATTTAGGTCAA
** * * * *
210165 AAATGGAATTTCAGAAAGATTAGGGGTAAAAATGTAATTTTTAG-AAATTTTGGGGTCAA
1 AAATGGAATTTTGGAAAGTTTAGGGGTAAAAATGTAATTTTTGGAAAAATTT-AGGTCAA
* * * ** *
210224 AAATGGAATTTTGGGAAGTTTATGGGTAAAACGA-G-AATTCTTGGAAAAATCGAGAT-AA
1 AAATGGAATTTTGGAAAGTTTAGGGGTAAAA--ATGTAATTTTTGGAAAAATTTAGGTCAA
210282 AAATGGAATTTTGGAAAGTTTAGGGGTAAAAATGTAATTTTTAGGAA
1 AAATGGAATTTTGGAAAGTTTAGGGGTAAAAATGTAATTTTT-GGAA
210329 GTTCGGAGGT
Statistics
Matches: 134, Mismatches: 22, Indels: 19
0.77 0.13 0.11
Matches are distributed among these distances:
56 1 0.01
57 1 0.01
58 43 0.32
59 59 0.44
60 18 0.13
61 6 0.04
62 6 0.04
ACGTcount: A:0.40, C:0.03, G:0.25, T:0.32
Consensus pattern (59 bp):
AAATGGAATTTTGGAAAGTTTAGGGGTAAAAATGTAATTTTTGGAAAAATTTAGGTCAA
Found at i:210226 original size:30 final size:30
Alignment explanation
Indices: 210133--210235 Score: 104
Period size: 30 Copynumber: 3.4 Consensus size: 30
210123 TTTCGAGGGT
* *
210133 AAAATGGTAATTTTTGGAAAAATTT-AGGTCA
1 AAAATGG-AATTTTTAG-AAAATTTGGGGTCA
* *
210164 AAAATGGAA-TTTCAGAAAGATTAGGGGT-A
1 AAAATGGAATTTTTAGAAA-ATTTGGGGTCA
* *
210193 AAAATGTAATTTTTAGAAATTTTGGGGTCA
1 AAAATGGAATTTTTAGAAAATTTGGGGTCA
210223 AAAATGGAATTTT
1 AAAATGGAATTTT
210236 GGGAAGTTTA
Statistics
Matches: 59, Mismatches: 9, Indels: 9
0.77 0.12 0.12
Matches are distributed among these distances:
28 3 0.05
29 23 0.39
30 26 0.44
31 7 0.12
ACGTcount: A:0.42, C:0.03, G:0.21, T:0.34
Consensus pattern (30 bp):
AAAATGGAATTTTTAGAAAATTTGGGGTCA
Found at i:210235 original size:29 final size:30
Alignment explanation
Indices: 210159--210322 Score: 99
Period size: 29 Copynumber: 5.6 Consensus size: 30
210149 GAAAAATTTA
*
210159 GGTCAAAAATGGAATTTCAGAAAGATTAGG
1 GGTCAAAAATGGAATTTTAGAAAGATTAGG
* * *
210189 GGT-AAAAATGTAATTTTTAGAAA-TTTTGG
1 GGTCAAAAATGGAA-TTTTAGAAAGATTAGG
* * * *
210218 GGTCAAAAATGGAATTTTGGGAAGTTTATG
1 GGTCAAAAATGGAATTTTAGAAAGATTAGG
* * * * *
210248 GGT--AAAACGAGAATTCTTGGAAA-AATCGA
1 GGTCAAAAATG-GAATT-TTAGAAAGATTAGG
* * *
210277 GAT-AAAAATGGAATTTTGGAAAGTTTAGG
1 GGTCAAAAATGGAATTTTAGAAAGATTAGG
*
210306 GGT-AAAAATGTAATTTT
1 GGTCAAAAATGGAATTTT
210323 TAGGAAGTTC
Statistics
Matches: 103, Mismatches: 24, Indels: 15
0.73 0.17 0.11
Matches are distributed among these distances:
28 12 0.12
29 53 0.51
30 38 0.37
ACGTcount: A:0.40, C:0.04, G:0.25, T:0.31
Consensus pattern (30 bp):
GGTCAAAAATGGAATTTTAGAAAGATTAGG
Found at i:211470 original size:18 final size:17
Alignment explanation
Indices: 211392--211483 Score: 59
Period size: 18 Copynumber: 5.4 Consensus size: 17
211382 CTTTTTTTGG
211392 TTATTAATTATTAA--TA
1 TTATT-ATTATTAATTTA
*
211408 CTTATTATTATTACAGTTA
1 -TTATTATTATTA-ATTTA
*
211427 TTAATATTATTAATGTT-
1 TTATTATTATTAAT-TTA
*
211444 TCTAGTATTA-T-ATTTA
1 T-TATTATTATTAATTTA
*
211460 TTATTATTATTAAAATTA
1 TTATTATTATT-AATTTA
211478 TTATTA
1 TTATTA
211484 ATGATAGTTA
Statistics
Matches: 61, Mismatches: 5, Indels: 17
0.73 0.06 0.20
Matches are distributed among these distances:
15 9 0.15
16 11 0.18
17 9 0.15
18 30 0.49
19 2 0.03
ACGTcount: A:0.37, C:0.03, G:0.03, T:0.57
