Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.04
Sequence: scaffold257
Parameters: 2 7 7 80 10 50 500
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 500
Length: 1615106
ACGTcount: A:0.29, C:0.15, G:0.15, T:0.29
Warning! 208026 characters in sequence are not A, C, G, or T
File 2 of 5
Found at i:4103 original size:2 final size:2
Alignment explanation
Indices: 4096--4120 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
4086 TTGCAAGTAC
4096 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
4121 NNNNNNNNNN
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:8785 original size:2 final size:2
Alignment explanation
Indices: 8778--8872 Score: 57
Period size: 2 Copynumber: 47.5 Consensus size: 2
8768 CCTACCTTTG
* * * * *
8778 GA GA GA GA GA GA GA CA GA CA TA CA GA GA GA GA GA CA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
* * * * * * *
8820 GA GA CA GA TG- GA CA GA GA TA AA CA GA GA GA AA GA GA CA GA GA
1 GA GA GA GA -GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
*
8862 GA GA GT GA GA G
1 GA GA GA GA GA G
8873 TGTGATGTCT
Statistics
Matches: 69, Mismatches: 22, Indels: 4
0.73 0.23 0.04
Matches are distributed among these distances:
1 1 0.01
2 67 0.97
3 1 0.01
ACGTcount: A:0.49, C:0.08, G:0.38, T:0.04
Consensus pattern (2 bp):
GA
Found at i:8835 original size:32 final size:30
Alignment explanation
Indices: 8781--8866 Score: 86
Period size: 32 Copynumber: 2.9 Consensus size: 30
8771 ACCTTTGGAG
*
8781 AGAGAGAGAGACAGACATACAGAGAGAGAGAC
1 AGAGAGAGAGACAGACAGACAGAGAGA-A-AC
** *
8813 AGAGAGAGAGACAGATGGACAGAGATAAAC
1 AGAGAGAGAGACAGACAGACAGAGAGAAAC
* *
8843 AGAGAGA-A-AGAGACAGAGAGAGAG
1 AGAGAGAGAGACAGACAGACAGAGAG
8867 TGAGAGTGTG
Statistics
Matches: 45, Mismatches: 9, Indels: 4
0.78 0.16 0.07
Matches are distributed among these distances:
28 11 0.24
29 1 0.02
30 9 0.20
31 1 0.02
32 23 0.51
ACGTcount: A:0.51, C:0.09, G:0.36, T:0.03
Consensus pattern (30 bp):
AGAGAGAGAGACAGACAGACAGAGAGAAAC
Found at i:8866 original size:12 final size:12
Alignment explanation
Indices: 8778--8827 Score: 64
Period size: 12 Copynumber: 4.2 Consensus size: 12
8768 CCTACCTTTG
*
8778 GAGAGAGAGAGA
1 GAGAGAGAGACA
* * *
8790 GACAGACATACA
1 GAGAGAGAGACA
8802 GAGAGAGAGACA
1 GAGAGAGAGACA
8814 GAGAGAGAGACA
1 GAGAGAGAGACA
8826 GA
1 GA
8828 TGGACAGAGA
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 31 1.00
ACGTcount: A:0.50, C:0.10, G:0.38, T:0.02
Consensus pattern (12 bp):
GAGAGAGAGACA
Found at i:9057 original size:5 final size:5
Alignment explanation
Indices: 9049--9084 Score: 54
Period size: 5 Copynumber: 6.8 Consensus size: 5
9039 AAAAAAACAA
9049 AAAAC AAAAC AAAAAC AAAAC AAAAAC AAAAC AAAA
1 AAAAC AAAAC -AAAAC AAAAC -AAAAC AAAAC AAAA
9085 AAGAAAAGAG
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
5 19 0.66
6 10 0.34
ACGTcount: A:0.83, C:0.17, G:0.00, T:0.00
Consensus pattern (5 bp):
AAAAC
Found at i:9057 original size:6 final size:6
Alignment explanation
Indices: 9041--9085 Score: 60
Period size: 6 Copynumber: 7.8 Consensus size: 6
9031 GAAGATACAA
9041 AAAAAC AAAAA- ACAAAAC AAAAAC -AAAAC AAAAAC -AAAAC AAAAA
1 AAAAAC AAAAAC A-AAAAC AAAAAC AAAAAC AAAAAC AAAAAC AAAAA
9086 AGAAAAGAGC
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
5 11 0.31
6 23 0.66
7 1 0.03
ACGTcount: A:0.84, C:0.16, G:0.00, T:0.00
Consensus pattern (6 bp):
AAAAAC
Found at i:9064 original size:11 final size:11
Alignment explanation
Indices: 9042--9085 Score: 79
Period size: 11 Copynumber: 3.9 Consensus size: 11
9032 AAGATACAAA
9042 AAAACAAAAAAC
1 AAAAC-AAAAAC
9054 AAAACAAAAAC
1 AAAACAAAAAC
9065 AAAACAAAAAC
1 AAAACAAAAAC
9076 AAAACAAAAA
1 AAAACAAAAA
9086 AGAAAAGAGC
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
11 27 0.84
12 5 0.16
ACGTcount: A:0.84, C:0.16, G:0.00, T:0.00
Consensus pattern (11 bp):
AAAACAAAAAC
Found at i:9601 original size:21 final size:21
Alignment explanation
Indices: 9575--9652 Score: 129
Period size: 21 Copynumber: 3.7 Consensus size: 21
9565 GTGATAAAAA
9575 ATAATAAAGCACCATCATCAT
1 ATAATAAAGCACCATCATCAT
* *
9596 ATAATAAAGCACCATCTTTAT
1 ATAATAAAGCACCATCATCAT
9617 ATAATAAAGCACCATCATCAT
1 ATAATAAAGCACCATCATCAT
*
9638 ATAGTAAAGCACCAT
1 ATAATAAAGCACCAT
9653 TTTCTTATGA
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 52 1.00
ACGTcount: A:0.46, C:0.22, G:0.06, T:0.26
Consensus pattern (21 bp):
ATAATAAAGCACCATCATCAT
Found at i:19340 original size:13 final size:13
Alignment explanation
Indices: 19322--19354 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
19312 GCCCANGGTC
19322 AGGTCAAAGGGCA
1 AGGTCAAAGGGCA
*
19335 AGGTCAAAGGTCA
1 AGGTCAAAGGGCA
19348 AGGTCAA
1 AGGTCAA
19355 GGTCAAACCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.39, C:0.15, G:0.33, T:0.12
Consensus pattern (13 bp):
AGGTCAAAGGGCA
Found at i:19350 original size:6 final size:6
Alignment explanation
Indices: 19318--19360 Score: 52
Period size: 6 Copynumber: 7.0 Consensus size: 6
19308 GGCTGCCCAN
*
19318 GGTC-A GGTCAAA GGGCAA GGTCAAA GGTCAA GGTCAA GGTCAA
1 GGTCAA GGTC-AA GGTCAA GGTC-AA GGTCAA GGTCAA GGTCAA
19361 ACCTAAAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
5 4 0.12
6 19 0.58
7 10 0.30
ACGTcount: A:0.35, C:0.16, G:0.35, T:0.14
Consensus pattern (6 bp):
GGTCAA
Found at i:19355 original size:19 final size:20
Alignment explanation
Indices: 19322--19361 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
19312 GCCCANGGTC
19322 AGGTCAAAGGGCAAGGTCAA
1 AGGTCAAAGGGCAAGGTCAA
*
19342 AGGTC-AAGGTCAAGGTCAA
1 AGGTCAAAGGGCAAGGTCAA
19361 A
1 A
19362 CCTAAAAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.40, C:0.15, G:0.33, T:0.12
Consensus pattern (20 bp):
AGGTCAAAGGGCAAGGTCAA
Found at i:19662 original size:6 final size:7
Alignment explanation
Indices: 19631--19663 Score: 59
Period size: 7 Copynumber: 4.9 Consensus size: 7
19621 CAGTCCTAAG
19631 AGGTCAA
1 AGGTCAA
19638 AGGTCAA
1 AGGTCAA
19645 AGGTCAA
1 AGGTCAA
19652 AGGTC-A
1 AGGTCAA
19658 AGGTCA
1 AGGTCA
19664 CTCATAAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 6 0.24
7 19 0.76
ACGTcount: A:0.39, C:0.15, G:0.30, T:0.15
Consensus pattern (7 bp):
AGGTCAA
Found at i:28097 original size:1 final size:1
Alignment explanation
Indices: 28093--28117 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
28083 CACTTTTTCT
28093 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
28118 TGGAGCTTGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:28557 original size:196 final size:196
Alignment explanation
Indices: 28237--28598 Score: 697
Period size: 196 Copynumber: 1.8 Consensus size: 196
28227 ACAAGTTTTT
*
28237 ATATTACTTCTTTACATACTCTAGTATTTCTCCTTGTTCATATAGCATTCAAATATCCTCAACTT
1 ATATTACTTCTTTACATACTCTAGTATATCTCCTTGTTCATATAGCATTCAAATATCCTCAACTT
*
28302 CAATTTTTTTATTGTTTTGTTTACATAATTCCTAGATTCCAAACTGCAACAGATATTTTGAAGGA
66 CAATTTTTTTATTGTTTTGTTTAAATAATTCCTAGATTCCAAACTGCAACAGATATTTTGAAGGA
28367 TTTTCGCCTTCCTCCAACCAATGGGCACGAAACCTTGCGTAGTTTTTCCAAAGCATACAAACTCT
131 TTTTCGCCTTCCTCCAACCAATGGGCACGAAACCTTGCGTAGTTTTTCCAAAGCATACAAACTCT
28432 C
196 C
28433 ATATTACTTCTTTACATACTCTAGTATATCTCCTTGTTCATATAGCATTCAAATATCCTCAACTT
1 ATATTACTTCTTTACATACTCTAGTATATCTCCTTGTTCATATAGCATTCAAATATCCTCAACTT
28498 CAATTTTTTTATTGTTTTGTTTAAATAATTCCTAGATTCCAAACTGCAACAGATATTTTGAAGGA
66 CAATTTTTTTATTGTTTTGTTTAAATAATTCCTAGATTCCAAACTGCAACAGATATTTTGAAGGA
*
28563 TTTTCGCCTTCCTCCAACCAATGGGCACGAGACCTT
131 TTTTCGCCTTCCTCCAACCAATGGGCACGAAACCTT
28599 TGGTTGGTGG
Statistics
Matches: 163, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
196 163 1.00
ACGTcount: A:0.28, C:0.22, G:0.10, T:0.39
Consensus pattern (196 bp):
ATATTACTTCTTTACATACTCTAGTATATCTCCTTGTTCATATAGCATTCAAATATCCTCAACTT
CAATTTTTTTATTGTTTTGTTTAAATAATTCCTAGATTCCAAACTGCAACAGATATTTTGAAGGA
TTTTCGCCTTCCTCCAACCAATGGGCACGAAACCTTGCGTAGTTTTTCCAAAGCATACAAACTCT
C
Found at i:30715 original size:49 final size:49
Alignment explanation
Indices: 30652--30748 Score: 194
Period size: 49 Copynumber: 2.0 Consensus size: 49
30642 TGTTTTCATA
30652 ACAAATCCTCTCCGCAGTTTGACTCTGACTTGTAAACGAATTTTGTGGT
1 ACAAATCCTCTCCGCAGTTTGACTCTGACTTGTAAACGAATTTTGTGGT
30701 ACAAATCCTCTCCGCAGTTTGACTCTGACTTGTAAACGAATTTTGTGG
1 ACAAATCCTCTCCGCAGTTTGACTCTGACTTGTAAACGAATTTTGTGG
30749 ATGTCTTTTG
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 48 1.00
ACGTcount: A:0.25, C:0.23, G:0.19, T:0.34
Consensus pattern (49 bp):
ACAAATCCTCTCCGCAGTTTGACTCTGACTTGTAAACGAATTTTGTGGT
Found at i:33534 original size:2 final size:2
Alignment explanation
Indices: 33527--33569 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
33517 NNNNNNNNNN
33527 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
33569 T
1 T
33570 TGGAACAAGT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:40844 original size:30 final size:30
Alignment explanation
Indices: 40782--40876 Score: 120
Period size: 30 Copynumber: 3.2 Consensus size: 30
40772 ACTGCCGGTA
* * * *
40782 AATAGACTGCGATCTATTAGACTG-TCGTC
1 AATAGACTGTGATCTATTGGACCGCTGGTC
40811 AATAGACTGTGATCTATTGGACCGCTGGTC
1 AATAGACTGTGATCTATTGGACCGCTGGTC
* * *
40841 AATAGACTGTGTTCTAATGGACCGCCGGTC
1 AATAGACTGTGATCTATTGGACCGCTGGTC
40871 AATAGA
1 AATAGA
40877 TTGCAATCTC
Statistics
Matches: 58, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
29 21 0.36
30 37 0.64
ACGTcount: A:0.27, C:0.20, G:0.24, T:0.28
Consensus pattern (30 bp):
AATAGACTGTGATCTATTGGACCGCTGGTC
Found at i:42507 original size:8 final size:8
Alignment explanation
Indices: 42494--42540 Score: 51
Period size: 8 Copynumber: 5.9 Consensus size: 8
42484 TTTCCTCTGC
42494 GTCCGTCA
1 GTCCGTCA
*
42502 GTCCGTCT
1 GTCCGTCA
42510 GTCCGTCTA
1 GTCCGTC-A
* *
42519 -TCTGTCC
1 GTCCGTCA
42526 GTCCGTCA
1 GTCCGTCA
42534 GTCCGTC
1 GTCCGTC
42541 TGTCTGTCCC
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
