Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr02 ID=Chr02-JGI_221_v2.0
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: 62769430
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1067035 characters in sequence are not A, C, G, or T
File 150 of 206
Found at i:45588371 original size:11 final size:11
Alignment explanation
Indices: 45588357--45588390 Score: 59
Period size: 11 Copynumber: 3.1 Consensus size: 11
45588347 AAATTTAAAT
45588357 ATTTTTCTATA
1 ATTTTTCTATA
*
45588368 ATTTTTTTATA
1 ATTTTTCTATA
45588379 ATTTTTCTATA
1 ATTTTTCTATA
45588390 A
1 A
45588391 CTTCTATTGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.29, C:0.06, G:0.00, T:0.65
Consensus pattern (11 bp):
ATTTTTCTATA
Found at i:45590760 original size:21 final size:21
Alignment explanation
Indices: 45590723--45590762 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
45590713 AAATAAATGT
*
45590723 AAAGAAAAGGAATGGAAAGAA
1 AAAGAAAAGGAAAGGAAAGAA
45590744 AAAGAAAA-GAAGAGGAAAG
1 AAAGAAAAGGAA-AGGAAAG
45590763 GAAATGAGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 3 0.18
21 14 0.82
ACGTcount: A:0.68, C:0.00, G:0.30, T:0.03
Consensus pattern (21 bp):
AAAGAAAAGGAAAGGAAAGAA
Found at i:45593421 original size:11 final size:11
Alignment explanation
Indices: 45593405--45593435 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
45593395 AGGCGGTTAT
45593405 TTTTATTTTCA
1 TTTTATTTTCA
*
45593416 TTTTATTTTCG
1 TTTTATTTTCA
45593427 TTTTATTTT
1 TTTTATTTT
45593436 TGCTTAATAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.13, C:0.06, G:0.03, T:0.77
Consensus pattern (11 bp):
TTTTATTTTCA
Found at i:45597782 original size:2 final size:2
Alignment explanation
Indices: 45597777--45597841 Score: 130
Period size: 2 Copynumber: 32.5 Consensus size: 2
45597767 TGTATTTACA
45597777 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
45597819 AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT A
45597842 CATACAAGCA
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 63 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:45598087 original size:16 final size:15
Alignment explanation
Indices: 45598061--45598092 Score: 55
Period size: 16 Copynumber: 2.1 Consensus size: 15
45598051 GTATAAGTAT
45598061 ATATAAATATATAAA
1 ATATAAATATATAAA
45598076 ATATAAAGTATATAAA
1 ATATAAA-TATATAAA
45598092 A
1 A
45598093 GTTTTAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (15 bp):
ATATAAATATATAAA
Found at i:45598307 original size:12 final size:12
Alignment explanation
Indices: 45598290--45598327 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
45598280 TATAGAAAAT
45598290 ATGATAATAATA
1 ATGATAATAATA
*
45598302 ATGATAGTAAATA
1 ATGATAAT-AATA
45598315 ATG-TAATAATA
1 ATGATAATAATA
45598326 AT
1 AT
45598328 AGTAATGGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
11 6 0.26
12 10 0.43
13 7 0.30
ACGTcount: A:0.55, C:0.00, G:0.11, T:0.34
Consensus pattern (12 bp):
ATGATAATAATA
Found at i:45598313 original size:24 final size:24
Alignment explanation
Indices: 45598281--45598327 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
45598271 ATGTATATGT
45598281 ATAGAAAAT-ATGATAATAATAATG
1 ATAGAAAATAATG-TAATAATAATG
*
45598305 ATAGTAAATAATGTAATAATAAT
1 ATAGAAAATAATGTAATAATAAT
