Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr7
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 21614486
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 1093914 characters in sequence are not A, C, G, or T
File 53 of 54
Found at i:20952019 original size:21 final size:21
Alignment explanation
Indices: 20951995--20952045 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
20951985 ATTTCTCGCT
*
20951995 ACAGTGAGATTCATTCTCACG
1 ACAGAGAGATTCATTCTCACG
* *
20952016 ACAGCGAGATTCATTCTCACT
1 ACAGAGAGATTCATTCTCACG
20952037 ACAGAGAGA
1 ACAGAGAGA
20952046 AACTTTCGGG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.33, C:0.24, G:0.20, T:0.24
Consensus pattern (21 bp):
ACAGAGAGATTCATTCTCACG
Found at i:20963680 original size:13 final size:13
Alignment explanation
Indices: 20963662--20963686 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
20963652 TTTCAAAAAA
20963662 TTTATAAAATCAT
1 TTTATAAAATCAT
20963675 TTTATAAAATCA
1 TTTATAAAATCA
20963687 CAATTTCTCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (13 bp):
TTTATAAAATCAT
Found at i:20975444 original size:2 final size:2
Alignment explanation
Indices: 20975437--20975462 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
20975427 CCTTTTTCCC
20975437 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
20975463 GTGTTCTAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:20979505 original size:2 final size:2
Alignment explanation
Indices: 20979498--20979558 Score: 113
Period size: 2 Copynumber: 30.5 Consensus size: 2
20979488 CTCACAACTT
*
20979498 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC GC 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
20979540 TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC T
20979559 AAGCGGCTGC
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.00, C:0.49, G:0.02, T:0.49
Consensus pattern (2 bp):
TC
Found at i:20980286 original size:2 final size:2
Alignment explanation
Indices: 20980281--20980323 Score: 68
Period size: 2 Copynumber: 21.5 Consensus size: 2
20980271 CCATATATCC
* *
20980281 AT AT AT TT AT AT AT AT AT AT AT AT GT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
20980323 A
1 A
20980324 CGTACATGAC
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
AT
Found at i:20989045 original size:54 final size:54
Alignment explanation
Indices: 20988970--20989121 Score: 277
Period size: 54 Copynumber: 2.8 Consensus size: 54
20988960 TTGAGTCCAA
20988970 CTATGTGCACGATGTGGTGGGATGCACATGAGCTGGGTGAGATGGGAAGTCCGG
1 CTATGTGCACGATGTGGTGGGATGCACATGAGCTGGGTGAGATGGGAAGTCCGG
* *
20989024 CTATGTGCACGATGTGGTGGGATGCACATGAGTTGGGTGAGATGGGATGTCCGG
1 CTATGTGCACGATGTGGTGGGATGCACATGAGCTGGGTGAGATGGGAAGTCCGG
*
20989078 CTATGTGCACGATGTGGTGGGATGCACATGGGCTGGGTGAGATG
1 CTATGTGCACGATGTGGTGGGATGCACATGAGCTGGGTGAGATG
20989122 CATATGATGA
Statistics
Matches: 94, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
54 94 1.00
ACGTcount: A:0.19, C:0.14, G:0.43, T:0.24
Consensus pattern (54 bp):
CTATGTGCACGATGTGGTGGGATGCACATGAGCTGGGTGAGATGGGAAGTCCGG
Found at i:20999943 original size:39 final size:40
Alignment explanation
Indices: 20999864--20999956 Score: 125
Period size: 39 Copynumber: 2.4 Consensus size: 40
20999854 AAATGCATTC
* * *
20999864 TCGCTGCAGCGAGAAACTTTCTGTTTTCTAGGTTGCAATT
1 TCGCTGCAGCGAGAAACATTCTGTTTTCTAGGTAGAAATT
*
20999904 TCGCTGCAGCGAGAAACATTCTG-TTTCTGGGTAGAAATT
1 TCGCTGCAGCGAGAAACATTCTGTTTTCTAGGTAGAAATT
* *
20999943 TTGCTACAGCGAGA
1 TCGCTGCAGCGAGA
20999957 TTCAGCGAAA
Statistics
Matches: 47, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
39 25 0.53
40 22 0.47
ACGTcount: A:0.24, C:0.19, G:0.25, T:0.32
Consensus pattern (40 bp):
TCGCTGCAGCGAGAAACATTCTGTTTTCTAGGTAGAAATT
Found at i:21001628 original size:43 final size:43
Alignment explanation
Indices: 21001580--21001709 Score: 170
Period size: 43 Copynumber: 3.0 Consensus size: 43
21001570 ACTCTCCCTC
* *
21001580 AGCTCACGTGCACTCCCACACCACACATAATTGGGTCATCATT
1 AGCTCATGTGCACTCCCACACCGCACATAATTGGGTCATCATT
* * * * *
21001623 AGCTCATGTCCACTCCCGCATCGCACATAGTTGGGTCATCATC
1 AGCTCATGTGCACTCCCACACCGCACATAATTGGGTCATCATT
* * *
21001666 AGCTCATGTGCACTCCTACACCGCACATATTTGGGTCATAATT
1 AGCTCATGTGCACTCCCACACCGCACATAATTGGGTCATCATT
21001709 A
1 A
21001710 TCACACAATA
Statistics
Matches: 73, Mismatches: 14, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
43 73 1.00
ACGTcount: A:0.25, C:0.32, G:0.16, T:0.26
Consensus pattern (43 bp):
AGCTCATGTGCACTCCCACACCGCACATAATTGGGTCATCATT
Found at i:21012291 original size:38 final size:37
Alignment explanation
Indices: 21012203--21012342 Score: 145
Period size: 38 Copynumber: 3.7 Consensus size: 37
21012193 ATTCAATTTT
* * * *
21012203 ATGTCCTATATAGTGGGGACCGTACCAATATCCGAGA
1 ATGTCCTAGATAGTGAGGACCATACCAATATCCAAGA
* * * *
21012240 ATGTCCTAAATAGTGAGAACCATACCACTATCCAAAA
1 ATGTCCTAGATAGTGAGGACCATACCAATATCCAAGA
* * *
21012277 ACTGTCCTAGATAGTAAGGACCATAACATTATCCAAGA
1 A-TGTCCTAGATAGTGAGGACCATACCAATATCCAAGA
* *
21012315 ATTGTCCTAGATAGTGGGGACCGTACCA
1 A-TGTCCTAGATAGTGAGGACCATACCA
21012343 TTGTCCTTAT
Statistics
Matches: 84, Mismatches: 18, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
37 31 0.37
38 53 0.63
ACGTcount: A:0.35, C:0.22, G:0.19, T:0.24
Consensus pattern (37 bp):
ATGTCCTAGATAGTGAGGACCATACCAATATCCAAGA
Found at i:21014323 original size:2 final size:2
Alignment explanation
Indices: 21014309--21014399 Score: 100
Period size: 2 Copynumber: 45.5 Consensus size: 2
21014299 TCAAATAAGG
*
21014309 TA TA TA TCA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA GNA -A
1 TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA
21014351 TA -A GTA TA TA TCA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA -TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
21014393 GA TA TA T
1 TA TA TA T
21014400 TACATATACA
Statistics
Matches: 78, Mismatches: 3, Indels: 16
0.80 0.03 0.16
Matches are distributed among these distances:
1 4 0.05
2 70 0.90
3 4 0.05
ACGTcount: A:0.49, C:0.02, G:0.03, T:0.44
Consensus pattern (2 bp):
TA
Found at i:21021412 original size:14 final size:14
Alignment explanation
Indices: 21021389--21021453 Score: 71
Period size: 13 Copynumber: 4.8 Consensus size: 14
21021379 GGGAGGGAAT
21021389 TTTCCCTCCAAAAG
1 TTTCCCTCCAAAAG
**
21021403 TTTCTGTCC-AAAG
1 TTTCCCTCCAAAAG
*
21021416 TTTCCCTCCAAAGG
1 TTTCCCTCCAAAAG
* *
21021430 TTTCCCTTCAGAA-
1 TTTCCCTCCAAAAG
21021443 TTTCCCTCCAA
1 TTTCCCTCCAA
21021454 CATGCAAGAC
Statistics
Matches: 40, Mismatches: 10, Indels: 3
0.75 0.19 0.06
Matches are distributed among these distances:
13 20 0.50
14 20 0.50
ACGTcount: A:0.23, C:0.34, G:0.09, T:0.34
Consensus pattern (14 bp):
TTTCCCTCCAAAAG
Found at i:21021446 original size:27 final size:27
Alignment explanation
Indices: 21021389--21021453 Score: 78
Period size: 27 Copynumber: 2.4 Consensus size: 27
21021379 GGGAGGGAAT
**
21021389 TTTCCCTCCAAAAGTTTCTGTCCAAAG
1 TTTCCCTCCAAAAGTTTCCCTCCAAAG
* *
21021416 TTTCCCTCCAAAGGTTTCCCTTCAGAA-
1 TTTCCCTCCAAAAGTTTCCCTCCA-AAG
21021443 TTTCCCTCCAA
1 TTTCCCTCCAA
21021454 CATGCAAGAC
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
27 31 0.94
28 2 0.06
ACGTcount: A:0.23, C:0.34, G:0.09, T:0.34
Consensus pattern (27 bp):
TTTCCCTCCAAAAGTTTCCCTCCAAAG
Found at i:21028048 original size:18 final size:19
Alignment explanation
Indices: 21028001--21028047 Score: 71
Period size: 19 Copynumber: 2.6 Consensus size: 19
21027991 TTAATATTTT
21028001 AATATTATTTTATTCATAA
1 AATATTATTTTATTCATAA
*
21028020 AATATTATTTTATT-TTAA
1 AATATTATTTTATTCATAA
21028038 AATATT-TTTT
1 AATATTATTTT
21028048 TCGCCGATCA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
17 4 0.15
18 9 0.33
19 14 0.52
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (19 bp):
AATATTATTTTATTCATAA
Found at i:21029877 original size:18 final size:18
Alignment explanation
Indices: 21029851--21029898 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 18
21029841 GTGATGGATA
*
21029851 AAAAGAATATTTT-GAAAT
1 AAAATAATATTTTAG-AAT
21029869 AAAATAATATTTTATGAAT
1 AAAATAATATTTTA-GAAT
21029888 AAAATAATATT
1 AAAATAATATT
21029899 AAAATATTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
18 12 0.44
19 14 0.52
20 1 0.04
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.38
Consensus pattern (18 bp):
AAAATAATATTTTAGAAT
Found at i:21031176 original size:41 final size:41
Alignment explanation
Indices: 21031122--21031202 Score: 153
Period size: 41 Copynumber: 2.0 Consensus size: 41
21031112 CCACAAAGTC
*
21031122 TTTAGCAAATATATATCTATTGGATTAACAATTTTTTATCT
1 TTTAGCAAATATATATCCATTGGATTAACAATTTTTTATCT
21031163 TTTAGCAAATATATATCCATTGGATTAACAATTTTTTATC
1 TTTAGCAAATATATATCCATTGGATTAACAATTTTTTATC
21031203 CTTTCTTTTC
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.35, C:0.11, G:0.07, T:0.47
Consensus pattern (41 bp):
TTTAGCAAATATATATCCATTGGATTAACAATTTTTTATCT
Found at i:21032177 original size:17 final size:19
Alignment explanation
Indices: 21032137--21032183 Score: 71
Period size: 19 Copynumber: 2.6 Consensus size: 19
21032127 TTAATATTTT
21032137 AATATTATTTTATTTACAA
1 AATATTATTTTATTTACAA
21032156 AATATTATTTTATTT-C-A
1 AATATTATTTTATTTACAA
*
21032173 AATATTCTTTT
1 AATATTATTTT
21032184 CACCCGTCAC
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
17 11 0.41
18 1 0.04
19 15 0.56