8 31 1.00
ACGTcount: A:0.06, C:0.38, G:0.23, T:0.32
Consensus pattern (8 bp):
GTCCGTCA
Found at i:42522 original size:12 final size:12
Alignment explanation
Indices: 42506--42549 Score: 61
Period size: 12 Copynumber: 3.7 Consensus size: 12
42496 CCGTCAGTCC
42506 GTCTGTCCGTCT
1 GTCTGTCCGTCT
* *
42518 ATCTGTCCGTCC
1 GTCTGTCCGTCT
*
42530 GTCAGTCCGTCT
1 GTCTGTCCGTCT
42542 GTCTGTCC
1 GTCTGTCC
42550 CACTTCAGTT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.05, C:0.36, G:0.23, T:0.36
Consensus pattern (12 bp):
GTCTGTCCGTCT
Found at i:45800 original size:4 final size:4
Alignment explanation
Indices: 45793--45854 Score: 65
Period size: 4 Copynumber: 15.8 Consensus size: 4
45783 GCGTCCGTCA
* * *
45793 GTCT GTCT GTCT G-CAT GTCC GTCC GTCT GTCT GTCT GTCT -TCT GTCC
1 GTCT GTCT GTCT GTC-T GTCT GTCT GTCT GTCT GTCT GTCT GTCT GTCT
*
45840 GTCC GTCT GTCT GTC
1 GTCT GTCT GTCT GTC
45855 CCACTTCAGT
Statistics
Matches: 51, Mismatches: 4, Indels: 6
0.84 0.07 0.10
Matches are distributed among these distances:
3 4 0.08
4 46 0.90
5 1 0.02
ACGTcount: A:0.02, C:0.32, G:0.24, T:0.42
Consensus pattern (4 bp):
GTCT
Found at i:45861 original size:27 final size:27
Alignment explanation
Indices: 45808--45861 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
45798 TCTGTCTGCA
***
45808 TGTCCGTCCGTCTGTCTGTCTGTCTTC
1 TGTCCGTCCGTCTGTCTGTCCCACTTC
45835 TGTCCGTCCGTCTGTCTGTCCCACTTC
1 TGTCCGTCCGTCTGTCTGTCCCACTTC
45862 AGTTTTCCAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.02, C:0.37, G:0.20, T:0.41
Consensus pattern (27 bp):
TGTCCGTCCGTCTGTCTGTCCCACTTC
Found at i:57036 original size:21 final size:21
Alignment explanation
Indices: 57011--57087 Score: 93
Period size: 21 Copynumber: 3.7 Consensus size: 21
57001 ATGTTGTGTT
57011 CACCGCATATAATGTTAGAA-
1 CACCGCATATAATGTTAGAAG
57031 CGACCGCATATAATGTTAGAAG
1 C-ACCGCATATAATGTTAGAAG
* * *
57053 CACCTCTTATAATGTTGGAAG
1 CACCGCATATAATGTTAGAAG
* *
57074 CCCCTCATATAATG
1 CACCGCATATAATG
57088 ATAATTGTAC
Statistics
Matches: 50, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
20 1 0.02
21 48 0.96
22 1 0.02
ACGTcount: A:0.34, C:0.22, G:0.17, T:0.27
Consensus pattern (21 bp):
CACCGCATATAATGTTAGAAG
Found at i:72165 original size:2 final size:2
Alignment explanation
Indices: 72158--72202 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
72148 TCAGTACAAA
72158 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
72200 TC T
1 TC T
72203 GAGAGTCCCT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:80505 original size:324 final size:324
Alignment explanation
Indices: 80038--80640 Score: 856
Period size: 324 Copynumber: 1.8 Consensus size: 324
80028 AAATAGAAGA
* * * * * *
80038 TTTTTAAAGATTTTTTCTATCTATCCTATGTAAAAATTCATCCCCCATTGTGGCCTCACCGTACC
1 TTTTTAAAGATTTTCTCTATATATCCTATATAAAAATTCATCCCCAATTGTGGCCCCACCCTACC
* * * * *
80103 CCTGGACTATGATTTAAACAAACTTGAATCTATACGATCTGGGGATGCTTCCACTCAAGTTTGGG
66 CCGGGACCATGATTTAAACAAACTTGAATCTACACGATCTGAGGATGCTTCCACTCAAGTTTGAG
80168 CTTTCCTGGCCAAATAGTTTTTGAGAAGAAGATTTTTAAAGATTTTCTCTATATA-TA-AAAA-T
131 CTTTCCTGGCCAAATAGTTTTTGAGAAGAAGATTTTTAAAGATTTTCTCTATATACTATAAAACT
* * *
80230 TTATCCCCC-ATTGTGGCCCCGCCCTACCCCCGGGGACCATGATTTGAACAAACTTGAATCTACA
196 TGATCCCCCTATTGTGGCCCCACCCTACCCACGGGGACCATGATTTGAACAAACTTGAATCTACA
*
80294 CTACTTAAGGATGCTTACAAGCCAATTTGAGCTTTCCTGGCCAAATAGTTTCAAAAATTTTTTT
261 CTACCTAAGGATGCTTACAAGCCAATTTGAGCTTTCCTGGCCAAATAGTTTCAAAAATTTTTTT
* *
80358 TTTTTAAAGATTTTCTCTATATATTCCTTTATAAAAATTCATACTCCAATTGTGGCCCCACCCTA
1 TTTTTAAAGATTTTCTCTATATA-TCCTATATAAAAATTCAT-CCCCAATTGTGGCCCCACCCTA
* * * *
80423 CCCCCGGGGACCATGATTTGAACAAACTTGAATCTACACTATCTGAGGATGCTTCCATTTTAA-T
64 -CCCC-GGGACCATGATTTAAACAAACTTGAATCTACACGATCTGAGGATGCTTCCA-CTCAAGT
*
80487 TTGAGCTTTTCTGGCCAAATAGTTTTTGAGAAGAAGATTTTTAAAGATTTTCTCTATATATTCCT
126 TTGAGCTTTCCTGGCCAAATAGTTTTTGAGAAGAAGATTTTTAAAGATTTTCTCTATATA---CT
* *
80552 ATGTAAAACTTGATCCCCCTATTTTGGCCCCACCCTATCCACGGGGACCATGATTTGAACAAACT
188 A--TAAAACTTGATCCCCCTATTGTGGCCCCACCCTACCCACGGGGACCATGATTTGAACAAACT
*
80617 TGAATCTACACTACCTGAGGATGC
251 TGAATCTACACTACCTAAGGATGC
80641 CTCCACATAT
Statistics
Matches: 244, Mismatches: 25, Indels: 15
0.86 0.09 0.05
Matches are distributed among these distances:
320 21 0.09
321 16 0.07
322 18 0.07
323 4 0.02
324 104 0.43
325 3 0.01
328 2 0.01
331 4 0.02
332 9 0.04
333 63 0.26
ACGTcount: A:0.28, C:0.23, G:0.15, T:0.34
Consensus pattern (324 bp):
TTTTTAAAGATTTTCTCTATATATCCTATATAAAAATTCATCCCCAATTGTGGCCCCACCCTACC
CCGGGACCATGATTTAAACAAACTTGAATCTACACGATCTGAGGATGCTTCCACTCAAGTTTGAG
CTTTCCTGGCCAAATAGTTTTTGAGAAGAAGATTTTTAAAGATTTTCTCTATATACTATAAAACT
TGATCCCCCTATTGTGGCCCCACCCTACCCACGGGGACCATGATTTGAACAAACTTGAATCTACA
CTACCTAAGGATGCTTACAAGCCAATTTGAGCTTTCCTGGCCAAATAGTTTCAAAAATTTTTTT
Found at i:80637 original size:166 final size:164
Alignment explanation
Indices: 79866--80694 Score: 860
Period size: 166 Copynumber: 5.1 Consensus size: 164
79856 AAAACTTTCC
* * * * **
79866 AAGAATATTTTTATAGTTTTTCTCTATATATTCCTATGTAAAAATTCAACCCGCCATTGCAGCCC
1 AAGAAGATTTTTAAAGATTTTCTCTATATATTCCTATGTAAAAATTCATCCC-CCATTGTGGCCC
* * * * * * ** * *
79931 CGCCCTACCCCCAGGGACTATGATTT-TACAAACTTGAATTTACACTACCCGAAAATGCCTCTAC
65 CACCCTACCCCCGGGGACCATGATTTGAACAAACTTGAATCTACACTACCTGAGGATGCTTCCAC
* *
79995 ACAAGTTTAAGCTTTTCTGGCCAAATAGTTTTT-AA
130 ACAA-TTTGAGCTTTTCTGGCCAAATAGTTTTTGAG
* * *
80030 ATAGAAGATTTTTAAAGATTTTTTCTATCTA-TCCTATGTAAAAATTCATCCCCCATTGTGGCCT
1 A-AGAAGATTTTTAAAGATTTTCTCTATATATTCCTATGTAAAAATTCATCCCCCATTGTGGCCC
* * * * * * * *
80094 CACCGTA-CCCC-TGGACTATGATTTAAACAAACTTGAATCTATACGATCTGGGGATGCTTCCAC
65 CACCCTACCCCCGGGGACCATGATTTGAACAAACTTGAATCTACACTACCTGAGGATGCTTCCAC
* * *
80157 TCAAGTTTGGGCTTTCCTGGCCAAATAGTTTTTGAG
130 ACAA-TTTGAGCTTTTCTGGCCAAATAGTTTTTGAG
*
80193 AAGAAGATTTTTAAAGATTTTCTC--TATA----TA--TAAAAATTTATCCCCCATTGTGGCCCC
1 AAGAAGATTTTTAAAGATTTTCTCTATATATTCCTATGTAAAAATTCATCCCCCATTGTGGCCCC
* * * *
80250 GCCCTACCCCCGGGGACCATGATTTGAACAAACTTGAATCTACACTACTTAAGGATGCTTACA-A
66 ACCCTACCCCCGGGGACCATGATTTGAACAAACTTGAATCTACACTACCTGAGGATGCTTCCACA
* ** *
80314 GCCAATTTGAGCTTTCCTGGCCAAATAG-TTTCAAA
131 --CAATTTGAGCTTTTCTGGCCAAATAGTTTTTGAG
***** * * * *
80349 AATTTTTTTTTTTTAAAGATTTTCTCTATATATTCCTTTATAAAAATTCATACTCCAATTGTGGC
1 AA--GAAGATTTTTAAAGATTTTCTCTATATATTCCTATGTAAAAATTCAT-CCCCCATTGTGGC
*
80414 CCCACCCTACCCCCGGGGACCATGATTTGAACAAACTTGAATCTACACTATCTGAGGATGCTTCC
63 CCCACCCTACCCCCGGGGACCATGATTTGAACAAACTTGAATCTACACTACCTGAGGATGCTTCC
***
80479 ATTTTAATTTGAGCTTTTCTGGCCAAATAGTTTTTGAG
128 A-CACAATTTGAGCTTTTCTGGCCAAATAGTTTTTGAG
* * *
80517 AAGAAGATTTTTAAAGATTTTCTCTATATATTCCTATGTAAAACTTGATCCCCCTATTTTGGCCC
1 AAGAAGATTTTTAAAGATTTTCTCTATATATTCCTATGTAAAAATTCATCCCCC-ATTGTGGCCC
* * *
80582 CACCCTATCCACGGGGACCATGATTTGAACAAACTTGAATCTACACTACCTGAGGATGCCTCCAC
65 CACCCTACCCCCGGGGACCATGATTTGAACAAACTTGAATCTACACTACCTGAGGATGCTTCCAC
* * * * *
80647 ATATGTTTAAGCTTTTCTGGCCAAAAAGTGTTTGAG
130 ACA-ATTTGAGCTTTTCTGGCCAAATAGTTTTTGAG
80683 AAGAAGATTTTT
1 AAGAAGATTTTT
80695 GAAAAATACC
Statistics
Matches: 551, Mismatches: 91, Indels: 44
0.80 0.13 0.06
Matches are distributed among these distances:
155 29 0.05
156 10 0.02
157 65 0.12
158 20 0.04
160 7 0.01
161 12 0.02
162 82 0.15
163 16 0.03
164 22 0.04
165 29 0.05
166 157 0.28
167 96 0.17
168 6 0.01
ACGTcount: A:0.29, C:0.22, G:0.14, T:0.34
Consensus pattern (164 bp):
AAGAAGATTTTTAAAGATTTTCTCTATATATTCCTATGTAAAAATTCATCCCCCATTGTGGCCCC
ACCCTACCCCCGGGGACCATGATTTGAACAAACTTGAATCTACACTACCTGAGGATGCTTCCACA
CAATTTGAGCTTTTCTGGCCAAATAGTTTTTGAG
Found at i:80882 original size:12 final size:12
Alignment explanation
Indices: 80865--80891 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
80855 GAAAAGTTTA
80865 CAACGACAACGC
1 CAACGACAACGC
80877 CAACGACAACGC
1 CAACGACAACGC
80889 CAA
1 CAA
80892 TGCCGACGAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.44, C:0.41, G:0.15, T:0.00
Consensus pattern (12 bp):
CAACGACAACGC
Found at i:80887 original size:18 final size:18
Alignment explanation
Indices: 80864--80902 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
80854 TGAAAAGTTT
80864 ACAACGACAACGCCAACG
1 ACAACGACAACGCCAACG
* * *
80882 ACAACGCCAATGCCGACG
1 ACAACGACAACGCCAACG
80900 ACA
1 ACA
80903 GACAACGGAC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.41, C:0.38, G:0.18, T:0.03
Consensus pattern (18 bp):
ACAACGACAACGCCAACG
Found at i:83916 original size:21 final size:21
Alignment explanation
Indices: 83892--83978 Score: 61
Period size: 21 Copynumber: 4.2 Consensus size: 21
83882 TTTTTCTATC
*
83892 AAATATGTCGACATGCAAGAT
1 AAATATGTCAACATGCAAGAT
* ** *
83913 AAATATATTGACATGCAAAAT
1 AAATATGTCAACATGCAAGAT
* *
83934 -AGTAATGTCAACATGCAACAT
1 AAAT-ATGTCAACATGCAAGAT
* * *
83955 GACTATGTTAACATGCAAGA-
1 AAATATGTCAACATGCAAGAT
83975 AAAT
1 AAAT
83979 TGCAATCAAA
Statistics
Matches: 51, Mismatches: 13, Indels: 5
0.74 0.19 0.07
Matches are distributed among these distances:
20 4 0.08
21 45 0.88
22 2 0.04
ACGTcount: A:0.46, C:0.14, G:0.15, T:0.25
Consensus pattern (21 bp):
AAATATGTCAACATGCAAGAT
Found at i:84085 original size:21 final size:21
Alignment explanation
Indices: 84056--84215 Score: 196
Period size: 21 Copynumber: 7.5 Consensus size: 21
84046 AAGATCCTGG
* *
84056 ATGCTACTTATTTATGTCGAC
1 ATGCAACTTATTTATGTTGAC
* *
84077 ATGCAACTTATTGACGTTGAC
1 ATGCAACTTATTTATGTTGAC
84098 ATGCAACTTATCTATATGTTGAC
1 ATGCAACTTAT-T-TATGTTGAC
* * *
84121 ATACAACTTATCTATGTCGAC
1 ATGCAACTTATTTATGTTGAC
*
84142 ATGCAACTAATTTATGTTGAC
1 ATGCAACTTATTTATGTTGAC
*
84163 ATGCAACTTATTTATGTTAAC
1 ATGCAACTTATTTATGTTGAC
84184 ATGCAACTT-TGTTATGTTGAC
1 ATGCAACTTAT-TTATGTTGAC
*
84205 ATGCAATTTAT
1 ATGCAACTTAT
84216 AACTTGAATG
Statistics
Matches: 118, Mismatches: 17, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
20 1 0.01
21 98 0.83
22 2 0.02
23 17 0.14