45598328 AGTAATGGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 18 0.86
25 3 0.14
ACGTcount: A:0.57, C:0.00, G:0.11, T:0.32
Consensus pattern (24 bp):
ATAGAAAATAATGTAATAATAATG
Found at i:45599938 original size:44 final size:44
Alignment explanation
Indices: 45599810--45600299 Score: 630
Period size: 44 Copynumber: 11.1 Consensus size: 44
45599800 AAGACTTGTA
* * * *
45599810 TCTTCGATCTA-TT-TCGCCAATATATGGGAAGACTAGATCTACTT
1 TCTTCGATCTACTTCACGCCAATACAT--GAAGACAAGATCTGCTT
* *
45599854 TCTTCGATCTACTTTGC-CCCCAATACAT-AGAGACAGGATCTGCTT
1 TCTTCGATCTAC-TT-CACGCCAATACATGA-AGACAAGATCTGCTT
*
45599899 TCTTCGATCTACTTCACGCTAATACATGAAGACAAGATCTGCTT
1 TCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTT
* *
45599943 TCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCCGTTT
1 TCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTT
* *
45599987 TCTTTGATCTACTTCACGCCAATACATGAAGATAAGATCTG-TT
1 TCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTT
* * *** * *
45600030 ATCTTCGATCTACTTCACCACCAGTATGGGAAGATAAGATCTGCTA
1 -TCTTCGATCTACTTCA-CGCCAATACATGAAGACAAGATCTGCTT
* *
45600076 TCTTTGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTA
1 TCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTT
*
45600120 TCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGTTT
1 TCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTT
**
45600164 TCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTTTTT
1 TCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTT
* *
45600208 TCTTCGATCTACTTCACGCCAATACATGAAGACAGGATCTGTTT
1 TCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTT
** *
45600252 TCTTCGATCTACTTCACGCTGATACATAAAGACAAGATCTGCTT
1 TCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTT
45600296 TCTT
1 TCTT
45600300 TCAACCTGCC
Statistics
Matches: 397, Mismatches: 39, Indels: 20
0.87 0.09 0.04
Matches are distributed among these distances:
43 3 0.01
44 322 0.81
45 60 0.15
46 3 0.01
47 9 0.02
ACGTcount: A:0.29, C:0.25, G:0.14, T:0.32
Consensus pattern (44 bp):
TCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTT
Found at i:45601596 original size:13 final size:14
Alignment explanation
Indices: 45601578--45601626 Score: 57
Period size: 13 Copynumber: 3.6 Consensus size: 14
45601568 CCTTAGCCTC
45601578 TCCATTTT-ACTTT
1 TCCATTTTCACTTT
*
45601591 TCCATTTTTCAGTTT
1 TCCA-TTTTCACTTT
45601606 T-CATTTTCACTTT
1 TCCATTTTCACTTT
*
45601619 TTCATTTT
1 TCCATTTT
45601627 TCATGTCGTC
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
13 14 0.45
14 12 0.39
15 5 0.16
ACGTcount: A:0.14, C:0.20, G:0.02, T:0.63
Consensus pattern (14 bp):
TCCATTTTCACTTT
Found at i:45601606 original size:7 final size:7
Alignment explanation
Indices: 45601588--45601630 Score: 52
Period size: 7 Copynumber: 6.1 Consensus size: 7
45601578 TCCATTTTAC
*
45601588 TTTTCCA
1 TTTTTCA
45601595 TTTTTCA
1 TTTTTCA
*
45601602 GTTTTCA
1 TTTTTCA
45601609 -TTTTCA
1 TTTTTCA
45601615 CTTTTTCA
1 -TTTTTCA
45601623 TTTTTCA
1 TTTTTCA
45601630 T
1 T
45601631 GTCGTCATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
6 6 0.19
7 20 0.62
8 6 0.19
ACGTcount: A:0.14, C:0.19, G:0.02, T:0.65
Consensus pattern (7 bp):
TTTTTCA
Found at i:45601610 original size:14 final size:15
Alignment explanation
Indices: 45601588--45601629 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