ACGTcount: A:0.36, C:0.06, G:0.00, T:0.57
Consensus pattern (19 bp):
AATATTATTTTATTTACAA
Found at i:21045062 original size:13 final size:13
Alignment explanation
Indices: 21045037--21045073 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
21045027 CCTCTTTATG
21045037 TTTATACTCCAATC
1 TTTATA-TCCAATC
21045051 TTTATATCCAATC
1 TTTATATCCAATC
*
21045064 TTTTTATCCA
1 TTTATATCCA
21045074 TTGTAAGGCA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 16 0.73
14 6 0.27
ACGTcount: A:0.27, C:0.24, G:0.00, T:0.49
Consensus pattern (13 bp):
TTTATATCCAATC
Found at i:21045320 original size:53 final size:52
Alignment explanation
Indices: 21045253--21045362 Score: 150
Period size: 53 Copynumber: 2.1 Consensus size: 52
21045243 CTTCCCAGTT
* *
21045253 AAAAGCAAGAATCCCTT-TGCGAATTGTTTAAAGGTTATCACTTGATCTCGTTA
1 AAAAACAAGAATCCCTTATG-G-ATTGTATAAAGGTTATCACTTGATCTCGTTA
* *
21045306 AAAAACAAGAATCCCTTCATGGATTGTATAAAGGTTTTCACTTGATCTTGTTA
1 AAAAACAAGAATCCCTT-ATGGATTGTATAAAGGTTATCACTTGATCTCGTTA
21045359 AAAA
1 AAAA
21045363 GTAAACATCT
Statistics
Matches: 51, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
53 48 0.94
54 1 0.02
55 2 0.04
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.34
Consensus pattern (52 bp):
AAAAACAAGAATCCCTTATGGATTGTATAAAGGTTATCACTTGATCTCGTTA
Found at i:21048183 original size:27 final size:27
Alignment explanation
Indices: 21048132--21048183 Score: 63
Period size: 28 Copynumber: 1.9 Consensus size: 27
21048122 TTATCCTGGT
*
21048132 GGTGGAAAATTATAATTTTGCCCCTAA
1 GGTGGAAAATTATAATTTTGACCCTAA
21048159 GGTGGCAAAATTACT-ATTTT-ACCCT
1 GGTGG-AAAATTA-TAATTTTGACCCT
21048184 TATACTCTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
27 9 0.41
28 12 0.55
29 1 0.05
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.35
Consensus pattern (27 bp):
GGTGGAAAATTATAATTTTGACCCTAA
Found at i:21048252 original size:19 final size:19
Alignment explanation
Indices: 21048228--21048265 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
21048218 ACTTCTAAAC
21048228 CTCAAATCATACTCCAATA
1 CTCAAATCATACTCCAATA
21048247 CTCAAATCATACTCCAATA
1 CTCAAATCATACTCCAATA
21048266 AGTCAAATGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.42, C:0.32, G:0.00, T:0.26
Consensus pattern (19 bp):
CTCAAATCATACTCCAATA
Found at i:21049592 original size:31 final size:31
Alignment explanation
Indices: 21049554--21049616 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
21049544 ATCATAAGAA
21049554 TGAACAATAATAACATATTGATTTGAAACTC
1 TGAACAATAATAACATATTGATTTGAAACTC
21049585 TGAACAATAATAACATATTGATTTGAAACTC
1 TGAACAATAATAACATATTGATTTGAAACTC
21049616 T
1 T
21049617 AATGTAACTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.44, C:0.13, G:0.10, T:0.33
Consensus pattern (31 bp):
TGAACAATAATAACATATTGATTTGAAACTC
Found at i:21050291 original size:4 final size:4
Alignment explanation
Indices: 21050282--21050307 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
21050272 TGAAGATAAG
21050282 AATA AATA AATA AATA AATA AATA AA
1 AATA AATA AATA AATA AATA AATA AA
21050308 AGTTATTCCC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AATA
Found at i:21051477 original size:79 final size:79
Alignment explanation
Indices: 21051327--21051526 Score: 292
Period size: 79 Copynumber: 2.5 Consensus size: 79
21051317 AAAGAGAAAG
* *
21051327 AAAGGGAAGCTTTGGGTTATCTGCCGCCGGTTAGAAAGGAAAAGCTTGGGGTTAGAGTCACCGGT
1 AAAGGGGAGCTTTGGGTTATCTGCCGCCGGTTAGAGAGGAAAAGCTTGGGGTTAGAGTCACCGGT
*
21051392 CTGTAAGGTTAGAA
66 CGGTAAGGTTAGAA
* * * * * *
21051406 AAATGGGAGCTTTGGGTTATCTGTCGCCGATTAGAGAGGAAAAGTTTGGGGTTAGAGTCGCTGGT
1 AAAGGGGAGCTTTGGGTTATCTGCCGCCGGTTAGAGAGGAAAAGCTTGGGGTTAGAGTCACCGGT
21051471 CGGTAAGGTTAGAA
66 CGGTAAGGTTAGAA
* * *
21051485 AAGGGGGAGCTTTGGGTTATTTGCCGTCGGTTAGAGAGGAAA
1 AAAGGGGAGCTTTGGGTTATCTGCCGCCGGTTAGAGAGGAAA
21051527 GATTCGGGGT
Statistics
Matches: 106, Mismatches: 15, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
79 106 1.00
ACGTcount: A:0.26, C:0.12, G:0.36, T:0.26
Consensus pattern (79 bp):
AAAGGGGAGCTTTGGGTTATCTGCCGCCGGTTAGAGAGGAAAAGCTTGGGGTTAGAGTCACCGGT
CGGTAAGGTTAGAA
Found at i:21055396 original size:38 final size:38
Alignment explanation
Indices: 21055345--21055482 Score: 179
Period size: 38 Copynumber: 3.6 Consensus size: 38
21055335 TGATGATTCC
*
21055345 CAATTGTGCTATTATAAATAGCACCTTCCAAAGATTAA
1 CAATTGTGCTATTATAAAGAGCACCTTCCAAAGATTAA
* *
21055383 CAATTGTGCTATTATAAAGAGCACCTTCCAAGGATCAA
1 CAATTGTGCTATTATAAAGAGCACCTTCCAAAGATTAA
* * * * * *
21055421 TAATTGTACTATCATAAAGAGCACCCTT-TAACGATTAG
1 CAATTGTGCTATTATAAAGAGCA-CCTTCCAAAGATTAA
21055459 CAATTGTGCTATTATAAAGAGCAC
1 CAATTGTGCTATTATAAAGAGCAC
21055483 ACTCTAAGGA
Statistics
Matches: 86, Mismatches: 13, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
37 1 0.01
38 81 0.94
39 4 0.05
ACGTcount: A:0.38, C:0.19, G:0.14, T:0.30
Consensus pattern (38 bp):
CAATTGTGCTATTATAAAGAGCACCTTCCAAAGATTAA
Found at i:21055472 original size:76 final size:76
Alignment explanation
Indices: 21055346--21055496 Score: 207
Period size: 76 Copynumber: 2.0 Consensus size: 76
21055336 GATGATTCCC
* * *
21055346 AATTGTGCTATTATAAATAGCACCTTCCAAAGATTAACAATTGTGCTATTATAAAGAGCAC-CTT
1 AATTGTACTATCATAAAGAGCACCTTCCAAAGATTAACAATTGTGCTATTATAAAGAGCACAC-T
21055410 CCAAGGATCAAT
65 CCAAGGATCAAT
* * *
21055422 AATTGTACTATCATAAAGAGCACCCTT-TAACGATTAGCAATTGTGCTATTATAAAGAGCACACT
1 AATTGTACTATCATAAAGAGCA-CCTTCCAAAGATTAACAATTGTGCTATTATAAAGAGCACACT
*
21055486 CTAAGGATCAA
65 CCAAGGATCAA
21055497 GTTGAAATTG
Statistics
Matches: 66, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
76 61 0.92
77 5 0.08
ACGTcount: A:0.38, C:0.19, G:0.14, T:0.29
Consensus pattern (76 bp):
AATTGTACTATCATAAAGAGCACCTTCCAAAGATTAACAATTGTGCTATTATAAAGAGCACACTC
CAAGGATCAAT
Found at i:21056539 original size:16 final size:16
Alignment explanation
Indices: 21056518--21056560 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
21056508 TTTAATTATT
*
21056518 TTTAGTTATTTTTTTA
1 TTTAGTTATATTTTTA
21056534 TTTAGTT-TATTTTTA
1 TTTAGTTATATTTTTA
*
21056549 TTAAGTTA-ATTT
1 TTTAGTTATATTT
21056561 AATTTTAGAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 17 0.71
16 7 0.29
ACGTcount: A:0.23, C:0.00, G:0.07, T:0.70
Consensus pattern (16 bp):
TTTAGTTATATTTTTA
Found at i:21071693 original size:28 final size:28
Alignment explanation
Indices: 21071485--21071731 Score: 237
Period size: 29 Copynumber: 8.5 Consensus size: 28
21071475 TCTTGTTATT
* *
21071485 AATTAAAACAAAAATATTTTATCTTGTCTA
1 AATTAAGACAAACATA-TTT-TCTTGTCTA
* *
21071515 AATTGAA-ACAAATATGTTTTCTTGTCTA
1 AATT-AAGACAAACATATTTTCTTGTCTA
* *
21071543 GATTAAGACAAAAAATATTTTTCTTGTCTTA
1 AATTAAGAC-AAACATA-TTTTCTTGTC-TA
* *
21071574 AATTATGACAAATATATTTTCTTGTCTTA
1 AATTAAGACAAACATATTTTCTTGTC-TA
* *
21071603 AATTATGACAAATATATTTTCTTGTCTA
1 AATTAAGACAAACATATTTTCTTGTCTA
*
21071631 AATTAAGGCCAAACATGA-TTTCTTGTCTA
1 AATTAA-GACAAACAT-ATTTTCTTGTCTA
*
21071660 AATTAAGACAAACATATTTTTTTGTCTA
1 AATTAAGACAAACATATTTTCTTGTCTA
* ** *
21071688 AATTAAGACATAACATGTTCGCTTGTGTA
1 AATTAAGACA-AACATATTTTCTTGTCTA
*
21071717 AATTAATACAAACAT
1 AATTAAGACAAACAT
21071732 TTAAAGCTGT
Statistics
Matches: 189, Mismatches: 19, Indels: 20
0.83 0.08 0.09
Matches are distributed among these distances:
27 3 0.02
28 54 0.29
29 93 0.49
30 28 0.15
31 11 0.06
ACGTcount: A:0.39, C:0.12, G:0.09, T:0.40
Consensus pattern (28 bp):
AATTAAGACAAACATATTTTCTTGTCTA
Found at i:21071731 original size:57 final size:57
Alignment explanation
Indices: 21071485--21071728 Score: 269
Period size: 57 Copynumber: 4.2 Consensus size: 57
21071475 TCTTGTTATT
* *
21071485 AATTAAAACAAAAATATTTTATCTTGTCTAAATTGAA-ACAAATATGTTTTCTTGTCTA
1 AATTAAGACAAAAATATTTT-TCTTGTCTAAATT-AAGACAAACATGTTTTCTTGTCTA
* * * *
21071543 GATTAAGACAAAAAATATTTTTCTTGTCTTAAATTATGACAAATATATTTTCTTGTCTTA
1 AATTAAGAC-AAAAATATTTTTCTTGTC-TAAATTAAGACAAACATGTTTTCTTGTC-TA
* * * *
21071603 AATTATGACAAATATA-TTTTCTTGTCTAAATTAAGGCCAAACATGATTTCTTGTCTA
1 AATTAAGACAAAAATATTTTTCTTGTCTAAATTAA-GACAAACATGTTTTCTTGTCTA
* ** *
21071660 AATTAAGACAAACATATTTTT-TTGTCTAAATTAAGACATAACATGTTCGCTTGTGTA
1 AATTAAGACAAAAATATTTTTCTTGTCTAAATTAAGACA-AACATGTTTTCTTGTCTA
*
21071717 AATTAATACAAA
1 AATTAAGACAAA
21071729 CATTTAAAGC
Statistics
Matches: 159, Mismatches: 20, Indels: 15
0.82 0.10 0.08
Matches are distributed among these distances:
56 3 0.02
57 61 0.38
58 45 0.28
59 41 0.26
60 9 0.06
ACGTcount: A:0.39, C:0.11, G:0.09, T:0.41
Consensus pattern (57 bp):
AATTAAGACAAAAATATTTTTCTTGTCTAAATTAAGACAAACATGTTTTCTTGTCTA
Found at i:21077952 original size:28 final size:27
Alignment explanation
Indices: 21077921--21077977 Score: 78
Period size: 28 Copynumber: 2.1 Consensus size: 27
21077911 ATTTTTGGAG
** *
21077921 CATAGGGTTAAAATGGTAATTTTGCCAC
1 CATAGGGGCAAAATAGTAATTTT-CCAC
21077949 CATAGGGGCAAAATAGTAATTTTCCAC
1 CATAGGGGCAAAATAGTAATTTTCCAC
21077976 CA
1 CA
21077978 CCAAGACACT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
27 6 0.23
28 20 0.77
ACGTcount: A:0.35, C:0.18, G:0.19, T:0.28
Consensus pattern (27 bp):
CATAGGGGCAAAATAGTAATTTTCCAC
Found at i:21081798 original size:27 final size:28
Alignment explanation
Indices: 21081767--21081819 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
21081757 AGTGTTGGGT
* *
21081767 GGTGT-AAAATTACAATTTTTCCCTTGG
1 GGTGTCAAAATAACAATTTTGCCCTTGG
*
21081794 GGTGTCAAAATAACTATTTTGCCCTT