ACGTcount: A:0.30, C:0.17, G:0.14, T:0.39
Consensus pattern (21 bp):
ATGCAACTTATTTATGTTGAC
Found at i:84142 original size:65 final size:63
Alignment explanation
Indices: 84061--84215 Score: 204
Period size: 65 Copynumber: 2.4 Consensus size: 63
84051 CCTGGATGCT
*
84061 ACTTATTTATGTCGACATGCAACTTATTGACGTTGACATGCAACTTATCTATATGTTGACATACA
1 ACTTATTTATGTCGACATGCAACTTATTGACGTTGACATGCAACTTAT-T-TATGTTAACATACA
* * * * *
84126 ACTTATCTATGTCGACATGCAACTAATTTATGTTGACATGCAACTTATTTATGTTAACATGCA
1 ACTTATTTATGTCGACATGCAACTTATTGACGTTGACATGCAACTTATTTATGTTAACATACA
* *
84189 ACTT-TGTTATGTTGACATGCAATTTAT
1 ACTTAT-TTATGTCGACATGCAACTTAT
84216 AACTTGAATG
Statistics
Matches: 79, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
62 1 0.01
63 33 0.42
64 1 0.01
65 44 0.56
ACGTcount: A:0.30, C:0.17, G:0.14, T:0.39
Consensus pattern (63 bp):
ACTTATTTATGTCGACATGCAACTTATTGACGTTGACATGCAACTTATTTATGTTAACATACA
Found at i:84266 original size:21 final size:21
Alignment explanation
Indices: 84242--84410 Score: 173
Period size: 21 Copynumber: 8.0 Consensus size: 21
84232 TATTTATTTC
* *
84242 GCATGTGTACATAACTAAGTT
1 GCATGTGAACATAAATAAGTT
*
84263 GCATGTTG-ACATAAATAAGTA
1 GCATG-TGAACATAAATAAGTT
*
84284 GCATGTGAACATAACTAAGTT
1 GCATGTGAACATAAATAAGTT
* *
84305 GCATGTCAACATAAATAAGTA
1 GCATGTGAACATAAATAAGTT
*
84326 GCATGTGAACATAACTAAGTT
1 GCATGTGAACATAAATAAGTT
84347 GCATGTCG-ACATAAATAAGTT
1 GCATGT-GAACATAAATAAGTT
* * * *
84368 GCATGTCAGCAT-ATTAATCTT
1 GCATGTGAACATAAATAA-GTT
* *
84389 GCATGTTAACATACATAAGTT
1 GCATGTGAACATAAATAAGTT
84410 G
1 G
84411 TATTTCGATA
Statistics
Matches: 122, Mismatches: 20, Indels: 12
0.79 0.13 0.08
Matches are distributed among these distances:
20 6 0.05
21 110 0.90
22 6 0.05
ACGTcount: A:0.38, C:0.14, G:0.18, T:0.30
Consensus pattern (21 bp):
GCATGTGAACATAAATAAGTT
Found at i:84288 original size:42 final size:42
Alignment explanation
Indices: 84242--84373 Score: 228
Period size: 42 Copynumber: 3.1 Consensus size: 42
84232 TATTTATTTC
* *
84242 GCATGTGTACATAACTAAGTTGCATGTTGACATAAATAAGTA
1 GCATGTGAACATAACTAAGTTGCATGTCGACATAAATAAGTA
*
84284 GCATGTGAACATAACTAAGTTGCATGTCAACATAAATAAGTA
1 GCATGTGAACATAACTAAGTTGCATGTCGACATAAATAAGTA
*
84326 GCATGTGAACATAACTAAGTTGCATGTCGACATAAATAAGTT
1 GCATGTGAACATAACTAAGTTGCATGTCGACATAAATAAGTA
84368 GCATGT
1 GCATGT
84374 CAGCATATTA
Statistics
Matches: 85, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 85 1.00
ACGTcount: A:0.39, C:0.14, G:0.19, T:0.29
Consensus pattern (42 bp):
GCATGTGAACATAACTAAGTTGCATGTCGACATAAATAAGTA
Found at i:84393 original size:63 final size:63
Alignment explanation
Indices: 84250--84429 Score: 170
Period size: 63 Copynumber: 2.9 Consensus size: 63
84240 TCGCATGTGT
* * * * *
84250 ACATAACTAAGTTGCATGTTG-ACATAAATAAGTAGCATGT-GAACATAACTAAGTTGCATGTCA
1 ACATAAATAACTTGCATG-TGAACATAACTAAGTTGCATGTCG-ACATAAATAAGTTGCATGTCA
* *
84313 ACATAAATAAGTAGCATGTGAACATAACTAAGTTGCATGTCGACATAAATAAGTTGCATGTCA
1 ACATAAATAACTTGCATGTGAACATAACTAAGTTGCATGTCGACATAAATAAGTTGCATGTCA
* * * * * * *
84376 GCAT-ATTAATCTTGCATGTTAACAT-ACATAAGTTGTATTTCGATATAAACAAGT
1 ACATAAATAA-CTTGCATGTGAACATAAC-TAAGTTGCATGTCGACATAAATAAGT
84430 ATCATCTAGC
Statistics
Matches: 99, Mismatches: 14, Indels: 8
0.82 0.12 0.07
Matches are distributed among these distances:
62 8 0.08
63 90 0.91
64 1 0.01
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.31
Consensus pattern (63 bp):
ACATAAATAACTTGCATGTGAACATAACTAAGTTGCATGTCGACATAAATAAGTTGCATGTCA
Found at i:84410 original size:42 final size:42
Alignment explanation
Indices: 84242--84408 Score: 219
Period size: 42 Copynumber: 4.0 Consensus size: 42
84232 TATTTATTTC
* **
84242 GCATGTGTACATAACTAAGTTGCATGTTGACATAAATAAGTA
1 GCATGTGAACATAACTAAGTTGCATGTCAACATAAATAAGTA
84284 GCATGTGAACATAACTAAGTTGCATGTCAACATAAATAAGTA
1 GCATGTGAACATAACTAAGTTGCATGTCAACATAAATAAGTA
* *
84326 GCATGTGAACATAACTAAGTTGCATGTCGACATAAATAAGTT
1 GCATGTGAACATAACTAAGTTGCATGTCAACATAAATAAGTA
* * * * * *
84368 GCATGTCAGCAT-ATTAATCTTGCATGTTAACATACATAAGT
1 GCATGTGAACATAACTAA-GTTGCATGTCAACATAAATAAGT
84409 TGTATTTCGA
Statistics
Matches: 112, Mismatches: 12, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
41 4 0.04
42 108 0.96
ACGTcount: A:0.38, C:0.14, G:0.17, T:0.30
Consensus pattern (42 bp):
GCATGTGAACATAACTAAGTTGCATGTCAACATAAATAAGTA
Found at i:84592 original size:21 final size:21
Alignment explanation
Indices: 84553--84595 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
84543 TTGAAATAAC
*
84553 TATCTTGCATGTCAGCATATT
1 TATCTTGCATATCAGCATATT
84574 TATCTTGCATATC-GACATATT
1 TATCTTGCATATCAG-CATATT
84595 T
1 T
84596 GATAGAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 1 0.05
21 19 0.95
ACGTcount: A:0.26, C:0.19, G:0.12, T:0.44
Consensus pattern (21 bp):
TATCTTGCATATCAGCATATT
Found at i:85406 original size:16 final size:17
Alignment explanation
Indices: 85387--85444 Score: 52
Period size: 16 Copynumber: 3.5 Consensus size: 17
85377 AGTTTCAGTG
85387 TTAG-TTGTTTTCATAT
1 TTAGATTGTTTTCATAT
*
85403 TTAGATTGTATTT-AGT-G
1 TTAGATTGT-TTTCA-TAT
*
85420 TTAG-TTGTTTACATAT
1 TTAGATTGTTTTCATAT
85436 TTAGATTGT
1 TTAGATTGT
85445 ATTTAGATTT
Statistics
Matches: 33, Mismatches: 3, Indels: 11
0.70 0.06 0.23
Matches are distributed among these distances:
15 3 0.09
16 13 0.39
17 13 0.39
18 4 0.12
ACGTcount: A:0.22, C:0.03, G:0.17, T:0.57
Consensus pattern (17 bp):
TTAGATTGTTTTCATAT
Found at i:85425 original size:33 final size:33
Alignment explanation
Indices: 85383--85450 Score: 127
Period size: 33 Copynumber: 2.1 Consensus size: 33
85373 TGACAGTTTC
*
85383 AGTGTTAGTTGTTTTCATATTTAGATTGTATTT
1 AGTGTTAGTTGTTTACATATTTAGATTGTATTT
85416 AGTGTTAGTTGTTTACATATTTAGATTGTATTT
1 AGTGTTAGTTGTTTACATATTTAGATTGTATTT
85449 AG
1 AG
85451 ATTTCCCTTG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.24, C:0.03, G:0.19, T:0.54
Consensus pattern (33 bp):
AGTGTTAGTTGTTTACATATTTAGATTGTATTT
Found at i:85584 original size:28 final size:28
Alignment explanation
Indices: 85544--85791 Score: 444
Period size: 28 Copynumber: 8.9 Consensus size: 28
85534 CAAGAAAGTA
85544 TCAGACAGTAGGGCCAATACAGTGAGTG
1 TCAGACAGTAGGGCCAATACAGTGAGTG
85572 TCAGACAGTAGGGCCAATACAGT-ATGTG
1 TCAGACAGTAGGGCCAATACAGTGA-GTG
85600 TCAGACAGTAGGGCCAATACAGTGAGTG
1 TCAGACAGTAGGGCCAATACAGTGAGTG
* *
85628 TCAGACAGTTGGGCCAATACAGTGAGTA
1 TCAGACAGTAGGGCCAATACAGTGAGTG
85656 TCAGACAGTAGGGCCAATACAGTGAGTG
1 TCAGACAGTAGGGCCAATACAGTGAGTG
*
85684 TCGGACAGTAGGGCCAATACAGTGAGTG
1 TCAGACAGTAGGGCCAATACAGTGAGTG
*
85712 TCAGACAGTAGGGCCAATACAGTGAGTA
1 TCAGACAGTAGGGCCAATACAGTGAGTG
85740 TCAGACAGTAGGGCCAATACAGTGAGTG
1 TCAGACAGTAGGGCCAATACAGTGAGTG
85768 TCAGACAGTAGGGCCAATACAGTG
1 TCAGACAGTAGGGCCAATACAGTG
85792 CGTAGCGTTC
Statistics
Matches: 210, Mismatches: 8, Indels: 4
0.95 0.04 0.02
Matches are distributed among these distances:
27 1 0.00
28 208 0.99
29 1 0.00
ACGTcount: A:0.32, C:0.18, G:0.31, T:0.19
Consensus pattern (28 bp):
TCAGACAGTAGGGCCAATACAGTGAGTG
Found at i:88613 original size:15 final size:16
Alignment explanation
Indices: 88583--88620 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
88573 TCAACCTCAA
88583 CAAACACGTTCAGGTT
1 CAAACACGTTCAGGTT
*
88599 CAAAC-CGTTCTGGTT
1 CAAACACGTTCAGGTT
88614 CACAACA
1 CA-AACA
88621 ATATTCAAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
15 11 0.58
16 8 0.42
ACGTcount: A:0.32, C:0.29, G:0.16, T:0.24
Consensus pattern (16 bp):
CAAACACGTTCAGGTT
Found at i:93423 original size:2 final size:2
Alignment explanation
Indices: 93418--93506 Score: 178
Period size: 2 Copynumber: 44.5 Consensus size: 2
93408 TCTTATTCCT
93418 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
93460 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
93502 GA GA G
1 GA GA G
93507 TTTAAGTAGG
Statistics
Matches: 87, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 87 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:94286 original size:12 final size:12
Alignment explanation
Indices: 94269--94294 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
94259 TATCGCTCTG
94269 CAATGTACAAAA
1 CAATGTACAAAA
94281 CAATGTACAAAA
1 CAATGTACAAAA
94293 CA
1 CA
94295 TGAACAAATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.58, C:0.19, G:0.08, T:0.15
Consensus pattern (12 bp):
CAATGTACAAAA
Found at i:97656 original size:43 final size:43
Alignment explanation
Indices: 97595--97706 Score: 215
Period size: 43 Copynumber: 2.6 Consensus size: 43
97585 TCAAATTGCC
97595 ATAGGCCCAAATAGGCCCTATGGCACTTAACGTAGATATTCAA
1 ATAGGCCCAAATAGGCCCTATGGCACTTAACGTAGATATTCAA
97638 ATAGGCCCAAATAGGCCCTATGGCACTTAACGTAGATATTCAA
1 ATAGGCCCAAATAGGCCCTATGGCACTTAACGTAGATATTCAA
*
97681 ATAGGCCCAAATAGGCCCTGTGGCAC
1 ATAGGCCCAAATAGGCCCTATGGCAC
97707 AGAAATGGTT
Statistics
Matches: 68, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
43 68 1.00
ACGTcount: A:0.33, C:0.25, G:0.21, T:0.21
Consensus pattern (43 bp):
ATAGGCCCAAATAGGCCCTATGGCACTTAACGTAGATATTCAA
Found at i:106149 original size:15 final size:17
Alignment explanation
Indices: 106112--106156 Score: 67
Period size: 17 Copynumber: 2.8 Consensus size: 17
106102 ATTTATTTCT
106112 ATTTCAAAATAAGCGGA
1 ATTTCAAAATAAGCGGA
106129 ATTTCAAAATAAGC-G-
1 ATTTCAAAATAAGCGGA
*
106144 ATTTCAATATAAG
1 ATTTCAAAATAAG
106157 TGGAGTATTA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
15 12 0.44
16 1 0.04
17 14 0.52
ACGTcount: A:0.47, C:0.11, G:0.13, T:0.29
Consensus pattern (17 bp):
ATTTCAAAATAAGCGGA
Found at i:110201 original size:2 final size:2
Alignment explanation
Indices: 110196--110253 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
110186 CCTCATTCGT
110196 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
110238 TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC
110254 ATTACAATAT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:115668 original size:24 final size:24
