Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold23
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: 3824748
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 177433 characters in sequence are not A, C, G, or T
File 1 of 14
Found at i:2225 original size:16 final size:17
Alignment explanation
Indices: 2192--2225 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
2182 TTAACTTGTG
*
2192 TATTTAATCAATTTTAA
1 TATTTAATCAATTATAA
2209 TATTTAAT-AATTATAA
1 TATTTAATCAATTATAA
2225 T
1 T
2226 TAAATTTATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (17 bp):
TATTTAATCAATTATAA
Found at i:2660 original size:5 final size:5
Alignment explanation
Indices: 2650--2676 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
2640 CTCAATCCTT
2650 ATATA ATATA ATATA ATATA ATATA AT
1 ATATA ATATA ATATA ATATA ATATA AT
2677 CTCTATTTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (5 bp):
ATATA
Found at i:4477 original size:39 final size:39
Alignment explanation
Indices: 4423--4500 Score: 147
Period size: 39 Copynumber: 2.0 Consensus size: 39
4413 ATTCTACTAT
4423 CATATGCTGTTCCTTCCCAACCAGGAAATGCAAAAATAA
1 CATATGCTGTTCCTTCCCAACCAGGAAATGCAAAAATAA
*
4462 CATATGTTGTTCCTTCCCAACCAGGAAATGCAAAAATAA
1 CATATGCTGTTCCTTCCCAACCAGGAAATGCAAAAATAA
4501 AGCACATGTT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.38, C:0.24, G:0.13, T:0.24
Consensus pattern (39 bp):
CATATGCTGTTCCTTCCCAACCAGGAAATGCAAAAATAA
Found at i:12250 original size:5 final size:5
Alignment explanation
Indices: 12215--12290 Score: 101
Period size: 5 Copynumber: 16.2 Consensus size: 5
12205 ATCATTCTTA
12215 AAAAT -AAAT -AAAT -AAAT -AAAT -AAAT -AAAT AAAAT AAAAT AAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT
12259 AAAAT AAAAT AAAAT AAAAT AAAAT ATAAAT A
1 AAAAT AAAAT AAAAT AAAAT AAAAT A-AAAT A
12291 TAAANNNNNN
Statistics
Matches: 69, Mismatches: 0, Indels: 3
0.96 0.00 0.04
Matches are distributed among these distances:
4 24 0.35
5 40 0.58
6 5 0.07
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (5 bp):
AAAAT
Found at i:12630 original size:44 final size:44
Alignment explanation
Indices: 12581--12724 Score: 130
Period size: 44 Copynumber: 3.3 Consensus size: 44
12571 AGACACCAGC
*
12581 CTTGCCTCCCTGGGTTGCAGCGGAGCAGGTTAAAAATAGCAGAT
1 CTTGCCTCCCTGGGTTGCAGCGGAGCAGGATAAAAATAGCAGAT
* ***** * * * * *
12625 CTTGCCTTCCTACACCGACAGCGAAGC-GGATCAAAGTCACCAG-C
1 CTTGCCTCCCTGGGTTG-CAGCGGAGCAGGATAAAAAT-AGCAGAT
*
12669 CTTGCCTCCCTGGGTTGCAGCGGAGCAGGCTAAAAATAGCAGAT
1 CTTGCCTCCCTGGGTTGCAGCGGAGCAGGATAAAAATAGCAGAT
*
12713 CTTGCCTTCCTG
1 CTTGCCTCCCTG
12725 CACCGACAAC
Statistics
Matches: 71, Mismatches: 25, Indels: 8
0.68 0.24 0.08
Matches are distributed among these distances:
43 12 0.17
44 47 0.66
45 12 0.17
ACGTcount: A:0.24, C:0.29, G:0.26, T:0.22
Consensus pattern (44 bp):
CTTGCCTCCCTGGGTTGCAGCGGAGCAGGATAAAAATAGCAGAT
Found at i:12681 original size:88 final size:88
Alignment explanation
Indices: 12555--12743 Score: 324
Period size: 88 Copynumber: 2.1 Consensus size: 88
12545 CTTGTACTGG
* *
12555 CAGCGAAGTAGATCAAAGACACCAGCCTTGCCTCCCTGGGTTGCAGCGGAGCAGGTTAAAAATAG
1 CAGCGAAGCAGATCAAAGACACCAGCCTTGCCTCCCTGGGTTGCAGCGGAGCAGGCTAAAAATAG
12620 CAGATCTTGCCTTCCTACACCGA
66 CAGATCTTGCCTTCCTACACCGA
* *
12643 CAGCGAAGCGGATCAAAGTCACCAGCCTTGCCTCCCTGGGTTGCAGCGGAGCAGGCTAAAAATAG
1 CAGCGAAGCAGATCAAAGACACCAGCCTTGCCTCCCTGGGTTGCAGCGGAGCAGGCTAAAAATAG
*
12708 CAGATCTTGCCTTCCTGCACCGA
66 CAGATCTTGCCTTCCTACACCGA
*
12731 CAACGAAGCAGAT
1 CAGCGAAGCAGAT
12744 NNNNNNNNNN
Statistics
Matches: 94, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
88 94 1.00
ACGTcount: A:0.28, C:0.29, G:0.25, T:0.18
Consensus pattern (88 bp):
CAGCGAAGCAGATCAAAGACACCAGCCTTGCCTCCCTGGGTTGCAGCGGAGCAGGCTAAAAATAG
CAGATCTTGCCTTCCTACACCGA
Found at i:13034 original size:88 final size:88
Alignment explanation
Indices: 12866--13037 Score: 245
Period size: 88 Copynumber: 2.0 Consensus size: 88
12856 NNNNNNNNNN
* * * * *
12866 CAGCGGAGTAGGCTAAAAATAGTAGATCTTGCCTTCCTGCACCGACAGCGATGGAGATCGAAGTC
1 CAGCGGAGCAGGCTAAAAATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGAC
* *
12931 ACCAGCCTTGCCTCCCTGGGTTG
66 ACCAGCCCTACCTCCCTGGGTTG
* *
12954 CAGCGGAGCAGGTTAAAAATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGATGAC
1 CAGCGGAGCAGGCTAAAAATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGAC
* *
13019 CCCAGCCCTATCTCCCTGG
66 ACCAGCCCTACCTCCCTGG
13038 ACAGTAGTGA
Statistics
Matches: 73, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
88 73 1.00
ACGTcount: A:0.25, C:0.30, G:0.26, T:0.20
Consensus pattern (88 bp):
CAGCGGAGCAGGCTAAAAATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGAC
ACCAGCCCTACCTCCCTGGGTTG
Found at i:13150 original size:44 final size:44
Alignment explanation
Indices: 13025--13150 Score: 189
Period size: 44 Copynumber: 2.9 Consensus size: 44
13015 TGACCCCAGC
* * * *
13025 CCTATCTCCCTGGACAGTAGTGAAATAGGTTGAAGATCCTGAAT
1 CCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTCTGAAT
* * *
13069 TCTATCTCCGTGGTCAGCAGTGGAATAGGTTGAAGATTGTGAAT
1 CCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTCTGAAT
13113 CCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATT
1 CCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATT
13151 ACGAATCTTA
Statistics
Matches: 73, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
44 73 1.00
ACGTcount: A:0.26, C:0.18, G:0.26, T:0.29
Consensus pattern (44 bp):
CCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTCTGAAT
Found at i:13364 original size:50 final size:48
Alignment explanation
Indices: 13310--13473 Score: 122
Period size: 50 Copynumber: 3.3 Consensus size: 48
13300 GCCGCAACGA
13310 CGAATCTTACTTCCCTGGCGGTATAGTGGAACAGATTGAAGCTACGACGG
1 CGAATCTTACTTCCCTGGCGGT-TAGTGGAACAGATTGAAG-TACGACGG
* * ** *
13360 CGAATCTTATTTGCTCAACATTGCAATT--T--AAAAGATTGAAGT-CGCAACGG
1 CGAATCTTACTT-C-C--C-TGGCGGTTAGTGGAACAGATTGAAGTACG--ACGG
* * *
13410 TGAATCTTACTTCCTTGGTGGTTAGTGGAACAGATTGAAGGTACGACGG
1 CGAATCTTACTTCCCTGGCGGTTAGTGGAACAGATTGAA-GTACGACGG
*
13459 CGAATCTTGCTTCCC
1 CGAATCTTACTTCCC
13474 CGACATTCCA
Statistics
Matches: 85, Mismatches: 16, Indels: 27
0.66 0.12 0.21
Matches are distributed among these distances:
45 4 0.05
47 1 0.01
48 3 0.04
49 28 0.33
50 38 0.45
51 3 0.04
52 2 0.02
54 2 0.02
55 4 0.05
ACGTcount: A:0.27, C:0.20, G:0.24, T:0.29
Consensus pattern (48 bp):
CGAATCTTACTTCCCTGGCGGTTAGTGGAACAGATTGAAGTACGACGG
Found at i:13480 original size:99 final size:100
Alignment explanation
Indices: 13291--13499 Score: 269
Period size: 99 Copynumber: 2.1 Consensus size: 100
13281 TACAGTGGAG
*
13291 CAGATTAAAGCCGCAACGACGAATCTTACTTCCCTGGCGGTATAGTGGAACAGATTGAAGCTACG
1 CAGATTGAAGCCGCAACGACGAATCTTACTTCCCTGGCGGTATAGTGGAACAGATTGAAGCTACG
* * * *
13356 ACGGCGAATCTTATTTGCTCAACATTGCAATTTAAA
66 ACGGCGAATCTTACTTCCCCAACATT-CAAGTTAAA
* ** * * *
13392 -AGATTGAAGTCGCAACGGTGAATCTTACTTCCTTGGTGGT-TAGTGGAACAGATTGAAGGTACG
1 CAGATTGAAGCCGCAACGACGAATCTTACTTCCCTGGCGGTATAGTGGAACAGATTGAAGCTACG
* * *
13455 ACGGCGAATCTTGCTTCCCCGACATTCCAGTTAAA
66 ACGGCGAATCTTACTTCCCCAACATTCAAGTTAAA
13490 CAGATTGAAG
1 CAGATTGAAG
13500 ATATCAGGTC
Statistics
Matches: 93, Mismatches: 14, Indels: 4
0.84 0.13 0.04
Matches are distributed among these distances:
98 7 0.08
99 52 0.56
100 34 0.37
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.26
Consensus pattern (100 bp):
CAGATTGAAGCCGCAACGACGAATCTTACTTCCCTGGCGGTATAGTGGAACAGATTGAAGCTACG
ACGGCGAATCTTACTTCCCCAACATTCAAGTTAAA
Found at i:13655 original size:44 final size:44
Alignment explanation
Indices: 13595--13889 Score: 185
Period size: 44 Copynumber: 6.8 Consensus size: 44
13585 GAAGATGGCG
* *
13595 AATCTTATCTCCCTGAAGTTGTAGTGGGGCAGATTAAAGCCAAT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAAT
* * * ** *
13639 AATCCTATCTCCCTGAATTTGTAGTGGAGTGGATTAAAG-TAAT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAAT
* * ** ***
13682 AGATCTTATCTCTCTGAAGTTGTAG-AAAGCAGATT---GCGTCT
1 A-ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAAT
* * * **
13723 AGTCTTATCTTCCTGAAGTTGCAGT-GAGGCAGACTGAAAGATGACA-
1 AATCTTATCTCCCTGAAGTTGCAGTGGA-GCAGA-TTAAAG-CCA-AT
* **
13769 AATCTTATCTCCTTGAAGTTGCAGTGGAGCAGATTAAAGCTGAT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAAT
* * * * *
13813 AATCCTATCTCCCTAAAGGTGCAGTGGAGCGGATTAAAACCACA-
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCA-AT
* * * *
13857 GATCTTATCTCTCTGAAGTTTCAG-AGAGCAGAT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGAT
13890 CGCATCTGGT
Statistics
Matches: 190, Mismatches: 48, Indels: 27
0.72 0.18 0.10
Matches are distributed among these distances:
40 21 0.11
41 7 0.04
42 1 0.01
43 18 0.09
44 106 0.56
45 7 0.04
46 28 0.15
47 2 0.01
ACGTcount: A:0.30, C:0.18, G:0.22, T:0.30
Consensus pattern (44 bp):
AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAAT
Found at i:13808 original size:174 final size:172
Alignment explanation
Indices: 13550--13920 Score: 492
Period size: 174 Copynumber: 2.1 Consensus size: 172
13540 TATGTAAGCA
* *
13550 AGTCTTATCCTCCTAAAGTTGCAGTGAGGCAGACTGAAGATGGCGAATCTTATCTCCCTGAAGTT
1 AGTCTTAT-CTCCTAAAGTTGCAGTGAGGCAGACTGAAGATGACAAATCTTATCTCCCTGAAGTT
* * * ** * * **
13615 GTAGTGGGGCAGATTAAAGCCAATAATCCTATCTCCCTGAATTTGTAGTGGAGTGGATTAAAGTA
65 GCAGTGGAGCAGATTAAAGCCAATAATCCTATCTCCCTAAAGGTGCAGTGGAGCGGATTAAAACA
* * *
13680 ATAGATCTTATCTCTCTGAAGTTGT-AGAAAGCAGATTGCGTCT
130 ACAGATCTTATCTCTCTGAAGTT-TCAGAAAGCAGATCGCATCT
* *
13723 AGTCTTATCTTCCTGAAGTTGCAGTGAGGCAGACTGAAAGATGACAAATCTTATCTCCTTGAAGT
1 AGTCTTATC-TCCTAAAGTTGCAGTGAGGCAGACTG-AAGATGACAAATCTTATCTCCCTGAAGT