45601578 TCCATTTTAC
45601588 TTTTCCATTTTTCA-G
1 TTTT-CATTTTTCACG
*
45601603 TTTTCA-TTTTCACT
1 TTTTCATTTTTCACG
45601617 TTTTCATTTTTCA
1 TTTTCATTTTTCA
45601630 TGTCGTCATT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
13 6 0.25
14 8 0.33
15 10 0.42
ACGTcount: A:0.14, C:0.19, G:0.02, T:0.64
Consensus pattern (15 bp):
TTTTCATTTTTCACG
Found at i:45606502 original size:16 final size:15
Alignment explanation
Indices: 45606476--45606507 Score: 55
Period size: 16 Copynumber: 2.1 Consensus size: 15
45606466 GTATAAGTAT
45606476 ATATAAATATATAAA
1 ATATAAATATATAAA
45606491 ATATAAAGTATATAAA
1 ATATAAA-TATATAAA
45606507 A
1 A
45606508 GTTTTAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (15 bp):
ATATAAATATATAAA
Found at i:45606739 original size:27 final size:28
Alignment explanation
Indices: 45606696--45606760 Score: 82
Period size: 27 Copynumber: 2.4 Consensus size: 28
45606686 ATGTATATGT
45606696 ATAGAAAAT-ATGATAATAATAATAATA
1 ATAGAAAATAATGATAATAATAATAATA
* *
45606723 ATAGTAAATAATG-TAATAATAATAGTA
1 ATAGAAAATAATGATAATAATAATAATA
*
45606750 AT-GGAAATAAT
1 ATAGAAAATAAT
45606761 AAATAAAAAC
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
26 8 0.24
27 23 0.68
28 3 0.09
ACGTcount: A:0.58, C:0.00, G:0.11, T:0.31
Consensus pattern (28 bp):
ATAGAAAATAATGATAATAATAATAATA
Found at i:45608606 original size:11 final size:11
Alignment explanation
Indices: 45608587--45608630 Score: 56
Period size: 11 Copynumber: 4.2 Consensus size: 11
45608577 AACACCGAAC
*
45608587 TTTTTGGGTAA
1 TTTTCGGGTAA
45608598 TTTTCGGGTAA
1 TTTTCGGGTAA
45608609 --TTCGGGTAA
1 TTTTCGGGTAA
*
45608618 TTTTCAGGTAA
1 TTTTCGGGTAA
45608629 TT
1 TT
45608631 CGGTTAATTC
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
9 9 0.31
11 20 0.69
ACGTcount: A:0.20, C:0.07, G:0.25, T:0.48
Consensus pattern (11 bp):
TTTTCGGGTAA
Found at i:45608614 original size:9 final size:9
Alignment explanation
Indices: 45608600--45608683 Score: 89
Period size: 9 Copynumber: 9.2 Consensus size: 9
45608590 TTGGGTAATT
45608600 TTCGGGTAA
1 TTCGGGTAA
45608609 TTCGGGTAA
1 TTCGGGTAA
*
45608618 TTTTCAGGTAA
1 --TTCGGGTAA
*
45608629 TTCGGTTAA
1 TTCGGGTAA
*
45608638 TTCGGTTAA
1 TTCGGGTAA
* *
45608647 TTCAGTTAA
1 TTCGGGTAA
*
45608656 TTCGGTTAA
1 TTCGGGTAA
45608665 -TCGGGTAA
1 TTCGGGTAA
45608673 TTCGGGTAA
1 TTCGGGTAA
45608682 TT
1 TT
45608684 TTTAACCCAA
Statistics
Matches: 66, Mismatches: 6, Indels: 6
0.85 0.08 0.08
Matches are distributed among these distances:
8 7 0.11
9 51 0.77
11 8 0.12
ACGTcount: A:0.24, C:0.11, G:0.25, T:0.40
Consensus pattern (9 bp):
TTCGGGTAA
Found at i:45608658 original size:27 final size:27
Alignment explanation
Indices: 45608600--45608683 Score: 107
Period size: 27 Copynumber: 3.1 Consensus size: 27
45608590 TTGGGTAATT
*
45608600 TTCGGGTAATTCGGGTAATTTTCAGGTAA
1 TTCGGTTAATTCGGGTAA--TTCAGGTAA
* *
45608629 TTCGGTTAATTCGGTTAATTCAGTTAA
1 TTCGGTTAATTCGGGTAATTCAGGTAA
*
45608656 TTCGGTTAA-TCGGGTAATTCGGGTAA
1 TTCGGTTAATTCGGGTAATTCAGGTAA
45608682 TT
1 TT
45608684 TTTAACCCAA
Statistics
Matches: 49, Mismatches: 6, Indels: 3
0.84 0.10 0.05
Matches are distributed among these distances:
26 16 0.33
27 17 0.35
29 16 0.33
ACGTcount: A:0.24, C:0.11, G:0.25, T:0.40
Consensus pattern (27 bp):