Alignment explanation
Indices: 115639--115696 Score: 80
Period size: 24 Copynumber: 2.4 Consensus size: 24
115629 GTCCATGGTT
115639 ATGACCTCCGCCATGACTATGACC
1 ATGACCTCCGCCATGACTATGACC
* * * *
115663 ATGACCTCCACCGTGACTGTGTCC
1 ATGACCTCCGCCATGACTATGACC
115687 ATGACCTCCG
1 ATGACCTCCG
115697 TGCCCATGAG
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.21, C:0.38, G:0.19, T:0.22
Consensus pattern (24 bp):
ATGACCTCCGCCATGACTATGACC
Found at i:116764 original size:113 final size:113
Alignment explanation
Indices: 116566--116782 Score: 434
Period size: 113 Copynumber: 1.9 Consensus size: 113
116556 GGGACTAGAA
116566 AGAATTGTATAAAATTGTCTTGCATGCTATAGCTTTTATGTTATAATATTCTTTTGTCTGTCATA
1 AGAATTGTATAAAATTGTCTTGCATGCTATAGCTTTTATGTTATAATATTCTTTTGTCTGTCATA
116631 TGATTTCATTTTGACTGTTTGCCAAAATGGTGATGTCTGTCATATGAT
66 TGATTTCATTTTGACTGTTTGCCAAAATGGTGATGTCTGTCATATGAT
116679 AGAATTGTATAAAATTGTCTTGCATGCTATAGCTTTTATGTTATAATATTCTTTTGTCTGTCATA
1 AGAATTGTATAAAATTGTCTTGCATGCTATAGCTTTTATGTTATAATATTCTTTTGTCTGTCATA
116744 TGATTTCATTTTGACTGTTTGCCAAAATGGTGATGTCTG
66 TGATTTCATTTTGACTGTTTGCCAAAATGGTGATGTCTG
116783 ATAAACCATT
Statistics
Matches: 104, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
113 104 1.00
ACGTcount: A:0.25, C:0.12, G:0.17, T:0.46
Consensus pattern (113 bp):
AGAATTGTATAAAATTGTCTTGCATGCTATAGCTTTTATGTTATAATATTCTTTTGTCTGTCATA
TGATTTCATTTTGACTGTTTGCCAAAATGGTGATGTCTGTCATATGAT
Found at i:119725 original size:17 final size:17
Alignment explanation
Indices: 119703--119739 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
119693 GAAATCATTA
119703 TTCATTATCTGAAACAT
1 TTCATTATCTGAAACAT
*
119720 TTCATTATCTGATACAT
1 TTCATTATCTGAAACAT
119737 TTC
1 TTC
119740 CTTAGTGTGC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.30, C:0.19, G:0.05, T:0.46
Consensus pattern (17 bp):
TTCATTATCTGAAACAT
Found at i:124416 original size:29 final size:29
Alignment explanation
Indices: 124374--124469 Score: 183
Period size: 29 Copynumber: 3.3 Consensus size: 29
124364 GATGTTCAGC
124374 TTTGTGTATCTTTATAATGTTGATTTAGA
1 TTTGTGTATCTTTATAATGTTGATTTAGA
124403 TTTGTGTATCTTTATAATGTTGATTTAGA
1 TTTGTGTATCTTTATAATGTTGATTTAGA
124432 TTTGTGTATCTTTATAATGTTGATTTAGA
1 TTTGTGTATCTTTATAATGTTGATTTAGA
*
124461 TTTGCGTAT
1 TTTGTGTAT
124470 GATTTTTAGA
Statistics
Matches: 66, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
29 66 1.00
ACGTcount: A:0.23, C:0.04, G:0.18, T:0.55
Consensus pattern (29 bp):
TTTGTGTATCTTTATAATGTTGATTTAGA
Found at i:127396 original size:23 final size:23
Alignment explanation
Indices: 127370--127532 Score: 116
Period size: 23 Copynumber: 7.4 Consensus size: 23
127360 AATATTAAGC
127370 ATCAGAAGTAAGTAAATACATGG
1 ATCAGAAGTAAGTAAATACATGG
127393 ATCAGAAGTAAGTAAATACATGG
1 ATCAGAAGTAAGTAAATACATGG
* **
127416 ATCAGAAATACA-TGGAT-CA--G
1 ATCAGAAGTA-AGTAAATACATGG
* * ** *
127436 A--AGTAAGTAAATACATGGATCAG
1 ATCAG-AAGTAAGTAAATACAT-GG
127459 A--AGTAAGT-A--A-ATACATGG
1 ATCAG-AAGTAAGTAAATACATGG
*
127477 ATCAAAAGTAAGTAAATACATGG
1 ATCAGAAGTAAGTAAATACATGG
127500 ATCAGAAGTAAGTAAATACATGG
1 ATCAGAAGTAAGTAAATACATGG
127523 ATCAGTAAGT
1 ATCAG-AAGT
127533 TTATACAGTA
Statistics
Matches: 114, Mismatches: 12, Indels: 27
0.75 0.08 0.18
Matches are distributed among these distances:
18 5 0.04
19 15 0.13
20 6 0.05
22 4 0.04
23 79 0.69
24 5 0.04
ACGTcount: A:0.48, C:0.09, G:0.21, T:0.22
Consensus pattern (23 bp):
ATCAGAAGTAAGTAAATACATGG
Found at i:127426 original size:15 final size:15
Alignment explanation
Indices: 127406--127437 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
127396 AGAAGTAAGT
127406 AAATACATGGATCAG
1 AAATACATGGATCAG
127421 AAATACATGGATCAG
1 AAATACATGGATCAG
127436 AA
1 AA
127438 GTAAGTAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.50, C:0.12, G:0.19, T:0.19
Consensus pattern (15 bp):
AAATACATGGATCAG
Found at i:127434 original size:38 final size:38
Alignment explanation
Indices: 127383--127506 Score: 167
Period size: 38 Copynumber: 3.1 Consensus size: 38
127373 AGAAGTAAGT
127383 AAATACATGGATCAGAAGTAAGTAAATACATGGATCAG
1 AAATACATGGATCAGAAGTAAGTAAATACATGGATCAG
127421 AAATACATGGATCAGAAGTAAGTAAATACATGGATCAGAAGTAAG
1 AAATACATGGATCAGAAGTAAGTAAATACATGGATC-------AG
*
127466 TAAATACATGGATCAAAAGTAAGTAAATACATGGATCAG
1 -AAATACATGGATCAGAAGTAAGTAAATACATGGATCAG
127505 AA
1 AA
127507 GTAAGTAAAT
Statistics
Matches: 77, Mismatches: 1, Indels: 16
0.82 0.01 0.17
Matches are distributed among these distances:
38 38 0.49
39 2 0.03
45 2 0.03
46 35 0.45
ACGTcount: A:0.49, C:0.10, G:0.20, T:0.21
Consensus pattern (38 bp):
AAATACATGGATCAGAAGTAAGTAAATACATGGATCAG
Found at i:127465 original size:61 final size:63
Alignment explanation
Indices: 127370--127532 Score: 249
Period size: 61 Copynumber: 2.5 Consensus size: 63
127360 AATATTAAGC
127370 ATCAGAAGTAAGTAAATACATGGATCAGAAGTAAGTAAATACATGGATC-AG-AAATACATGG
1 ATCAGAAGTAAGTAAATACATGGATCAGAAGTAAGTAAATACATGGATCAAGTAAATACATGG
127431 ATCAGAAGTAAGTAAATACATGGATCAGAAGTAAGTAAATACATGGATCAAAAGTAAGTAAATAC
1 ATCAGAAGTAAGTAAATACATGGATCAGAAGTAAGTAAATACATGGATC------AAGTAAATAC
127496 ATGG
60 ATGG
127500 ATCAGAAGTAAGTAAATACATGGATCAGTAAGT
1 ATCAGAAGTAAGTAAATACATGGATCAG-AAGT
127533 TTATACAGTA
Statistics
Matches: 93, Mismatches: 0, Indels: 9
0.91 0.00 0.09
Matches are distributed among these distances:
61 49 0.53
68 2 0.02
69 38 0.41
70 4 0.04
ACGTcount: A:0.48, C:0.09, G:0.21, T:0.22
Consensus pattern (63 bp):
ATCAGAAGTAAGTAAATACATGGATCAGAAGTAAGTAAATACATGGATCAAGTAAATACATGG
Found at i:127473 original size:46 final size:46
Alignment explanation
Indices: 127421--127532 Score: 206
Period size: 46 Copynumber: 2.4 Consensus size: 46
127411 CATGGATCAG
127421 AAATACATGGATCAGAAGTAAGTAAATACATGGATCAGAAGTAAGT
1 AAATACATGGATCAGAAGTAAGTAAATACATGGATCAGAAGTAAGT
*
127467 AAATACATGGATCAAAAGTAAGTAAATACATGGATCAGAAGTAAGT
1 AAATACATGGATCAGAAGTAAGTAAATACATGGATCAGAAGTAAGT
127513 AAATACATGGATCAGTAAGT
1 AAATACATGGATCAG-AAGT
127533 TTATACAGTA
Statistics
Matches: 63, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
46 59 0.94
47 4 0.06
ACGTcount: A:0.48, C:0.09, G:0.21, T:0.22
Consensus pattern (46 bp):
AAATACATGGATCAGAAGTAAGTAAATACATGGATCAGAAGTAAGT
Found at i:128612 original size:4 final size:4
Alignment explanation
Indices: 128597--128634 Score: 51
Period size: 4 Copynumber: 9.8 Consensus size: 4
128587 ATCACCCGTT
* *
128597 GTCC GT-C GTCC GTCC GTCC GTCT GTCT GTCC GTCC GTC
1 GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTC
128635 TGTAAACTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
3 3 0.10
4 28 0.90
ACGTcount: A:0.00, C:0.42, G:0.26, T:0.32
Consensus pattern (4 bp):
GTCC
Found at i:128629 original size:16 final size:16
Alignment explanation
Indices: 128597--128637 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
128587 ATCACCCGTT
128597 GTCCGTC-GTCCGTCC
1 GTCCGTCTGTCCGTCC
*
128612 GTCCGTCTGTCTGTCC
1 GTCCGTCTGTCCGTCC
128628 GTCCGTCTGT
1 GTCCGTCTGT
128638 AAACTTTTCA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 7 0.29
16 17 0.71
ACGTcount: A:0.00, C:0.39, G:0.27, T:0.34
Consensus pattern (16 bp):
GTCCGTCTGTCCGTCC
Found at i:129078 original size:166 final size:166
Alignment explanation
Indices: 128804--129653 Score: 1529
Period size: 166 Copynumber: 5.1 Consensus size: 166
128794 GGTGCATGTC
* * * *
128804 TTTAAAAATCTTCTTCTCAAGAACCACTGCACCAGAAATACCAATTTTTACAAAAAAGCATGTAT
1 TTTAAAAATCTTCTTCTCAAGAACCACTGCACCAGAAATGCCAATATTTACACAAAAGCTTGTAT
* * *
128869 ATATAGTTAAGATTCTAAATTGTAAAAATCGTAACCCCCGGACCAAAACTGGGGCCCCAGGCGGG
66 ATATAGTGAATATTCTAAATTGTAAAAATCGTGACCCCCGGACCAAAACTGGGGCCCCAGGCGGG
* *
128934 GTTCATAATTTAACATGGAAATACATTAGAAAAATG
131 GTTCAAAATTTAACATGGAAATACATTGGAAAAATG
*
128970 TTTAAAAATCTTCTTCTCAAGAACCACTGCACCAGAAATGCCAATATTAACACAAAAGCTTGTAT
1 TTTAAAAATCTTCTTCTCAAGAACCACTGCACCAGAAATGCCAATATTTACACAAAAGCTTGTAT
129035 ATATAGTGAATATTCTAAATTGTAAAAATCGTGACCCCCGGACCAAAACTGGGGCCCCAGGCGGG
66 ATATAGTGAATATTCTAAATTGTAAAAATCGTGACCCCCGGACCAAAACTGGGGCCCCAGGCGGG
129100 GTTCAAAATTTAACATGGAAATACATTGGAAAAATG
131 GTTCAAAATTTAACATGGAAATACATTGGAAAAATG
* * *
129136 TTTAAAAATCTTCTTCTCAAGAACCACTGCAACAGAAATGCTATTATTTACACAAAAGCTTGTAT
1 TTTAAAAATCTTCTTCTCAAGAACCACTGCACCAGAAATGCCAATATTTACACAAAAGCTTGTAT
* *
129201 ATAAAGTGAATATTCTAAATTGTAAAAATCGTGACCCCTGGACCAAAACTGGGGCCCCAGGCGGG
66 ATATAGTGAATATTCTAAATTGTAAAAATCGTGACCCCCGGACCAAAACTGGGGCCCCAGGCGGG
129266 GTTCAAAATTTAACATGGAAATACATTGGAAAAATG
131 GTTCAAAATTTAACATGGAAATACATTGGAAAAATG
129302 TTTAAAAATCTTCTTCTCAAGAACCACTGCACCAGAAATGCCAATATTTACACAAAAGCTTGTAT
1 TTTAAAAATCTTCTTCTCAAGAACCACTGCACCAGAAATGCCAATATTTACACAAAAGCTTGTAT
*
129367 ATATAGTGAATATTCTAAATTGTAAAAATCGTGACCCCCGGACCAAAACTGGAGCCCCAGGCGGG
66 ATATAGTGAATATTCTAAATTGTAAAAATCGTGACCCCCGGACCAAAACTGGGGCCCCAGGCGGG
129432 GTTCAAAATTTAACATGGAAATACATTGGAAAAATG
131 GTTCAAAATTTAACATGGAAATACATTGGAAAAATG
*
129468 TTTAAAAATCTTCTTCTCAAGAACCACTGCACCAGAAATGCCAATATTTACACATAAGCTTGTAT
1 TTTAAAAATCTTCTTCTCAAGAACCACTGCACCAGAAATGCCAATATTTACACAAAAGCTTGTAT
* *
129533 ATATAGTGAAGATTCTAAATTGTAAAAATCATGACCCCCGGACCAAAACTGGGGCCCCAGGCGGG
66 ATATAGTGAATATTCTAAATTGTAAAAATCGTGACCCCCGGACCAAAACTGGGGCCCCAGGCGGG
129598 GTTCAAAATTTAACATGGAAATACATTGGAAAAATG
131 GTTCAAAATTTAACATGGAAATACATTGGAAAAATG
129634 TTTAAAAATCTTCTTCTCAA
1 TTTAAAAATCTTCTTCTCAA
129654 ATCTAATGGA
Statistics
Matches: 658, Mismatches: 26, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
166 658 1.00
ACGTcount: A:0.39, C:0.19, G:0.16, T:0.26
Consensus pattern (166 bp):
TTTAAAAATCTTCTTCTCAAGAACCACTGCACCAGAAATGCCAATATTTACACAAAAGCTTGTAT
ATATAGTGAATATTCTAAATTGTAAAAATCGTGACCCCCGGACCAAAACTGGGGCCCCAGGCGGG
GTTCAAAATTTAACATGGAAATACATTGGAAAAATG
Found at i:141073 original size:234 final size:233
Alignment explanation
Indices: 140664--141130 Score: 925