1 GGTGTCAAAATAACAATTTTGCCCTT
21081820 ATCCTCGGAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 5 0.23
28 17 0.77
ACGTcount: A:0.26, C:0.17, G:0.17, T:0.40
Consensus pattern (28 bp):
GGTGTCAAAATAACAATTTTGCCCTTGG
Found at i:21087146 original size:17 final size:17
Alignment explanation
Indices: 21087124--21087159 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
21087114 AAATATGAAT
21087124 TTATAAAATAAATGGAA
1 TTATAAAATAAATGGAA
*
21087141 TTATAAAATAAATTGAA
1 TTATAAAATAAATGGAA
21087158 TT
1 TT
21087160 TTTATAATTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.56, C:0.00, G:0.08, T:0.36
Consensus pattern (17 bp):
TTATAAAATAAATGGAA
Found at i:21092875 original size:18 final size:18
Alignment explanation
Indices: 21092832--21092875 Score: 63
Period size: 17 Copynumber: 2.4 Consensus size: 18
21092822 TTTATGAGAA
*
21092832 AAATATGAATTTATAAAAT
1 AAAT-TGAAATTATAAAAT
21092851 AAA-TGAAATTATAAAAT
1 AAATTGAAATTATAAAAT
21092868 AAATTGAA
1 AAATTGAA
21092876 TTTTTTATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 16 0.70
18 4 0.17
19 3 0.13
ACGTcount: A:0.61, C:0.00, G:0.07, T:0.32
Consensus pattern (18 bp):
AAATTGAAATTATAAAAT
Found at i:21105402 original size:20 final size:20
Alignment explanation
Indices: 21105377--21105420 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
21105367 TTTGACCCCA
21105377 TTGACTTATTGGAGTATAAT
1 TTGACTTATTGGAGTATAAT
* *
21105397 TTGACTTATTGGATTATGAT
1 TTGACTTATTGGAGTATAAT
21105417 TTGA
1 TTGA
21105421 GGTTTAGAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.27, C:0.05, G:0.20, T:0.48
Consensus pattern (20 bp):
TTGACTTATTGGAGTATAAT
Found at i:21113955 original size:19 final size:19
Alignment explanation
Indices: 21113918--21113955 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
21113908 CCATTGAACT
* *
21113918 TATTGGAGTATGATTTGAG
1 TATTGGAGTATAATATGAG
21113937 TATTGGAGTATAATATGAG
1 TATTGGAGTATAATATGAG
21113956 GGTTTGGCAG
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:0.32, C:0.00, G:0.29, T:0.39
Consensus pattern (19 bp):
TATTGGAGTATAATATGAG
Found at i:21116563 original size:15 final size:16
Alignment explanation
Indices: 21116543--21116583 Score: 59
Period size: 15 Copynumber: 2.7 Consensus size: 16
21116533 CAGAGATTTT
21116543 GATTTTAAAG-CTTTG
1 GATTTTAAAGTCTTTG
*
21116558 GATTTTAAAGTTTTTG
1 GATTTTAAAGTCTTTG
21116574 G-TTTTAAAGT
1 GATTTTAAAGT
21116584 TGTTTTAAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 19 0.79
16 5 0.21
ACGTcount: A:0.27, C:0.02, G:0.20, T:0.51
Consensus pattern (16 bp):
GATTTTAAAGTCTTTG
Found at i:21116584 original size:15 final size:15
Alignment explanation
Indices: 21116539--21116584 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
21116529 AGATCAGAGA
*
21116539 TTTTGATTTTAAAG-
1 TTTTGGTTTTAAAGT
*
21116553 CTTTGGATTTTAAAGT
1 TTTTGG-TTTTAAAGT
21116569 TTTTGGTTTTAAAGT
1 TTTTGGTTTTAAAGT
21116584 T
1 T
21116585 GTTTTAAGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
14 4 0.15
15 18 0.67
16 5 0.19
ACGTcount: A:0.24, C:0.02, G:0.17, T:0.57
Consensus pattern (15 bp):
TTTTGGTTTTAAAGT
Found at i:21122386 original size:13 final size:13
Alignment explanation
Indices: 21122368--21122392 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
21122358 AAAGAAATTG
21122368 TGATTTTATAAAA
1 TGATTTTATAAAA
21122381 TGATTTTATAAA
1 TGATTTTATAAA
21122393 TTTTCTAGAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (13 bp):
TGATTTTATAAAA
Found at i:21131884 original size:10 final size:11
Alignment explanation
Indices: 21131866--21131902 Score: 51
Period size: 10 Copynumber: 3.5 Consensus size: 11
21131856 GTGGTTGAAA
21131866 TTGATGATATT
1 TTGATGATATT
21131877 TT-ATGATATT
1 TTGATGATATT
*
21131887 TTGGTGATA-T
1 TTGATGATATT
21131897 TTGATG
1 TTGATG
21131903 TTTGGTGAGG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
10 16 0.70
11 7 0.30
ACGTcount: A:0.24, C:0.00, G:0.22, T:0.54
Consensus pattern (11 bp):
TTGATGATATT
Found at i:21134078 original size:75 final size:74
Alignment explanation
Indices: 21133987--21134138 Score: 286
Period size: 75 Copynumber: 2.0 Consensus size: 74
21133977 AAGATAACAT
21133987 TACAACGTTTGGTTTACAAATACTTTGTTGGGAATATAATATTAATTTTCAAAATTACCCCTATT
1 TACAACGTTTGGTTTACAAATACTTTGTTGGGAATATAATATTAATTTTCAAAATTACCCCTATT
21134052 TATTAAATA
66 TATTAAATA
21134061 TNACAACGTTTGGTTTACAAATACTTTGTTGGGAATATAATATTAATTTTCAAAATTACCCCTAT
1 T-ACAACGTTTGGTTTACAAATACTTTGTTGGGAATATAATATTAATTTTCAAAATTACCCCTAT
21134126 TTATTAAAATA
65 TTATT-AAATA
21134137 TA
1 TA
21134139 AGTTTAATAT
Statistics
Matches: 76, Mismatches: 0, Indels: 3
0.96 0.00 0.04
Matches are distributed among these distances:
74 1 0.01
75 69 0.91
76 6 0.08
ACGTcount: A:0.37, C:0.12, G:0.09, T:0.41
Consensus pattern (74 bp):
TACAACGTTTGGTTTACAAATACTTTGTTGGGAATATAATATTAATTTTCAAAATTACCCCTATT
TATTAAATA
Found at i:21134267 original size:29 final size:28
Alignment explanation
Indices: 21134220--21134275 Score: 76
Period size: 29 Copynumber: 2.0 Consensus size: 28
21134210 ATATATTTTA
*
21134220 TTTTTATTTCTTATTATAATCTTTTATT
1 TTTTTATTTCTTAATATAATCTTTTATT
* *
21134248 TTTTTATTTTTTTAATATAATTTTTTAT
1 TTTTTA-TTTCTTAATATAATCTTTTAT
21134276 ATTATATATT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
28 6 0.25
29 18 0.75
ACGTcount: A:0.23, C:0.04, G:0.00, T:0.73
Consensus pattern (28 bp):
TTTTTATTTCTTAATATAATCTTTTATT
Found at i:21134287 original size:29 final size:28
Alignment explanation
Indices: 21134215--21134287 Score: 69
Period size: 29 Copynumber: 2.6 Consensus size: 28
21134205 ATGTCATATA
* *
21134215 TTTTATTT-T-TATTTCTTATTATAATC
1 TTTTATTTATATATTTTTTAATATAATC
* * *
21134241 TTTTATTTTTTTATTTTTTTAATATAATT
1 TTTTATTTATATA-TTTTTTAATATAATC
21134270 TTTTATATTATATATTTT
1 TTTTAT-TTATATATTTT
21134288 ATTGTAATTT
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
26 8 0.21
27 1 0.03
28 2 0.05
29 22 0.58
30 5 0.13
ACGTcount: A:0.25, C:0.03, G:0.00, T:0.73
Consensus pattern (28 bp):
TTTTATTTATATATTTTTTAATATAATC
Found at i:21134302 original size:29 final size:29
Alignment explanation
Indices: 21134270--21134378 Score: 95
Period size: 29 Copynumber: 3.9 Consensus size: 29
21134260 TAATATAATT
* *
21134270 TTTTATATTATATATTTTATTGTAATTTC
1 TTTTATATTATATATTATATTTTAATTTC
** *
21134299 TTTTACCTTAT-TATATAAATTTTAATTTC
1 TTTTATATTATATAT-TATATTTTAATTTC
* *
21134328 TTATATA-TATATA-TATATTTT--TAT-
1 TTTTATATTATATATTATATTTTAATTTC
*
21134352 TTTTATATTATATATTTTATTTTAATT
1 TTTTATATTATATATTATATTTTAATT
21134379 ATAACGTTAC
Statistics
Matches: 61, Mismatches: 13, Indels: 13
0.70 0.15 0.15
Matches are distributed among these distances:
24 6 0.10
25 8 0.13
26 7 0.11
27 7 0.11
28 7 0.11
29 26 0.43
ACGTcount: A:0.31, C:0.04, G:0.01, T:0.64
Consensus pattern (29 bp):
TTTTATATTATATATTATATTTTAATTTC
Found at i:21134358 original size:20 final size:20
Alignment explanation
Indices: 21134333--21134374 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 20
21134323 ATTTCTTATA
21134333 TATATATATATATTTTTATTTT
1 TATAT-TATATA-TTTTATTTT
21134355 TATATTATATATTTTATTTT
1 TATATTATATATTTTATTTT
21134375 AATTATAACG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 9 0.45
21 6 0.30
22 5 0.25
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (20 bp):
TATATTATATATTTTATTTT
Found at i:21134380 original size:29 final size:28
Alignment explanation
Indices: 21134268--21134378 Score: 88
Period size: 27 Copynumber: 4.0 Consensus size: 28
21134258 TTTAATATAA
* *
21134268 TTTTTTATATTATATATTTTATTGTAAT
1 TTTTTTATATTATATATTATATTTTAAT
** *
21134296 TTCTTTTACCTTAT-TATATAAATTTTAA-
1 TT-TTTTATATTATATAT-TATATTTTAAT
*
21134324 TTTCTTATA-TATATATATATATTTT--T
1 TTTTTTATATTATATAT-TATATTTTAAT
* *
21134350 ATTTTTATATTATATATTTTATTTTAAT
1 TTTTTTATATTATATATTATATTTTAAT
21134378 T
1 T
21134379 ATAACGTTAC
Statistics
Matches: 63, Mismatches: 13, Indels: 14
0.70 0.14 0.16
Matches are distributed among these distances:
26 17 0.27
27 22 0.35
28 8 0.13
29 16 0.25
ACGTcount: A:0.31, C:0.04, G:0.01, T:0.65
Consensus pattern (28 bp):
TTTTTTATATTATATATTATATTTTAAT
Found at i:21136557 original size:21 final size:21
Alignment explanation
Indices: 21136528--21136599 Score: 90
Period size: 21 Copynumber: 3.4 Consensus size: 21
21136518 TCAAAATTGC
*
21136528 TTGAATGATCTCTGAACTTGT
1 TTGAGTGATCTCTGAACTTGT
*
21136549 TTGAGTGATCCCTGAACTTGT
1 TTGAGTGATCTCTGAACTTGT
* * *
21136570 TTAAGTGATTTTTGAACTTGT
1 TTGAGTGATCTCTGAACTTGT
*
21136591 TTGATTGAT
1 TTGAGTGAT
21136600 TTTTAAAGTT
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 43 1.00
ACGTcount: A:0.22, C:0.11, G:0.21, T:0.46
Consensus pattern (21 bp):
TTGAGTGATCTCTGAACTTGT
Found at i:21136600 original size:21 final size:21
Alignment explanation
Indices: 21136540--21136628 Score: 97
Period size: 21 Copynumber: 4.2 Consensus size: 21
21136530 GAATGATCTC
***
21136540 TGAACTTGTTTGAGTGATCCC
1 TGAACTTGTTTGAGTGATTTT
*
21136561 TGAACTTGTTTAAGTGATTTT
1 TGAACTTGTTTGAGTGATTTT
*
21136582 TGAACTTGTTTGATTGATTTT
1 TGAACTTGTTTGAGTGATTTT
* * *
21136603 TAAAGTTGTTTGAATGAGTTTT
1 TGAACTTGTTTGAGTGA-TTTT
21136625 TGAA
1 TGAA
21136629 TTTAATTTAT
Statistics
Matches: 57, Mismatches: 10, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
21 50 0.88
22 7 0.12
ACGTcount: A:0.24, C:0.07, G:0.21, T:0.48
Consensus pattern (21 bp):
TGAACTTGTTTGAGTGATTTT