TTCGGTTAATTCGGGTAATTCAGGTAA
Found at i:45608856 original size:12 final size:12
Alignment explanation
Indices: 45608839--45608863 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
45608829 AGTAATTTCG
45608839 GGTCGGTTAACC
1 GGTCGGTTAACC
45608851 GGTCGGTTAACC
1 GGTCGGTTAACC
45608863 G
1 G
45608864 AATGAACACC
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:0.16, C:0.24, G:0.36, T:0.24
Consensus pattern (12 bp):
GGTCGGTTAACC
Found at i:45612557 original size:14 final size:16
Alignment explanation
Indices: 45612528--45612560 Score: 52
Period size: 14 Copynumber: 2.2 Consensus size: 16
45612518 AATTAAACCG
45612528 AATTCAAAATTAAATA
1 AATTCAAAATTAAATA
45612544 AATT-AAAA-TAAATA
1 AATTCAAAATTAAATA
45612558 AAT
1 AAT
45612561 ATGGGTTGCC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 9 0.53
15 4 0.24
16 4 0.24
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (16 bp):
AATTCAAAATTAAATA
Found at i:45619436 original size:27 final size:28
Alignment explanation
Indices: 45619406--45619458 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
45619396 TGAAATTCTT
*
45619406 ACTTTAATTA-TAAAATAATTAATTTAC
1 ACTTAAATTATTAAAATAATTAATTTAC
* *
45619433 ACTTAAATTATTAACATATTTAATTT
1 ACTTAAATTATTAAAATAATTAATTT
45619459 TAATTATTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 9 0.41
28 13 0.59
ACGTcount: A:0.45, C:0.08, G:0.00, T:0.47
Consensus pattern (28 bp):
ACTTAAATTATTAAAATAATTAATTTAC
Found at i:45621552 original size:17 final size:18
Alignment explanation
Indices: 45621515--45621554 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
45621505 TTGTTTTTTC
45621515 TTTTCTTCCTTCATTCGT
1 TTTTCTTCCTTCATTCGT
* *
45621533 TTTTCTTCTTTC-TTCTT
1 TTTTCTTCCTTCATTCGT
45621550 TTTTC
1 TTTTC
45621555 CACAACCCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 9 0.45
18 11 0.55
ACGTcount: A:0.03, C:0.25, G:0.03, T:0.70
Consensus pattern (18 bp):
TTTTCTTCCTTCATTCGT
Found at i:45623388 original size:22 final size:22
Alignment explanation
Indices: 45623363--45623454 Score: 103
Period size: 22 Copynumber: 4.2 Consensus size: 22
45623353 AAATTCAATA
* *
45623363 TCAATTTCTTTCAAAAATTCTC
1 TCAATTCCCTTCAAAAATTCTC
* *
45623385 TCAATTCCTTTCAAAATTTCTC
1 TCAATTCCCTTCAAAAATTCTC
* * *
45623407 TCAATTCCCTTCAATATTTCTA
1 TCAATTCCCTTCAAAAATTCTC
* *
45623429 TCAATTTCCTTCCAAAATTCTC
1 TCAATTCCCTTCAAAAATTCTC
45623451 TCAA
1 TCAA
45623455 ACTCTCAAAT
Statistics
Matches: 60, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 60 1.00
ACGTcount: A:0.29, C:0.27, G:0.00, T:0.43
Consensus pattern (22 bp):
TCAATTCCCTTCAAAAATTCTC
Found at i:45623420 original size:44 final size:44
Alignment explanation
Indices: 45623363--45623454 Score: 114
Period size: 44 Copynumber: 2.1 Consensus size: 44
45623353 AAATTCAATA
* * * *
45623363 TCAATTTCTTTCAAAAATTCTCTCAA-TTCCTTTCAAAATTTCTC
1 TCAATTCCCTTCAAAAATTCTATCAATTTCCTTCCAAAA-TTCTC
* *
45623407 TCAATTCCCTTCAATATTTCTATCAATTTCCTTCCAAAATTCTC
1 TCAATTCCCTTCAAAAATTCTATCAATTTCCTTCCAAAATTCTC
45623451 TCAA
1 TCAA
45623455 ACTCTCAAAT
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
44 30 0.73
45 11 0.27
ACGTcount: A:0.29, C:0.27, G:0.00, T:0.43
Consensus pattern (44 bp):
TCAATTCCCTTCAAAAATTCTATCAATTTCCTTCCAAAATTCTC
Found at i:45623470 original size:52 final size:51