Period size: 234 Copynumber: 2.0 Consensus size: 233
140654 GGTAATCTTA
140664 TGTGTATTTCTGTGTATTGCAGTAAATAAATTCACTGAAACCAGTACTTTTTTTAATGTACATTG
1 TGTGTATTTCTGTGTATTGCAGTAAATAAATTCACTGAAACCAGTACTTTTTTTAATGTACATTG
140729 GATACACTTTTTAAACATGACTGAAATGGGGGGTTTCAGTGAATTTATTTACTGCAATACACAGA
66 GATACACTTTTTAAACATGACTGAAATGGGGGGTTTCAGTGAATTTATTTACTGCAATACACAGA
140794 AATACACATAAGATTACCAATTTTAATCAATTTTTTCTTCGGGCACAAATAATTAGGAAATTCAC
131 AATACACATAAGATTACCAATTTTAATCAATTTTTTCTTCGGGCACAAATAATTAGGAAATTCAC
140859 TATCCAACAACCAAGCCCCTGTGGTACATCATGCATGT
196 TATCCAACAACCAAGCCCCTGTGGTACATCATGCATGT
140897 NTGTGTATTTCTGTGTATTGCAGTAAATAAATTCACTGAAACCAGTACTTTTTTTAATGTACATT
1 -TGTGTATTTCTGTGTATTGCAGTAAATAAATTCACTGAAACCAGTACTTTTTTTAATGTACATT
140962 GGATACACTTTTTAAACATGACTGAAATGGGGGGTTTCAGTGAATTTATTTACTGCAATACACAG
65 GGATACACTTTTTAAACATGACTGAAATGGGGGGTTTCAGTGAATTTATTTACTGCAATACACAG
141027 AAATACACATAAGATTACCAATTTTAATCAATTTTTTCTTCGGGCACAAATAATTAGGAAATTCA
130 AAATACACATAAGATTACCAATTTTAATCAATTTTTTCTTCGGGCACAAATAATTAGGAAATTCA
141092 CTATCCAACAACCAAGCCCCTGTGGTACATCATGCATGT
195 CTATCCAACAACCAAGCCCCTGTGGTACATCATGCATGT
141131 AGTCTAGTTT
Statistics
Matches: 233, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
234 233 1.00
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.34
Consensus pattern (233 bp):
TGTGTATTTCTGTGTATTGCAGTAAATAAATTCACTGAAACCAGTACTTTTTTTAATGTACATTG
GATACACTTTTTAAACATGACTGAAATGGGGGGTTTCAGTGAATTTATTTACTGCAATACACAGA
AATACACATAAGATTACCAATTTTAATCAATTTTTTCTTCGGGCACAAATAATTAGGAAATTCAC
TATCCAACAACCAAGCCCCTGTGGTACATCATGCATGT
Found at i:141625 original size:2 final size:2
Alignment explanation
Indices: 141618--141668 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
141608 TCGAATTGAG
141618 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
141660 TC TC TC TC T
1 TC TC TC TC T
141669 TCTTCTTCTT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:141674 original size:3 final size:3
Alignment explanation
Indices: 141666--141693 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
141656 TCTCTCTCTC
141666 TCT TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT T
141694 AACACTAACA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:147822 original size:2 final size:2
Alignment explanation
Indices: 147815--147863 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
147805 TTTAACATGC
147815 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
147857 CT CT CT C
1 CT CT CT C
147864 ATAATTATAA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:158253 original size:55 final size:55
Alignment explanation
Indices: 158205--158878 Score: 891
Period size: 55 Copynumber: 12.3 Consensus size: 55
158195 GTCGCGGACC
* * * * *
158205 TTGTTCTATAACGTAACCATCAGTTACTGTTAGCATTGGACGAGGGTCGTTGACG
1 TTGTACTATAACGTTACAATCAGTTAATGTAAGCATTGGACGAGGGTCGTTGACG
** ** *
158260 TTGTAC-AGTAACGCAACACCCAGTTAATGTAAGCATTGGACGAGGGTCTTTGACG
1 TTGTACTA-TAACGTTACAATCAGTTAATGTAAGCATTGGACGAGGGTCGTTGACG
** * * * * * *
158315 TAATGCTGTAACATAACAATCAGTTAATATAAGCATTGGACGAGGGTCGTAGACG
1 TTGTACTATAACGTTACAATCAGTTAATGTAAGCATTGGACGAGGGTCGTTGACG
* *
158370 TTGTACTGTAACGTTACAATCAGTTAATGTAAGCATTGGACGAGGGTCGTAGACG
1 TTGTACTATAACGTTACAATCAGTTAATGTAAGCATTGGACGAGGGTCGTTGACG
* * *
158425 TTGTACTGTAACGTTACAATCAGTTAATGTTAGCACTGGACGAGGGTCGTTGACG
1 TTGTACTATAACGTTACAATCAGTTAATGTAAGCATTGGACGAGGGTCGTTGACG
* * * * *
158480 TTGTACTATAGCATAACAATCAGTTACTGTAAGCTTTGGACGAGGGTCGTTGACG
1 TTGTACTATAACGTTACAATCAGTTAATGTAAGCATTGGACGAGGGTCGTTGACG
* ** *
158535 TTGTACTATAACGTTACAATCAGTTACTGTAAGCATTATACGAGGGTCGTAGACG
1 TTGTACTATAACGTTACAATCAGTTAATGTAAGCATTGGACGAGGGTCGTTGACG
* **
158590 TTGTACTGTAACGTTACAATCAGTTAATGTAAGCATTATACGAGGGTCGTTGACG
1 TTGTACTATAACGTTACAATCAGTTAATGTAAGCATTGGACGAGGGTCGTTGACG
* *
158645 TTGTACTGTAACGTTACAATCAGTTAATGTAAGCATTGGACGAGGGTCGTAGACG
1 TTGTACTATAACGTTACAATCAGTTAATGTAAGCATTGGACGAGGGTCGTTGACG
* * *
158700 TTGTACTGTAACGTTACAATCAGTTAATGTTAGCACTGGACGAGGGTCGTTGACG
1 TTGTACTATAACGTTACAATCAGTTAATGTAAGCATTGGACGAGGGTCGTTGACG
* * * * * *
158755 TTGTACTATAACATAACAATCAGCTACTGTAAGCTTTGGACGAGGGTAGTTGACG
1 TTGTACTATAACGTTACAATCAGTTAATGTAAGCATTGGACGAGGGTCGTTGACG
* *
158810 TTGTACTATAACGTTACAATCAGTTACTGTATGCATTGGACGAGGGTCGTTGACG
1 TTGTACTATAACGTTACAATCAGTTAATGTAAGCATTGGACGAGGGTCGTTGACG
*
158865 TTGTACTGTAACGT
1 TTGTACTATAACGT
158879 ACGTGTAACA
Statistics
Matches: 549, Mismatches: 68, Indels: 4
0.88 0.11 0.01
Matches are distributed among these distances:
54 1 0.00
55 548 1.00
ACGTcount: A:0.28, C:0.16, G:0.25, T:0.30
Consensus pattern (55 bp):
TTGTACTATAACGTTACAATCAGTTAATGTAAGCATTGGACGAGGGTCGTTGACG
Found at i:161505 original size:30 final size:30
Alignment explanation
Indices: 161480--161569 Score: 130
Period size: 30 Copynumber: 3.0 Consensus size: 30
161470 TCAGAATCCG
*
161480 ATCAGCACAATTCTGGCCAATCAGAATTTT
1 ATCAGCACAATTCTGACCAATCAGAATTTT
*
161510 ATCAGGCAC-TTTCTGACCAATCAGAATTTT
1 ATCA-GCACAATTCTGACCAATCAGAATTTT
161540 ATCAGC-CAATTTCTGACCAATCAGAATTTT
1 ATCAGCACAA-TTCTGACCAATCAGAATTTT
161570 GCCCCTCTAC
Statistics
Matches: 54, Mismatches: 3, Indels: 6
0.86 0.05 0.10
Matches are distributed among these distances:
28 1 0.02
29 2 0.04
30 47 0.87
31 4 0.07
ACGTcount: A:0.32, C:0.23, G:0.12, T:0.32
Consensus pattern (30 bp):
ATCAGCACAATTCTGACCAATCAGAATTTT
Found at i:168682 original size:55 final size:55
Alignment explanation
Indices: 168559--168686 Score: 184
Period size: 55 Copynumber: 2.3 Consensus size: 55
168549 ACTGACGTAA
* * *
168559 ACGTTGTACTATGACGTAACACTCAGTTACTGTTAGCATTGGACGAGGGTCGTTG
1 ACGTTGTACTGTAACGTAACACTCAGTTACTGTAAGCATTGGACGAGGGTCGTTG
* * * * *
168614 ATGTTTTAATGTAATGTAATACTCAGTTACTGTAAGCATTGGACGAGGGTCGTTG
1 ACGTTGTACTGTAACGTAACACTCAGTTACTGTAAGCATTGGACGAGGGTCGTTG
168669 ACGTTGTACTGTAACGTA
1 ACGTTGTACTGTAACGTA
168687 CGTGTAACAC
Statistics
Matches: 61, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
55 61 1.00
ACGTcount: A:0.26, C:0.15, G:0.26, T:0.34
Consensus pattern (55 bp):
ACGTTGTACTGTAACGTAACACTCAGTTACTGTAAGCATTGGACGAGGGTCGTTG
Found at i:168704 original size:61 final size:59
Alignment explanation
Indices: 168574--168737 Score: 187
Period size: 55 Copynumber: 2.8 Consensus size: 59
168564 GTACTATGAC
* *
168574 GTAACACTCAGTTACTGTTAGCATTGGACGAGGGTCGTTGA---TGT-TTTAATGTAAT
1 GTAACACTCAGTTACTGTTAGCATTGGACGAGGGTCGTTGACGTTGTATGTAACGTAAT
* * *
168629 GTAATACTCAGTTACTGTAAGCATTGGACGAGGGTCGTTGACGTTGTACTGTAACGTACGT
1 GTAACACTCAGTTACTGTTAGCATTGGACGAGGGTCGTTGACGTTGTA-TGTAACGTA-AT
* *
168690 GTAACACTCAGTTACTGTTGGCATTGG-CGTAGGGACG-TGTACGTTGTA
1 GTAACACTCAGTTACTGTTAGCATTGGACG-AGGGTCGTTG-ACGTTGTA
168738 ATTATAGTTT
Statistics
Matches: 92, Mismatches: 9, Indels: 10
0.83 0.08 0.09
Matches are distributed among these distances:
55 39 0.42
58 3 0.03
60 11 0.12
61 39 0.42
ACGTcount: A:0.24, C:0.15, G:0.28, T:0.33
Consensus pattern (59 bp):
GTAACACTCAGTTACTGTTAGCATTGGACGAGGGTCGTTGACGTTGTATGTAACGTAAT
Found at i:172329 original size:30 final size:30
Alignment explanation
Indices: 172295--172354 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
172285 TCAGAATCCG
172295 ATCAGTACA-ATTCTGGCCAATCAGAATTTT
1 ATCAG-ACACATTCTGGCCAATCAGAATTTT
* *
172325 ATCAGCCACTTTCTGGCCAATCAGAATTTT
1 ATCAGACACATTCTGGCCAATCAGAATTTT
172355 GCCCCTCTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 2 0.07
30 25 0.93
ACGTcount: A:0.30, C:0.23, G:0.13, T:0.33
Consensus pattern (30 bp):
ATCAGACACATTCTGGCCAATCAGAATTTT
Found at i:174906 original size:2 final size:2
Alignment explanation
Indices: 174899--174935 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
174889 TGGCGGATCC
174899 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
174936 TGGCAAAGGC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:180448 original size:165 final size:165
Alignment explanation
Indices: 180064--180858 Score: 1128
Period size: 165 Copynumber: 4.8 Consensus size: 165
180054 GGAGTAGAGA
* * * * * *
180064 AGAAGATTTTTTAAGATTTAAAACATTTTTACTATATGGCCATATTGGTCCCACCCTAGAGCCTG
1 AGAAGGTTTTCTAAGATTTCATACATTTTAACTATATGGCCATTTTGGTCCCACCCTAGAGCCTG
* * ** ** *
180129 AACACCTAACAAAGGATTCATGAATTTCACAATAATTTTAGA-AGA-CGCTCTCATGGACATCAT
66 AACCCCTGACCCAGGGGTCATGAATTTCAC---AA-TTTAGATAGAGGGCT-TCATGGACATCAT
* * * *
180192 AATCATGCATTTAGTTTTTTACAAATATATATGGGA-TAAAAG
126 AACCAGGCATTTAGTTTTTAACAAATATATATGAGAGT---AG
* * *
180234 AACAAGATTTTCTAAGATTTCATACATTTTGACTATATGGCCATTTTGGTCCCACCCTAGAGCCT
1 -AGAAGGTTTTCTAAGATTTCATACATTTTAACTATATGGCCATTTTGGTCCCACCCTAGAGCCT
180299 GAACCCCTGACCCAGGGGTCATGAATTTCACAATTTAGATAGAGGGCTTCATGGACATCATAACC
65 GAACCCCTGACCCAGGGGTCATGAATTTCACAATTTAGATAGAGGGCTTCATGGACATCATAACC
180364 AGGCATTTAGTTTTTAACAAATATATATGAGAGTAG
130 AGGCATTTAGTTTTTAACAAATATATATGAGAGTAG
*
180400 AGAAGGTTTTCTAAGATTTCATACATTTTAACTATATTGCCATTTTGGTCCCACCCTAGAGCCTG
1 AGAAGGTTTTCTAAGATTTCATACATTTTAACTATATGGCCATTTTGGTCCCACCCTAGAGCCTG
*
180465 AACCCCTGACCCAGGGGTCATGAATTTCACAATTTAGATAGAGGGCTTCATGGACATCTTAACCA
66 AACCCCTGACCCAGGGGTCATGAATTTCACAATTTAGATAGAGGGCTTCATGGACATCATAACCA
180530 GGCATTTAGTTTTTAACAAATATATATGAGAGTAG
131 GGCATTTAGTTTTTAACAAATATATATGAGAGTAG
* * *
180565 AGAAGGTTTTCTAAGATTTCATACATTTCAACTATATTGCCATTTTGGTCCCACCCTAGAGCCTA
1 AGAAGGTTTTCTAAGATTTCATACATTTTAACTATATGGCCATTTTGGTCCCACCCTAGAGCCTG
* *
180630 AACCCCTGACCCAGGGGTCATGAATTTCACAATTTAGGTAGAGGGCCTCATGGACATCATAACCA
66 AACCCCTGACCCAGGGGTCATGAATTTCACAATTTAGATAGAGGGCTTCATGGACATCATAACCA
* *
180695 GGCATTTAGTTTTTAACAAATGTATATGAGACTAG
131 GGCATTTAGTTTTTAACAAATATATATGAGAGTAG
* * * * *
180730 AGAAGAAGAATTTCTAAGATTTAATACATTTTTACTATATGGCCATATTGGCCCCACCCTAGAGC
1 AGAAG--G-TTTTCTAAGATTTCATACATTTTAACTATATGGCCATTTTGGTCCCACCCTAGAGC
* * *
180795 CTGAACCCCTGACCCAGGGGTCATGAATTTCACAATTTTGGTAGAGGGCCTCATGGACATCATA
63 CTGAACCCCTGACCCAGGGGTCATGAATTTCACAATTTAGATAGAGGGCTTCATGGACATCATA