Found at i:21136736 original size:21 final size:21
Alignment explanation
Indices: 21136712--21136786 Score: 78
Period size: 21 Copynumber: 3.5 Consensus size: 21
21136702 TCAAGATGAC
*
21136712 TTGAATGATCTTTGAACTTGT
1 TTGAATGATTTTTGAACTTGT
* * *
21136733 TTGAATTATTTTTGAAGTTTT
1 TTGAATGATTTTTGAACTTGT
* *
21136754 TTTAATGAGTTTTTAAACTTGT
1 TTGAATGA-TTTTTGAACTTGT
21136776 TTGAATAGATT
1 TTGAAT-GATT
21136787 ATAAACTTTT
Statistics
Matches: 42, Mismatches: 10, Indels: 3
0.76 0.18 0.05
Matches are distributed among these distances:
21 23 0.55
22 17 0.40
23 2 0.05
ACGTcount: A:0.27, C:0.04, G:0.16, T:0.53
Consensus pattern (21 bp):
TTGAATGATTTTTGAACTTGT
Found at i:21137495 original size:34 final size:33
Alignment explanation
Indices: 21137451--21137514 Score: 101
Period size: 34 Copynumber: 1.9 Consensus size: 33
21137441 AAGGCACTGT
* *
21137451 ATTGTGAAGGTTGTGCTTGATCCTTTGAAAAGGC
1 ATTGTAAAGGTTGTGCTTGAGCC-TTGAAAAGGC
21137485 ATTGTAAAGGTTGTGCTTGAGCCTTGAAAA
1 ATTGTAAAGGTTGTGCTTGAGCCTTGAAAA
21137515 AATAGTTGTT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
33 7 0.25
34 21 0.75
ACGTcount: A:0.27, C:0.11, G:0.28, T:0.34
Consensus pattern (33 bp):
ATTGTAAAGGTTGTGCTTGAGCCTTGAAAAGGC
Found at i:21143407 original size:64 final size:64
Alignment explanation
Indices: 21143329--21143452 Score: 221
Period size: 64 Copynumber: 1.9 Consensus size: 64
21143319 ATTTTATAAC
*
21143329 ACAATACTTGAAAAAATAATAATTCACTAAAATTGAACACCTACCCTAATTAAATAAAAGTAAG
1 ACAATACTTAAAAAAATAATAATTCACTAAAATTGAACACCTACCCTAATTAAATAAAAGTAAG
* *
21143393 ACAATACTTAAAAAATTAATAATTCACTAAAATTGAACACCTACCCTGATTAAATAAAAG
1 ACAATACTTAAAAAAATAATAATTCACTAAAATTGAACACCTACCCTAATTAAATAAAAG
21143453 CTAATTAGAT
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
64 57 1.00
ACGTcount: A:0.52, C:0.16, G:0.06, T:0.26
Consensus pattern (64 bp):
ACAATACTTAAAAAAATAATAATTCACTAAAATTGAACACCTACCCTAATTAAATAAAAGTAAG
Found at i:21154166 original size:24 final size:24
Alignment explanation
Indices: 21154134--21154180 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
21154124 TCTATTTCTT
21154134 AACTTGAGTGGTTATACCTTAACC
1 AACTTGAGTGGTTATACCTTAACC
*
21154158 AACTTGAGTGGTTATATCTTAAC
1 AACTTGAGTGGTTATACCTTAAC
21154181 TAATTGAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.36
Consensus pattern (24 bp):
AACTTGAGTGGTTATACCTTAACC
Found at i:21163150 original size:3 final size:3
Alignment explanation
Indices: 21163137--21163168 Score: 55
Period size: 3 Copynumber: 10.3 Consensus size: 3
21163127 CTCATTTGCT
21163137 ATA ATTA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA A-TA ATA ATA ATA ATA ATA ATA ATA ATA A
21163169 AGATTGAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 25 0.89
4 3 0.11
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:21163627 original size:3 final size:3
Alignment explanation
Indices: 21163619--21163644 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
21163609 GGAAAACTAA
21163619 TGC TGC TGC TGC TGC TGC TGC TGC TG
1 TGC TGC TGC TGC TGC TGC TGC TGC TG
21163645 TGTGTATGTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.31, G:0.35, T:0.35
Consensus pattern (3 bp):
TGC
Found at i:21164069 original size:20 final size:22
Alignment explanation
Indices: 21164044--21164087 Score: 65
Period size: 20 Copynumber: 2.1 Consensus size: 22
21164034 AATTCAATTA
21164044 TAAATAATAATTTT-TA-ATAT
1 TAAATAATAATTTTATAGATAT
*
21164064 TAAATATTAATTTTATAGATAT
1 TAAATAATAATTTTATAGATAT
21164086 TA
1 TA
21164088 TTTTTTATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 13 0.62
21 2 0.10
22 6 0.29
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (22 bp):
TAAATAATAATTTTATAGATAT
Found at i:21176388 original size:28 final size:29
Alignment explanation
Indices: 21176347--21176411 Score: 69
Period size: 30 Copynumber: 2.2 Consensus size: 29
21176337 GTCTATGGGC
*
21176347 AATTTTTCAATTTT-TGGGGCAAAAATGT
1 AATTTTTCAATTTTAGGGGGCAAAAATGT
* * *
21176375 AATTTTTGACTTTTACGGGGGCAAAAGTGT
1 AATTTTTCAATTTTA-GGGGGCAAAAATGT
*
21176405 AAATTTT
1 AATTTTT
21176412 AAAAATTACT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
28 12 0.40
30 18 0.60
ACGTcount: A:0.31, C:0.08, G:0.20, T:0.42
Consensus pattern (29 bp):
AATTTTTCAATTTTAGGGGGCAAAAATGT
Found at i:21178571 original size:12 final size:12
Alignment explanation
Indices: 21178554--21178578 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
21178544 AAGAAAATAG
21178554 AATATTTCTTTT
1 AATATTTCTTTT
21178566 AATATTTCTTTT
1 AATATTTCTTTT
21178578 A
1 A
21178579 TTTTCTTATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.28, C:0.08, G:0.00, T:0.64
Consensus pattern (12 bp):
AATATTTCTTTT
Found at i:21179331 original size:90 final size:90
Alignment explanation
Indices: 21179220--21179404 Score: 232
Period size: 90 Copynumber: 2.1 Consensus size: 90
21179210 CTAATTTCTC
* *
21179220 AAGTTTTGGTATTAGTTTGTTTTCATCATCT-TCAAG-TTTCAAAAAGATTTCAATTATTAGGT-
1 AAGTGTTGGTATTAGTTTGTTTTCATCATCTCT-AAGCTTT-AAAAAGATTTCAATGATT-GGTC
* * *
21179282 TTTGATTTCTAGTTTTACCAAATCAAGT
63 TTTAATTTCTAGTTGTAACAAATCAAGT
* * *
21179310 AAGTGTTGGTATTATTTTGTTTTCATCATCTCTAAGCTTTAAAAGGATTTCAATGGTTGGTCTTT
1 AAGTGTTGGTATTAGTTTGTTTTCATCATCTCTAAGCTTTAAAAAGATTTCAATGATTGGTCTTT
* *
21179375 AATTTCTGGTTGTAATAAATCAAGT
66 AATTTCTAGTTGTAACAAATCAAGT
21179400 AAGTG
1 AAGTG
21179405 ACTTAATATC
Statistics
Matches: 82, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
89 3 0.04
90 75 0.91
91 4 0.05
ACGTcount: A:0.28, C:0.10, G:0.16, T:0.45
Consensus pattern (90 bp):
AAGTGTTGGTATTAGTTTGTTTTCATCATCTCTAAGCTTTAAAAAGATTTCAATGATTGGTCTTT
AATTTCTAGTTGTAACAAATCAAGT
Found at i:21179670 original size:59 final size:59
Alignment explanation
Indices: 21179598--21179710 Score: 145
Period size: 59 Copynumber: 1.9 Consensus size: 59
21179588 AAAAATTATA
* * * ** *
21179598 AATCCATCCATTCCCTGAAATGAATGTGACACCATTTAATAACTATGATCATGGTCACG
1 AATCCATCAATTCCCTAAAATAAATGCAACACCATTTAATAACTATAATCATGGTCACG
* * *
21179657 AATCCATCAATTCCTTAAAATAAATGCAACATCATTTAATAATTATAATCATGG
1 AATCCATCAATTCCCTAAAATAAATGCAACACCATTTAATAACTATAATCATGG
21179711 ACATGGAAGA
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
59 45 1.00
ACGTcount: A:0.39, C:0.20, G:0.10, T:0.31
Consensus pattern (59 bp):
AATCCATCAATTCCCTAAAATAAATGCAACACCATTTAATAACTATAATCATGGTCACG
Found at i:21179835 original size:26 final size:26
Alignment explanation
Indices: 21179763--21179845 Score: 87
Period size: 26 Copynumber: 3.2 Consensus size: 26
21179753 TAATTCTAAA
* *
21179763 GATAATTTTACCACCAGAAATGAATG
1 GATAATTTTACCACTAGAAGTGAATG
* * * *
21179789 AATAATTTTACTA-TCAAAAGTAAATG
1 GATAATTTTACCACT-AGAAGTGAATG
*
21179815 GATAATTTTACCACTAGAAGTGGATG
1 GATAATTTTACCACTAGAAGTGAATG
21179841 GATAA
1 GATAA
21179846 CTTAACTCAC
Statistics
Matches: 44, Mismatches: 11, Indels: 4
0.75 0.19 0.07
Matches are distributed among these distances:
26 43 0.98
27 1 0.02
ACGTcount: A:0.43, C:0.11, G:0.16, T:0.30
Consensus pattern (26 bp):
GATAATTTTACCACTAGAAGTGAATG
Found at i:21179921 original size:28 final size:28
Alignment explanation
Indices: 21179889--21179948 Score: 93
Period size: 28 Copynumber: 2.1 Consensus size: 28
21179879 AATCAAGAAA
*
21179889 TGGATGAATACTTGTAACCCACCAAAAG
1 TGGATGAATACTTGTAACCCACCAAAAC
* *
21179917 TGGATGAATACTTTTAACCCACGAAAAC
1 TGGATGAATACTTGTAACCCACCAAAAC
21179945 TGGA
1 TGGA
21179949 CGGATAACGA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.38, C:0.20, G:0.18, T:0.23
Consensus pattern (28 bp):
TGGATGAATACTTGTAACCCACCAAAAC
Found at i:21180426 original size:92 final size:92
Alignment explanation
Indices: 21180282--21180467 Score: 356
Period size: 92 Copynumber: 2.0 Consensus size: 92
21180272 TGTTGGTATG
21180282 TTCTAATATAACTATATTATAAAGATACTTTTATATGTTCTCATTA-TTTTTTTTTTTTATAATT
1 TTCTAATATAACTATATTATAAAGATACTTTTATATGTTCTCATTATTTTTTTTTTTTTATAATT
21180346 GAGGGAGAGGGGATTTGAACCCTGTTC
66 GAGGGAGAGGGGATTTGAACCCTGTTC
21180373 TNTCTAATATAACTATATTATAAAGATACTTTTATATGTTCTCATTATTTTTTTTTTTTTATAAT
1 T-TCTAATATAACTATATTATAAAGATACTTTTATATGTTCTCATTATTTTTTTTTTTTTATAAT
21180438 TGAGGGAGAGGGGATTTGAACCCTGTTC
65 TGAGGGAGAGGGGATTTGAACCCTGTTC
21180466 TT
1 TT
21180468 TAAGTAGGGG
Statistics
Matches: 93, Mismatches: 0, Indels: 3
0.97 0.00 0.03
Matches are distributed among these distances:
91 1 0.01
92 46 0.49
93 46 0.49
ACGTcount: A:0.28, C:0.10, G:0.14, T:0.48
Consensus pattern (92 bp):
TTCTAATATAACTATATTATAAAGATACTTTTATATGTTCTCATTATTTTTTTTTTTTTATAATT
GAGGGAGAGGGGATTTGAACCCTGTTC
Found at i:21183127 original size:19 final size:19
Alignment explanation
Indices: 21183100--21183145 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
21183090 AGGAGACAAG
*
21183100 ATAAAATTTT-TAGAATAAA
1 ATAATATTTTATA-AATAAA
*
21183119 ATAATATTTTATAAATGAA
1 ATAATATTTTATAAATAAA
21183138 ATAATATT
1 ATAATATT
21183146 AAAATATTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 22 0.92
20 2 0.08
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.41
Consensus pattern (19 bp):
ATAATATTTTATAAATAAA
Found at i:21183594 original size:20 final size:20
Alignment explanation
Indices: 21183549--21183586 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
21183539 TTTTGGCCCC
21183549 ATTTGACTTATTGGAGTATA
1 ATTTGACTTATTGGAGTATA
21183569 ATTTGACTTATTGGAGTA
1 ATTTGACTTATTGGAGTA
21183587 AGATTTGAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.29, C:0.05, G:0.21, T:0.45