Alignment explanation
Indices: 45623404--45623506 Score: 120
Period size: 52 Copynumber: 2.0 Consensus size: 51
45623394 TTCAAAATTT
* * * *
45623404 CTCTCAATTCCCTT-CAATATTTCTATCAATTTCCTTCCAAAATTCTCTCAAA
1 CTCTCAATTCCCTTCCAA-AATCCTATCAATTTCCTTCAAAAAATCTC-CAAA
*
45623456 CTCTCAAATT-CCTTCCAAAATCCTCTCAATTTCCTTCAAAAAATCTCCAAA
1 CTCTC-AATTCCCTTCCAAAATCCTATCAATTTCCTTCAAAAAATCTCCAAA
45623507 TCCATATTAA
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
51 4 0.09
52 33 0.75
53 7 0.16
ACGTcount: A:0.32, C:0.32, G:0.00, T:0.36
Consensus pattern (51 bp):
CTCTCAATTCCCTTCCAAAATCCTATCAATTTCCTTCAAAAAATCTCCAAA
Found at i:45623495 original size:21 final size:22
Alignment explanation
Indices: 45623456--45623497 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
45623446 TTCTCTCAAA
45623456 CTCTCAAATTCCTTCCAAAATC
1 CTCTCAAATTCCTTCCAAAATC
* *
45623478 CTCTCAATTTCCTTCAAAAA
1 CTCTCAAATTCCTTCCAAAA
45623498 ATCTCCAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (22 bp):
CTCTCAAATTCCTTCCAAAATC
Found at i:45623594 original size:29 final size:29
Alignment explanation
Indices: 45623539--45623594 Score: 96
Period size: 28 Copynumber: 2.0 Consensus size: 29
45623529 ATTAAATTTC
45623539 ATTTTTTTAAGAAAATTTTAAAATTTTTT
1 ATTTTTTTAAGAAAATTTTAAAATTTTTT
*
45623568 ATTTTTTTAA-ATAATTTTAAAATTTTT
1 ATTTTTTTAAGAAAATTTTAAAATTTTT
45623595 AATATTTTCA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
28 16 0.62
29 10 0.38
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.61
Consensus pattern (29 bp):
ATTTTTTTAAGAAAATTTTAAAATTTTTT
Found at i:45623602 original size:29 final size:29
Alignment explanation
Indices: 45623539--45623602 Score: 94
Period size: 28 Copynumber: 2.2 Consensus size: 29
45623529 ATTAAATTTC
*
45623539 ATTTTTTTAAGAAAATTTTAAAATTTTTT
1 ATTTTTTTAAGAAAATTTTAAAATTTTTA
*
45623568 ATTTTTTTAA-ATAATTTTAAAATTTTTA
1 ATTTTTTTAAGAAAATTTTAAAATTTTTA
*
45623596 ATATTTT
1 ATTTTTT
45623603 CAACAATGGC
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
28 22 0.69
29 10 0.31
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.61
Consensus pattern (29 bp):
ATTTTTTTAAGAAAATTTTAAAATTTTTA
Found at i:45668958 original size:17 final size:17
Alignment explanation
Indices: 45668919--45668959 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
45668909 CTTGTTTTAG
* *
45668919 AAGGGGGTTTGTATGCA
1 AAGGGGGTTTGCATACA
45668936 AAGGGGGTTTGCATACA
1 AAGGGGGTTTGCATACA
*
45668953 ATGGGGG
1 AAGGGGG
45668960 GTTCGCGTAC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.24, C:0.07, G:0.44, T:0.24
Consensus pattern (17 bp):
AAGGGGGTTTGCATACA
Found at i:45676478 original size:15 final size:16
Alignment explanation
Indices: 45676458--45676487 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
45676448 AGCATATAAA
45676458 AAGAGAC-TGTCTAAG
1 AAGAGACATGTCTAAG
45676473 AAGAGACATGTCTAA
1 AAGAGACATGTCTAA
45676488 ACATAATCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.43, C:0.13, G:0.23, T:0.20
Consensus pattern (16 bp):
AAGAGACATGTCTAAG
Found at i:45677002 original size:16 final size:16
Alignment explanation
Indices: 45676969--45677002 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
45676959 AATTCACAAT
*
45676969 TTGGTGAACTTTAAGG
1 TTGGTGAACTCTAAGG
*
45676985 TTGGTGAACTCTAGGG
1 TTGGTGAACTCTAAGG