180859 GATATGCAAC
Statistics
Matches: 580, Mismatches: 38, Indels: 15
0.92 0.06 0.02
Matches are distributed among these distances:
165 323 0.56
166 2 0.00
167 7 0.01
168 161 0.28
169 4 0.01
171 83 0.14
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.31
Consensus pattern (165 bp):
AGAAGGTTTTCTAAGATTTCATACATTTTAACTATATGGCCATTTTGGTCCCACCCTAGAGCCTG
AACCCCTGACCCAGGGGTCATGAATTTCACAATTTAGATAGAGGGCTTCATGGACATCATAACCA
GGCATTTAGTTTTTAACAAATATATATGAGAGTAG
Found at i:183337 original size:17 final size:17
Alignment explanation
Indices: 183317--183349 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
183307 TAAGTGTGTT
183317 AATTATGTAAGCATTTG
1 AATTATGTAAGCATTTG
*
183334 AATTGTGTAAGCATTT
1 AATTATGTAAGCATTT
183350 TATGTACTCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.33, C:0.06, G:0.18, T:0.42
Consensus pattern (17 bp):
AATTATGTAAGCATTTG
Found at i:185397 original size:19 final size:19
Alignment explanation
Indices: 185373--185416 Score: 79
Period size: 19 Copynumber: 2.3 Consensus size: 19
185363 AGAGATAGTT
185373 TTGATATTTTATGATGTTC
1 TTGATATTTTATGATGTTC
185392 TTGATATTTTATGATGTTC
1 TTGATATTTTATGATGTTC
*
185411 TCGATA
1 TTGATA
185417 AAGAATGCCT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.23, C:0.07, G:0.16, T:0.55
Consensus pattern (19 bp):
TTGATATTTTATGATGTTC
Found at i:185435 original size:2 final size:2
Alignment explanation
Indices: 185428--185486 Score: 118
Period size: 2 Copynumber: 29.5 Consensus size: 2
185418 AGAATGCCTA
185428 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
185470 AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG A
185487 AATGATAACA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:188524 original size:2 final size:2
Alignment explanation
Indices: 188517--188577 Score: 122
Period size: 2 Copynumber: 30.5 Consensus size: 2
188507 AGACAGATCA
188517 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
188559 TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC T
188578 GTTAACACGT
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:189686 original size:2 final size:2
Alignment explanation
Indices: 189679--189734 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
189669 GTAACGTAAT
189679 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
189721 TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC
189735 AGTTACCAAA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:192104 original size:11 final size:11
Alignment explanation
Indices: 192088--192126 Score: 78
Period size: 11 Copynumber: 3.5 Consensus size: 11
192078 AATTTAAAAT
192088 TGATCGATATC
1 TGATCGATATC
192099 TGATCGATATC
1 TGATCGATATC
192110 TGATCGATATC
1 TGATCGATATC
192121 TGATCG
1 TGATCG
192127 GTAATTTGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 28 1.00
ACGTcount: A:0.26, C:0.18, G:0.21, T:0.36
Consensus pattern (11 bp):
TGATCGATATC
Found at i:195553 original size:23 final size:23
Alignment explanation
Indices: 195520--195579 Score: 75
Period size: 23 Copynumber: 2.6 Consensus size: 23
195510 TTGTCTTTTA
*
195520 GTCAAACGAATATACCTACCATT
1 GTCAAAAGAATATACCTACCATT
* * * *
195543 TTCATAAGAATGTATCTACCATT
1 GTCAAAAGAATATACCTACCATT
195566 GTCAAAAGAATATA
1 GTCAAAAGAATATA
195580 GTATTACATG
Statistics
Matches: 29, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.42, C:0.18, G:0.10, T:0.30
Consensus pattern (23 bp):
GTCAAAAGAATATACCTACCATT
Found at i:196317 original size:2 final size:2
Alignment explanation
Indices: 196310--196361 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
196300 AACTAACCAA
196310 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
196352 CT CT CT CT CT
1 CT CT CT CT CT
196362 GGTACCTCTT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:200182 original size:21 final size:21
Alignment explanation
Indices: 200158--200226 Score: 77
Period size: 21 Copynumber: 3.3 Consensus size: 21
200148 GGTATATCTT
*
200158 TTATATGCAATAGTAATATCA
1 TTATATGCAATAGTAACATCA
* *
200179 TTATATGCAGTGGTAACATCA
1 TTATATGCAATAGTAACATCA
* *
200200 TTATATGCAGT-GCTTACATCA
1 TTATATGCAATAG-TAACATCA
200221 TTATAT
1 TTATAT
200227 ACTGTTATTT
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
20 1 0.02
21 42 0.98
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.39
Consensus pattern (21 bp):
TTATATGCAATAGTAACATCA
Found at i:200221 original size:42 final size:42
Alignment explanation
Indices: 200175--200286 Score: 107
Period size: 42 Copynumber: 2.7 Consensus size: 42
200165 CAATAGTAAT
* * *
200175 ATCATTATATGCAGTGGTAACATCATTATATGCAGTGCTTAC
1 ATCATTATATGCAGTGGTAACATCATTATATGCAGGGCTAAA
* * ** ** * *
200217 ATCATTATATACTGTTATTTCATCATTATATTCAGGGGTAAA
1 ATCATTATATGCAGTGGTAACATCATTATATGCAGGGCTAAA
* *
200259 ATCTTTATATGAAGTGGTAACATCATTA
1 ATCATTATATGCAGTGGTAACATCATTA
200287 CGTTATGTCG
Statistics
Matches: 51, Mismatches: 19, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
42 51 1.00
ACGTcount: A:0.33, C:0.13, G:0.14, T:0.39
Consensus pattern (42 bp):
ATCATTATATGCAGTGGTAACATCATTATATGCAGGGCTAAA
Found at i:200578 original size:21 final size:21
Alignment explanation
Indices: 200527--200579 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
200517 TATGGTTTAT
*
200527 TAAAACCATTATGTATGGTGG
1 TAAAACCTTTATGTATGGTGG
*
200548 TAAAACCTTTATGTATTGTGG
1 TAAAACCTTTATGTATGGTGG
* *
200569 TGAAAGCTTTA
1 TAAAACCTTTA
200580 AATGCAATTG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.32, C:0.09, G:0.21, T:0.38
Consensus pattern (21 bp):
TAAAACCTTTATGTATGGTGG
Found at i:200739 original size:21 final size:21
Alignment explanation
Indices: 200682--200726 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
200672 GATCATTTCA
* *
200682 TTATATGGAGTGGTAACTTCT
1 TTATATGCAGTCGTAACTTCT
200703 TTATATGCAGTCGTAAC-TCT
1 TTATATGCAGTCGTAACTTCT
200723 TTAT
1 TTAT
200727 GATGAGGTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 7 0.32
21 15 0.68
ACGTcount: A:0.24, C:0.13, G:0.18, T:0.44
Consensus pattern (21 bp):
TTATATGCAGTCGTAACTTCT
Found at i:202404 original size:2 final size:2
Alignment explanation
Indices: 202397--202436 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
202387 AAAGAACACA
202397 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
202437 GCTTCGAAAC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:202737 original size:21 final size:21
Alignment explanation
Indices: 202713--202757 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
202703 CAATTGCCTG
202713 TAAAGCTTTCACCAAAATACA
1 TAAAGCTTTCACCAAAATACA
* * **
202734 TAAAGGTTTTACCACCATACA
1 TAAAGCTTTCACCAAAATACA
202755 TAA
1 TAA
202758 TGGTTTTAAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.44, C:0.22, G:0.07, T:0.27
Consensus pattern (21 bp):
TAAAGCTTTCACCAAAATACA
Found at i:203076 original size:42 final size:42
Alignment explanation
Indices: 203029--203144 Score: 133
Period size: 42 Copynumber: 2.8 Consensus size: 42
203019 GTTGCCACTT
* * * *
203029 CATATAAAGATTTTACCCCTGAATATAATGATGAAATAACAG
1 CATATAATGATGTTACCACTGAATATAATGATGAAAGAACAG
* * * * * *
203071 TATATAATGATGTTAGCACTGTATATAATGATGTAAGCACTG
1 CATATAATGATGTTACCACTGAATATAATGATGAAAGAACAG
*
203113 CATATAATGATGTTACCACTGCATATAATGAT
1 CATATAATGATGTTACCACTGAATATAATGAT
203145 ATTACTATTG
Statistics
Matches: 61, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
42 61 1.00
ACGTcount: A:0.40, C:0.13, G:0.15, T:0.33
Consensus pattern (42 bp):
CATATAATGATGTTACCACTGAATATAATGATGAAAGAACAG
Found at i:203094 original size:21 final size:21
Alignment explanation
Indices: 203072--203161 Score: 119
Period size: 21 Copynumber: 4.3 Consensus size: 21
203062 AAATAACAGT
*
203072 ATATAATGATGTTAGCACTGT
1 ATATAATGATGTTAGCACTGC
*
203093 ATATAATGATGTAAGCACTGC
1 ATATAATGATGTTAGCACTGC
*
203114 ATATAATGATGTTACCACTGC
1 ATATAATGATGTTAGCACTGC
* *
203135 ATATAATGATATTA-CTATTGC
1 ATATAATGATGTTAGC-ACTGC
203156 ATATAA
1 ATATAA
203162 AAGATATACC
Statistics
Matches: 62, Mismatches: 6, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
20 1 0.02
21 61 0.98
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.36
Consensus pattern (21 bp):
ATATAATGATGTTAGCACTGC
Found at i:203312 original size:2 final size:2
Alignment explanation
Indices: 203305--203349 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
203295 AATACTTCCN
*
203305 TC TC TC TC TC TC TC TC TC TC TC TC TC CC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
203347 TC T
1 TC T
203350 TCAAAACAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
TC
Found at i:203487 original size:21 final size:21
Alignment explanation
Indices: 203463--203520 Score: 57
Period size: 21 Copynumber: 2.8 Consensus size: 21
203453 GAGAACCAGT
203463 TTACAACCT-CATCATAAAG-AG
1 TTACAA-CTGCAT-ATAAAGAAG
*
203484 TTACGACTGCATATAAAGAAG
1 TTACAACTGCATATAAAGAAG
* *
203505 TTACCACTCCATATAA
1 TTACAACTGCATATAA
203521 TGAAAAGATC
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
20 8 0.25
21 24 0.75
ACGTcount: A:0.41, C:0.22, G:0.10, T:0.26
Consensus pattern (21 bp):
TTACAACTGCATATAAAGAAG
Found at i:203501 original size:20 final size:21
Alignment explanation
Indices: 203476--203520 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
203466 CAACCTCATC
* *
203476 ATAAAG-AGTTACGACTGCAT
1 ATAAAGAAGTTACCACTCCAT
203496 ATAAAGAAGTTACCACTCCAT
1 ATAAAGAAGTTACCACTCCAT
203517 ATAA
1 ATAA
203521 TGAAAAGATC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 6 0.27
21 16 0.73
ACGTcount: A:0.44, C:0.18, G:0.13, T:0.24
Consensus pattern (21 bp):
ATAAAGAAGTTACCACTCCAT
Found at i:203672 original size:21 final size:21
Alignment explanation
Indices: 203623--203675 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
203613 CAATTGCATG
* *
203623 TAAAGCTTTCACCACAATACA
1 TAAAGGTTTTACCACAATACA
*
203644 TAAAGGTTTTACCACCATACA
1 TAAAGGTTTTACCACAATACA
*