Consensus pattern (20 bp):
ATTTGACTTATTGGAGTATA
Found at i:21187296 original size:25 final size:24
Alignment explanation
Indices: 21187268--21187354 Score: 104
Period size: 25 Copynumber: 3.5 Consensus size: 24
21187258 ATAGACTTCT
21187268 CCCATCTCTT-TTTAATTGGACCATG
1 CCCAT-TCTTCTTT-ATTGGACCATG
21187293 CCCATTCTTCCTTTATTGGACCATG
1 CCCATTCTT-CTTTATTGGACCATG
*
21187318 TCCATTCTTCCTTTATTGGACCATG
1 CCCATTCTT-CTTTATTGGACCATG
* *
21187343 TCCATTTTTCTT
1 CCCATTCTTCTT
21187355 GCTTGTTGGG
Statistics
Matches: 58, Mismatches: 2, Indels: 5
0.89 0.03 0.08
Matches are distributed among these distances:
24 7 0.12
25 48 0.83
26 3 0.05
ACGTcount: A:0.16, C:0.29, G:0.10, T:0.45
Consensus pattern (24 bp):
CCCATTCTTCTTTATTGGACCATG
Found at i:21187374 original size:27 final size:27
Alignment explanation
Indices: 21187283--21187388 Score: 89
Period size: 25 Copynumber: 4.1 Consensus size: 27
21187273 CTCTTTTTAA
*
21187283 TTGGACCATGCCCATTCTTCC-T--TTA
1 TTGGACCATGCCCATT-TTCCTTGCTTG
* *
21187308 TTGGACCATGTCCATTCTTCC-T--TTA
1 TTGGACCATGCCCATT-TTCCTTGCTTG
* *
21187333 TTGGACCATGTCCATTTTTCTTGCTTG
1 TTGGACCATGCCCATTTTCCTTGCTTG
* *
21187360 TTGGGCCATGCCCATTTTCCTTTCTTG
1 TTGGACCATGCCCATTTTCCTTGCTTG
21187387 TT
1 TT
21187389 ATTTTTTTTT
Statistics
Matches: 71, Mismatches: 7, Indels: 4
0.87 0.09 0.05
Matches are distributed among these distances:
24 3 0.04
25 41 0.58
27 27 0.38
ACGTcount: A:0.12, C:0.27, G:0.15, T:0.45
Consensus pattern (27 bp):
TTGGACCATGCCCATTTTCCTTGCTTG
Found at i:21187398 original size:5 final size:5
Alignment explanation
Indices: 21187374--21187441 Score: 75
Period size: 5 Copynumber: 13.6 Consensus size: 5
21187364 GCCATGCCCA
* * * *
21187374 TTTTC CTTTC TTGTTA TTTTT TTTTC TTTTC TTTTC TTTTC TTTTC CTTTC
1 TTTTC TTTTC TT-TTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC
*
21187425 TTCTC TTTTC -TTTC TTT
1 TTTTC TTTTC TTTTC TTT
21187442 CTTCCACCGT
Statistics
Matches: 52, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
4 4 0.08
5 44 0.85
6 4 0.08
ACGTcount: A:0.01, C:0.21, G:0.01, T:0.76
Consensus pattern (5 bp):
TTTTC
Found at i:21191319 original size:2 final size:2
Alignment explanation
Indices: 21191312--21191363 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
21191302 NNNNNNNNNN
21191312 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
21191354 AT AT AT AT AT
1 AT AT AT AT AT
21191364 TATTCTTTCT
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:21192956 original size:27 final size:28
Alignment explanation
Indices: 21192917--21192977 Score: 72
Period size: 27 Copynumber: 2.2 Consensus size: 28
21192907 TCCAACGAAA
* *
21192917 TTTTCGTTGGAAAATTCCAATG-GAAAAT
1 TTTTTGTTGGAAAA-TCCAATGAAAAAAT
*
21192945 TTTTTGTT-GAAAATCCATTGAAAAAAT
1 TTTTTGTTGGAAAATCCAATGAAAAAAT
21192972 TTTTTG
1 TTTTTG
21192978 GAAGCAAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
26 6 0.21
27 16 0.55
28 7 0.24
ACGTcount: A:0.34, C:0.08, G:0.15, T:0.43
Consensus pattern (28 bp):
TTTTTGTTGGAAAATCCAATGAAAAAAT
Found at i:21192969 original size:113 final size:112
Alignment explanation
Indices: 21192836--21193072 Score: 332
Period size: 112 Copynumber: 2.1 Consensus size: 112
21192826 ATGGAATTTC
*
21192836 CGTTGGAAATCCATTAAAAAAAATTTTTGGCAAGCAAAAAAAGACAGGAGACCACCATTTCTGAC
1 CGTTGGAAATCCATTAAAAAAAATTTTTGG-AAGCAAAAAAAGACAGGAGACCACCATTTCAGAC
* * *
21192901 GGAATTTCCAACGA-AATTTTCGTTGGAAAATTCCAATGGAAAATTTTT
65 GAAATTTCCAA-GAGAATTTTCGTTGGAAAATTCCAACGAAAAATTTTT
* * * * * *
21192949 TGTTGAAAATCCATTGAAAAAATTTTTTGGAAGCAAAAAAAGATAGGAGACCACCATTTCAGATG
1 CGTTGGAAATCCATTAAAAAAAATTTTTGGAAGCAAAAAAAGACAGGAGACCACCATTTCAGACG
* * *
21193014 AAATTTCCAATAGAATTTTTGTTGGAAATTTCCAACGAAAAATTTTT
66 AAATTTCCAAGAGAATTTTCGTTGGAAAATTCCAACGAAAAATTTTT
21193061 CGTTGGAAATCC
1 CGTTGGAAATCC
21193073 GTCCAAAAGT
Statistics
Matches: 108, Mismatches: 15, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
111 1 0.01
112 81 0.75
113 26 0.24
ACGTcount: A:0.40, C:0.14, G:0.16, T:0.30
Consensus pattern (112 bp):
CGTTGGAAATCCATTAAAAAAAATTTTTGGAAGCAAAAAAAGACAGGAGACCACCATTTCAGACG
AAATTTCCAAGAGAATTTTCGTTGGAAAATTCCAACGAAAAATTTTT
Found at i:21193978 original size:11 final size:11
Alignment explanation
Indices: 21193961--21194004 Score: 51
Period size: 11 Copynumber: 4.3 Consensus size: 11
21193951 TATGGCCGGC
21193961 CAAAGGAA-AA
1 CAAAGGAAGAA
21193971 CAAAAGGAAGAA
1 C-AAAGGAAGAA
21193983 CAAAGGAAG-A
1 CAAAGGAAGAA
21193993 -AAA-GAAGAA
1 CAAAGGAAGAA
21194002 CAA
1 CAA
21194005 GAACCCTAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
8 4 0.13
9 4 0.13
10 4 0.13
11 15 0.50
12 3 0.10
ACGTcount: A:0.68, C:0.09, G:0.23, T:0.00
Consensus pattern (11 bp):
CAAAGGAAGAA
Found at i:21201970 original size:20 final size:20
Alignment explanation
Indices: 21201953--21201990 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
21201943 CTTCAAATCT
21201953 TACTCCAATAAGTCAAATTA
1 TACTCCAATAAGTCAAATTA
21201973 TACTCCAATAAGTCAAAT
1 TACTCCAATAAGTCAAAT
21201991 GGAGCCAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.45, C:0.21, G:0.05, T:0.29
Consensus pattern (20 bp):
TACTCCAATAAGTCAAATTA
Found at i:21205833 original size:13 final size:14
Alignment explanation
Indices: 21205790--21205846 Score: 60
Period size: 15 Copynumber: 3.8 Consensus size: 14
21205780 TTTTTAATTT
21205790 TAATTTTTATTATA
1 TAATTTTTATTATA
* *
21205804 TTATTTGATTATTTTA
1 TAATTT--TTATTATA
21205820 TTAATTTTTATTATA
1 -TAATTTTTATTATA
21205835 TATATTTTTATT
1 TA-ATTTTTATT
21205847 TGGGGAATAG
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
14 7 0.20
15 16 0.46
16 7 0.20
17 5 0.14
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (14 bp):
TAATTTTTATTATA
Found at i:21206332 original size:23 final size:23
Alignment explanation
Indices: 21206302--21206347 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
21206292 TGATGCATAA
* *
21206302 TCTCGTTACTGTTGCTTTTGATT
1 TCTCGTTACTGCTGCCTTTGATT
21206325 TCTCGTTACTGCTGCCTTTGATT
1 TCTCGTTACTGCTGCCTTTGATT
21206348 ACAGCTGCTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.09, C:0.22, G:0.17, T:0.52
Consensus pattern (23 bp):
TCTCGTTACTGCTGCCTTTGATT
Found at i:21206985 original size:15 final size:15
Alignment explanation
Indices: 21206965--21206994 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
21206955 TTGGAAACCA
21206965 ATTTCCAACGGAATT
1 ATTTCCAACGGAATT
*
21206980 ATTTCCAATGGAATT
1 ATTTCCAACGGAATT
21206995 TTCTGTCGGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.33, C:0.17, G:0.13, T:0.37
Consensus pattern (15 bp):
ATTTCCAACGGAATT
Found at i:21212366 original size:34 final size:35
Alignment explanation
Indices: 21212291--21212380 Score: 112
Period size: 35 Copynumber: 2.6 Consensus size: 35
21212281 GGGAAATGAG
*
21212291 TTTTCTAAGGGATCCAGCAAAACCCTCACAATAGCT
1 TTTTC-AAGGGATCAAGCAAAACCCTCACAATAGCT
* **
21212327 TTTTCACGGGATCAAGCAAAACCCTTGCAA-AGCT
1 TTTTCAAGGGATCAAGCAAAACCCTCACAATAGCT
21212361 TTTTCAAGAGG-TCAAGCAAA
1 TTTTCAAG-GGATCAAGCAAA
21212381 TCCTTTCAAT
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
34 20 0.42
35 23 0.48
36 5 0.10
ACGTcount: A:0.34, C:0.24, G:0.17, T:0.24
Consensus pattern (35 bp):
TTTTCAAGGGATCAAGCAAAACCCTCACAATAGCT
Found at i:21214281 original size:20 final size:20
Alignment explanation
Indices: 21214224--21214286 Score: 101
Period size: 20 Copynumber: 3.2 Consensus size: 20
21214214 TATATACCCA
*
21214224 TCATCATCATC-TCACCAAC
1 TCATCATCATCATCACCAGC
*
21214243 CCATCATCATCATCACCAGC
1 TCATCATCATCATCACCAGC
21214263 TCATCATCATCATCACCAGC
1 TCATCATCATCATCACCAGC
21214283 TCAT
1 TCAT
21214287 GCGCACTCCC
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
19 10 0.25
20 30 0.75
ACGTcount: A:0.30, C:0.41, G:0.03, T:0.25
Consensus pattern (20 bp):
TCATCATCATCATCACCAGC
Found at i:21214333 original size:43 final size:43
Alignment explanation
Indices: 21214285--21214403 Score: 168
Period size: 43 Copynumber: 2.8 Consensus size: 43
21214275 TCACCAGCTC
** * *
21214285 ATGCGCACTCCCTACTCGCACATGGCTGGGTCATCAC-CGGGTT
1 ATGCGCACTCCCTACTCGCACATAACCGGGTCATC-CTCGGCTT
21214328 ATGCGCACTCCCTACTCGCACATAACCGGGTCATCCTCGGCTT
1 ATGCGCACTCCCTACTCGCACATAACCGGGTCATCCTCGGCTT
* *
21214371 ATGCGCACTCCCTACTCGCACATAGCCGAGTCA
1 ATGCGCACTCCCTACTCGCACATAACCGGGTCA
21214404 ACATAATTAC
Statistics
Matches: 69, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
42 1 0.01
43 68 0.99
ACGTcount: A:0.19, C:0.38, G:0.21, T:0.22
Consensus pattern (43 bp):
ATGCGCACTCCCTACTCGCACATAACCGGGTCATCCTCGGCTT
Found at i:21217507 original size:17 final size:17
Alignment explanation
Indices: 21217487--21217539 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
21217477 TTTTAACAAC
21217487 AAACACATATCACCAAT
1 AAACACATATCACCAAT
* * *
21217504 AAACA-ATAATAAACAAC
1 AAACACAT-ATCACCAAT
*
21217521 AAATACATATCACCAAT
1 AAACACATATCACCAAT
21217538 AA
1 AA
21217540 CCAACAAATA
Statistics
Matches: 27, Mismatches: 7, Indels: 4
0.71 0.18 0.11
Matches are distributed among these distances:
16 2 0.07
17 23 0.85
18 2 0.07
ACGTcount: A:0.60, C:0.23, G:0.00, T:0.17
Consensus pattern (17 bp):
AAACACATATCACCAAT
Found at i:21217529 original size:34 final size:34
Alignment explanation
Indices: 21217480--21217557 Score: 113
Period size: 34 Copynumber: 2.3 Consensus size: 34
21217470 TTTCACATTT