**
13788 TGCAGTGGAGCAGATTAAAGCTGATAATCCTATCTCCCTAAAGGTGCAGTGGAGCGGATTAAAAC
64 TGCAGTGGAGCAGATTAAAGCCAATAATCCTATCTCCCTAAAGGTGCAGTGGAGCGGATTAAAAC
* *
13853 CACAGATCTTATCTCTCTGAAGTTTCAGAGAGCAGATCGCATCT
129 AACAGATCTTATCTCTCTGAAGTTTCAGAAAGCAGATCGCATCT
* *
13897 GGTCTCATCTCACTAAAGTTGCAG
1 AGTCTTATCTC-CTAAAGTTGCAG
13921 AGGAGTAGAT
Statistics
Matches: 171, Mismatches: 23, Indels: 7
0.85 0.11 0.03
Matches are distributed among these distances:
172 1 0.01
173 36 0.21
174 134 0.78
ACGTcount: A:0.29, C:0.19, G:0.23, T:0.29
Consensus pattern (172 bp):
AGTCTTATCTCCTAAAGTTGCAGTGAGGCAGACTGAAGATGACAAATCTTATCTCCCTGAAGTTG
CAGTGGAGCAGATTAAAGCCAATAATCCTATCTCCCTAAAGGTGCAGTGGAGCGGATTAAAACAA
CAGATCTTATCTCTCTGAAGTTTCAGAAAGCAGATCGCATCT
Found at i:42987 original size:16 final size:16
Alignment explanation
Indices: 42968--43032 Score: 62
Period size: 16 Copynumber: 4.1 Consensus size: 16
42958 AAGTAAAAAG
42968 AGTTATAATAATTAAA
1 AGTTATAATAATTAAA
**
42984 AG-T-TAATAAGCAAA
1 AGTTATAATAATTAAA
* *
42998 AGTTCTAATATTCTTAAA
1 AGTTATAATA--ATTAAA
43016 AGTTATAATAATTAAA
1 AGTTATAATAATTAAA
43032 A
1 A
43033 AATGAGGGAA
Statistics
Matches: 38, Mismatches: 7, Indels: 8
0.72 0.13 0.15
Matches are distributed among these distances:
14 11 0.29
15 2 0.05
16 13 0.34
18 12 0.32
ACGTcount: A:0.52, C:0.05, G:0.08, T:0.35
Consensus pattern (16 bp):
AGTTATAATAATTAAA
Found at i:44041 original size:9 final size:9
Alignment explanation
Indices: 44005--44052 Score: 55
Period size: 9 Copynumber: 5.6 Consensus size: 9
43995 AAAAAACAGC
44005 AAAAAG-AA
1 AAAAAGCAA
*
44013 AAAAAACAA
1 AAAAAGCAA
44022 AAAAAGC-A
1 AAAAAGCAA
44030 AAAAAGCAA
1 AAAAAGCAA
**
44039 AAAGCGCAA
1 AAAAAGCAA
44048 AAAAA
1 AAAAA
44053 AAAGTTGCCT
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
8 13 0.41
9 19 0.59
ACGTcount: A:0.79, C:0.10, G:0.10, T:0.00
Consensus pattern (9 bp):
AAAAAGCAA
Found at i:44042 original size:7 final size:8
Alignment explanation
Indices: 43996--44051 Score: 51
Period size: 8 Copynumber: 6.8 Consensus size: 8
43986 TATTCTTTAA
43996 AAAAACAGC
1 AAAAA-AGC
*
44005 -AAAAAGA
1 AAAAAAGC
*
44012 AAAAAAAC
1 AAAAAAGC
44020 AAAAAAAGC
1 -AAAAAAGC
44029 AAAAAAGC
1 AAAAAAGC
*
44037 AAAAAGCGC
1 AAAAA-AGC
44046 AAAAAA
1 AAAAAA
44052 AAAAGTTGCC
Statistics
Matches: 38, Mismatches: 6, Indels: 7
0.75 0.12 0.14
Matches are distributed among these distances:
7 2 0.05
8 22 0.58
9 14 0.37
ACGTcount: A:0.77, C:0.12, G:0.11, T:0.00
Consensus pattern (8 bp):
AAAAAAGC
Found at i:44047 original size:17 final size:17
Alignment explanation
Indices: 43994--44052 Score: 64
Period size: 17 Copynumber: 3.4 Consensus size: 17
43984 CTTATTCTTT
* *
43994 AAAAAAACAGCAAAAAGA
1 AAAAAAACA-AAAAAAGC
44012 AAAAAAACAAAAAAAGC
1 AAAAAAACAAAAAAAGC
* **
44029 AAAAAAGCAAAAAGCGC
1 AAAAAAACAAAAAAAGC
44046 AAAAAAA
1 AAAAAAA
44053 AAAGTTGCCT
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
17 26 0.74
18 9 0.26
ACGTcount: A:0.78, C:0.12, G:0.10, T:0.00
Consensus pattern (17 bp):
AAAAAAACAAAAAAAGC
Found at i:51184 original size:16 final size:16
Alignment explanation
Indices: 51165--51197 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
51155 TTATTCTCGT
51165 TTTTATTTCTAATTTG
1 TTTTATTTCTAATTTG
51181 TTTTATTTCTAATTTG
1 TTTTATTTCTAATTTG
51197 T
1 T
51198 GTTTCTCTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.18, C:0.06, G:0.06, T:0.70
Consensus pattern (16 bp):
TTTTATTTCTAATTTG
Found at i:57034 original size:58 final size:55
Alignment explanation
Indices: 56972--57080 Score: 139
Period size: 57 Copynumber: 1.9 Consensus size: 55
56962 GAAATTATTA
* * *
56972 TGGTTTTCTCCTAAATTAAAATGAAAATAGAGAAGATGGAA-TCATTTGGAAATGAATG
1 TGGTTTTCT-CAAAATGAAAATGAAAAT-GAGAA-AT-GAATTCATTTAGAAATGAATG
*
57030 TGGTTTTCTCAAAATGGAAATGAAAATGAGAAATGAATTCATTTAGAAATG
1 TGGTTTTCTCAAAATGAAAATGAAAATGAGAAATGAATTCATTTAGAAATG
57081 TACAAGGAAT
Statistics
Matches: 46, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
54 3 0.07
55 14 0.30
56 5 0.11
57 15 0.33
58 9 0.20
ACGTcount: A:0.42, C:0.06, G:0.20, T:0.31
Consensus pattern (55 bp):
TGGTTTTCTCAAAATGAAAATGAAAATGAGAAATGAATTCATTTAGAAATGAATG
Found at i:59290 original size:12 final size:13
Alignment explanation
Indices: 59263--59296 Score: 52
Period size: 12 Copynumber: 2.6 Consensus size: 13
59253 ATAAATATGT
59263 AAAATTGAATAAGA
1 AAAATT-AATAAGA
59277 AAAATTAA-AAGA
1 AAAATTAATAAGA
59289 AAAATTAA
1 AAAATTAA
59297 GGAAGCCATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 12 0.60
13 2 0.10
14 6 0.30
ACGTcount: A:0.71, C:0.00, G:0.09, T:0.21
Consensus pattern (13 bp):
AAAATTAATAAGA
Found at i:59615 original size:40 final size:40
Alignment explanation
Indices: 59571--59655 Score: 152
Period size: 40 Copynumber: 2.1 Consensus size: 40
59561 ATAAAGTATA
*
59571 AATATTTTGAAATTTAAATGAATTTTCTGTAATTATAGAT
1 AATATTTTGAAATTTAAATGAATTTTCTATAATTATAGAT
*
59611 AATATTTTGAAATTTACATGAATTTTCTATAATTATAGAT
1 AATATTTTGAAATTTAAATGAATTTTCTATAATTATAGAT
59651 AATAT
1 AATAT
59656 ATGGTTGTAG
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 43 1.00
ACGTcount: A:0.41, C:0.04, G:0.08, T:0.47
Consensus pattern (40 bp):
AATATTTTGAAATTTAAATGAATTTTCTATAATTATAGAT
Found at i:60620 original size:25 final size:26
Alignment explanation
Indices: 60592--60658 Score: 84
Period size: 26 Copynumber: 2.6 Consensus size: 26
60582 ATTTTCTTAA
* *
60592 CTAGTGTTAGCAA-CATCGA-ACTAAG
1 CTAGTGTTAGCAACCCT-GATACGAAG
*
60617 CTAGTGTTAGCAACCCTGATTCGAAG
1 CTAGTGTTAGCAACCCTGATACGAAG
60643 CTAGTGTTAGCAACCC
1 CTAGTGTTAGCAACCC
60659 AATATTGCTA
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
25 15 0.41
26 22 0.59
ACGTcount: A:0.30, C:0.24, G:0.21, T:0.25
Consensus pattern (26 bp):
CTAGTGTTAGCAACCCTGATACGAAG
Found at i:61895 original size:33 final size:35
Alignment explanation
Indices: 61830--61895 Score: 91
Period size: 33 Copynumber: 1.9 Consensus size: 35
61820 TTTTCAGTTC
*
61830 CATTTCCATTTTTTGAGACACCCACATTCATTTTT
1 CATTTCCATTTTTTGAGAAACCCACATTCATTTTT
* *
61865 CATTTCTA-TTTTTG-GAAACCTACATTCATTT
1 CATTTCCATTTTTTGAGAAACCCACATTCATTT
61896 CCAAATGATT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
33 15 0.54
34 6 0.21
35 7 0.25
ACGTcount: A:0.24, C:0.23, G:0.06, T:0.47
Consensus pattern (35 bp):
CATTTCCATTTTTTGAGAAACCCACATTCATTTTT
Found at i:70084 original size:25 final size:24
Alignment explanation
Indices: 70056--70102 Score: 76
Period size: 25 Copynumber: 1.9 Consensus size: 24
70046 ATCCGGGTAA
70056 TATAACGGGAAGCTCACAAAGAGCC
1 TATAACGGGAAGCTC-CAAAGAGCC
*
70081 TATAACGGGTAGCTCCAAAGAG
1 TATAACGGGAAGCTCCAAAGAG
70103 TAATTAATGG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 7 0.33
25 14 0.67
ACGTcount: A:0.38, C:0.21, G:0.26, T:0.15
Consensus pattern (24 bp):
TATAACGGGAAGCTCCAAAGAGCC
Found at i:70114 original size:24 final size:24
Alignment explanation
Indices: 70087--70136 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
70077 AGCCTATAAC
*
70087 GGGTAGCTCCAAAGAGTAATTAAT
1 GGGTAGCTCCAAAGAGCAATTAAT
*
70111 GGGTAGCTCCGAAGAGCAATTAAT
1 GGGTAGCTCCAAAGAGCAATTAAT
70135 GG
1 GG
70137 AAAGCACCGG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.34, C:0.14, G:0.30, T:0.22
Consensus pattern (24 bp):
GGGTAGCTCCAAAGAGCAATTAAT
Found at i:72400 original size:12 final size:12
Alignment explanation
Indices: 72385--72423 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
72375 CATGTCCCTG
72385 CCCGTGTCCATA
1 CCCGTGTCCATA
72397 CCCGTGTCCATA
1 CCCGTGTCCATA
* *
72409 CCCATCTCCATA
1 CCCGTGTCCATA
72421 CCC
1 CCC
72424 TTCTCACTCT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.18, C:0.49, G:0.10, T:0.23
Consensus pattern (12 bp):
CCCGTGTCCATA
Found at i:73517 original size:23 final size:24
Alignment explanation
Indices: 73487--73596 Score: 134
Period size: 23 Copynumber: 4.7 Consensus size: 24
73477 AATAATTTGT
*
73487 CGTCAATTCATCCTTTACA-TTAC
1 CGTCAATTCATCCTTTACATTTTC
73510 CGTCAATTCATCCTTTACATTTTC
1 CGTCAATTCATCCTTTACATTTTC
* * * *
73534 TGTCAGTTCCTCCATTACATTTTC
1 CGTCAATTCATCCTTTACATTTTC
* *
73558 CATCAATTCATCCTTTCCA-TTTC
1 CGTCAATTCATCCTTTACATTTTC
*
73581 CATCAATTCATCCTTT
1 CGTCAATTCATCCTTT
73597 CCCAATAATG
Statistics
Matches: 75, Mismatches: 11, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
23 39 0.52
24 36 0.48
ACGTcount: A:0.22, C:0.31, G:0.04, T:0.44
Consensus pattern (24 bp):
CGTCAATTCATCCTTTACATTTTC
Found at i:80894 original size:50 final size:50
Alignment explanation
Indices: 80827--81017 Score: 229
Period size: 50 Copynumber: 3.7 Consensus size: 50
80817 NNGTGCCCAT
**
80827 GCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGGTGCCAAC
1 GCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAAC
* *
80877 GCCATGTCCCAGACATGGTCTTACATGGGACCCCCCATCTCGGTGCCAAC
1 GCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAAC
* * * *
80927 ACCATGTCCCAGACATGGTCTTACATGGAACCTCTCATAATCTCAATGATGCCAAT
1 GCCATGTCCCAGACATGGTCTTACATGGGACCTCTC---ATCTC---GGTGCCAAC
* * *
80983 ACCATGTCTCAGACATGGTCTTACATGGGATCTCT
1 GCCATGTCCCAGACATGGTCTTACATGGGACCTCT
81018 TTACCCAAAT
Statistics
Matches: 122, Mismatches: 13, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
50 78 0.64
53 5 0.04
56 39 0.32
ACGTcount: A:0.23, C:0.32, G:0.20, T:0.25
Consensus pattern (50 bp):
GCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAAC
Found at i:86291 original size:67 final size:67
Alignment explanation
Indices: 86165--86523 Score: 336
Period size: 67 Copynumber: 5.4 Consensus size: 67
86155 ATGGTCTATA
* * * * * *