203665 TAATGGTTTTA
1 TAAAGGTTTTA
203676 ATAAACCATA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.38, C:0.21, G:0.09, T:0.32
Consensus pattern (21 bp):
TAAAGGTTTTACCACAATACA
Found at i:204053 original size:21 final size:21
Alignment explanation
Indices: 203916--204053 Score: 123
Period size: 21 Copynumber: 6.6 Consensus size: 21
203906 CGACAAAACG
* *
203916 TAATGATGTTACAACTTCATA
1 TAATGATGTTACCACTGCATA
* * * *
203937 TAAAGATTTTACCCCTGAATA
1 TAATGATGTTACCACTGCATA
** ** * *
203958 TAATGATGAAATAACAGTATA
1 TAATGATGTTACCACTGCATA
* *
203979 TAATGATGTTAGCACTGGATA
1 TAATGATGTTACCACTGCATA
* *
204000 TAATGATGTAAGCACTGCATA
1 TAATGATGTTACCACTGCATA
204021 TAATGATGTTACCACTGCATA
1 TAATGATGTTACCACTGCATA
*
204042 TAATGATATTAC
1 TAATGATGTTAC
204054 TATTGCTTAT
Statistics
Matches: 91, Mismatches: 26, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 91 1.00
ACGTcount: A:0.39, C:0.13, G:0.14, T:0.33
Consensus pattern (21 bp):
TAATGATGTTACCACTGCATA
Found at i:211117 original size:24 final size:24
Alignment explanation
Indices: 211078--211148 Score: 83
Period size: 24 Copynumber: 3.0 Consensus size: 24
211068 GCGATTCATT
* *
211078 CAGCTTCAAATTTGTTTTGTTTAC
1 CAGCTCCAAATGTGTTTTGTTTAC
* *
211102 GAGC-CCTAAATGTGTTTTCTTTAC
1 CAGCTCC-AAATGTGTTTTGTTTAC
211126 CAGCTCC-AATGTGTTTTGTTTAC
1 CAGCTCCAAATGTGTTTTGTTTAC
211149 AGGCAAATCA
Statistics
Matches: 39, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
23 16 0.41
24 21 0.54
25 2 0.05
ACGTcount: A:0.20, C:0.20, G:0.15, T:0.45
Consensus pattern (24 bp):
CAGCTCCAAATGTGTTTTGTTTAC
Found at i:211991 original size:20 final size:20
Alignment explanation
Indices: 211966--212047 Score: 157
Period size: 20 Copynumber: 4.2 Consensus size: 20
211956 TCTTTTAGTG
211966 CTTACTATAAGTACTAATGT
1 CTTACTATAAGTACTAATGT
211986 CTTACTATAAGTACTAATGT
1 CTTACTATAAGTACTAATGT
212006 CTTACTATAAGTACTAATGT
1 CTTACTATAAGTACTAATGT
212026 CTTACTA-AAGTACTAATGT
1 CTTACTATAAGTACTAATGT
212045 CTT
1 CTT
212048 GGTTGTTTTT
Statistics
Matches: 62, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
19 15 0.24
20 47 0.76
ACGTcount: A:0.34, C:0.16, G:0.10, T:0.40
Consensus pattern (20 bp):
CTTACTATAAGTACTAATGT
Found at i:214974 original size:2 final size:2
Alignment explanation
Indices: 214967--215030 Score: 121
Period size: 2 Copynumber: 32.5 Consensus size: 2
214957 ATTCGACTAT
214967 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
215009 TC TC -C TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC T
215031 GTTGAGAATT
Statistics
Matches: 61, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 60 0.98
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:232788 original size:6 final size:6
Alignment explanation
Indices: 232777--232829 Score: 63
Period size: 6 Copynumber: 8.8 Consensus size: 6
232767 GTCACAGGGC
* * *
232777 TTTTTT TTTTTT TTTTTG CTTATT- TTTTTG TTTTTG TTTTTG TTTTTG
1 TTTTTG TTTTTG TTTTTG -TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG
232825 TTTTT
1 TTTTT
232830 TTTAGGGGGG
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
5 4 0.10
6 34 0.81
7 4 0.10
ACGTcount: A:0.02, C:0.02, G:0.09, T:0.87
Consensus pattern (6 bp):
TTTTTG
Found at i:232804 original size:18 final size:16
Alignment explanation
Indices: 232777--232832 Score: 60
Period size: 15 Copynumber: 3.4 Consensus size: 16
232767 GTCACAGGGC
232777 TTTTTTTTTTTTTT-T
1 TTTTTTTTTTTTTTGT
** *
232792 TTGCTTATTTTTTTGT
1 TTTTTTTTTTTTTTGT
232808 TTTTGTTTTTGTTTTTGT
1 TTTT-TTTTT-TTTTTGT
232826 TTTTTTT
1 TTTTTTT
232833 AGGGGGGGGG
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
15 11 0.34
16 3 0.09
17 7 0.22
18 11 0.34
ACGTcount: A:0.02, C:0.02, G:0.09, T:0.88
Consensus pattern (16 bp):
TTTTTTTTTTTTTTGT
Found at i:233430 original size:3 final size:3
Alignment explanation
Indices: 233422--233466 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
233412 CATCGCCTTT
233422 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA
233467 ACATCATCAG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (3 bp):
TGA
Found at i:235433 original size:20 final size:19
Alignment explanation
Indices: 235395--235432 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
235385 GTGTCATTGT
* *
235395 TTTAATGCAGTATAAAAAA
1 TTTAAAGCAGAATAAAAAA
235414 TTTAAAGCAGAATAAAAAA
1 TTTAAAGCAGAATAAAAAA
235433 AAAGCACACG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.58, C:0.05, G:0.11, T:0.26
Consensus pattern (19 bp):
TTTAAAGCAGAATAAAAAA
Found at i:235808 original size:21 final size:21
Alignment explanation
Indices: 235767--235896 Score: 107
Period size: 21 Copynumber: 6.6 Consensus size: 21
235757 TAGGTTAACT
235767 TTAAAGTTGAAAA-TCCAAGA
1 TTAAAGTTGAAAATTCCAAGA
*
235787 TTAAAGTTGAAAATTTCAAGA
1 TTAAAGTTGAAAATTCCAAGA
* *
235808 TTAAAGTT-TAAAGTCCAA-A
1 TTAAAGTTGAAAATTCCAAGA
* **
235827 -T----TTAAAAATTCCAACT
1 TTAAAGTTGAAAATTCCAAGA
235843 TTAAAGTTGAGAAA-TCCAAGA
1 TTAAAGTTGA-AAATTCCAAGA
* **
235864 TTAAAGTTGAAATTTTTAAGA
1 TTAAAGTTGAAAATTCCAAGA
235885 TTAAAGTTGAAA
1 TTAAAGTTGAAA
235897 GTCCAACTTT
Statistics
Matches: 87, Mismatches: 13, Indels: 19
0.73 0.11 0.16
Matches are distributed among these distances:
14 2 0.02
15 8 0.09
17 1 0.01
18 1 0.01
19 1 0.01
20 22 0.25
21 49 0.56
22 3 0.03
ACGTcount: A:0.47, C:0.08, G:0.13, T:0.32
Consensus pattern (21 bp):
TTAAAGTTGAAAATTCCAAGA
Found at i:235867 original size:77 final size:76
Alignment explanation
Indices: 235763--235913 Score: 248
Period size: 77 Copynumber: 2.0 Consensus size: 76
235753 ATTATAGGTT
*
235763 AACTTTAAAGTTGAAAATCCAAGATTAAAGTTGAAAATTTCAAGATTAAAGTTTAAAGTCCAAAT
1 AACTTTAAAGTTGAAAATCCAAGATTAAAGTTGAAAATTTCAAGATTAAAGTTGAAAGTCCAAAT
235828 TTAAAAATTCC
66 TTAAAAATTCC
* * *
235839 AACTTTAAAGTTGAGAAATCCAAGATTAAAGTTGAAATTTTTAAGATTAAAGTTGAAAGTCCAAC
1 AACTTTAAAGTTGA-AAATCCAAGATTAAAGTTGAAAATTTCAAGATTAAAGTTGAAAGTCCAAA
*
235904 TTTAAGAATT
65 TTTAAAAATT
235914 TCATAACACT
Statistics
Matches: 69, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
76 14 0.20
77 55 0.80
ACGTcount: A:0.46, C:0.09, G:0.13, T:0.32
Consensus pattern (76 bp):
AACTTTAAAGTTGAAAATCCAAGATTAAAGTTGAAAATTTCAAGATTAAAGTTGAAAGTCCAAAT
TTAAAAATTCC
Found at i:237035 original size:4 final size:4
Alignment explanation
Indices: 237026--237057 Score: 64
Period size: 4 Copynumber: 8.0 Consensus size: 4
237016 AACTAACATT
237026 TAAC TAAC TAAC TAAC TAAC TAAC TAAC TAAC
1 TAAC TAAC TAAC TAAC TAAC TAAC TAAC TAAC
237058 ATTTAAAAAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
TAAC
Found at i:240320 original size:3 final size:3
Alignment explanation
Indices: 240312--240345 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
240302 TCGCCTTTTT
* *
240312 ATC ATC ATC ATC ATC ATC ATC GTC ATC AAC ATC A
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC A
240346 ATAACGTTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.35, C:0.32, G:0.03, T:0.29
Consensus pattern (3 bp):
ATC
Found at i:243121 original size:21 final size:22
Alignment explanation
Indices: 243097--243142 Score: 85
Period size: 21 Copynumber: 2.1 Consensus size: 22
243087 ATTTAGTCTC
243097 AAAGTATTTAGTAGTTAAAA-T
1 AAAGTATTTAGTAGTTAAAAGT
243118 AAAGTATTTAGTAGTTAAAAGT
1 AAAGTATTTAGTAGTTAAAAGT
243140 AAA
1 AAA
243143 CGTTGCTATT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.50, C:0.00, G:0.15, T:0.35
Consensus pattern (22 bp):
AAAGTATTTAGTAGTTAAAAGT
Found at i:244376 original size:20 final size:21
Alignment explanation
Indices: 244348--244396 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
244338 CACGTTATTA
* *
244348 ATAACGTAATGG-ACTTTGAC
1 ATAATGTAATGGTAATTTGAC
244368 ATAATGTAATGGTAATTTGAC
1 ATAATGTAATGGTAATTTGAC
244389 ATAATGTA
1 ATAATGTA
244397 CACGTCTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.39, C:0.08, G:0.18, T:0.35
Consensus pattern (21 bp):
ATAATGTAATGGTAATTTGAC
Found at i:251903 original size:2 final size:2
Alignment explanation
Indices: 251896--251954 Score: 109
Period size: 2 Copynumber: 29.0 Consensus size: 2
251886 TGTATGTGTA
251896 AT AT AT AT AT AT AT AT AT AT AT ANT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT
251939 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
251955 TCAAATCAAA
Statistics
Matches: 56, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 54 0.96
3 2 0.04
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:252686 original size:21 final size:22
Alignment explanation
Indices: 252662--252718 Score: 73
Period size: 22 Copynumber: 2.6 Consensus size: 22
252652 CACCCTCTTT
*
252662 TGCAAAGCCAACAGA-CACCGA
1 TGCAAAACCAACAGATCACCGA
*
252683 TGCAAAAACTAAC-GATCACCGA
1 TGC-AAAACCAACAGATCACCGA
252705 TGCAAAACCAACAG
1 TGCAAAACCAACAG
252719 TCATGCACTG
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
21 13 0.43
22 17 0.57
ACGTcount: A:0.46, C:0.30, G:0.16, T:0.09
Consensus pattern (22 bp):
TGCAAAACCAACAGATCACCGA
Found at i:256061 original size:60 final size:59
Alignment explanation
Indices: 255988--256106 Score: 229
Period size: 60 Copynumber: 2.0 Consensus size: 59
255978 AAATTTTGCG
255988 CACATATACCTTTAATGAAATAGAATTACTACGCTCACGTATTTATGCCCGTGCTTGTT
1 CACATATACCTTTAATGAAATAGAATTACTACGCTCACGTATTTATGCCCGTGCTTGTT
256047 NCACATATACCTTTAATGAAATAGAATTACTACGCTCACGTATTTATGCCCGTGCTTGTT
1 -CACATATACCTTTAATGAAATAGAATTACTACGCTCACGTATTTATGCCCGTGCTTGTT
256107 AAAAGTTCTT
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
60 59 1.00
ACGTcount: A:0.29, C:0.22, G:0.13, T:0.35
Consensus pattern (59 bp):
CACATATACCTTTAATGAAATAGAATTACTACGCTCACGTATTTATGCCCGTGCTTGTT
Found at i:258227 original size:21 final size:21
Alignment explanation
Indices: 258203--258242 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
258193 TGACAATTTT
258203 ACGAATCGTAAACTATAGTAA
1 ACGAATCGTAAACTATAGTAA
* * *
258224 ACGATTTGTTAACTATAGT