*
21217480 TAACAACAAACACATATCACCAATAAACAA-TAA
1 TAACAACAAACACATATCACCAATAAACAACAAA
* *
21217513 TAAACAACAAATACATATCACCAATAACCAACAAA
1 T-AACAACAAACACATATCACCAATAAACAACAAA
21217548 TAACAACAAA
1 TAACAACAAA
21217558 ATTATTTTAC
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
33 1 0.03
34 36 0.90
35 3 0.08
ACGTcount: A:0.62, C:0.24, G:0.00, T:0.14
Consensus pattern (34 bp):
TAACAACAAACACATATCACCAATAAACAACAAA
Found at i:21223227 original size:2 final size:2
Alignment explanation
Indices: 21223220--21223271 Score: 95
Period size: 2 Copynumber: 26.0 Consensus size: 2
21223210 TTAAATGATA
21223220 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
21223262 CT AT AT AT AT
1 AT AT AT AT AT
21223272 TCCTTTACCA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:21229039 original size:17 final size:17
Alignment explanation
Indices: 21229017--21229053 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
21229007 CTATAGCGTA
*
21229017 GGGCTCATGGTGAATGG
1 GGGCTCATGGTGAACGG
21229034 GGGCTCATGGTGAACGG
1 GGGCTCATGGTGAACGG
21229051 GGG
1 GGG
21229054 TTATTCCATC
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:0.16, C:0.14, G:0.51, T:0.19
Consensus pattern (17 bp):
GGGCTCATGGTGAACGG
Found at i:21231258 original size:39 final size:39
Alignment explanation
Indices: 21231214--21231292 Score: 158
Period size: 39 Copynumber: 2.0 Consensus size: 39
21231204 ATAAAAAGAG
21231214 AATGATTTTTCTCTAAAAAAGAGAAAGCTTTTGTTTTCA
1 AATGATTTTTCTCTAAAAAAGAGAAAGCTTTTGTTTTCA
21231253 AATGATTTTTCTCTAAAAAAGAGAAAGCTTTTGTTTTCA
1 AATGATTTTTCTCTAAAAAAGAGAAAGCTTTTGTTTTCA
21231292 A
1 A
21231293 GTTAACTTTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.37, C:0.10, G:0.13, T:0.41
Consensus pattern (39 bp):
AATGATTTTTCTCTAAAAAAGAGAAAGCTTTTGTTTTCA
Found at i:21231499 original size:17 final size:18
Alignment explanation
Indices: 21231477--21231515 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
21231467 TATAAATCCT
*
21231477 TTTATTTATTA-TATTAA
1 TTTATTAATTATTATTAA
*
21231494 TTTATTAATTATTTTTAA
1 TTTATTAATTATTATTAA
21231512 TTTA
1 TTTA
21231516 CTTTGCTAGG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 10 0.53
18 9 0.47
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (18 bp):
TTTATTAATTATTATTAA
Found at i:21236393 original size:19 final size:20
Alignment explanation
Indices: 21236369--21236407 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
21236359 TAAGAGAACA
*
21236369 AATAAA-ATAAAAGTGATAC
1 AATAAAGATAAAAGGGATAC
21236388 AATAAAGTATAAAAGGGATA
1 AATAAAG-ATAAAAGGGATA
21236408 GATAAAAGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 6 0.35
21 11 0.65
ACGTcount: A:0.62, C:0.03, G:0.15, T:0.21
Consensus pattern (20 bp):
AATAAAGATAAAAGGGATAC
Found at i:21238454 original size:17 final size:16
Alignment explanation
Indices: 21238432--21238467 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
21238422 TATTTTTGTC
*
21238432 AAAAAAAGGAAAAAAGA
1 AAAAAAAAGAAAAAA-A
21238449 AAAAAAAAGAAAAAAA
1 AAAAAAAAGAAAAAAA
21238465 AAA
1 AAA
21238468 CCAAAGATCT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 4 0.22
17 14 0.78
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (16 bp):
AAAAAAAAGAAAAAAA
Found at i:21238467 original size:11 final size:10
Alignment explanation
Indices: 21238441--21238466 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
21238431 CAAAAAAAGG
21238441 AAAAAAGAAA
1 AAAAAAGAAA
21238451 AAAAAAGAAA
1 AAAAAAGAAA
21238461 AAAAAA
1 AAAAAA
21238467 ACCAAAGATC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (10 bp):
AAAAAAGAAA
Found at i:21245230 original size:120 final size:120
Alignment explanation
Indices: 21245015--21245256 Score: 367
Period size: 120 Copynumber: 2.0 Consensus size: 120
21245005 ACATTTCAGA
* * * *
21245015 TAATTAATGTCAAGATTTTTTAAAGTTACGTTGCCTTAGTTTTCGAGGAGCCATATTTCCTAAAT
1 TAATTAATGTCAAGATTTTTTAAAGTTACGTTGCCTCAGTTTTCGAGGAACAACATTTCCTAAAT
* *
21245080 TCTCCAAGTACATTCTGAAGACCTCCGGGCACATTATTCTCTTAAATCCTCCGGG
66 CCTCCAAGTACATTCTGAAGACCTCCGGGCACATTATTCTCTTAAAACCTCCGGG
* *
21245135 TAATTAGTGTCAAGATTTTTTAAAGTTACGTTGCCTCAGTTTTCGAGGAACAACATTTCTTAAAT
1 TAATTAATGTCAAGATTTTTTAAAGTTACGTTGCCTCAGTTTTCGAGGAACAACATTTCCTAAAT
** * **
21245200 CCTCCGGGTACATTCTTAAGACCTTTGGGCACATTATTCTCTTAAAACCTCCGGG
66 CCTCCAAGTACATTCTGAAGACCTCCGGGCACATTATTCTCTTAAAACCTCCGGG
21245255 TA
1 TA
21245257 CATTTCCAAA
Statistics
Matches: 109, Mismatches: 13, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
120 109 1.00
ACGTcount: A:0.27, C:0.21, G:0.16, T:0.36
Consensus pattern (120 bp):
TAATTAATGTCAAGATTTTTTAAAGTTACGTTGCCTCAGTTTTCGAGGAACAACATTTCCTAAAT
CCTCCAAGTACATTCTGAAGACCTCCGGGCACATTATTCTCTTAAAACCTCCGGG
Found at i:21245419 original size:44 final size:44
Alignment explanation
Indices: 21245342--21245463 Score: 133
Period size: 44 Copynumber: 2.8 Consensus size: 44
21245332 ATTTTCAAAA
* **
21245342 CCTCCGGGTACATTTT-TAAAACCTCCAAGTACATTCTATAAAG
1 CCTCTGGGTACATTTTCTAAAACCTCCGGGTACATTCTATAAAG
* * *
21245385 CCTCTGGGTACATTTTCTAAAGCCTCCGGGTACATTTTTTAAAG
1 CCTCTGGGTACATTTTCTAAAACCTCCGGGTACATTCTATAAAG
* * *
21245429 TCT-TCGGGTACATTTTC-AAAACCTTCGGGCACATT
1 CCTCT-GGGTACATTTTCTAAAACCTCCGGGTACATT
21245464 TTTCTCTCAA
Statistics
Matches: 67, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
43 31 0.46
44 36 0.54
ACGTcount: A:0.26, C:0.25, G:0.16, T:0.34
Consensus pattern (44 bp):
CCTCTGGGTACATTTTCTAAAACCTCCGGGTACATTCTATAAAG
Found at i:21245444 original size:22 final size:22
Alignment explanation
Indices: 21245346--21245466 Score: 104
Period size: 22 Copynumber: 5.6 Consensus size: 22
21245336 TCAAAACCTC
* *
21245346 CGGGTACA-TTTTTAAAACCTC
1 CGGGTACATTTTTTAAAGCCTT
** * *
21245367 CAAGTACATTCTATAAAGCC-T
1 CGGGTACATTTTTTAAAGCCTT
* *
21245388 CTGGGTACATTTTCTAAAGCCTC
1 C-GGGTACATTTTTTAAAGCCTT
*
21245411 CGGGTACATTTTTTAAAGTCTT
1 CGGGTACATTTTTTAAAGCCTT
* *
21245433 CGGGTACA-TTTTCAAAACCTT
1 CGGGTACATTTTTTAAAGCCTT
*
21245454 CGGGCACATTTTT
1 CGGGTACATTTTT
21245467 CTCTCAAAAC
Statistics
Matches: 78, Mismatches: 18, Indels: 7
0.76 0.17 0.07
Matches are distributed among these distances:
21 24 0.31
22 53 0.68
23 1 0.01
ACGTcount: A:0.26, C:0.22, G:0.16, T:0.36
Consensus pattern (22 bp):
CGGGTACATTTTTTAAAGCCTT
Found at i:21245454 original size:21 final size:21
Alignment explanation
Indices: 21245317--21245465 Score: 120
Period size: 21 Copynumber: 7.0 Consensus size: 21
21245307 TTTTTCTCTT
* * *
21245317 AAAACCTCCAGATATATTTTC
1 AAAACCTCCGGGTACATTTTC
*
21245338 AAAACCTCCGGGTACATTTTT
1 AAAACCTCCGGGTACATTTTC
**
21245359 AAAACCTCCAAGTACATTCTAT-
1 AAAACCTCCGGGTACATT-T-TC
* *
21245381 AAAGCCTCTGGGTACATTTTC
1 AAAACCTCCGGGTACATTTTC
* *
21245402 TAAAGCCTCCGGGTACATTTTTT
1 -AAAACCTCCGGGTACA-TTTTC
** *
21245425 AAAGTCTTCGGGTACATTTTC
1 AAAACCTCCGGGTACATTTTC
* *
21245446 AAAACCTTCGGGCACATTTT
1 AAAACCTCCGGGTACATTTT
21245466 TCTCTCAAAA
Statistics
Matches: 105, Mismatches: 18, Indels: 10
0.79 0.14 0.08
Matches are distributed among these distances:
20 1 0.01
21 55 0.52
22 44 0.42
23 5 0.05
ACGTcount: A:0.30, C:0.23, G:0.13, T:0.34
Consensus pattern (21 bp):
AAAACCTCCGGGTACATTTTC
Found at i:21245553 original size:1 final size:1
Alignment explanation
Indices: 21245547--21245590 Score: 52
Period size: 1 Copynumber: 44.0 Consensus size: 1
21245537 TTTAAACGAC
* * * *
21245547 AAAAAAAAAACAAAAAAAACAAAAAAACAAAAAACAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
21245591 CCTTGGTAAG
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
1 35 1.00
ACGTcount: A:0.91, C:0.09, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:21245563 original size:9 final size:9
Alignment explanation
Indices: 21245549--21245591 Score: 63
Period size: 8 Copynumber: 5.0 Consensus size: 9
21245539 TAAACGACAA
21245549 AAAAAAAAC
1 AAAAAAAAC
21245558 AAAAAAAAC
1 AAAAAAAAC
21245567 -AAAAAAAC
1 AAAAAAAAC
*
21245575 AAAAAACA-
1 AAAAAAAAC
21245583 AAAAAAAAC
1 AAAAAAAAC
21245592 CTTGGTAAGA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
8 15 0.50
9 15 0.50
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (9 bp):
AAAAAAAAC
Found at i:21245572 original size:17 final size:17
Alignment explanation
Indices: 21245548--21245591 Score: 72
Period size: 17 Copynumber: 2.6 Consensus size: 17
21245538 TTAAACGACA
21245548 AAAAAAAAACAAAAAA-
1 AAAAAAAAACAAAAAAC
21245564 AACAAAAAAACAAAAAAC
1 AA-AAAAAAACAAAAAAC
21245582 AAAAAAAAAC
1 AAAAAAAAAC
21245592 CTTGGTAAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
16 2 0.08
17 22 0.85
18 2 0.08
ACGTcount: A:0.89, C:0.11, G:0.00, T:0.00
Consensus pattern (17 bp):
AAAAAAAAACAAAAAAC
Found at i:21246495 original size:21 final size:21
Alignment explanation
Indices: 21246456--21246495 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
21246446 AGATTTCACC
*
21246456 TTGGGGAAGTCAGATTCGGCT
1 TTGGGGAAGTCAGAATCGGCT
21246477 TTGGGGAAGTCCA-AATCGG
1 TTGGGGAAGT-CAGAATCGG
21246496 AGTTGAGTAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 15 0.88
22 2 0.12
ACGTcount: A:0.23, C:0.15, G:0.38, T:0.25
Consensus pattern (21 bp):
TTGGGGAAGTCAGAATCGGCT
Found at i:21255802 original size:17 final size:17
Alignment explanation
Indices: 21255771--21255804 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
21255761 CCTTAAAACT
21255771 AAGAAAAGCAAAAAAGA
1 AAGAAAAGCAAAAAAGA
21255788 AAGAAAAG-AAGAAAAGA