86165 ATGGGGTAAAGTGTGTAAGACCATGGCTCAACTATGGAAACATAAAAAGCCCGTCAGGACATTAA
1 ATGGGGTAAAATGTGTAAGACCATAGCTCAACTATGGAAACATAGAGAGTCTGTCAGGACATTAA
86230 AC
66 AC
* ** * * *
86232 ATTGGGTAAAATGCATAAGATCATAGCTCAACTATGGCAACATAGAGAGTCTGTTAGGACATTAA
1 ATGGGGTAAAATGTGTAAGACCATAGCTCAACTATGGAAACATAGAGAGTCTGTCAGGACATTAA
*
86297 GC
66 AC
* * **
86299 ATGGGGTAAAATGTGTAAGACCATAGCTCAGCTATAGAAACATAGAGAGTCT-TCCAAAACATTA
1 ATGGGGTAAAATGTGTAAGACCATAGCTCAACTATGGAAACATAGAGAGTCTGT-CAGGACATTA
86363 AAC
65 AAC
* * * *
86366 ATGGGGCAAAATGTGTAAGACCATAACTCGACTAT-GACAACATAGAGAGTCTGTC---A-A-GA
1 ATGGGGTAAAATGTGTAAGACCATAGCTCAACTATGGA-AACATAGAGAGTCTGTCAGGACATTA
86425 AAC
65 AAC
* * * * ** * * * *
86428 ATGGGGTATATTATGTAAGACGATAGCTTGACTATTGCAACATAGAAAGTCCGTCAGGACATTAA
1 ATGGGGTAAAATGTGTAAGACCATAGCTCAACTATGGAAACATAGAGAGTCTGTCAGGACATTAA
86493 AC
66 AC
* * * *
86495 ATAGGGTATATTGTGTAAGACTATAGCTC
1 ATGGGGTAAAATGTGTAAGACCATAGCTC
86524 GGCTATGTGT
Statistics
Matches: 239, Mismatches: 44, Indels: 18
0.79 0.15 0.06
Matches are distributed among these distances:
62 47 0.20
63 2 0.01
64 1 0.00
65 1 0.00
66 4 0.02
67 183 0.77
68 1 0.00
ACGTcount: A:0.38, C:0.16, G:0.22, T:0.24
Consensus pattern (67 bp):
ATGGGGTAAAATGTGTAAGACCATAGCTCAACTATGGAAACATAGAGAGTCTGTCAGGACATTAA
AC
Found at i:92242 original size:25 final size:27
Alignment explanation
Indices: 92194--92243 Score: 77
Period size: 25 Copynumber: 1.9 Consensus size: 27
92184 AGATTTTAAA
*
92194 ATTTTACCCCTATTTTTCAGATTTTGC
1 ATTTTACCCCTATTTTTCAAATTTTGC
92221 ATTTT-CCCCTA-TTTTCAAATTTT
1 ATTTTACCCCTATTTTTCAAATTTT
92244 ACAATTTTGT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 11 0.50
26 6 0.27
27 5 0.23
ACGTcount: A:0.20, C:0.22, G:0.04, T:0.54
Consensus pattern (27 bp):
ATTTTACCCCTATTTTTCAAATTTTGC
Found at i:92250 original size:26 final size:28
Alignment explanation
Indices: 92114--92251 Score: 111
Period size: 28 Copynumber: 5.0 Consensus size: 28
92104 GATCGTATGT
* * * *
92114 CCCCTATTTTTTAGATTTTACAGTTTTG
1 CCCCTATTTTTCAAATTTTACAATTTTA
* * * *
92142 CCCATTTTTTTTAAATTTTACAAATTTA
1 CCCCTATTTTTCAAATTTTACAATTTTA
* * * *
92170 CCCTTAGTTTTTTTAGATTTTAAAATTTTA
1 CCCCTA--TTTTTCAAATTTTACAATTTTA
* *
92200 CCCCTATTTTTCAGATTTTGC-ATTTT-
1 CCCCTATTTTTCAAATTTTACAATTTTA
92226 CCCCTA-TTTTCAAATTTTACAATTTT
1 CCCCTATTTTTCAAATTTTACAATTTT
92252 GTCTGCAACT
Statistics
Matches: 90, Mismatches: 17, Indels: 8
0.78 0.15 0.07
Matches are distributed among these distances:
25 12 0.13
26 11 0.12
27 5 0.06
28 38 0.42
30 24 0.27
ACGTcount: A:0.24, C:0.17, G:0.05, T:0.54
Consensus pattern (28 bp):
CCCCTATTTTTCAAATTTTACAATTTTA
Found at i:92577 original size:34 final size:34
Alignment explanation
Indices: 92534--92610 Score: 93
Period size: 34 Copynumber: 2.3 Consensus size: 34
92524 AAACATGACA
*
92534 ATTTGCTACTA-AGTTGATATGCTATAAGCATATT
1 ATTTGCTACTATA-TTGAGATGCTATAAGCATATT
* *
92568 ATTTGCTACTATATTGAGCTGTTATAAGCATATT
1 ATTTGCTACTATATTGAGATGCTATAAGCATATT
**
92602 GGTTGCTAC
1 ATTTGCTAC
92611 CGTATTGTTC
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
34 36 0.97
35 1 0.03
ACGTcount: A:0.29, C:0.13, G:0.17, T:0.42
Consensus pattern (34 bp):
ATTTGCTACTATATTGAGATGCTATAAGCATATT
Found at i:97121 original size:16 final size:17
Alignment explanation
Indices: 97100--97135 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
97090 TTTAAATTAC
*
97100 ATAAAAAATTAAA-AAA
1 ATAAAAAATAAAATAAA
97116 ATAAAAAATAAAATAAA
1 ATAAAAAATAAAATAAA
97133 ATA
1 ATA
97136 TTTCANNNNN
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 12 0.67
17 6 0.33
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (17 bp):
ATAAAAAATAAAATAAA
Found at i:98198 original size:80 final size:79
Alignment explanation
Indices: 98092--98250 Score: 293
Period size: 80 Copynumber: 2.0 Consensus size: 79
98082 CTTTTTATGT
98092 TTTGGATTGTCAAAACTATATAGGTTGATAAGGTTTGA-TGTCAGAAAAAAATAAATATTAAAAG
1 TTTGGATTGTCAAAACTATATAGGTTGATAAGGTTTGATTGTCAG-AAAAAATAAATATTAAAAG
98156 TTAAAATTATTTTTA
65 TTAAAATTATTTTTA
98171 TTTGGTATTGTCAAAACTATATAGGTTGATAAGGTTTGATTGTCAGAAAAAATAAATATTAAAAG
1 TTTGG-ATTGTCAAAACTATATAGGTTGATAAGGTTTGATTGTCAGAAAAAATAAATATTAAAAG
98236 TTAAAATTATTTTTA
65 TTAAAATTATTTTTA
98251 AAATTCAAAA
Statistics
Matches: 78, Mismatches: 0, Indels: 3
0.96 0.00 0.04
Matches are distributed among these distances:
79 5 0.06
80 67 0.86
81 6 0.08
ACGTcount: A:0.42, C:0.04, G:0.15, T:0.39
Consensus pattern (79 bp):
TTTGGATTGTCAAAACTATATAGGTTGATAAGGTTTGATTGTCAGAAAAAATAAATATTAAAAGT
TAAAATTATTTTTA
Found at i:107658 original size:25 final size:25
Alignment explanation
Indices: 107630--107678 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
107620 CTTAGTTTCA
107630 TGTAATAAGCCTATATCATTAACGG
1 TGTAATAAGCCTATATCATTAACGG
107655 TGTAATAAGCCTATATCATTAACG
1 TGTAATAAGCCTATATCATTAACG
107679 ATAAGCAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.33
Consensus pattern (25 bp):
TGTAATAAGCCTATATCATTAACGG
Found at i:113166 original size:10 final size:10
Alignment explanation
Indices: 113151--113284 Score: 69
Period size: 10 Copynumber: 13.1 Consensus size: 10
113141 ATTTTTAAAT
113151 AAATTTTTTA
1 AAATTTTTTA
113161 AAATTTTTTA
1 AAATTTTTTA
**
113171 ATAATTACTTA
1 A-AATTTTTTA
*
113182 CAATTTTTTA
1 AAATTTTTTA
*
113192 ATAATTATTTGA
1 A-AATT-TTTTA
*
113204 AAGTTTTTTA
1 AAATTTTTTA
* *
113214 ATATTTTTTTC
1 A-AATTTTTTA
*
113225 TAA-TTTTTA
1 AAATTTTTTA
113234 ATAA-TTTTTA
1 A-AATTTTTTA
* * *
113244 AAAATTCTAA
1 AAATTTTTTA
113254 ATAATTTTTTA
1 A-AATTTTTTA
*
113265 CAA--TTTTA
1 AAATTTTTTA
113273 AAATATTTTTA
1 AAAT-TTTTTA
113284 A
1 A
113285 CAATATTTAA
Statistics
Matches: 92, Mismatches: 22, Indels: 19
0.69 0.17 0.14
Matches are distributed among these distances:
8 7 0.08
9 7 0.08
10 40 0.43
11 33 0.36
12 5 0.05
ACGTcount: A:0.39, C:0.04, G:0.01, T:0.56
Consensus pattern (10 bp):
AAATTTTTTA
Found at i:113176 original size:21 final size:21
Alignment explanation
Indices: 113140--113304 Score: 117
Period size: 21 Copynumber: 8.0 Consensus size: 21
113130 ACCGATTCAC
*
113140 AATTTTTAAATAAATTTTTTAA
1 AATTTTTTAAT-AATTTTTTAA
** *
113162 AATTTTTTAATAATTACTTAC
1 AATTTTTTAATAATTTTTTAA
*
113183 AATTTTTTAATAATTATTTGAA
1 AATTTTTTAATAATT-TTTTAA
* * **
113205 AGTTTTTTAATATTTTTTTCT
1 AATTTTTTAATAATTTTTTAA
113226 AA-TTTTTAATAA-TTTTTAA
1 AATTTTTTAATAATTTTTTAA
* * * *
113245 AAATTCTAAATAATTTTTTAC
1 AATTTTTTAATAATTTTTTAA
113266 AA--TTTTAA-AATATTTTTAA
1 AATTTTTTAATAAT-TTTTTAA
* *
113285 CAA-TATTTAATAATTATTTA
1 -AATTTTTTAATAATTTTTTA
113305 CGATATTTAT
Statistics
Matches: 111, Mismatches: 25, Indels: 15
0.74 0.17 0.10
Matches are distributed among these distances:
18 3 0.03
19 17 0.15
20 19 0.17
21 44 0.40
22 28 0.25
ACGTcount: A:0.40, C:0.04, G:0.01, T:0.55
Consensus pattern (21 bp):
AATTTTTTAATAATTTTTTAA
Found at i:113231 original size:9 final size:10
Alignment explanation
Indices: 113208--113304 Score: 70
Period size: 10 Copynumber: 9.6 Consensus size: 10
113198 ATTTGAAAGT
*
113208 TTTTTAATAT
1 TTTTTAATAA
**
113218 TTTTTTCTAA
1 TTTTTAATAA
113228 TTTTTAATAA
1 TTTTTAATAA
*
113238 TTTTTAAAAA
1 TTTTTAATAA
* *
113248 TTCTAAATAA
1 TTTTTAATAA
* *
113258 TTTTTTACAA
1 TTTTTAATAA
*
113268 -TTTTAAAATA
1 TTTTTAATA-A
*
113278 TTTTTAACAA
1 TTTTTAATAA
*
113288 TATTTAATAA
1 TTTTTAATAA
113298 TTATTTA
1 TT-TTTA
113305 CGATATTTAT
Statistics
Matches: 65, Mismatches: 19, Indels: 5
0.73 0.21 0.06
Matches are distributed among these distances:
9 6 0.09
10 48 0.74
11 11 0.17
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.57
Consensus pattern (10 bp):
TTTTTAATAA
Found at i:113249 original size:20 final size:20
Alignment explanation
Indices: 113140--113304 Score: 98
Period size: 20 Copynumber: 7.9 Consensus size: 20
113130 ACCGATTCAC
113140 AATTTTTAAATAAATTTTTTAAA
1 AATTTTT-AAT-AA-TTTTTAAA
* * *
113163 ATTTTTTAATAATTACTTACA
1 AATTTTTAATAATT-TTTAAA
*
113184 ATTTTTTAATAATTATTTGAAA
1 AATTTTTAATAATT-TTT-AAA
** * ***
113206 GTTTTTTAATATTTTTTTCT
1 AATTTTTAATAATTTTTAAA
113226 AATTTTTAATAATTTTTAAA
1 AATTTTTAATAATTTTTAAA
* * * *
113246 AATTCTAAATAATTTTTTAC
1 AATTTTTAATAATTTTTAAA
* *
113266 AA-TTTTAAAATATTTTTAAC
1 AATTTTTAATA-ATTTTTAAA
*
113286 AATATTTAATAATTATTTA
1 AATTTTTAATAATT-TTTA
113305 CGATATTTAT
Statistics
Matches: 111, Mismatches: 26, Indels: 12
0.74 0.17 0.08
Matches are distributed among these distances:
19 5 0.05
20 47 0.42
21 36 0.32
22 17 0.15
23 6 0.05
ACGTcount: A:0.40, C:0.04, G:0.01, T:0.55
Consensus pattern (20 bp):
AATTTTTAATAATTTTTAAA
Found at i:113346 original size:20 final size:20
Alignment explanation
Indices: 113141--113358 Score: 85
Period size: 21 Copynumber: 10.3 Consensus size: 20
113131 CCGATTCACA
113141 ATTTTTAAATAAATTTTTTAAA-
1 ATTTTT-AAT-AA-TTTTTAAAT
*
113163 ATTTTTTAATAATTACTTACAAT
1 A-TTTTTAATAATT-TTTA-AAT
113186 -TTTTTAATAATTATTTGAAAGT
1 ATTTTTAATAATT-TTT-AAA-T
***
113208 -TTTTTAAT-ATTTTTTTCT
1 ATTTTTAATAATTTTTAAAT
*
113226 AATTTTTAATAATTTTTAAAA
1 -ATTTTTAATAATTTTTAAAT
* * *
113247 ATTCTAAATAATTTTTTACA-
1 ATTTTTAATAA-TTTTTAAAT
*
113267 A-TTTTAAAATATTTTTAACA-
1 ATTTTTAATA-ATTTTTAA-AT
*
113287 ATATTTAATAATTATTTACGATATTT
1 ATTTTTAATAATT-TTTA--A-A--T
* *
113313 ATTTTTTTACAATTTTTAAAT
1 A-TTTTTAATAATTTTTAAAT
113334 ATTTTTAATAA--TTTAAAT
1 ATTTTTAATAATTTTTAAAT
113352 ATTTTTA
1 ATTTTTA
113359 CAATTTTTTG
Statistics
Matches: 152, Mismatches: 24, Indels: 44
0.69 0.11 0.20
Matches are distributed among these distances:
18 15 0.10
19 11 0.07
20 37 0.24
21 50 0.33
22 16 0.11
23 8 0.05
24 1 0.01
26 5 0.03
27 9 0.06
ACGTcount: A:0.39, C:0.04, G:0.01, T:0.56
Consensus pattern (20 bp):