1 ACGAATCGTAAACTATAGT
258243 TTTCATATGA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.40, C:0.12, G:0.15, T:0.33
Consensus pattern (21 bp):
ACGAATCGTAAACTATAGTAA
Found at i:260032 original size:14 final size:14
Alignment explanation
Indices: 260015--260041 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
260005 TACAATCATG
260015 TATATTTTTATGCA
1 TATATTTTTATGCA
260029 TATATTTTTATGC
1 TATATTTTTATGC
260042 TTCATCATAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.26, C:0.07, G:0.07, T:0.59
Consensus pattern (14 bp):
TATATTTTTATGCA
Found at i:260210 original size:186 final size:185
Alignment explanation
Indices: 259896--260241 Score: 683
Period size: 186 Copynumber: 1.9 Consensus size: 185
259886 ATGCATATCN
259896 AAGTAGTACACTTATGCTGTAATTGTACTATTTAAGTTTTTTATTGTTTTTCTGTTTCTTTTTCC
1 AAGTAGTACACTTATGCTGTAATTGTACTATTTAAGTTTTTTATTGTTTTTCTGTTTCTTTTTCC
259961 ACAAACCGGTTTTTGCCAACCCTTTTTTTTGGCCCATCTGAATATACAATCATGTATATTTTTAT
66 ACAAACCGGTTTTTGCCAACCCTTTTTTTTGGCCCATCTGAATATACAATCATGTATATTTTTAT
260026 GCATATATTTTTATGCTTCATCATACTATNTATATATATATAAAACATGTACATAA
131 GCATATATTTTTATGCTTCATCATACTAT-TATATATATATAAAACATGTACATAA
260082 AAGTAGTACACTTATGCTGTAATTGTACTATTTAAGTTTTTTATTGTTTTTCTGTTTCTTTTTCC
1 AAGTAGTACACTTATGCTGTAATTGTACTATTTAAGTTTTTTATTGTTTTTCTGTTTCTTTTTCC
260147 ACAAACCGGTTTTTGCCAACCCTTTTTTTTGGCCCATCTGAATATACAATCATGTATATTTTTAT
66 ACAAACCGGTTTTTGCCAACCCTTTTTTTTGGCCCATCTGAATATACAATCATGTATATTTTTAT
260212 GCATATATTTTTATGCTTCATCATACTATT
131 GCATATATTTTTATGCTTCATCATACTATT
260242 CTACAAATAA
Statistics
Matches: 160, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
185 1 0.01
186 159 0.99
ACGTcount: A:0.26, C:0.16, G:0.10, T:0.47
Consensus pattern (185 bp):
AAGTAGTACACTTATGCTGTAATTGTACTATTTAAGTTTTTTATTGTTTTTCTGTTTCTTTTTCC
ACAAACCGGTTTTTGCCAACCCTTTTTTTTGGCCCATCTGAATATACAATCATGTATATTTTTAT
GCATATATTTTTATGCTTCATCATACTATTATATATATATAAAACATGTACATAA
Found at i:260218 original size:14 final size:14
Alignment explanation
Indices: 260201--260227 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
260191 TACAATCATG
260201 TATATTTTTATGCA
1 TATATTTTTATGCA
260215 TATATTTTTATGC
1 TATATTTTTATGC
260228 TTCATCATAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.26, C:0.07, G:0.07, T:0.59
Consensus pattern (14 bp):
TATATTTTTATGCA
Found at i:264502 original size:18 final size:18
Alignment explanation
Indices: 264472--264506 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
264462 ACCAAAAACT
264472 ATTAATAGTTAATAGTTC
1 ATTAATAGTTAATAGTTC
264490 ATTAACTAG-TAATAGTT
1 ATTAA-TAGTTAATAGTT
264507 TTCATCTGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 13 0.81
19 3 0.19
ACGTcount: A:0.40, C:0.06, G:0.11, T:0.43
Consensus pattern (18 bp):
ATTAATAGTTAATAGTTC
Found at i:265643 original size:21 final size:21
Alignment explanation
Indices: 265593--265664 Score: 83
Period size: 21 Copynumber: 3.4 Consensus size: 21
265583 TCAATTTTAT
*
265593 ACTTTAATCTGT-AATTTCCAC
1 ACTTTAATCTGTAAAATT-CAC
*
265614 ACTTCAATCTGTAAAATTCAC
1 ACTTTAATCTGTAAAATTCAC
* *
265635 TCTTTAATCTGTAAAATTCGC
1 ACTTTAATCTGTAAAATTCAC
*
265656 CCTTTAATC
1 ACTTTAATC
265665 ATTACTTTTA
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
21 40 0.91
22 4 0.09
ACGTcount: A:0.31, C:0.24, G:0.06, T:0.40
Consensus pattern (21 bp):
ACTTTAATCTGTAAAATTCAC
Found at i:268276 original size:18 final size:18
Alignment explanation
Indices: 268253--268293 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
268243 CCCTCTTGTA
* *
268253 TATGTTTATTGAATGTTT
1 TATGTTCATTGAATGTTG
*
268271 TATGTTCATTGGATGTTG
1 TATGTTCATTGAATGTTG
268289 TATGT
1 TATGT
268294 CAACAGTCTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.20, C:0.02, G:0.22, T:0.56
Consensus pattern (18 bp):
TATGTTCATTGAATGTTG
Found at i:288166 original size:24 final size:24
Alignment explanation
Indices: 288139--288210 Score: 135
Period size: 24 Copynumber: 3.0 Consensus size: 24
288129 AGCAGCCACA
288139 GGTACTTTGATGGTTTTAAAATGC
1 GGTACTTTGATGGTTTTAAAATGC
*
288163 GGTACTTTGCTGGTTTTAAAATGC
1 GGTACTTTGATGGTTTTAAAATGC
288187 GGTACTTTGATGGTTTTAAAATGC
1 GGTACTTTGATGGTTTTAAAATGC
288211 TGTATCGCGT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 46 1.00
ACGTcount: A:0.24, C:0.10, G:0.25, T:0.42
Consensus pattern (24 bp):
GGTACTTTGATGGTTTTAAAATGC
Found at i:289188 original size:21 final size:20
Alignment explanation
Indices: 289162--289200 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
289152 CCAACAACAA
289162 CAAAAAACAACAAAAAAACCC
1 CAAAAAACAA-AAAAAAACCC
*
289183 CAAAAAACAAAATAAAAC
1 CAAAAAACAAAAAAAAAC
289201 GGTTACGGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.74, C:0.23, G:0.00, T:0.03
Consensus pattern (20 bp):
CAAAAAACAAAAAAAAACCC
Found at i:289512 original size:200 final size:200
Alignment explanation
Indices: 289169--289568 Score: 800
Period size: 200 Copynumber: 2.0 Consensus size: 200
289159 CAACAAAAAA
289169 CAACAAAAAAACCCCAAAAAACAAAATAAAACGGTTACGGAATTCGATATCTTTTCTAAAAAAAA
1 CAACAAAAAAACCCCAAAAAACAAAATAAAACGGTTACGGAATTCGATATCTTTTCTAAAAAAAA
289234 AAAGACTATTACAGGATATACAGCTTAGCCATTACGCGTGTAACGATGCCAAGAATGTAACATTA
66 AAAGACTATTACAGGATATACAGCTTAGCCATTACGCGTGTAACGATGCCAAGAATGTAACATTA
289299 TGCTAAAGATATAAACTTATTTGTAGAAATCTCAATCGCCATATTGGAGATCACTATCATTTTTG
131 TGCTAAAGATATAAACTTATTTGTAGAAATCTCAATCGCCATATTGGAGATCACTATCATTTTTG
289364 CTAAC
196 CTAAC
289369 CAACAAAAAAACCCCAAAAAACAAAATAAAACGGTTACGGAATTCGATATCTTTTCTAAAAAAAA
1 CAACAAAAAAACCCCAAAAAACAAAATAAAACGGTTACGGAATTCGATATCTTTTCTAAAAAAAA
289434 AAAGACTATTACAGGATATACAGCTTAGCCATTACGCGTGTAACGATGCCAAGAATGTAACATTA
66 AAAGACTATTACAGGATATACAGCTTAGCCATTACGCGTGTAACGATGCCAAGAATGTAACATTA
289499 TGCTAAAGATATAAACTTATTTGTAGAAATCTCAATCGCCATATTGGAGATCACTATCATTTTTG
131 TGCTAAAGATATAAACTTATTTGTAGAAATCTCAATCGCCATATTGGAGATCACTATCATTTTTG
289564 CTAAC
196 CTAAC
289569 AATCATTTCA
Statistics
Matches: 200, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
200 200 1.00
ACGTcount: A:0.42, C:0.18, G:0.13, T:0.27
Consensus pattern (200 bp):
CAACAAAAAAACCCCAAAAAACAAAATAAAACGGTTACGGAATTCGATATCTTTTCTAAAAAAAA
AAAGACTATTACAGGATATACAGCTTAGCCATTACGCGTGTAACGATGCCAAGAATGTAACATTA
TGCTAAAGATATAAACTTATTTGTAGAAATCTCAATCGCCATATTGGAGATCACTATCATTTTTG
CTAAC
Found at i:295810 original size:2 final size:2
Alignment explanation
Indices: 295803--295863 Score: 95
Period size: 2 Copynumber: 30.5 Consensus size: 2
295793 AGTCAAAAAT
* * *
295803 TC TC TC TC TC TC TT TC TC TT TC TC TC TC TC TC TT TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
295845 TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC T
295864 GCGTATCACC
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.00, C:0.44, G:0.00, T:0.56
Consensus pattern (2 bp):
TC
Found at i:299278 original size:23 final size:23
Alignment explanation
Indices: 299252--299298 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
299242 ATGTCTTCCA
299252 CTGTAATACACCCAGTATGAGTG
1 CTGTAATACACCCAGTATGAGTG
299275 CTGTAATACACCCAGTATGAGTG
1 CTGTAATACACCCAGTATGAGTG
299298 C
1 C
299299 CTTCTTTTAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.30, C:0.23, G:0.21, T:0.26
Consensus pattern (23 bp):
CTGTAATACACCCAGTATGAGTG
Found at i:299693 original size:21 final size:21
Alignment explanation
Indices: 299663--299742 Score: 88
Period size: 21 Copynumber: 3.8 Consensus size: 21
299653 TTCTATTAAT
299663 TATGTCGACATGCAAGATAAA
1 TATGTCGACATGCAAGATAAA
* * **
299684 GATGTTGACATGCAAGATAGT
1 TATGTCGACATGCAAGATAAA
* * *
299705 TATGTCAACATGCAACATAAC
1 TATGTCGACATGCAAGATAAA
*
299726 TATGTTGACATGCAAGA
1 TATGTCGACATGCAAGA
299743 AAACTGCAAT
Statistics
Matches: 46, Mismatches: 13, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 46 1.00
ACGTcount: A:0.39, C:0.15, G:0.20, T:0.26
Consensus pattern (21 bp):
TATGTCGACATGCAAGATAAA
Found at i:299731 original size:42 final size:42
Alignment explanation
Indices: 299662--299742 Score: 126
Period size: 42 Copynumber: 1.9 Consensus size: 42
299652 TTTCTATTAA
* *
299662 TTATGTCGACATGCAAGATAAAGATGTTGACATGCAAGATAG
1 TTATGTCAACATGCAACATAAAGATGTTGACATGCAAGATAG
**
299704 TTATGTCAACATGCAACATAACTATGTTGACATGCAAGA
1 TTATGTCAACATGCAACATAAAGATGTTGACATGCAAGA
299743 AAACTGCAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.38, C:0.15, G:0.20, T:0.27
Consensus pattern (42 bp):
TTATGTCAACATGCAACATAAAGATGTTGACATGCAAGATAG
Found at i:299882 original size:21 final size:21
Alignment explanation
Indices: 299856--299994 Score: 152
Period size: 21 Copynumber: 6.6 Consensus size: 21
299846 ATGTTAATTA
*
299856 ACATGCAACTTCTTTATGTCG
1 ACATGCAACTTATTTATGTCG
299877 ACATGCAACTTATTTATGTCG
1 ACATGCAACTTATTTATGTCG
* **
299898 ACATGCAACTTAGTTATGTTA
1 ACATGCAACTTATTTATGTCG
*** ** *
299919 ACATGCAGGATAAATATGTTG
1 ACATGCAACTTATTTATGTCG
*
299940 ACATGCAACATATTTATGTCG
1 ACATGCAACTTATTTATGTCG
* *
299961 ACATGCAACTTAGTTATGTTG
1 ACATGCAACTTATTTATGTCG
*
299982 ACATACAACTTAT
1 ACATGCAACTTAT
299995 AAGTTGCATG
Statistics
Matches: 98, Mismatches: 20, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 98 1.00
ACGTcount: A:0.32, C:0.17, G:0.15, T:0.35
Consensus pattern (21 bp):
ACATGCAACTTATTTATGTCG
Found at i:300058 original size:42 final size:41
Alignment explanation
Indices: 299994--300094 Score: 175
Period size: 42 Copynumber: 2.4 Consensus size: 41
299984 ATACAACTTA
299994 TAAGTTGCATGTCAACATATTTATCTCGCATGTAAACATAAC
1 TAAGTTGCATGTCAAC-TATTTATCTCGCATGTAAACATAAC
*
300036 TAAGTTGCATGTCAACTCATTTATCTCGCATGTCAACATAAC
1 TAAGTTGCATGTCAACT-ATTTATCTCGCATGTAAACATAAC
300078 TAAGTTGCATGTCAACT
1 TAAGTTGCATGTCAACT
300095 TAAATAAGTT
Statistics
Matches: 57, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
41 1 0.02
42 56 0.98
ACGTcount: A:0.33, C:0.21, G:0.13, T:0.34
Consensus pattern (41 bp):
TAAGTTGCATGTCAACTATTTATCTCGCATGTAAACATAAC
Done.