Consensus pattern (17 bp):
TTATTATTATTAATTTA
Found at i:211624 original size:55 final size:55
Alignment explanation
Indices: 211560--211665 Score: 203
Period size: 55 Copynumber: 1.9 Consensus size: 55
211550 TATTAATAAC
*
211560 AAAACATTTGAAATTTGAACAATAAATAAAAAGTAATTAATAATCAATGCAAGTG
1 AAAACATTTGAAATTTGAACAATAAATAAAAAGCAATTAATAATCAATGCAAGTG
211615 AAAACATTTGAAATTTGAACAATAAATAAAAAGCAATTAATAATCAATGCA
1 AAAACATTTGAAATTTGAACAATAAATAAAAAGCAATTAATAATCAATGCA
211666 TGTGTTAAAT
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
55 50 1.00
ACGTcount: A:0.56, C:0.08, G:0.09, T:0.26
Consensus pattern (55 bp):
AAAACATTTGAAATTTGAACAATAAATAAAAAGCAATTAATAATCAATGCAAGTG
Found at i:212241 original size:6 final size:6
Alignment explanation
Indices: 212219--212294 Score: 56
Period size: 6 Copynumber: 13.3 Consensus size: 6
212209 GTTTTAAATC
* **
212219 AATTCA AATTT- AA-TTA AATTTA AATTTA AA-GAA AATTTA AATTTA
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA
*
212264 AGA--TA AATTTA AATTTA AGA-ATA AATTTA AA
1 A-ATTTA AATTTA AATTTA A-ATTTA AATTTA AA
212295 CCAATTTAAA
Statistics
Matches: 55, Mismatches: 7, Indels: 16
0.71 0.09 0.21
Matches are distributed among these distances:
4 3 0.05
5 11 0.20
6 39 0.71
7 2 0.04
ACGTcount: A:0.55, C:0.01, G:0.04, T:0.39
Consensus pattern (6 bp):
AATTTA
Found at i:212256 original size:17 final size:17
Alignment explanation
Indices: 212219--212294 Score: 102
Period size: 17 Copynumber: 4.5 Consensus size: 17
212209 GTTTTAAATC
* *
212219 AATTCAAATTTAA-TTA
1 AATTTAAATTTAAGATA
212235 AATTTAAATTTAAAGA-A
1 AATTTAAATTT-AAGATA
212252 AATTTAAATTTAAGATA
1 AATTTAAATTTAAGATA
212269 AATTTAAATTTAAGAATA
1 AATTTAAATTTAAG-ATA
212287 AATTTAAA
1 AATTTAAA
212295 CCAATTTAAA
Statistics
Matches: 54, Mismatches: 2, Indels: 6
0.87 0.03 0.10
Matches are distributed among these distances:
16 14 0.26
17 29 0.54
18 11 0.20
ACGTcount: A:0.55, C:0.01, G:0.04, T:0.39
Consensus pattern (17 bp):
AATTTAAATTTAAGATA
Found at i:212305 original size:34 final size:34
Alignment explanation
Indices: 212232--212305 Score: 80
Period size: 34 Copynumber: 2.2 Consensus size: 34
212222 TCAAATTTAA
**
212232 TTAAATTTAAATTTAAAGAAAATTTAAATTTAAG
1 TTAAATTTAAATTTAAAGAAAATTTAAATCCAAG
* *
212266 ATAAATTTAAATTT-AAGAATAAATTTAAA-CCAAT
1 TTAAATTTAAATTTAAAG-A-AAATTTAAATCCAAG
212300 TTAAAT
1 TTAAAT
212306 CAAACTTAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
33 3 0.09
34 21 0.64
35 9 0.27
ACGTcount: A:0.54, C:0.03, G:0.04, T:0.39
Consensus pattern (34 bp):
TTAAATTTAAATTTAAAGAAAATTTAAATCCAAG
Found at i:214515 original size:13 final size:13
Alignment explanation
Indices: 214497--214530 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
214487 TTTTAAAATT
*
214497 TTAAAAATTAAAA
1 TTAAAAATAAAAA
214510 TTAAAAATAAAAA
1 TTAAAAATAAAAA
214523 TTCAAAAA
1 TT-AAAAA
214531 AATTATAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 14 0.74
14 5 0.26
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (13 bp):
TTAAAAATAAAAA
Found at i:216285 original size:30 final size:30
Alignment explanation