ATTTTTAATAATTTTTAAAT
Found at i:113694 original size:41 final size:39
Alignment explanation
Indices: 113649--113797 Score: 156
Period size: 40 Copynumber: 3.7 Consensus size: 39
113639 AGCGGCGCTT
* *
113649 TTAGCGGCGTTTGGACAAAAAACGCCACTAACAATCGAGCA
1 TTAGCGGCGTTT-TACAAAAAACGCCGCTAA-AATCGAGCA
* *
113690 TTAGCGGCATTTTACGAAAAACGCCGC-AAAGTATCGAGCA
1 TTAGCGGCGTTTTACAAAAAACGCCGCTAAA--ATCGAGCA
* * * *
113730 TTAGCGGCGTTACATAAAAAAAACGCCGCTAAAACCAAGCA
1 TTAGCGGCGTT--TTACAAAAAACGCCGCTAAAATCGAGCA
*
113771 TTAGCGGCGTTTTACAAAAAGCGCCGC
1 TTAGCGGCGTTTTACAAAAAACGCCGC
113798 AATAGAGTAA
Statistics
Matches: 90, Mismatches: 13, Indels: 12
0.78 0.11 0.10
Matches are distributed among these distances:
38 1 0.01
39 15 0.17
40 30 0.33
41 28 0.31
42 13 0.14
43 3 0.03
ACGTcount: A:0.36, C:0.24, G:0.21, T:0.18
Consensus pattern (39 bp):
TTAGCGGCGTTTTACAAAAAACGCCGCTAAAATCGAGCA
Found at i:115037 original size:10 final size:10
Alignment explanation
Indices: 115022--115155 Score: 69
Period size: 10 Copynumber: 13.1 Consensus size: 10
115012 ATTTTTAAAT
115022 AAATTTTTTA
1 AAATTTTTTA
115032 AAATTTTTTA
1 AAATTTTTTA
**
115042 ATAATTACTTA
1 A-AATTTTTTA
*
115053 CAATTTTTTA
1 AAATTTTTTA
*
115063 ATAATTATTTGA
1 A-AATT-TTTTA
*
115075 AAGTTTTTTA
1 AAATTTTTTA
* *
115085 ATATTTTTTTC
1 A-AATTTTTTA
*
115096 TAA-TTTTTA
1 AAATTTTTTA
115105 ATAA-TTTTTA
1 A-AATTTTTTA
* * *
115115 AAAATTCTAA
1 AAATTTTTTA
115125 ATAATTTTTTA
1 A-AATTTTTTA
*
115136 CAA--TTTTA
1 AAATTTTTTA
115144 AAATATTTTTA
1 AAAT-TTTTTA
115155 A
1 A
115156 CAATATTTAA
Statistics
Matches: 92, Mismatches: 22, Indels: 19
0.69 0.17 0.14
Matches are distributed among these distances:
8 7 0.08
9 7 0.08
10 40 0.43
11 33 0.36
12 5 0.05
ACGTcount: A:0.39, C:0.04, G:0.01, T:0.56
Consensus pattern (10 bp):
AAATTTTTTA
Found at i:115047 original size:21 final size:21
Alignment explanation
Indices: 115011--115175 Score: 117
Period size: 21 Copynumber: 8.0 Consensus size: 21
115001 ACCGATTCAC
*
115011 AATTTTTAAATAAATTTTTTAA
1 AATTTTTTAAT-AATTTTTTAA
** *
115033 AATTTTTTAATAATTACTTAC
1 AATTTTTTAATAATTTTTTAA
*
115054 AATTTTTTAATAATTATTTGAA
1 AATTTTTTAATAATT-TTTTAA
* * **
115076 AGTTTTTTAATATTTTTTTCT
1 AATTTTTTAATAATTTTTTAA
115097 AA-TTTTTAATAA-TTTTTAA
1 AATTTTTTAATAATTTTTTAA
* * * *
115116 AAATTCTAAATAATTTTTTAC
1 AATTTTTTAATAATTTTTTAA
115137 AA--TTTTAA-AATATTTTTAA
1 AATTTTTTAATAAT-TTTTTAA
* *
115156 CAA-TATTTAATAATTATTTA
1 -AATTTTTTAATAATTTTTTA
115176 CGATATTTAT
Statistics
Matches: 111, Mismatches: 25, Indels: 15
0.74 0.17 0.10
Matches are distributed among these distances:
18 3 0.03
19 17 0.15
20 19 0.17
21 44 0.40
22 28 0.25
ACGTcount: A:0.40, C:0.04, G:0.01, T:0.55
Consensus pattern (21 bp):
AATTTTTTAATAATTTTTTAA
Found at i:115102 original size:9 final size:10
Alignment explanation
Indices: 115079--115175 Score: 70
Period size: 10 Copynumber: 9.6 Consensus size: 10
115069 ATTTGAAAGT
*
115079 TTTTTAATAT
1 TTTTTAATAA
**
115089 TTTTTTCTAA
1 TTTTTAATAA
115099 TTTTTAATAA
1 TTTTTAATAA
*
115109 TTTTTAAAAA
1 TTTTTAATAA
* *
115119 TTCTAAATAA
1 TTTTTAATAA
* *
115129 TTTTTTACAA
1 TTTTTAATAA
*
115139 -TTTTAAAATA
1 TTTTTAATA-A
*
115149 TTTTTAACAA
1 TTTTTAATAA
*
115159 TATTTAATAA
1 TTTTTAATAA
115169 TTATTTA
1 TT-TTTA
115176 CGATATTTAT
Statistics
Matches: 65, Mismatches: 19, Indels: 5
0.73 0.21 0.06
Matches are distributed among these distances:
9 6 0.09
10 48 0.74
11 11 0.17
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.57
Consensus pattern (10 bp):
TTTTTAATAA
Found at i:115120 original size:20 final size:20
Alignment explanation
Indices: 115011--115175 Score: 98
Period size: 20 Copynumber: 7.9 Consensus size: 20
115001 ACCGATTCAC
115011 AATTTTTAAATAAATTTTTTAAA
1 AATTTTT-AAT-AA-TTTTTAAA
* * *
115034 ATTTTTTAATAATTACTTACA
1 AATTTTTAATAATT-TTTAAA
*
115055 ATTTTTTAATAATTATTTGAAA
1 AATTTTTAATAATT-TTT-AAA
** * ***
115077 GTTTTTTAATATTTTTTTCT
1 AATTTTTAATAATTTTTAAA
115097 AATTTTTAATAATTTTTAAA
1 AATTTTTAATAATTTTTAAA
* * * *
115117 AATTCTAAATAATTTTTTAC
1 AATTTTTAATAATTTTTAAA
* *
115137 AA-TTTTAAAATATTTTTAAC
1 AATTTTTAATA-ATTTTTAAA
*
115157 AATATTTAATAATTATTTA
1 AATTTTTAATAATT-TTTA
115176 CGATATTTAT
Statistics
Matches: 111, Mismatches: 26, Indels: 12
0.74 0.17 0.08
Matches are distributed among these distances:
19 5 0.05
20 47 0.42
21 36 0.32
22 17 0.15
23 6 0.05
ACGTcount: A:0.40, C:0.04, G:0.01, T:0.55
Consensus pattern (20 bp):
AATTTTTAATAATTTTTAAA
Found at i:115217 original size:20 final size:20
Alignment explanation
Indices: 115012--115229 Score: 85
Period size: 21 Copynumber: 10.3 Consensus size: 20
115002 CCGATTCACA
115012 ATTTTTAAATAAATTTTTTAAA-
1 ATTTTT-AAT-AA-TTTTTAAAT
*
115034 ATTTTTTAATAATTACTTACAAT
1 A-TTTTTAATAATT-TTTA-AAT
115057 -TTTTTAATAATTATTTGAAAGT
1 ATTTTTAATAATT-TTT-AAA-T
***
115079 -TTTTTAAT-ATTTTTTTCT
1 ATTTTTAATAATTTTTAAAT
*
115097 AATTTTTAATAATTTTTAAAA
1 -ATTTTTAATAATTTTTAAAT
* * *
115118 ATTCTAAATAATTTTTTACA-
1 ATTTTTAATAA-TTTTTAAAT
*
115138 A-TTTTAAAATATTTTTAACA-
1 ATTTTTAATA-ATTTTTAA-AT
*
115158 ATATTTAATAATTATTTACGATATTT
1 ATTTTTAATAATT-TTTA--A-A--T
* *
115184 ATTTTTTTACAATTTTTAAAT
1 A-TTTTTAATAATTTTTAAAT
115205 ATTTTTAATAA--TTTAAAT
1 ATTTTTAATAATTTTTAAAT
115223 ATTTTTA
1 ATTTTTA
115230 CAATTTTTTG
Statistics
Matches: 152, Mismatches: 24, Indels: 44
0.69 0.11 0.20
Matches are distributed among these distances:
18 15 0.10
19 11 0.07
20 37 0.24
21 50 0.33
22 16 0.11
23 8 0.05
24 1 0.01
26 5 0.03
27 9 0.06
ACGTcount: A:0.39, C:0.04, G:0.01, T:0.56
Consensus pattern (20 bp):
ATTTTTAATAATTTTTAAAT
Found at i:115565 original size:41 final size:39
Alignment explanation
Indices: 115520--115668 Score: 156
Period size: 40 Copynumber: 3.7 Consensus size: 39
115510 AGCGGCGCTT
* *
115520 TTAGCGGCGTTTGGACAAAAAACGCCACTAACAATCGAGCA
1 TTAGCGGCGTTT-TACAAAAAACGCCGCTAA-AATCGAGCA
* *
115561 TTAGCGGCATTTTACGAAAAACGCCGC-AAAGTATCGAGCA
1 TTAGCGGCGTTTTACAAAAAACGCCGCTAAA--ATCGAGCA
* * * *
115601 TTAGCGGCGTTACATAAAAAAAACGCCGCTAAAACCAAGCA
1 TTAGCGGCGTT--TTACAAAAAACGCCGCTAAAATCGAGCA
*
115642 TTAGCGGCGTTTTACAAAAAGCGCCGC
1 TTAGCGGCGTTTTACAAAAAACGCCGC
115669 AATAGAGTAA
Statistics
Matches: 90, Mismatches: 13, Indels: 12
0.78 0.11 0.10
Matches are distributed among these distances:
38 1 0.01
39 15 0.17
40 30 0.33
41 28 0.31
42 13 0.14
43 3 0.03
ACGTcount: A:0.36, C:0.24, G:0.21, T:0.18
Consensus pattern (39 bp):
TTAGCGGCGTTTTACAAAAAACGCCGCTAAAATCGAGCA
Found at i:115883 original size:40 final size:40
Alignment explanation
Indices: 115798--115892 Score: 109
Period size: 40 Copynumber: 2.4 Consensus size: 40
115788 ACCGGTATTT
* * ** ** *
115798 TAGCCGCGTTTTTGTGTATGCGCCGCTAATGGTCTTATCTT
1 TAGCGGCGTTTTT-TGTATGCGCCGCAAATAATCCGATCTA
*
115839 TAGCGGCGTTTTTTTTATGCGCCGCAAATAATCCGATCTA
1 TAGCGGCGTTTTTTGTATGCGCCGCAAATAATCCGATCTA
115879 TAGCGGCGTTTTTT
1 TAGCGGCGTTTTTT
115893 ATAAACCGCC
Statistics
Matches: 46, Mismatches: 8, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
40 34 0.74
41 12 0.26
ACGTcount: A:0.16, C:0.21, G:0.23, T:0.40
Consensus pattern (40 bp):
TAGCGGCGTTTTTTGTATGCGCCGCAAATAATCCGATCTA
Found at i:115985 original size:41 final size:41
Alignment explanation
Indices: 115940--116032 Score: 107
Period size: 41 Copynumber: 2.3 Consensus size: 41
115930 TATGGAGAAT
*
115940 CGCCGCTAATGT-TCCGGTCTATAGCGGCATTTGTGTAACAG
1 CGCCGCTAAT-TCTCCGGTCTATAGCAGCATTTGTGTAACAG
* * * * *
115981 CGCCGGTAATTCTTCGGTCTATAGCAGCGTTTGTGTAAAAA
1 CGCCGCTAATTCTCCGGTCTATAGCAGCATTTGTGTAACAG
*
116022 CGCTGCTAATT
1 CGCCGCTAATT
116033 AGAAAATCTA
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
40 1 0.02
41 42 0.98
ACGTcount: A:0.22, C:0.23, G:0.25, T:0.31
Consensus pattern (41 bp):
CGCCGCTAATTCTCCGGTCTATAGCAGCATTTGTGTAACAG
Found at i:116956 original size:23 final size:23
Alignment explanation
Indices: 116920--116964 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
116910 GCCTTTAATT
116920 TTAATGCTTACGGGTTATAGGGA
1 TTAATGCTTACGGGTTATAGGGA
*
116943 TTAATAGCTT-CGGGTTTTAGGG
1 TTAAT-GCTTACGGGTTATAGGG
116965 TACAAAAGCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 16 0.80
24 4 0.20
ACGTcount: A:0.22, C:0.09, G:0.31, T:0.38
Consensus pattern (23 bp):
TTAATGCTTACGGGTTATAGGGA
Found at i:122866 original size:28 final size:28
Alignment explanation
Indices: 122826--122881 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
122816 GCACACAGTT
122826 GGGTCGAGAAGTTTTGCGTGTGTAGCTC
1 GGGTCGAGAAGTTTTGCGTGTGTAGCTC
122854 GGGTCGAGAAGTTTTGCGTGTGTAGCTC
1 GGGTCGAGAAGTTTTGCGTGTGTAGCTC
122882 AGGCCGAGGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.14, C:0.14, G:0.39, T:0.32
Consensus pattern (28 bp):
GGGTCGAGAAGTTTTGCGTGTGTAGCTC
Found at i:122897 original size:28 final size:28
Alignment explanation
Indices: 122830--122889 Score: 102
Period size: 28 Copynumber: 2.1 Consensus size: 28
122820 ACAGTTGGGT
* *
122830 CGAGAAGTTTTGCGTGTGTAGCTCGGGT
1 CGAGAAGTTTTGCGTGTGTAGCTCAGGC
122858 CGAGAAGTTTTGCGTGTGTAGCTCAGGC
1 CGAGAAGTTTTGCGTGTGTAGCTCAGGC
122886 CGAG
1 CGAG
122890 GTATTTTGAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.17, C:0.17, G:0.38, T:0.28
Consensus pattern (28 bp):
CGAGAAGTTTTGCGTGTGTAGCTCAGGC
Found at i:123611 original size:87 final size:86
Alignment explanation
Indices: 123499--123697 Score: 222
Period size: 87 Copynumber: 2.3 Consensus size: 86
123489 ACACAACTTA
* * * *
123499 AAGCGGAGGCAACATCGAGAAAAGCTGAGGTTCAA-AAAAGATATGAAGAACTCCAGCTA-CAAC
1 AAGCAGAGGC-ACAGCGAGAGAAGCTGAGGTTCAACAAAAG-TATGAACAACTCCAGC-AGCAAC
* *
123562 TTAAAACAGATGCGGCAGCGAGAG
63 TTAAAACAGAGGCGGCAGCAAGAG