45677001 TT
1 TT
45677003 TGTTGGACTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.21, C:0.09, G:0.32, T:0.38
Consensus pattern (16 bp):
TTGGTGAACTCTAAGG
Found at i:45680319 original size:50 final size:50
Alignment explanation
Indices: 45680209--45680332 Score: 142
Period size: 50 Copynumber: 2.5 Consensus size: 50
45680199 GGTAAAGAGA
* * * ***
45680209 TCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATAAGGGG
1 TCCCATGTAAGACCATGTCTGGGACATAGCATGGGCACCGAGATAAGAAC
** *
45680259 TCCC-TCGTAAGACCATGTCTGGGACATAGCATGGGCACCGTTATGAGAAC
1 TCCCAT-GTAAGACCATGTCTGGGACATAGCATGGGCACCGAGATAAGAAC
*
45680309 TCCCATGTAAGACCATATCTGGGA
1 TCCCATGTAAGACCATGTCTGGGA
45680333 TAAGGAATTG
Statistics
Matches: 62, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
49 1 0.02
50 60 0.97
51 1 0.02
ACGTcount: A:0.26, C:0.24, G:0.28, T:0.22
Consensus pattern (50 bp):
TCCCATGTAAGACCATGTCTGGGACATAGCATGGGCACCGAGATAAGAAC
Found at i:45685536 original size:15 final size:16
Alignment explanation
Indices: 45685506--45685537 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
45685496 ACTTTAGGGG
45685506 CAAAAATGTAATTTTT
1 CAAAAATGTAATTTTT
*
45685522 CAAAAATGTGATTTTT
1 CAAAAATGTAATTTTT
45685538 GGATTGGATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.41, C:0.06, G:0.09, T:0.44
Consensus pattern (16 bp):
CAAAAATGTAATTTTT
Found at i:45685878 original size:101 final size:102
Alignment explanation
Indices: 45685767--45685949 Score: 289
Period size: 102 Copynumber: 1.8 Consensus size: 102
45685757 TGATTGTCAC
* *
45685767 GTGTGTAGTACTATGTGCTGGCTACTACGTGTACCAGA-A-TGATAGGTCGCATGTGTAGTACTA
1 GTGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGATAGTGA-AGGTCACATGTGTAGTACTA
45685830 TCTGCAGGCTACTATGTGTACCGGATAGCTTCGATCAT
65 TCTGCAGGCTACTATGTGTACCGGATAGCTTCGATCAT
* * *
45685868 GTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGATAGTGACGGTCACATGTGTAGTACTAT
1 GTGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGATAGTGAAGGTCACATGTGTAGTACTAT
*
45685933 GTGCAGGCTACTATGTG
66 CTGCAGGCTACTATGTG
45685950 AACCAGTATC
Statistics
Matches: 74, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
101 35 0.47
102 36 0.49
103 3 0.04
ACGTcount: A:0.22, C:0.17, G:0.28, T:0.32
Consensus pattern (102 bp):
GTGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGATAGTGAAGGTCACATGTGTAGTACTAT
CTGCAGGCTACTATGTGTACCGGATAGCTTCGATCAT
Found at i:45685887 original size:51 final size:48
Alignment explanation
Indices: 45685762--45685945 Score: 192
Period size: 51 Copynumber: 3.6 Consensus size: 48
45685752 GAAAGTGATT
* *
45685762 GTCACGTGTGTAGTACTATGTGCTGGCTACTACGTGTACCAGAATGATAGGTC
1 GTCA-GTGTGTAGTACTATGTGCAGGCTACTACGTGTACC-G---GATAGTTC
* *
45685815 G-CA-TGTGTAGTACTATCTGCAGGCTACTATGTGTACCGGATAGCTTC
1 GTCAGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATAG-TTC
* *
45685862 GATCATGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGATAGTGAC
1 G-TCA-GTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATAGT-TC
*
45685913 GGTCACATGTGTAGTACTATGTGCAGGCTACTA
1 -GTCA-GTGTGTAGTACTATGTGCAGGCTACTA
45685946 TGTGAACCAG
Statistics
Matches: 114, Mismatches: 10, Indels: 16
0.81 0.07 0.11
Matches are distributed among these distances:
46 5 0.04
47 3 0.03
49 3 0.03
50 32 0.28
51 67 0.59
52 3 0.03
53 1 0.01