1 AAGAAAAGCAA-AAAAGA
21255805 GTGAGCTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 2 0.12
17 14 0.88
ACGTcount: A:0.76, C:0.03, G:0.21, T:0.00
Consensus pattern (17 bp):
AAGAAAAGCAAAAAAGA
Found at i:21256394 original size:15 final size:15
Alignment explanation
Indices: 21256352--21256387 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
21256342 CAATACAATA
* *
21256352 TGATTACAAGTAATG
1 TGATTGCAAGAAATG
21256367 TGATTGCAAGAAATG
1 TGATTGCAAGAAATG
21256382 TGATTG
1 TGATTG
21256388 TATGAAAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.36, C:0.06, G:0.25, T:0.33
Consensus pattern (15 bp):
TGATTGCAAGAAATG
Found at i:21256686 original size:32 final size:32
Alignment explanation
Indices: 21256605--21256683 Score: 88
Period size: 32 Copynumber: 2.4 Consensus size: 32
21256595 TTTAATACCA
*
21256605 TATATTTT-ATTTTTTATTATAATCTTATATAT
1 TATATTTTCA-TTTTTAATATAATCTTATATAT
* * *
21256637 TTTATTTTCATTTTTAATATAATTTTTTATAT
1 TATATTTTCATTTTTAATATAATCTTATATAT
*
21256669 TATATGTTTTATTTT
1 TATAT-TTTCATTTT
21256684 AATTTCTTTT
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
32 30 0.77
33 9 0.23
ACGTcount: A:0.28, C:0.03, G:0.01, T:0.68
Consensus pattern (32 bp):
TATATTTTCATTTTTAATATAATCTTATATAT
Found at i:21256933 original size:16 final size:16
Alignment explanation
Indices: 21256908--21256981 Score: 58
Period size: 14 Copynumber: 5.2 Consensus size: 16
21256898 CTTTACGTCC
21256908 ATTA-ATTATAATATA
1 ATTATATTATAATATA
21256923 ATTATATTATAAT-T-
1 ATTATATTATAATATA
*
21256937 -TTATAATAT-A-ATA
1 ATTATATTATAATATA
*
21256950 ATT-TATTAAAATATA
1 ATTATATTATAATATA
*
21256965 A--ATAATATAATATA
1 ATTATATTATAATATA
21256979 ATT
1 ATT
21256982 TAATTAAACA
Statistics
Matches: 45, Mismatches: 5, Indels: 17
0.67 0.07 0.25
Matches are distributed among these distances:
12 2 0.04
13 12 0.27
14 14 0.31
15 9 0.20
16 8 0.18
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
ATTATATTATAATATA
Found at i:21256974 original size:24 final size:27
Alignment explanation
Indices: 21256915--21256975 Score: 67
Period size: 24 Copynumber: 2.4 Consensus size: 27
21256905 TCCATTAATT
* *
21256915 ATAATATAATTATATTATAATTTTATA
1 ATAATATAATTATATTATAAATATATA
21256942 AT-ATAATAATT-TATTA-AAATATA-A
1 ATAAT-ATAATTATATTATAAATATATA
21256966 ATAATATAAT
1 ATAATATAAT
21256976 ATAATTTAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
24 8 0.27
25 7 0.23
26 7 0.23
27 8 0.27
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (27 bp):
ATAATATAATTATATTATAAATATATA
Found at i:21278532 original size:32 final size:32
Alignment explanation
Indices: 21278496--21278598 Score: 75
Period size: 32 Copynumber: 3.2 Consensus size: 32
21278486 TCATATCACT
21278496 TTTAGTTTGAATTATTTTAGCTTTACATCAGA
1 TTTAGTTTGAATTATTTTAGCTTTACATCAGA
* * * * * * * **
21278528 TTTAG-GTCATCTTGAGCTTAATG-TTCATATCACT
1 TTTAGTTTGA-ATT-A-TTTTA-GCTTTACATCAGA
21278562 TTTAGTTTGAATTATTTTAGCTTTACATCAGA
1 TTTAGTTTGAATTATTTTAGCTTTACATCAGA
21278594 TTTAG
1 TTTAG
21278599 GTCATCTTGA
Statistics
Matches: 47, Mismatches: 18, Indels: 12
0.61 0.23 0.16
Matches are distributed among these distances:
31 3 0.06
32 22 0.47
33 2 0.04
34 17 0.36
35 3 0.06
ACGTcount: A:0.26, C:0.12, G:0.14, T:0.49
Consensus pattern (32 bp):
TTTAGTTTGAATTATTTTAGCTTTACATCAGA
Found at i:21278591 original size:66 final size:66
Alignment explanation
Indices: 21278485--21278621 Score: 274
Period size: 66 Copynumber: 2.1 Consensus size: 66
21278475 TTGTTTGGGA
21278485 TTCATATCACTTTTAGTTTGAATTATTTTAGCTTTACATCAGATTTAGGTCATCTTGAGCTTAAT
1 TTCATATCACTTTTAGTTTGAATTATTTTAGCTTTACATCAGATTTAGGTCATCTTGAGCTTAAT
21278550 G
66 G
21278551 TTCATATCACTTTTAGTTTGAATTATTTTAGCTTTACATCAGATTTAGGTCATCTTGAGCTTAAT
1 TTCATATCACTTTTAGTTTGAATTATTTTAGCTTTACATCAGATTTAGGTCATCTTGAGCTTAAT
21278616 G
66 G
21278617 TTCAT
1 TTCAT
21278622 GTCATTCAGG
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
66 71 1.00
ACGTcount: A:0.26, C:0.14, G:0.13, T:0.47
Consensus pattern (66 bp):
TTCATATCACTTTTAGTTTGAATTATTTTAGCTTTACATCAGATTTAGGTCATCTTGAGCTTAAT
G
Found at i:21279004 original size:111 final size:113
Alignment explanation
Indices: 21278805--21279019 Score: 317
Period size: 111 Copynumber: 1.9 Consensus size: 113
21278795 GAGATTTTAC
* * * * *
21278805 ATTTTCATTATCTTTCTTAAGTTATTCATCGATTAATAGTTTATATAATATAATATCTCTTCATT
1 ATTTTCATTATCTTTCTTAAGTTACTCATAGACTAATAGTTTATATAATATAATATATCTCCATT
* *
21278870 CTATATTAGATGTTTACGTTTGACTTGAATGAAAATTAATTTATTTTT
66 ATATATTAGATGTTTACGTTTGACTCGAATGAAAATTAATTTATTTTT
* *
21278918 ATTTTTATTATC-TTCTTAAGTTACTCATAGACTAATAGTTTATATTA-ATAATATATCTCCATT
1 ATTTTCATTATCTTTCTTAAGTTACTCATAGACTAATAGTTTATATAATATAATATATCTCCATT
* *
21278981 ATATATTAGATGTTTATGTTTGACTCGTATGAAAATTAA
66 ATATATTAGATGTTTACGTTTGACTCGAATGAAAATTAA
21279020 GAAAAATATT
Statistics
Matches: 91, Mismatches: 11, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
111 49 0.54
112 31 0.34
113 11 0.12
ACGTcount: A:0.33, C:0.10, G:0.08, T:0.49
Consensus pattern (113 bp):
ATTTTCATTATCTTTCTTAAGTTACTCATAGACTAATAGTTTATATAATATAATATATCTCCATT
ATATATTAGATGTTTACGTTTGACTCGAATGAAAATTAATTTATTTTT
Found at i:21281919 original size:53 final size:52
Alignment explanation
Indices: 21281784--21281955 Score: 191
Period size: 53 Copynumber: 3.2 Consensus size: 52
21281774 AAGGGTGTTA
* * ***
21281784 CAAGCATGGAAGCGCCTAGGGTGTTCCAAACACAGAAGCGCCCAAGGGCGTTC
1 CAAGCGTGGAAGCGCCTAGGGTGTTCCAAGCGTGGAAGCGCCCAA-GGCGTTC
* ** * *
21281837 CAAGTGCAGAAGCGCCTAGGGTGTTCCAAGCGTGGAAACGCCCAAGGAGTTC
1 CAAGCGTGGAAGCGCCTAGGGTGTTCCAAGCGTGGAAGCGCCCAAGGCGTTC
* * * *
21281889 CAAGCGTGGAAGCGCCTAGAGGCGTTCCAAGCGTGGAAGCTCCTAGAGGCGTTT
1 CAAGCGTGGAAGCGCCTAG-GGTGTTCCAAGCGTGGAAGCGCCCA-AGGCGTTC
21281943 CAAGCGTGGAAGC
1 CAAGCGTGGAAGC
21281956 ACACAGAAAC
Statistics
Matches: 98, Mismatches: 19, Indels: 3
0.82 0.16 0.03
Matches are distributed among these distances:
52 22 0.22
53 57 0.58
54 19 0.19
ACGTcount: A:0.26, C:0.26, G:0.33, T:0.15
Consensus pattern (52 bp):
CAAGCGTGGAAGCGCCTAGGGTGTTCCAAGCGTGGAAGCGCCCAAGGCGTTC
Found at i:21281923 original size:27 final size:27
Alignment explanation
Indices: 21281784--21281955 Score: 163
Period size: 27 Copynumber: 6.5 Consensus size: 27
21281774 AAGGGTGTTA
* *
21281784 CAAGCATGGAAGCGCCTAG-GGTGTTC
1 CAAGCGTGGAAGCGCCTAGAGGCGTTC
* *** *
21281810 CAAACACAGAAGCGCCCA-AGGGCGTTC
1 CAAGCGTGGAAGCGCCTAGA-GGCGTTC
* ** *
21281837 CAAGTGCAGAAGCGCCTAG-GGTGTTC
1 CAAGCGTGGAAGCGCCTAGAGGCGTTC
* * *
21281863 CAAGCGTGGAAACGCCCA-AGGAGTTC
1 CAAGCGTGGAAGCGCCTAGAGGCGTTC
21281889 CAAGCGTGGAAGCGCCTAGAGGCGTTC
1 CAAGCGTGGAAGCGCCTAGAGGCGTTC
* *
21281916 CAAGCGTGGAAGCTCCTAGAGGCGTTT
1 CAAGCGTGGAAGCGCCTAGAGGCGTTC
21281943 CAAGCGTGGAAGC
1 CAAGCGTGGAAGC
21281956 ACACAGAAAC
Statistics
Matches: 120, Mismatches: 21, Indels: 9
0.80 0.14 0.06
Matches are distributed among these distances:
26 55 0.46
27 65 0.54
ACGTcount: A:0.26, C:0.26, G:0.33, T:0.15
Consensus pattern (27 bp):
CAAGCGTGGAAGCGCCTAGAGGCGTTC
Found at i:21283744 original size:53 final size:53
Alignment explanation
Indices: 21283680--21283838 Score: 291
Period size: 53 Copynumber: 3.0 Consensus size: 53
21283670 TACTTAAGAA
* *
21283680 AATATTTTTTATTAACTCTCAACTTGAATGTCTCATAACTAAGCCTAAGGGTC
1 AATATTCTTTATTAACTCTCAACTTGAATGTCTTATAACTAAGCCTAAGGGTC
*
21283733 AATATTCTTTATTAACTCTCAACTTGAATATCTTATAACTAAGCCTAAGGGTC
1 AATATTCTTTATTAACTCTCAACTTGAATGTCTTATAACTAAGCCTAAGGGTC
21283786 AATATTCTTTATTAACTCTCAACTTGAATGTCTTATAACTAAGCCTAAGGGTC
1 AATATTCTTTATTAACTCTCAACTTGAATGTCTTATAACTAAGCCTAAGGGTC
21283839 TTATTTATAG
Statistics
Matches: 102, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
53 102 1.00
ACGTcount: A:0.33, C:0.19, G:0.11, T:0.38
Consensus pattern (53 bp):
AATATTCTTTATTAACTCTCAACTTGAATGTCTTATAACTAAGCCTAAGGGTC
Found at i:21284664 original size:9 final size:9
Alignment explanation
Indices: 21284652--21284688 Score: 58
Period size: 9 Copynumber: 4.2 Consensus size: 9
21284642 GAACTTATCA
21284652 TTATTATTG
1 TTATTATTG
*
21284661 TTATTATTA
1 TTATTATTG
21284670 TTATTATTG
1 TTATTATTG
21284679 TTATT-TTG
1 TTATTATTG
21284687 TT
1 TT
21284689 TATTTTGAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
8 5 0.19
9 21 0.81
ACGTcount: A:0.22, C:0.00, G:0.08, T:0.70
Consensus pattern (9 bp):
TTATTATTG
Found at i:21292587 original size:212 final size:213
Alignment explanation
Indices: 21292044--21292668 Score: 835
Period size: 219 Copynumber: 2.9 Consensus size: 213
21292034 AACTATAATG
* *
21292044 TTATAATGTTTTATATCAAAGTCTGTATAAATAATAACTAATTATAAACAATATGTTATAAAAAC
1 TTATAATATTTTATATCAAAGTTTGTATAAATAATAACTAATTATAAACAATATGTTATAAAAAC
* *
21292109 TAAGATGATAATTAATAAAGTTATTAAGTGTAATTGTATAAATAAAGTTTATTATAAATTATAAT
66 TAAGATGATAACTAATAAAGTTATTAAGTGTAATTGTATAAATAAAGTTTATTATAAGTTATAAT
* *
21292174 AATACTTATGTATAAATTAAATATTTGTATATATATAATATTATTTTATTATATATATATAATTA
131 AATACTTATGTATAAATTAAATATATGTATATATATAATATTACTTTATTATATATATATAATTA
21292239 ATGACACAATTTATATGT
196 ATGACACAATTTATATGT
** * * * * * *
21292257 TATAGTGTTTTAGTTGTTATAACAAAATTTTTATAAAAAATAACTAATTCTAAATAATATGTTAT
1 T-TA---TAATA-TT-TTATATCAAAGTTTGTATAAATAATAACTAATTATAAACAATATGTTAT
* * *
21292322 AAAAACTAAGATGATGACTAATAAAGTTATTAAGTGTAATTGTATAGATAAAGTCTATTATAAGT
60 AAAAACTAAGATGATAACTAATAAAGTTATTAAGTGTAATTGTATAAATAAAGTTTATTATAAGT
* **
21292387 TATAGTAATGGTTATGTATAAATTAAATATATGTATATATATAATATTACTTTATTATATATATG