* * *
123586 AAGCAGAGGCAGCAGCGAGAGAAGCTGGGGTTCAACGAAAGTATGAACAACTCTAGCAGCAACTT
1 AAGCAGAGGCA-CAGCGAGAGAAGCTGAGGTTCAACAAAAGTATGAACAACTCCAGCAGCAACTT
* * *
123651 AAAGCAGAGGCTGCAGCAAGGG
65 AAAACAGAGGCGGCAGCAAGAG
*
123673 AAGTAGAGGCTACAGCGAGAGAAGC
1 AAGCAGAGGC-ACAGCGAGAGAAGC
123698 AGAACAGCTT
Statistics
Matches: 95, Mismatches: 13, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
86 2 0.02
87 88 0.93
88 5 0.05
ACGTcount: A:0.40, C:0.19, G:0.30, T:0.12
Consensus pattern (86 bp):
AAGCAGAGGCACAGCGAGAGAAGCTGAGGTTCAACAAAAGTATGAACAACTCCAGCAGCAACTTA
AAACAGAGGCGGCAGCAAGAG
Found at i:123696 original size:21 final size:21
Alignment explanation
Indices: 123656--123696 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
123646 AACTTAAAGC
* *
123656 AGAGGCTGCAGCAAGGGAAGT
1 AGAGGCTACAGCAAGAGAAGT
*
123677 AGAGGCTACAGCGAGAGAAG
1 AGAGGCTACAGCAAGAGAAG
123697 CAGAACAGCT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.37, C:0.15, G:0.41, T:0.07
Consensus pattern (21 bp):
AGAGGCTACAGCAAGAGAAGT
Found at i:124158 original size:43 final size:43
Alignment explanation
Indices: 124092--124330 Score: 370
Period size: 43 Copynumber: 5.6 Consensus size: 43
124082 NNNNNNNNNN
* * *
124092 AGACCAAGGTCTATAGCGTCGTTTCATGGGTAAGCGCCGCTAA
1 AGACCATGGTCTATAGCGGCGTTTGATGGGTAAGCGCCGCTAA
124135 AGACCATGGTCTATAGCGGCGTTTGATGGGTAAGCGCCGCTAA
1 AGACCATGGTCTATAGCGGCGTTTGATGGGTAAGCGCCGCTAA
* * *
124178 AGACCATGGGCTATAGCGGCATTTGATGGGTAAGCGCCACTAA
1 AGACCATGGTCTATAGCGGCGTTTGATGGGTAAGCGCCGCTAA
* * *
124221 AGACCATGGTCTATAGCGTCGTTTTATGGATAAGCGCCGCTAA
1 AGACCATGGTCTATAGCGGCGTTTGATGGGTAAGCGCCGCTAA
* * *
124264 AGACCATGCTCTATAGCGGCGTTTTATGGATAAGCGCCGCTAA
1 AGACCATGGTCTATAGCGGCGTTTGATGGGTAAGCGCCGCTAA
124307 AGACCATGGTCTATAGCGGCGTTT
1 AGACCATGGTCTATAGCGGCGTTT
124331 ATTATAAAAA
Statistics
Matches: 181, Mismatches: 15, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
43 181 1.00
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (43 bp):
AGACCATGGTCTATAGCGGCGTTTGATGGGTAAGCGCCGCTAA
Found at i:128438 original size:44 final size:44
Alignment explanation
Indices: 128375--128462 Score: 158
Period size: 44 Copynumber: 2.0 Consensus size: 44
128365 GTTCTGTTGC
* *
128375 GATTGGCCTCTACAAGGGTGCGCTCAAGGGAGTCTATGAAAACA
1 GATTGGCCTCCACAAGGGTGCACTCAAGGGAGTCTATGAAAACA
128419 GATTGGCCTCCACAAGGGTGCACTCAAGGGAGTCTATGAAAACA
1 GATTGGCCTCCACAAGGGTGCACTCAAGGGAGTCTATGAAAACA
128463 AACATGCCCC
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 42 1.00
ACGTcount: A:0.31, C:0.22, G:0.28, T:0.19
Consensus pattern (44 bp):
GATTGGCCTCCACAAGGGTGCACTCAAGGGAGTCTATGAAAACA
Found at i:138868 original size:21 final size:22
Alignment explanation
Indices: 138827--138868 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
138817 TGATCTATTT
**
138827 TGCATCTATATCTGATTTGTTC
1 TGCATCTATATCTGAACTGTTC
138849 TGCATCT-TATCTGAACTGTT
1 TGCATCTATATCTGAACTGTT
138869 ACGATAATAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.19, C:0.19, G:0.14, T:0.48
Consensus pattern (22 bp):
TGCATCTATATCTGAACTGTTC
Found at i:140567 original size:48 final size:48
Alignment explanation
Indices: 140496--140593 Score: 196
Period size: 48 Copynumber: 2.0 Consensus size: 48
140486 ATAAGGTCAT
140496 TTCCAAGCCTTATTTCTCACCCAATCTTGTCTTCCACCTACATTAACA
1 TTCCAAGCCTTATTTCTCACCCAATCTTGTCTTCCACCTACATTAACA
140544 TTCCAAGCCTTATTTCTCACCCAATCTTGTCTTCCACCTACATTAACA
1 TTCCAAGCCTTATTTCTCACCCAATCTTGTCTTCCACCTACATTAACA
140592 TT
1 TT
140594 TAAACACATT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 50 1.00
ACGTcount: A:0.24, C:0.35, G:0.04, T:0.37
Consensus pattern (48 bp):
TTCCAAGCCTTATTTCTCACCCAATCTTGTCTTCCACCTACATTAACA
Found at i:141620 original size:23 final size:25
Alignment explanation
Indices: 141537--141663 Score: 91
Period size: 25 Copynumber: 5.1 Consensus size: 25
141527 TAACAGGTAT
* *
141537 CTCCGAAGAGCCAT-TAATCGAGAAG
1 CTCCGGAGAGCCATAT-ATCGGGAAG
*
141562 CTCCGGATAGCCATATATCGGGAAG
1 CTCCGGAGAGCCATATATCGGGAAG
* ** *
141587 TTCAAGTGAGCCATAT-T-GGGAAG
1 CTCCGGAGAGCCATATATCGGGAAG
*
141610 CTCCGGAGAGCCAT-TAATCAGGAAG
1 CTCCGGAGAGCCATAT-ATCGGGAAG
** * *
141635 CTCACAAAGAGCCATATATCTGGACG
1 CTC-CGGAGAGCCATATATCGGGAAG
141661 CTC
1 CTC
141664 ATAAGAGCTA
Statistics
Matches: 79, Mismatches: 17, Indels: 11
0.74 0.16 0.10
Matches are distributed among these distances:
22 1 0.01
23 16 0.20
24 2 0.03
25 39 0.49
26 20 0.25
27 1 0.01
ACGTcount: A:0.31, C:0.24, G:0.25, T:0.20
Consensus pattern (25 bp):
CTCCGGAGAGCCATATATCGGGAAG
Found at i:146439 original size:22 final size:22
Alignment explanation
Indices: 146392--146439 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
146382 TTTGAATCAT
** *
146392 AAAATTTTTATTATTATTGATT
1 AAAATTTTTATTACCATTGATG
146414 AAAATTTTTATTACCA-TGAATG
1 AAAATTTTTATTACCATTG-ATG
146436 AAAA
1 AAAA
146440 CAATTTTTAG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
21 2 0.09
22 20 0.91
ACGTcount: A:0.44, C:0.04, G:0.06, T:0.46
Consensus pattern (22 bp):
AAAATTTTTATTACCATTGATG
Found at i:146509 original size:23 final size:23
Alignment explanation
Indices: 146483--146540 Score: 73
Period size: 23 Copynumber: 2.5 Consensus size: 23
146473 ATTGTAATTA
146483 TTTTTAAAATTTTATTAACTATG
1 TTTTTAAAATTTTATTAACTATG
* *
146506 TTTTT-AAATGTTTTTTAATTATG
1 TTTTTAAAAT-TTTATTAACTATG
146529 TTTTTGAAAATT
1 TTTTT-AAAATT
146541 CATAATTTGT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
22 4 0.13
23 21 0.70
24 1 0.03
25 4 0.13
ACGTcount: A:0.31, C:0.02, G:0.07, T:0.60
Consensus pattern (23 bp):
TTTTTAAAATTTTATTAACTATG
Found at i:146608 original size:7 final size:7
Alignment explanation
Indices: 146591--146628 Score: 53
Period size: 7 Copynumber: 5.7 Consensus size: 7
146581 GGAGATGAGG
146591 AAGAA-A
1 AAGAAGA
146597 AAGAAGA
1 AAGAAGA
146604 AAGAAGA
1 AAGAAGA
*
146611 AAGAGGA
1 AAGAAGA
146618 AAGAA-A
1 AAGAAGA
146624 AAGAA
1 AAGAA
146629 AGGTAGCAGA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
6 11 0.38
7 18 0.62
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (7 bp):
AAGAAGA
Found at i:147758 original size:9 final size:9
Alignment explanation
Indices: 147701--147770 Score: 59
Period size: 9 Copynumber: 7.6 Consensus size: 9
147691 TTAATTTTTT
147701 AAATATAAA
1 AAATATAAA
*
147710 AAATTTGAAA
1 AAATAT-AAA
*
147720 AAAGCATAAA
1 AAA-TATAAA
* * *
147730 AATTATTAC
1 AAATATAAA
*
147739 AAATTTAAA
1 AAATATAAA
*
147748 AAGTATAAA
1 AAATATAAA
147757 AAATATAAA
1 AAATATAAA
147766 AAATA
1 AAATA
147771 ATAGTTTAAT
Statistics
Matches: 45, Mismatches: 14, Indels: 4
0.71 0.22 0.06
Matches are distributed among these distances:
9 33 0.73
10 11 0.24
11 1 0.02
ACGTcount: A:0.67, C:0.03, G:0.04, T:0.26
Consensus pattern (9 bp):
AAATATAAA
Found at i:148092 original size:31 final size:32
Alignment explanation
Indices: 148027--148100 Score: 89
Period size: 31 Copynumber: 2.3 Consensus size: 32
148017 AAAAACCACC
*
148027 ATTTTATCTTATCATCCCCTAAAATTTTACAA
1 ATTTTATTTTATCATCCCCTAAAATTTTACAA
* *
148059 ATTTTATTTTATC-TCCCTTAAAAGTTTT-TAA
1 ATTTTATTTTATCATCCCCTAAAA-TTTTACAA
*
148090 ATTTAATTTTA
1 ATTTTATTTTA
148101 ACTCATTGGA
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
31 21 0.57
32 16 0.43
ACGTcount: A:0.32, C:0.15, G:0.01, T:0.51
Consensus pattern (32 bp):
ATTTTATTTTATCATCCCCTAAAATTTTACAA
Found at i:158494 original size:24 final size:23
Alignment explanation
Indices: 158467--158511 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 23
158457 AGATTGTTGT
158467 TGAA-CTTAATAAATCATTTGTGAA
1 TGAATCTTAA-AAA-CATTTGTGAA
*
158491 TGAATGTTAAAAACATTTGTG
1 TGAATCTTAAAAACATTTGTG
158512 TCAGATTTGG
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 8 0.42
24 7 0.37
25 4 0.21
ACGTcount: A:0.40, C:0.07, G:0.16, T:0.38
Consensus pattern (23 bp):
TGAATCTTAAAAACATTTGTGAA
Found at i:160670 original size:19 final size:19
Alignment explanation
Indices: 160634--160673 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
160624 TTAGAAAATC
*
160634 TTAAAATTTTATGATTTTT
1 TTAAAATTTTAGGATTTTT
* *
160653 TTAAAATTTTGGGGTTTTT
1 TTAAAATTTTAGGATTTTT
160672 TT
1 TT
160674 TTTCATTTTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.25, C:0.00, G:0.12, T:0.62
Consensus pattern (19 bp):
TTAAAATTTTAGGATTTTT
Found at i:161085 original size:20 final size:20
Alignment explanation
Indices: 161062--161102 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
161052 AAAACTCAAT
* *
161062 ATTCTTTAAAAATATAAAAA
1 ATTCATTAAAAATACAAAAA
161082 ATTCATTAAAAATACAAAAA
1 ATTCATTAAAAATACAAAAA
161102 A
1 A
161103 ACCCTAATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.63, C:0.07, G:0.00, T:0.29
Consensus pattern (20 bp):
ATTCATTAAAAATACAAAAA
Found at i:161973 original size:16 final size:15
Alignment explanation
Indices: 161952--161982 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
161942 ACATGTGTCT
161952 TTTTTAAAAATATTTA
1 TTTTTAAAAAT-TTTA
161968 TTTTTAAAAATTTTA
1 TTTTTAAAAATTTTA
161983 CTATTCATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.27
16 11 0.73
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
TTTTTAAAAATTTTA
Found at i:164866 original size:20 final size:21
Alignment explanation
Indices: 164826--164865 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
164816 CTTAAATTTA
164826 TTTACGATTTATCTCTAAAAT
1 TTTACGATTTATCTCTAAAAT
* *
164847 TTTAGGATTTATTTCTAAA
1 TTTACGATTTATCTCTAAA
164866 TCCACTATTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.33, C:0.10, G:0.07, T:0.50
Consensus pattern (21 bp):
TTTACGATTTATCTCTAAAAT
Found at i:167082 original size:9 final size:9