ACGTcount: A:0.23, C:0.18, G:0.28, T:0.31
Consensus pattern (48 bp):
GTCAGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATAGTTC
Found at i:45685949 original size:26 final size:26
Alignment explanation
Indices: 45685869--45685949 Score: 73
Period size: 26 Copynumber: 3.2 Consensus size: 26
45685859 TTCGATCATG
45685869 TGTGTAGTACTATGTGCAGGCTACTA
1 TGTGTAGTACTATGTGCAGGCTACTA
* *
45685895 CGTGTA-T-CGGATAGTG-ACGG-TCAC-A
1 TGTGTAGTAC-TAT-GTGCA-GGCT-ACTA
45685920 TGTGTAGTACTATGTGCAGGCTACTA
1 TGTGTAGTACTATGTGCAGGCTACTA
45685946 TGTG
1 TGTG
45685950 AACCAGTATC
Statistics
Matches: 42, Mismatches: 4, Indels: 18
0.66 0.06 0.28
Matches are distributed among these distances:
24 1 0.02
25 18 0.43
26 22 0.52
27 1 0.02
ACGTcount: A:0.22, C:0.16, G:0.30, T:0.32
Consensus pattern (26 bp):
TGTGTAGTACTATGTGCAGGCTACTA
Found at i:45691116 original size:49 final size:50
Alignment explanation
Indices: 45690988--45691184 Score: 200
Period size: 49 Copynumber: 3.8 Consensus size: 50
45690978 ATTTGGGTAA
* *
45690988 AGAGATCCCATCTAAGACCATGTCTGGGACATGACATTGGCATCATTGAGGTTATG
1 AGAGGTCCCATCTAAGACCATGTCTGGGACATGACATTGGCA-C--CGA-G--ATG
* * *
45691044 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATCTAAGACCATGTCTGGGACATGACATTGGCACCGAGATG
* *
45691094 AGAGGTCCC-TCTAAGACCATGTCTGGGACATGACATGGGCACCGATATG
1 AGAGGTCCCATCTAAGACCATGTCTGGGACATGACATTGGCACCGAGATG
** * * * *
45691143 AGAACTCCCATGTAAAACCATATCTAGGG-TATGACATTGGCA
1 AGAGGTCCCATCTAAGACCATGTCT-GGGACATGACATTGGCA
45691185 GTACAAGAAA
Statistics
Matches: 122, Mismatches: 17, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
49 42 0.34
50 35 0.29
51 3 0.02
52 1 0.01
53 2 0.02
55 1 0.01
56 38 0.31
ACGTcount: A:0.28, C:0.22, G:0.27, T:0.23
Consensus pattern (50 bp):
AGAGGTCCCATCTAAGACCATGTCTGGGACATGACATTGGCACCGAGATG
Found at i:45691183 original size:99 final size:103
Alignment explanation
Indices: 45690988--45691184 Score: 233
Period size: 99 Copynumber: 1.9 Consensus size: 103
45690978 ATTTGGGTAA
* * **
45690988 AGAGATCCCATCTAAGACCATGTCTGGGACATGACATTGGCATCATTGAGGTTATGAGAGGTCCC
1 AGAGATCCCATCTAAGACCATGTCTGGGACATGACATGGGCATCA-CGA-G-TATGAGAACTCCC
* * * *
45691053 ATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
63 ATGTAAAACCATATCTGGGACATGACATTGGCACCGAGATG
*
45691094 AGAGGTCCC-TCTAAGACCATGTCTGGGACATGACATGGGCA-C-CGA-TATGAGAACTCCCATG
1 AGAGATCCCATCTAAGACCATGTCTGGGACATGACATGGGCATCACGAGTATGAGAACTCCCATG
*
45691155 TAAAACCATATCTAGGG-TATGACATTGGCA
66 TAAAACCATATCT-GGGACATGACATTGGCA
45691185 GTACAAGAAA
Statistics
Matches: 80, Mismatches: 10, Indels: 9
0.81 0.10 0.09
Matches are distributed among these distances:
99 35 0.44
100 3 0.04
102 2 0.03
104 1 0.01
105 31 0.39
106 8 0.10
ACGTcount: A:0.28, C:0.22, G:0.27, T:0.23
Consensus pattern (103 bp):
AGAGATCCCATCTAAGACCATGTCTGGGACATGACATGGGCATCACGAGTATGAGAACTCCCATG
TAAAACCATATCTGGGACATGACATTGGCACCGAGATG
Found at i:45697446 original size:45 final size:45
Alignment explanation
Indices: 45697395--45697489 Score: 190
Period size: 45 Copynumber: 2.1 Consensus size: 45
45697385 TTACTAGTTG
45697395 ATCATGATCACCCCATGGTGGCTTGATTCAATAGGTGAGGGAATT
1 ATCATGATCACCCCATGGTGGCTTGATTCAATAGGTGAGGGAATT
45697440 ATCATGATCACCCCATGGTGGCTTGATTCAATAGGTGAGGGAATT
1 ATCATGATCACCCCATGGTGGCTTGATTCAATAGGTGAGGGAATT