Indices: 216225--216291 Score: 75
Period size: 30 Copynumber: 2.3 Consensus size: 30
216215 TTTTAATAGA
** *
216225 AATAAATAATTTATTTTTTATTTAAGATAT
1 AATAAATAATTTATTTTTTATAAAAAATAT
*
216255 AATAACTAATTTATTTATTT-TAAAAAATAT
1 AATAAATAATTTATTT-TTTATAAAAAATAT
216285 -ATAAATA
1 AATAAATA
216292 TAATCAAACT
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
29 6 0.19
30 22 0.71
31 3 0.10
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (30 bp):
AATAAATAATTTATTTTTTATAAAAAATAT
Found at i:217254 original size:22 final size:22
Alignment explanation
Indices: 217228--217271 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
217218 ACAAAATTAT
* *
217228 TAAATATTAAAATAAAATAAAA
1 TAAATATTAAAAAAAAAAAAAA
217250 TAAATATTAAAAAAAAAAAAAA
1 TAAATATTAAAAAAAAAAAAAA
217272 GAATATAAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (22 bp):
TAAATATTAAAAAAAAAAAAAA
Found at i:217276 original size:21 final size:22
Alignment explanation
Indices: 217229--217277 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
217219 CAAAATTATT
*
217229 AAATATTAAAATAAAATAAAAT
1 AAATATTAAAATAAAATAAAAA
217251 AAATATTAAAA-AAAA-AAAAA
1 AAATATTAAAATAAAATAAAAA
217271 AGAATAT
1 A-AATAT
217278 AAACAGATCT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
20 5 0.20
21 9 0.36
22 11 0.44
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.22
Consensus pattern (22 bp):
AAATATTAAAATAAAATAAAAA
Found at i:220687 original size:37 final size:37
Alignment explanation
Indices: 220637--220710 Score: 148
Period size: 37 Copynumber: 2.0 Consensus size: 37
220627 ATTTATTCCA
220637 TGAGTTGGTCTTGCCTCGATTCAATCTTTGTGGTATG
1 TGAGTTGGTCTTGCCTCGATTCAATCTTTGTGGTATG
220674 TGAGTTGGTCTTGCCTCGATTCAATCTTTGTGGTATG
1 TGAGTTGGTCTTGCCTCGATTCAATCTTTGTGGTATG
220711 CCCATCAAGT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.14, C:0.16, G:0.27, T:0.43
Consensus pattern (37 bp):
TGAGTTGGTCTTGCCTCGATTCAATCTTTGTGGTATG
Found at i:224022 original size:14 final size:14
Alignment explanation
Indices: 224003--224036 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
223993 TCACAATTTG
*
224003 ATTCTCTATTTCTT
1 ATTCTCGATTTCTT
*
224017 ATTCTCGATTTGTT
1 ATTCTCGATTTCTT
224031 ATTCTC
1 ATTCTC
224037 AATTGTCAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.15, C:0.21, G:0.06, T:0.59
Consensus pattern (14 bp):
ATTCTCGATTTCTT
Found at i:226912 original size:49 final size:51
Alignment explanation
Indices: 226808--226914 Score: 157
Period size: 52 Copynumber: 2.1 Consensus size: 51
226798 AAATAGCAAG
226808 AAAATATTATTAAATTATTTAATTTTAATAAGTTAATTATTATGATGTTAAA
1 AAAATATTATTAAATTATTTAATTTTAATAAGTTAATTATTATGA-GTTAAA
* *
226860 AAAATATTATTGAATTATTTAATTTTAA-ATAGTTACTTATTAT-A-TTAAA
1 AAAATATTATTAAATTATTTAATTTTAATA-AGTTAATTATTATGAGTTAAA
226909 AAAATA
1 AAAATA
226915 GTTAATTATT
Statistics
Matches: 52, Mismatches: 2, Indels: 5
0.88 0.03 0.08
Matches are distributed among these distances:
49 11 0.21
51 2 0.04
52 39 0.75
ACGTcount: A:0.48, C:0.01, G:0.05, T:0.47
Consensus pattern (51 bp):
AAAATATTATTAAATTATTTAATTTTAATAAGTTAATTATTATGAGTTAAA
Done.