125 TATAATAATACTTATGTATAAATTAAATATATGTATATATATAATATTACTTTATTATATATAT-
*
21292452 A-AATTAATGATACAATTTATAT-T
189 ATAATTAATGACACAATTTATATGT
* *
21292475 TTATAATATTTTATATCACAGTTTGTATTAATAATAACTAATTATAAACAATATGTTATAAAAAC
1 TTATAATATTTTATATCAAAGTTTGTATAAATAATAACTAATTATAAACAATATGTTATAAAAAC
** *
21292540 TAATG-TGATAACTAATAAAGTTATTAAGTGTAATCATATAAATAAAGTTTAATATAAGTTATAA
66 TAA-GATGATAACTAATAAAGTTATTAAGTGTAATTGTATAAATAAAGTTTATTATAAGTTATAA
* * * * *
21292604 TAATACTTATGCAAAAATTAAATGTATGTATATA-ATATATTTATACAATTATATATATATATAT
130 TAATACTTATGTATAAATTAAATATATGTATATATATA-ATAT-TAC-TTTAT-TATATATATAT
21292668 A
191 A
21292669 TATATTTATA
Statistics
Matches: 354, Mismatches: 45, Indels: 24
0.84 0.11 0.06
Matches are distributed among these distances:
211 3 0.01
212 134 0.38
213 7 0.02
214 10 0.03
215 10 0.03
217 4 0.01
218 4 0.01
219 181 0.51
220 1 0.00
ACGTcount: A:0.46, C:0.04, G:0.08, T:0.42
Consensus pattern (213 bp):
TTATAATATTTTATATCAAAGTTTGTATAAATAATAACTAATTATAAACAATATGTTATAAAAAC
TAAGATGATAACTAATAAAGTTATTAAGTGTAATTGTATAAATAAAGTTTATTATAAGTTATAAT
AATACTTATGTATAAATTAAATATATGTATATATATAATATTACTTTATTATATATATATAATTA
ATGACACAATTTATATGT
Found at i:21295054 original size:26 final size:26
Alignment explanation
Indices: 21294994--21295055 Score: 97
Period size: 26 Copynumber: 2.4 Consensus size: 26
21294984 ACCATATACC
* * *
21294994 CATCATCAACTTGCACACCATTCCAT
1 CATCATCATCATGCACACCATCCCAT
21295020 CATCATCATCATGCACACCATCCCAT
1 CATCATCATCATGCACACCATCCCAT
21295046 CATCATCATC
1 CATCATCATC
21295056 TCATATGCAA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.31, C:0.40, G:0.03, T:0.26
Consensus pattern (26 bp):
CATCATCATCATGCACACCATCCCAT
Found at i:21295139 original size:42 final size:42
Alignment explanation
Indices: 21295075--21295216 Score: 239
Period size: 42 Copynumber: 3.4 Consensus size: 42
21295065 ACAGCTTATG
* *
21295075 CGCATATAGCCGGGTCAGCAACGGCTTATGTGCACTTCCACT
1 CGCACATAGCCGGGTCAGCAACGGCTTATGTGCACTCCCACT
21295117 CGCACATAGCCGGGTCAGCAACGGCTTATGTGCACTCCCACT
1 CGCACATAGCCGGGTCAGCAACGGCTTATGTGCACTCCCACT
**
21295159 CGCACATAATCGGGTCAGCAACGGCTTATGTGCACTCCCACT
1 CGCACATAGCCGGGTCAGCAACGGCTTATGTGCACTCCCACT
*
21295201 CACACATAGCCGGGTC
1 CGCACATAGCCGGGTC
21295217 CAAATCAACA
Statistics
Matches: 93, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 93 1.00
ACGTcount: A:0.23, C:0.34, G:0.23, T:0.20
Consensus pattern (42 bp):
CGCACATAGCCGGGTCAGCAACGGCTTATGTGCACTCCCACT
Found at i:21303405 original size:20 final size:20
Alignment explanation
Indices: 21303380--21303425 Score: 67
Period size: 20 Copynumber: 2.3 Consensus size: 20
21303370 TTTTGACCCC
21303380 ATTTGACTTATT-AGAGTATA
1 ATTTGACTTATTGA-AGTATA
*
21303400 ATTTGACTTATTGAAGTATG
1 ATTTGACTTATTGAAGTATA
21303420 ATTTGA
1 ATTTGA
21303426 GGTTTAGAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 23 0.96
21 1 0.04
ACGTcount: A:0.33, C:0.04, G:0.17, T:0.46
Consensus pattern (20 bp):
ATTTGACTTATTGAAGTATA
Found at i:21306889 original size:20 final size:20
Alignment explanation
Indices: 21306860--21306902 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
21306850 ATTAGGTTAC
21306860 TTTTAAGTTAGTT-ATTTTAA
1 TTTTAAGTTA-TTCATTTTAA
* *
21306880 TTTTATGTTATTCCTTTTAA
1 TTTTAAGTTATTCATTTTAA
21306900 TTT
1 TTT
21306903 GGTTATTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 2 0.10
20 18 0.90
ACGTcount: A:0.23, C:0.05, G:0.07, T:0.65
Consensus pattern (20 bp):
TTTTAAGTTATTCATTTTAA
Found at i:21316552 original size:32 final size:30
Alignment explanation
Indices: 21316511--21316569 Score: 75
Period size: 32 Copynumber: 1.9 Consensus size: 30
21316501 TTTTAAGTTA
*
21316511 TTTTATTTT-ATTTCATTTTTTTTACTTTAAT
1 TTTTATTTTAATCT-ATTTTTTTT-CTTTAAT
21316542 TTTTATTTTTAATCTATTTTTTTTCTTT
1 TTTTA-TTTTAATCTATTTTTTTTCTTT
21316570 TTGCAGGTCA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
31 9 0.36
32 13 0.52
33 3 0.12
ACGTcount: A:0.17, C:0.07, G:0.00, T:0.76
Consensus pattern (30 bp):
TTTTATTTTAATCTATTTTTTTTCTTTAAT
Found at i:21316752 original size:72 final size:72
Alignment explanation
Indices: 21316626--21316762 Score: 168
Period size: 72 Copynumber: 1.9 Consensus size: 72
21316616 CCTGAAAAGT
* * * ** *
21316626 GCTAAAATTTGGGCTGAAATAAAATGTTTCAGTGCCGCGGCCCTCAGAGGGAGTGTCGTGACACT
1 GCTAAAATCTGGGCTGAAACAAAATGTTACAACGCCGCGGCCCTCAGAGGGAGTGCCGTGACACT
21316691 GGACGAA
66 GGACGAA
* * * *
21316698 GCTAAAATCTGGGCTGAAACAGAATGTTACAACGTCGCGGCCCTC-GATGTGAGTGCCGTGGCAC
1 GCTAAAATCTGGGCTGAAACAAAATGTTACAACGCCGCGGCCCTCAGA-GGGAGTGCCGTGACAC
21316762 T
65 T
21316763 AAATAAAGCC
Statistics
Matches: 54, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
71 2 0.04
72 52 0.96
ACGTcount: A:0.26, C:0.22, G:0.30, T:0.22
Consensus pattern (72 bp):
GCTAAAATCTGGGCTGAAACAAAATGTTACAACGCCGCGGCCCTCAGAGGGAGTGCCGTGACACT
GGACGAA
Found at i:21317953 original size:30 final size:30
Alignment explanation
Indices: 21317917--21317976 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
21317907 CATGCTCCAC
21317917 AACAGATATTGGCGTCGATTTTCTAACCAA
1 AACAGATATTGGCGTCGATTTTCTAACCAA
21317947 AACAGATATTGGCGTCGATTTTCTAACCAA
1 AACAGATATTGGCGTCGATTTTCTAACCAA
21317977 CCTGAAGCTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.30
Consensus pattern (30 bp):
AACAGATATTGGCGTCGATTTTCTAACCAA
Found at i:21321225 original size:14 final size:14
Alignment explanation
Indices: 21321206--21321232 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
21321196 TTGGTTTTAA
21321206 TTTTAGTTAATTAG
1 TTTTAGTTAATTAG
21321220 TTTTAGTTAATTA
1 TTTTAGTTAATTA
21321233 ATAAATTTTG
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:0.30, C:0.00, G:0.11, T:0.59
Consensus pattern (14 bp):
TTTTAGTTAATTAG
Found at i:21322724 original size:43 final size:43
Alignment explanation
Indices: 21322660--21322783 Score: 160
Period size: 43 Copynumber: 2.9 Consensus size: 43
21322650 ACACTAAACT
* *
21322660 CATGTGCACTCCCTAC-TCGCACATAGCCGGGTCATCATCAGCC
1 CATGTGCACTCCC-ACACCGCACATAGCTGGGTCATCATCAGCC
*
21322703 CATGTGCACTCCCACACCGCACATAGCTGGGTCATCATCAGCT
1 CATGTGCACTCCCACACCGCACATAGCTGGGTCATCATCAGCC
** * * *
21322746 CATGTGCAAACTCACACCACATATAGCTGGGTCATCAT
1 CATGTGCACTCCCACACCGCACATAGCTGGGTCATCAT
21322784 TTTCACACAA
Statistics
Matches: 72, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
42 2 0.03
43 70 0.97
ACGTcount: A:0.25, C:0.35, G:0.18, T:0.22
Consensus pattern (43 bp):
CATGTGCACTCCCACACCGCACATAGCTGGGTCATCATCAGCC
Found at i:21328388 original size:17 final size:17
Alignment explanation
Indices: 21328368--21328400 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
21328358 TTTTCAGTCC
21328368 TCTTTTCCTTT-TTCTTT
1 TCTTTT-CTTTCTTCTTT
21328385 TCTTTTCTTTCTTCTT
1 TCTTTTCTTTCTTCTT
21328401 CATCTTACCA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (17 bp):
TCTTTTCTTTCTTCTTT
Found at i:21336245 original size:26 final size:26
Alignment explanation
Indices: 21336209--21336264 Score: 78
Period size: 26 Copynumber: 2.2 Consensus size: 26
21336199 AGCAAGTTGT
21336209 TGTTACATGCCA-AGTCAATAAAATGA
1 TGTTACATGCCATAGTCAA-AAAATGA
* *
21336235 TGTTACATGCCATGGTGAAAAAATGA
1 TGTTACATGCCATAGTCAAAAAATGA
21336261 TGTT
1 TGTT
21336265 GTTACATGTC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
26 23 0.85
27 4 0.15
ACGTcount: A:0.38, C:0.12, G:0.20, T:0.30
Consensus pattern (26 bp):
TGTTACATGCCATAGTCAAAAAATGA
Found at i:21367431 original size:63 final size:63
Alignment explanation
Indices: 21367279--21367431 Score: 234
Period size: 63 Copynumber: 2.4 Consensus size: 63
21367269 GATGTAACTG
** *
21367279 TGCATGTGCGGAGTGGGCAGTGCACACGCCAGTTGAATGACAATGTTGTGACAATTACAACCG
1 TGCATGTGCGGAGTGGGCAGTGCACATACCAGTTGAATGACAATGTTGTGACAATTACAACCA
* * * *
21367342 TGCATGTGCGAACTGGGCAGTGCACATACCGGTTGAATGACAATGTTGTGACAATTACAATCA
1 TGCATGTGCGGAGTGGGCAGTGCACATACCAGTTGAATGACAATGTTGTGACAATTACAACCA
*
21367405 TGCATGTGTGGAGTGGGCAGTGCACAT
1 TGCATGTGCGGAGTGGGCAGTGCACAT
21367432 GCCGACTATG
Statistics
Matches: 80, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
63 80 1.00
ACGTcount: A:0.27, C:0.19, G:0.30, T:0.24
Consensus pattern (63 bp):
TGCATGTGCGGAGTGGGCAGTGCACATACCAGTTGAATGACAATGTTGTGACAATTACAACCA
Found at i:21372124 original size:58 final size:57
Alignment explanation
Indices: 21372031--21372150 Score: 152
Period size: 58 Copynumber: 2.1 Consensus size: 57
21372021 AAGGTCTCAT
* * * * *
21372031 CTTTGCACGCATAGTATTTATTAAATCGTATAAAATAAATCTATCACAAGCACATTA
1 CTTTGCACGCATAGCATTTATTAAATCGGACAAAATAAATCTATCACAAGCAAACTA
* *
21372088 CTTTGCATTGCATAGCATTTATTAAA-CTGGACAAAATAAATCTATCACATGCAAACTA
1 CTTTGCA-CGCATAGCATTTATTAAATC-GGACAAAATAAATCTATCACAAGCAAACTA
21372146 CTTTG
1 CTTTG
21372151 GATGATTATG
Statistics
Matches: 54, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
57 8 0.15
58 46 0.85
ACGTcount: A:0.38, C:0.18, G:0.10, T:0.33
Consensus pattern (57 bp):
CTTTGCACGCATAGCATTTATTAAATCGGACAAAATAAATCTATCACAAGCAAACTA
Found at i:21374450 original size:2 final size:2
Alignment explanation
Indices: 21374438--21374470 Score: 57
Period size: 2 Copynumber: 16.0 Consensus size: 2
21374428 CGCAACAAGG
21374438 AT AT CAT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT
21374471 GTTAGAGCTA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 28 0.93
3 2 0.07
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.