Alignment explanation
Indices: 167068--167104 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
167058 TATAGTTTGA
167068 TATTCGAAT
1 TATTCGAAT
167077 TATTCGAAT
1 TATTCGAAT
*
167086 TATTCGAGT
1 TATTCGAAT
167095 TATTCGAAT
1 TATTCGAAT
167104 T
1 T
167105 CGAAAACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:167173 original size:9 final size:9
Alignment explanation
Indices: 167156--167186 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
167146 TCGAGTTGAT
167156 TCGAATAAC
1 TCGAATAAC
*
167165 TCGATTAAC
1 TCGAATAAC
167174 TCGAATAAC
1 TCGAATAAC
167183 TCGA
1 TCGA
167187 TTCGTTTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.26
Consensus pattern (9 bp):
TCGAATAAC
Found at i:172372 original size:48 final size:46
Alignment explanation
Indices: 172252--172374 Score: 147
Period size: 48 Copynumber: 2.6 Consensus size: 46
172242 AGGAGAGCCA
* *
172252 ATGTAAGACCATGTCTGGGACATGGCATCGGCTCGAGATGAGGGCC
1 ATGTAAGACCATGTCTGGGACATGGCATCGGATCGAGATGAGGCCC
* * * *
172298 AGAGTAAGACCATGTCTGGGACATGGCATCGGTATCGATATGTGATCCC
1 A-TGTAAGACCATGTCTGGGACATGGCATCGG-ATCGAGATGAG-GCCC
* *
172347 ATGTAAGACCATATCTGGGATATGGCAT
1 ATGTAAGACCATGTCTGGGACATGGCAT
172375 TGGCGTCCTA
Statistics
Matches: 65, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
46 1 0.02
47 29 0.45
48 32 0.49
49 3 0.05
ACGTcount: A:0.27, C:0.20, G:0.30, T:0.24
Consensus pattern (46 bp):
ATGTAAGACCATGTCTGGGACATGGCATCGGATCGAGATGAGGCCC
Found at i:172950 original size:45 final size:43
Alignment explanation
Indices: 172813--172976 Score: 127
Period size: 45 Copynumber: 3.7 Consensus size: 43
172803 CAGATATTAA
* * *
172813 TGAGAATAAAGGTAATTGCTATGTGCTGATTTCACTGGATACCAA
1 TGAGTATAAAGGT-GTTGCTATGTGCTGATTTCACTGG-TACCAT
* * *
172858 CG-GTTATATAA-GTGATTGCTATGTGTTGAATTCACCCT-GTACCAT
1 TGAG-TATA-AAGGTG-TTGCTATGTGCTGATTTCA--CTGGTACCAT
*
172903 TGAGTATAAAGGTAGTTGCTATGTGCTGATTTCACTGAGTACTAT
1 TGAGTATAAAGGT-GTTGCTATGTGCTGATTTCACTG-GTACCAT
* * * *
172948 TGATTATAAGGGTGGTGCTGTGTGCTGAT
1 TGAGTATAAAGGTGTTGCTATGTGCTGAT
172977 CCACCGTGTA
Statistics
Matches: 95, Mismatches: 14, Indels: 21
0.73 0.11 0.16
Matches are distributed among these distances:
43 2 0.02
44 17 0.18
45 69 0.73
46 5 0.05
47 2 0.02
ACGTcount: A:0.26, C:0.13, G:0.25, T:0.36
Consensus pattern (43 bp):
TGAGTATAAAGGTGTTGCTATGTGCTGATTTCACTGGTACCAT
Found at i:180764 original size:11 final size:11
Alignment explanation
Indices: 180748--180786 Score: 51
Period size: 11 Copynumber: 3.4 Consensus size: 11
180738 GATAAATATA
180748 TATAAATTAAT
1 TATAAATTAAT
*
180759 TATAAAGTATAT
1 TATAAATTA-AT
180771 TATTAAATTAAT
1 TA-TAAATTAAT
180783 TATA
1 TATA
180787 TTATAAATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
11 10 0.42
12 8 0.33
13 6 0.25
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (11 bp):
TATAAATTAAT
Found at i:180777 original size:24 final size:21
Alignment explanation
Indices: 180739--180786 Score: 69
Period size: 24 Copynumber: 2.1 Consensus size: 21
180729 ATTTATTTAG
180739 ATAAATATATATAAATTAATT
1 ATAAATATATATAAATTAATT
180760 ATAAAGTATATTATTAAATTAATT
1 ATAAA-TATA-TA-TAAATTAATT
180784 ATA
1 ATA
180787 TTATAAATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
21 5 0.21
22 4 0.17
23 2 0.08
24 13 0.54
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (21 bp):
ATAAATATATATAAATTAATT
Found at i:181999 original size:24 final size:25
Alignment explanation
Indices: 181946--181998 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 25
181936 TTTAATGCCT
181946 TATTGGTGTGTTGGGAGGATATGATA
1 TATTGGTGTGTTGGGAGGATAT-ATA
* *
181972 TATTGGTGTGTTATGGAGGATTTATA
1 TATTGGTGTGTT-GGGAGGATATATA
181998 T
1 T
181999 TTATTTCGGG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 16 0.67
27 8 0.33
ACGTcount: A:0.23, C:0.00, G:0.34, T:0.43
Consensus pattern (25 bp):
TATTGGTGTGTTGGGAGGATATATA
Found at i:184618 original size:31 final size:31
Alignment explanation
Indices: 184556--184619 Score: 92
Period size: 31 Copynumber: 2.1 Consensus size: 31
184546 CTTAACAGCC
**
184556 TAGTGACTTAAATAAAAACTTTTGAACAGTT
1 TAGTGACTTAAATAAAAACTTTCAAACAGTT
* *
184587 TAGTGACTTAAATGAAAACTTTCAAATAGTT
1 TAGTGACTTAAATAAAAACTTTCAAACAGTT
184618 TA
1 TA
184620 ATGATCATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.42, C:0.09, G:0.12, T:0.36
Consensus pattern (31 bp):
TAGTGACTTAAATAAAAACTTTCAAACAGTT
Found at i:185137 original size:95 final size:96
Alignment explanation
Indices: 185033--185223 Score: 375
Period size: 95 Copynumber: 2.0 Consensus size: 96
185023 TTTCTAAAAT
185033 ACGGTCGGTGGCTTGTAATCAAATTGAGGTTGAAGCGAATAAAATTCTAATTTTTTATGGTTTAT
1 ACGGTCGGTGGCTTGTAATCAAATTGAGGTTGAAGCGAATAAAATTCTAATTTTTTATGGTTTAT
185098 ATTTTTATAATTTTAAAAAT-TTAAATTAAA
66 ATTTTTATAATTTTAAAAATATTAAATTAAA
185128 ACGGTCGGTGGCTTGTAATCAAATTGAGGTTGAAGCGAATAAAATTCTAATTTTTTATGGTTTAT
1 ACGGTCGGTGGCTTGTAATCAAATTGAGGTTGAAGCGAATAAAATTCTAATTTTTTATGGTTTAT
185193 ATTTTTATAATTTTAAAAATATTAAATTAAA
66 ATTTTTATAATTTTAAAAATATTAAATTAAA
185224 TTTTTATAAT
Statistics
Matches: 95, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
95 85 0.89
96 10 0.11
ACGTcount: A:0.36, C:0.06, G:0.16, T:0.42
Consensus pattern (96 bp):
ACGGTCGGTGGCTTGTAATCAAATTGAGGTTGAAGCGAATAAAATTCTAATTTTTTATGGTTTAT
ATTTTTATAATTTTAAAAATATTAAATTAAA
Found at i:187163 original size:19 final size:20
Alignment explanation
Indices: 187139--187186 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 20
187129 ATTTATTAAT
187139 TAAAAAATAATTAAAA-AAC-
1 TAAAAAA-AATTAAAACAACA
187158 T-AAAAAAATTAAAACAACA
1 TAAAAAAAATTAAAACAACA
187177 TAAAATAAAA
1 TAAAA-AAAA
187187 AATATAAATG
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
17 8 0.32
18 8 0.32
19 2 0.08
20 3 0.12
21 4 0.16
ACGTcount: A:0.75, C:0.06, G:0.00, T:0.19
Consensus pattern (20 bp):
TAAAAAAAATTAAAACAACA
Found at i:187167 original size:17 final size:20
Alignment explanation
Indices: 187141--187181 Score: 61
Period size: 17 Copynumber: 2.2 Consensus size: 20
187131 TTATTAATTA
187141 AAAAATAATTAAAA-AAC-T
1 AAAAATAATTAAAACAACAT
187159 AAAAA-AATTAAAACAACAT
1 AAAAATAATTAAAACAACAT
187178 AAAA
1 AAAA
187182 TAAAAAATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 8 0.38
18 8 0.38
19 5 0.24
ACGTcount: A:0.76, C:0.07, G:0.00, T:0.17
Consensus pattern (20 bp):
AAAAATAATTAAAACAACAT
Found at i:187897 original size:6 final size:6
Alignment explanation
Indices: 187888--187918 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
187878 TATTTATATG
187888 ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT A
1 ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT A
187919 AAACATATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (6 bp):
ATTTTT
Found at i:193606 original size:23 final size:24
Alignment explanation
Indices: 193572--193623 Score: 72
Period size: 23 Copynumber: 2.2 Consensus size: 24
193562 GTTAGTGTAT
*
193572 TTAGT-TAGTTGGTTATT-TTTTA
1 TTAGTATAATTGGTTATTATTTTA
193594 TTAGTATAATTGGTTATTATTTTA
1 TTAGTATAATTGGTTATTATTTTA
*
193618 GTAGTA
1 TTAGTA
193624 ATTTATTTGT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
22 5 0.19
23 11 0.42
24 10 0.38
ACGTcount: A:0.25, C:0.00, G:0.17, T:0.58
Consensus pattern (24 bp):
TTAGTATAATTGGTTATTATTTTA
Found at i:195508 original size:50 final size:50
Alignment explanation
Indices: 195455--195738 Score: 302
Period size: 50 Copynumber: 5.7 Consensus size: 50
195445 ATTTGGGTAA
* * * *
195455 AGAGGTCCCATGTAAGACCGTGTATGGGAAATGGCGTTGGCACCGAGATA
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
* * *
195505 AGAGGTCCCATGTAAGACCATGTTTGGGACATGACGTTGGCACCGAGACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
195555 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
** ** * * * * *
195605 ATTGGTCCCCCGTAAGACCATGTTTGGGATATGGCATGGGCACCGATATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
** * * * *
195655 AGAACTCCCATGTAAGACCATATCTGGGATATGGCATTGGCA--GTACATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCG-AGATG
* ** **
195704 AAACATTTCATGTAAGACCATGTCTGGGACATGGC
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGC
195739 TTTGACATGT
Statistics
Matches: 198, Mismatches: 35, Indels: 3
0.84 0.15 0.01
Matches are distributed among these distances:
48 1 0.01
49 32 0.16
50 165 0.83
ACGTcount: A:0.27, C:0.21, G:0.30, T:0.23
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
Found at i:200141 original size:20 final size:20
Alignment explanation
Indices: 200102--200141 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
200092 AATAAATTAA
* *
200102 GTTAAAATAATATAATAAAG
1 GTTAAAATAATAAAAAAAAG
*
200122 GTTAAAATTATAAAAAAAAG
1 GTTAAAATAATAAAAAAAAG
200142 AGAAGAAATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.62, C:0.00, G:0.10, T:0.28
Consensus pattern (20 bp):
GTTAAAATAATAAAAAAAAG
Found at i:200170 original size:20 final size:20
Alignment explanation
Indices: 200145--200184 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
200135 AAAAAAGAGA
200145 AGAAATTATCATCATTTTTG
1 AGAAATTATCATCATTTTTG
200165 AGAAATTATCATCATTTTTG
1 AGAAATTATCATCATTTTTG
200185 CTCACCACCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.10, G:0.10, T:0.45
Consensus pattern (20 bp):
AGAAATTATCATCATTTTTG
Found at i:209968 original size:9 final size:9
Alignment explanation
Indices: 209954--209984 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
209944 CACTAATCTG
209954 TTATTCGAA
1 TTATTCGAA
*
209963 TTATTCGAG
1 TTATTCGAA
209972 TTATTCGAA
1 TTATTCGAA
209981 TTAT
1 TTAT
209985 AAAATTCAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.29, C:0.10, G:0.13, T:0.48
Consensus pattern (9 bp):
TTATTCGAA
Found at i:213930 original size:155 final size:156
Alignment explanation
Indices: 213711--214023 Score: 538
Period size: 155 Copynumber: 2.0 Consensus size: 156
213701 AAAGTGAAAA
* * * *
213711 TCTTAAAAATCTAAAACATTTAAAAACTTTAGAAAATTATTTATATAAAAAACTTGTAAACTAAA
1 TCTTAAAAATCTAAAAAATTTAAAAACTGTAGAAAATTATATATAAAAAAAACTTGTAAACTAAA
*
213776 ATAAAAACCTATTCCCTTTTGCCCCCAATAAAAACCCAGATTTTTCTTGGCACAAAAAGCTCTTG
66 ATAAAAACCAATTCCCTTTTGCCCCCAATAAAAACCCAGATTTTTCTTGGCACAAAAAGCTCTTG
*
213841 AAGCAACTTGGTTTGTGAGATTTTGT
131 AAGCAACTTGGTTTGTAAGATTTTGT
*
213867 TCTTAAAAATCTAAAAAATTT-AAAACTGTAGAAAATTATATATAAAAAAAACTTGTATACTAAA
1 TCTTAAAAATCTAAAAAATTTAAAAACTGTAGAAAATTATATATAAAAAAAACTTGTAAACTAAA
* *
213931 ATAAAAACCAATTCCTTTTTGCCCCCAATAAAAATCCAGATTTTTCTTGGCACAAAAAGCTCTTG
66 ATAAAAACCAATTCCCTTTTGCCCCCAATAAAAACCCAGATTTTTCTTGGCACAAAAAGCTCTTG
213996 AAGCAACTTGGTTTGTAAGATTTTGT
131 AAGCAACTTGGTTTGTAAGATTTTGT
214022 TC
1 TC
214024 ATTTGTAATT
Statistics
Matches: 148, Mismatches: 9, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
155 128 0.86
156 20 0.14
ACGTcount: A:0.41, C:0.16, G:0.10, T:0.33
Consensus pattern (156 bp):
TCTTAAAAATCTAAAAAATTTAAAAACTGTAGAAAATTATATATAAAAAAAACTTGTAAACTAAA
ATAAAAACCAATTCCCTTTTGCCCCCAATAAAAACCCAGATTTTTCTTGGCACAAAAAGCTCTTG
AAGCAACTTGGTTTGTAAGATTTTGT
Found at i:222714 original size:5 final size:5
Alignment explanation
Indices: 222679--222710 Score: 55
Period size: 5 Copynumber: 6.4 Consensus size: 5
222669 GGAAAGTAGT
*
222679 TCAAC TCAAC TCAAC TCAAC TCAAC TCCAC TC
1 TCAAC TCAAC TCAAC TCAAC TCAAC TCAAC TC
222711 CACTACTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.34, C:0.44, G:0.00, T:0.22
Consensus pattern (5 bp):
TCAAC
Found at i:228549 original size:18 final size:19
Alignment explanation
Indices: 228511--228554 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
228501 ATATTTAAAT
* *
228511 TTATTATATTTTTTATTTA
1 TTATTAAATTTATTATTTA
228530 TTATTAAATTTATT-TTTA
1 TTATTAAATTTATTATTTA
228548 TTATTAA
1 TTATTAA
228555 TTAAAATATT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 11 0.48
19 12 0.52
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (19 bp):
TTATTAAATTTATTATTTA
Found at i:228564 original size:21 final size:22
Alignment explanation
Indices: 228515--228570 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
228505 TTAAATTTAT
228515 TATATTTTTTATTTATTATTAAA
1 TATA-TTTTTATTTATTATTAAA
*
228538 TTTATTTTTA-TTATTAATTAAA
1 TATATTTTTATTTATT-ATTAAA
228560 -ATA-TTTTATTT
1 TATATTTTTATTT
228571 TAGAAAAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
20 5 0.17
21 9 0.31
22 12 0.41
23 3 0.10
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (22 bp):
TATATTTTTATTTATTATTAAA
Found at i:228700 original size:29 final size:29
Alignment explanation
Indices: 228631--228741 Score: 87
Period size: 31 Copynumber: 3.7 Consensus size: 29
228621 ATCTCAAAAT
* *
228631 TATACATAAACTTTGATTTAGTGTGCAATTG
1 TATACATGAACTTTAATTT-G-GTGCAATTG
* *
228662 TATAAATGAACTTTAATTTGGTGCAATTA
1 TATACATGAACTTTAATTTGGTGCAATTG
* * * *
228691 TATACCTGAAACTCTAATTGTGGTTCAAATG
1 TATACATG-AACTTTAATT-TGGTGCAATTG
* *
228722 TATACTTTAAACTTTAATTT
1 TATAC-ATGAACTTTAATTT
228742 TGATTTAATC
Statistics
Matches: 64, Mismatches: 13, Indels: 7
0.76 0.15 0.08
Matches are distributed among these distances:
29 14 0.22
30 11 0.17
31 38 0.59
32 1 0.02
ACGTcount: A:0.34, C:0.11, G:0.13, T:0.42
Consensus pattern (29 bp):
TATACATGAACTTTAATTTGGTGCAATTG
Found at i:230073 original size:24 final size:24
Alignment explanation
Indices: 230010--230061 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
230000 AATCTAGAAG
* * *
230010 ATTTAGTATTTATGAGTATAATAT
1 ATTTAGCATTTATTAGCATAATAT
230034 ATTTAGCATTTATTAGCATAATAT
1 ATTTAGCATTTATTAGCATAATAT
230058 ATTT
1 ATTT
230062 GACTTTGATT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.37, C:0.04, G:0.10, T:0.50
Consensus pattern (24 bp):
ATTTAGCATTTATTAGCATAATAT
Found at i:234454 original size:24 final size:24
Alignment explanation
Indices: 234391--234442 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
234381 TTTCTAGAAG
* * *
234391 ATTTAGTATTTATGAGTATAATAT
1 ATTTAGCATTTATTAGCATAATAT
234415 ATTTAGCATTTATTAGCATAATAT
1 ATTTAGCATTTATTAGCATAATAT
234439 ATTT
1 ATTT
234443 GACTTTGATT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.37, C:0.04, G:0.10, T:0.50
Consensus pattern (24 bp):
ATTTAGCATTTATTAGCATAATAT
Found at i:239047 original size:33 final size:35
Alignment explanation
Indices: 239010--239087 Score: 106
Period size: 36 Copynumber: 2.3 Consensus size: 35
239000 GGTTTGTCTT
* *
239010 TATTTGT-TTATTGGA-TTCTTTTTACGACAATAA
1 TATTTGTATTATTCGACTTCTTTTTACAACAATAA
*
239043 TATTTGTATTATTCGACTTTTTTTTTACAACAATAA
1 TATTTGTATTATTCGAC-TTCTTTTTACAACAATAA
239079 TATTTGTAT
1 TATTTGTAT
239088 AAGAATTTAT
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
33 7 0.18
34 7 0.18
36 25 0.64
ACGTcount: A:0.28, C:0.09, G:0.09, T:0.54
Consensus pattern (35 bp):
TATTTGTATTATTCGACTTCTTTTTACAACAATAA
Found at i:242040 original size:23 final size:23
Alignment explanation
Indices: 241996--242041 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
241986 GATAATAGGG
* *
241996 GTTTTAATTAATTTAGTTAATTA
1 GTTTTAATTAATTCACTTAATTA
242019 GTTTTAATTAA-TCACTTGAATTA
1 GTTTTAATTAATTCACTT-AATTA
242042 TTCGGTTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 4 0.20
23 16 0.80
ACGTcount: A:0.35, C:0.04, G:0.09, T:0.52
Consensus pattern (23 bp):
GTTTTAATTAATTCACTTAATTA
Found at i:250508 original size:24 final size:24
Alignment explanation
Indices: 250480--250531 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
250470 TTCGTAGGTC
250480 AAATAAATTATACTAATAAATACA
1 AAATAAATTATACTAATAAATACA
* * * *
250504 AAATATATTATATTAATAGATACT
1 AAATAAATTATACTAATAAATACA
250528 AAAT
1 AAAT
250532 CTTCTAAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.58, C:0.06, G:0.02, T:0.35
Consensus pattern (24 bp):
AAATAAATTATACTAATAAATACA
Found at i:250665 original size:119 final size:120
Alignment explanation
Indices: 250525--250762 Score: 388
Period size: 119 Copynumber: 2.0 Consensus size: 120
250515 ATTAATAGAT
* **
250525 ACTAAATCTTCTAAAAAGAAAATATATTTTGTTTAACTTGACTTGCAAGTAATCTCTTATTTTAT
1 ACTAAATCTTCTAAAAAGAAAATATATTTTGTTTAACTTGAATTGCAAACAATCTCTTATTTTAT
*
250590 TTAATAAGAATTTGGGTAACACATA-TTTATTAATTTATAATTAAAATTAATTAA
66 TTAACAAGAATTTGGGTAACACATAGTTTATTAATTTATAATTAAAATTAATTAA
* *
250644 ACTAAATCTTCTAGAAAGAAAATATATTTTGTTTAACTTGAATTGCAAACAATGTCTTATTTTAT
1 ACTAAATCTTCTAAAAAGAAAATATATTTTGTTTAACTTGAATTGCAAACAATCTCTTATTTTAT
* *
250709 TTGACAAGAATTTGGGTCACACATATGTTTATTAATTTATAATTAAAATTAATT
66 TTAACAAGAATTTGGGTAACACATA-GTTTATTAATTTATAATTAAAATTAATT
250763 TTTTTTAAAT
Statistics
Matches: 109, Mismatches: 8, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
119 82 0.75
121 27 0.25
ACGTcount: A:0.40, C:0.09, G:0.09, T:0.42
Consensus pattern (120 bp):
ACTAAATCTTCTAAAAAGAAAATATATTTTGTTTAACTTGAATTGCAAACAATCTCTTATTTTAT
TTAACAAGAATTTGGGTAACACATAGTTTATTAATTTATAATTAAAATTAATTAA
Found at i:251173 original size:23 final size:24
Alignment explanation
Indices: 251146--251192 Score: 69
Period size: 25 Copynumber: 2.0 Consensus size: 24
251136 CAATTAAATG
*
251146 CTAAAGTTCT-TTTTATCTGTTTA
1 CTAAAGTTCTCTTTTATATGTTTA
251169 CTAAAGTTCTCCTTTTATATGTTT
1 CTAAAGTTCT-CTTTTATATGTTT
251193 TTTTTTTGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 10 0.48
25 11 0.52
ACGTcount: A:0.21, C:0.15, G:0.09, T:0.55
Consensus pattern (24 bp):
CTAAAGTTCTCTTTTATATGTTTA
Found at i:252325 original size:17 final size:17
Alignment explanation
Indices: 252296--252328 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
252286 TATTGGTAAG
252296 CTTGCAGTCTTGGTGAA
1 CTTGCAGTCTTGGTGAA
252313 CTTGCAGAT-TTGGTGA
1 CTTGCAG-TCTTGGTGA
252329 GCTCACAGAC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 14 0.93
18 1 0.07
ACGTcount: A:0.18, C:0.15, G:0.30, T:0.36
Consensus pattern (17 bp):
CTTGCAGTCTTGGTGAA
Found at i:254969 original size:38 final size:38
Alignment explanation
Indices: 254918--254992 Score: 141
Period size: 38 Copynumber: 2.0 Consensus size: 38
254908 CATGTCCCAT
254918 TCTTCTATACCATAACTTGGTTTCATCTAGTGAGTTGG
1 TCTTCTATACCATAACTTGGTTTCATCTAGTGAGTTGG
*
254956 TCTTCTATGCCATAACTTGGTTTCATCTAGTGAGTTG
1 TCTTCTATACCATAACTTGGTTTCATCTAGTGAGTTG
254993 TTATATGCTA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.20, C:0.19, G:0.19, T:0.43
Consensus pattern (38 bp):
TCTTCTATACCATAACTTGGTTTCATCTAGTGAGTTGG
Found at i:261052 original size:19 final size:19
Alignment explanation
Indices: 261021--261075 Score: 71
Period size: 19 Copynumber: 2.9 Consensus size: 19
261011 TTTTTAAAAA
261021 TATAAAT-TTTTGAATTTT
1 TATAAATATTTTGAATTTT
261039 TATAAATATTTTGAA-TTT
1 TATAAATATTTTGAATTTT
261057 TA-AAATTTATTTTGAATTT
1 TATAAA--TATTTTGAATTT
261076 ATTTTGTAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
17 3 0.09
18 12 0.36
19 16 0.48
20 2 0.06
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.58
Consensus pattern (19 bp):
TATAAATATTTTGAATTTT
Found at i:265989 original size:3 final size:3
Alignment explanation
Indices: 265981--266007 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
265971 ACTCAACCCA
265981 TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT
266008 AAGAAGAAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:268506 original size:72 final size:72
Alignment explanation
Indices: 268314--268480 Score: 212
Period size: 72 Copynumber: 2.3 Consensus size: 72
268304 AAAATCATAT
* * * * *
268314 ATAAACAACTATTGATAAAACTA-ATTTA-ATAAAAATAAGTAGAACATAAATTCAATATTTAAA
1 ATAAACAACTATTAATAAAACTAGA-TTACACATAAACAAGTAGAACATAAATTCAATATTCAAA
*
268377 GACCAAAC
65 AACCAAAC
* * *
268385 ATAAACAACTATTAATAGAAGTAGATTACACATAAATAAGTAGAACATAAATTCAATATTCAAAA
1 ATAAACAACTATTAATAAAACTAGATTACACATAAACAAGTAGAACATAAATTCAATATTCAAAA
268450 ACCAAAC
66 ACCAAAC
* *
268457 ATAAATAACTATTGATAAAACTAG
1 ATAAACAACTATTAATAAAACTAG
268481 TTTAGCATTA
Statistics
Matches: 83, Mismatches: 11, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
71 23 0.28
72 60 0.72
ACGTcount: A:0.56, C:0.12, G:0.07, T:0.26
Consensus pattern (72 bp):
ATAAACAACTATTAATAAAACTAGATTACACATAAACAAGTAGAACATAAATTCAATATTCAAAA
ACCAAAC
Found at i:269505 original size:18 final size:18
Alignment explanation
Indices: 269468--269514 Score: 60
Period size: 18 Copynumber: 2.7 Consensus size: 18
269458 TCCATCAATT
* *
269468 TGAACATC-TTTGAGATG
1 TGAACATCATTTAAAATG
269485 TGAACATCATTTAAAATG
1 TGAACATCATTTAAAATG
*
269503 TGAGCATCATTT
1 TGAACATCATTT
269515 CTCATATTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
17 8 0.31
18 18 0.69
ACGTcount: A:0.34, C:0.13, G:0.17, T:0.36
Consensus pattern (18 bp):
TGAACATCATTTAAAATG
Found at i:269938 original size:25 final size:23
Alignment explanation
Indices: 269904--269958 Score: 74
Period size: 25 Copynumber: 2.3 Consensus size: 23
269894 AGTGGAGAAG
269904 AGGAACAAAGAACAAGCACCAGCAA
1 AGGAACAAAGAACAAGCA--AGCAA
* *
269929 AGGAACAAAGAACTAGCAAGCAG
1 AGGAACAAAGAACAAGCAAGCAA
269952 AGGAACA
1 AGGAACA
269959 CCAGCACTAG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
23 11 0.39
25 17 0.61
ACGTcount: A:0.55, C:0.20, G:0.24, T:0.02
Consensus pattern (23 bp):
AGGAACAAAGAACAAGCAAGCAA
Found at i:269985 original size:11 final size:11
Alignment explanation
Indices: 269969--269998 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
269959 CCAGCACTAG
269969 CAGAGAACCAA
1 CAGAGAACCAA
*
269980 CAGAGAACCAG
1 CAGAGAACCAA
269991 CAGAGAAC
1 CAGAGAAC
269999 AAAATTTGGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.50, C:0.27, G:0.23, T:0.00
Consensus pattern (11 bp):
CAGAGAACCAA
Found at i:270060 original size:14 final size:14
Alignment explanation
Indices: 270041--270068 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
270031 ACACCAGTAG
270041 CAGCAGAGAAGAAC
1 CAGCAGAGAAGAAC
270055 CAGCAGAGAAGAAC
1 CAGCAGAGAAGAAC
270069 AAATGTGTGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.21, G:0.29, T:0.00
Consensus pattern (14 bp):
CAGCAGAGAAGAAC
Found at i:276302 original size:9 final size:9
Alignment explanation
Indices: 276288--276317 Score: 60
Period size: 9 Copynumber: 3.3 Consensus size: 9
276278 AAGTCTAAAC
276288 ATTGAATTG
1 ATTGAATTG
276297 ATTGAATTG
1 ATTGAATTG
276306 ATTGAATTG
1 ATTGAATTG
276315 ATT
1 ATT
276318 AAATAGATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.20, T:0.47
Consensus pattern (9 bp):
ATTGAATTG
Found at i:276326 original size:18 final size:18
Alignment explanation
Indices: 276288--276326 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
276278 AAGTCTAAAC
* *
276288 ATTGAATTGATTGAATTG
1 ATTGAATTGATTAAATAG
276306 ATTGAATTGATTAAATAG
1 ATTGAATTGATTAAATAG
276324 ATT
1 ATT
276327 AATAAATATA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.38, C:0.00, G:0.18, T:0.44
Consensus pattern (18 bp):
ATTGAATTGATTAAATAG
Found at i:283612 original size:20 final size:21
Alignment explanation
Indices: 283583--283623 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
283573 ATATTTAAAA
*
283583 AATATGTAAAAAAA-TAATAT
1 AATATATAAAAAAATTAATAT
283603 AATATATAAAAAAATTAATAT
1 AATATATAAAAAAATTAATAT
283624 GGGTAGACGG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (21 bp):
AATATATAAAAAAATTAATAT
Found at i:284521 original size:18 final size:18
Alignment explanation
Indices: 284498--284536 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
284488 AGGGGTAAGA
284498 AATCGAGTTGAATTTTAC
1 AATCGAGTTGAATTTTAC
284516 AATCGAGTTGAATTTTAC
1 AATCGAGTTGAATTTTAC
284534 AAT
1 AAT
284537 TCAAATAACT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.36, C:0.10, G:0.15, T:0.38
Consensus pattern (18 bp):
AATCGAGTTGAATTTTAC
Found at i:296502 original size:25 final size:25
Alignment explanation
Indices: 296472--296542 Score: 74
Period size: 25 Copynumber: 2.8 Consensus size: 25
296462 TTATTTTTTA
296472 TATTTTT-GAATTTTATTTTATAAAAT
1 TATTTTTAG-ATTTTATTTTA-AAAAT
*
296498 T-TTTTTAGATTTTTTTATTAAAAAT
1 TATTTTTAGATTTTATT-TTAAAAAT
**
296523 TATTTTTATTTTTTATTTTA
1 TATTTTTAGATTTTATTTTA
296543 CTTTTTAAAG
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
25 21 0.55
26 17 0.45
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.68
Consensus pattern (25 bp):
TATTTTTAGATTTTATTTTAAAAAT
Found at i:307288 original size:79 final size:80
Alignment explanation
Indices: 307170--307331 Score: 317
Period size: 79 Copynumber: 2.0 Consensus size: 80
307160 AAATGATTCG
307170 AATGTAAAGTATTATTTATTTCCTATGCCATGATGTCATGTTAGTATTATTTTAGTATTAAATTA
1 AATGTAAAGTATTATTTATTTCCTATGCCATGATGTCATGTTAGTATTATTTTAGTATTAAATTA
307235 TAAT-AAATATAAGA
66 TAATAAAATATAAGA
307249 AATGTAAAGTATTATTTATTTCCTATGCCATGATGTCATGTTAGTATTATTTTAGTATTAAATTA
1 AATGTAAAGTATTATTTATTTCCTATGCCATGATGTCATGTTAGTATTATTTTAGTATTAAATTA
307314 TAATAAAATATAAGA
66 TAATAAAATATAAGA
307329 AAT
1 AAT
307332 TTTATAGTAA
Statistics
Matches: 82, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
79 69 0.84
80 13 0.16
ACGTcount: A:0.39, C:0.06, G:0.11, T:0.44
Consensus pattern (80 bp):
AATGTAAAGTATTATTTATTTCCTATGCCATGATGTCATGTTAGTATTATTTTAGTATTAAATTA
TAATAAAATATAAGA
Found at i:311988 original size:31 final size:31
Alignment explanation
Indices: 311953--312014 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
311943 CAACCCAATG
311953 TTTAAATAAAAACTTTTGAATAGTTCAGTGA
1 TTTAAATAAAAACTTTTGAATAGTTCAGTGA
** *
311984 TTTAAATGTAAACTTTTGAATAGTTTAGTGA
1 TTTAAATAAAAACTTTTGAATAGTTCAGTGA
312015 ACATTTTGAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.39, C:0.05, G:0.15, T:0.42
Consensus pattern (31 bp):
TTTAAATAAAAACTTTTGAATAGTTCAGTGA
Found at i:314299 original size:18 final size:18
Alignment explanation
Indices: 314267--314320 Score: 72
Period size: 18 Copynumber: 3.0 Consensus size: 18
314257 ATATTATTAA
* *
314267 GGTGAAGTGTGTTAATTT
1 GGTGAACTGTATTAATTT
* *
314285 GGTGATCTGTATTAATAT
1 GGTGAACTGTATTAATTT
314303 GGTGAACTGTATTAATTT
1 GGTGAACTGTATTAATTT
314321 TCCAAACTAT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.26, C:0.04, G:0.26, T:0.44
Consensus pattern (18 bp):
GGTGAACTGTATTAATTT
Found at i:315129 original size:17 final size:18
Alignment explanation
Indices: 315087--315130 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
315077 TGATCTGCCC
315087 ATTTTATGTGAATTACTT
1 ATTTTATGTGAATTACTT
* * *
315105 ATTATATGTGAGTTGC-T
1 ATTTTATGTGAATTACTT
315122 ATTTTATGT
1 ATTTTATGT
315131 AGACTGCAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.25, C:0.05, G:0.16, T:0.55
Consensus pattern (18 bp):
ATTTTATGTGAATTACTT
Found at i:320346 original size:13 final size:13
Alignment explanation
Indices: 320325--320358 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
320315 TCTTTGATTT
320325 ATTATTTTATTTTA
1 ATTA-TTTATTTTA
*
320339 GTTATTTATTTTA
1 ATTATTTATTTTA
320352 ATTATTT
1 ATTATTT
320359 TATCCGACTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
13 15 0.83
14 3 0.17
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (13 bp):
ATTATTTATTTTA
Found at i:324500 original size:18 final size:18
Alignment explanation
Indices: 324473--324512 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
324463 TAATCTTTGA
324473 TTTA-TTATTTT-ATTTT
1 TTTATTTATTTTAATTTT
324489 TGTTATTTATTTTAATTTT
1 T-TTATTTATTTTAATTTT
324508 TTTAT
1 TTTAT
324513 CTGACTTGGA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
16 1 0.05
17 3 0.14
18 11 0.52
19 6 0.29
ACGTcount: A:0.20, C:0.00, G:0.03, T:0.78
Consensus pattern (18 bp):
TTTATTTATTTTAATTTT
Found at i:324813 original size:14 final size:14
Alignment explanation
Indices: 324779--324835 Score: 53
Period size: 14 Copynumber: 4.1 Consensus size: 14
324769 TAAAATGAAT
* *
324779 AAATTAAGTGTAGA
1 AAATTAAGTATTGA
*
324793 AAA-TAAGTTTTGA
1 AAATTAAGTATTGA
*
324806 AAATTAAGTATTAA
1 AAATTAAGTATTGA
*
324820 AAATTTAAGAATTGA
1 AAA-TTAAGTATTGA
324835 A
1 A
324836 TTTAAGTTAT
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
13 11 0.31
14 14 0.40
15 10 0.29
ACGTcount: A:0.53, C:0.00, G:0.14, T:0.33
Consensus pattern (14 bp):
AAATTAAGTATTGA
Found at i:328069 original size:23 final size:23
Alignment explanation
Indices: 328026--328075 Score: 59
Period size: 22 Copynumber: 2.2 Consensus size: 23
328016 TCAAAACCAT
328026 TTTTAAACTTTTCTTTTATTT-A
1 TTTTAAACTTTTCTTTTATTTCA
*
328048 TTTTAAAGTTTT-TTTCTGATTTCA
1 TTTTAAACTTTTCTTT-T-ATTTCA
328072 TTTT
1 TTTT
328076 GCATTTTCAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
21 3 0.12
22 12 0.50
23 4 0.17
24 5 0.21
ACGTcount: A:0.20, C:0.08, G:0.04, T:0.68
Consensus pattern (23 bp):
TTTTAAACTTTTCTTTTATTTCA
Found at i:328284 original size:23 final size:23
Alignment explanation
Indices: 328258--328304 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
328248 TGTAAAATTG
328258 ATAATTTTAATATTTTAATTCTT
1 ATAATTTTAATATTTTAATTCTT
328281 ATAATTTTAATATTTTAATTCTT
1 ATAATTTTAATATTTTAATTCTT
328304 A
1 A
328305 CATAAATATT
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:0.36, C:0.04, G:0.00, T:0.60
Consensus pattern (23 bp):
ATAATTTTAATATTTTAATTCTT
Done.