45697485 ATCAT
1 ATCAT
45697490 TATAATGGCT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 50 1.00
ACGTcount: A:0.27, C:0.18, G:0.25, T:0.29
Consensus pattern (45 bp):
ATCATGATCACCCCATGGTGGCTTGATTCAATAGGTGAGGGAATT
Found at i:45700241 original size:20 final size:22
Alignment explanation
Indices: 45700206--45700250 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
45700196 GGATTTGAGG
*
45700206 TTTTATATATATTTAAAA-CTC
1 TTTTAAATATATTTAAAATCTC
45700227 TTTTAAATA-ATTTAAAATCTC
1 TTTTAAATATATTTAAAATCTC
45700248 TTT
1 TTT
45700251 CCTCATCTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 8 0.36
21 14 0.64
ACGTcount: A:0.38, C:0.09, G:0.00, T:0.53
Consensus pattern (22 bp):
TTTTAAATATATTTAAAATCTC
Found at i:45700352 original size:26 final size:25
Alignment explanation
Indices: 45700323--45700405 Score: 69
Period size: 26 Copynumber: 3.2 Consensus size: 25
45700313 TTAAATTCTA
45700323 TTTAATTATCTTTTATTTAAAACTCT
1 TTTAATTAT-TTTTATTTAAAACTCT
* ** * *
45700349 TTTACA-TAATAATAATTAAATTCTCT
1 TTTA-ATTATTTTTATTTAAA-ACTCT
*
45700375 TTTAATTATTATTTATCTAAAACTCT
1 TTTAATTATT-TTTATTTAAAACTCT
45700401 TTTAA
1 TTTAA
45700406 ATAATAATTA
Statistics
Matches: 42, Mismatches: 11, Indels: 8
0.69 0.18 0.13
Matches are distributed among these distances:
25 9 0.21
26 26 0.62
27 7 0.17
ACGTcount: A:0.36, C:0.11, G:0.00, T:0.53
Consensus pattern (25 bp):
TTTAATTATTTTTATTTAAAACTCT
Found at i:45700382 original size:52 final size:48
Alignment explanation
Indices: 45700292--45700425 Score: 189
Period size: 52 Copynumber: 2.7 Consensus size: 48
45700282 TTGAATTTTA
*
45700292 AAAACTCTTTTAAATAATAAGTTAAATTCTATTTAATTATCT-TTTATTT
1 AAAACTCTTTTAAATAATAA-TTAAATTCTATTTAATTAT-TATTTATCT
*
45700341 AAAACTCTTTTACATAATAATAATTAAATTCTCTTTTAATTATTATTTATCT
1 AAAACTCTTTT--A-AATAATAATTAAATTCT-ATTTAATTATTATTTATCT
45700393 AAAACTCTTTTAAATAATAATTAAATTCTATTT
1 AAAACTCTTTTAAATAATAATTAAATTCTATTT
45700426 CCTTTTCTAA
Statistics
Matches: 77, Mismatches: 3, Indels: 11
0.85 0.03 0.12
Matches are distributed among these distances:
48 3 0.04
49 28 0.36
50 1 0.01
51 11 0.14
52 34 0.44
ACGTcount: A:0.40, C:0.10, G:0.01, T:0.49
Consensus pattern (48 bp):
AAAACTCTTTTAAATAATAATTAAATTCTATTTAATTATTATTTATCT
Found at i:45700545 original size:94 final size:94
Alignment explanation
Indices: 45700374--45700547 Score: 253
Period size: 94 Copynumber: 1.9 Consensus size: 94
45700364 TTAAATTCTC
*
45700374 TTTTAATTATTATTTATCTAAAACTCTTTTAAATAATAATTAAATTCTATTTCCTTTTCTAATAA
1 TTTTAATTATTATTTATCTAAAACTCTTTTAAATAATAATAAAATTCTATTTCCTTTTCTAATAA
* * *
45700439 GGAGTATGTCAAATCCTTTTGATTTTGAA
66 AGAATATATCAAATCCTTTTGATTTTGAA
* * *
45700468 TTTTAATTATTATTTATCTAAAACT-TTGTTAAGTAATTATAAAATTCTATTTCCTTATT-TGAT
1 TTTTAATTATTATTTATCTAAAACTCTT-TTAAATAATAATAAAATTCTATTTCCTT-TTCTAAT
45700531 AAAGAATATATCAAATC
64 AAAGAATATATCAAATC
45700548 ACCTTTTTAT
Statistics
Matches: 71, Mismatches: 7, Indels: 4
0.87 0.09 0.05
Matches are distributed among these distances:
93 2 0.03
94 67 0.94
95 2 0.03
ACGTcount: A:0.36, C:0.10, G:0.06, T:0.48
Consensus pattern (94 bp):
TTTTAATTATTATTTATCTAAAACTCTTTTAAATAATAATAAAATTCTATTTCCTTTTCTAATAA
AGAATATATCAAATCCTTTTGATTTTGAA
Found at i:45708400 original size:43 final size:43
Alignment explanation
Indices: 45708353--45708437 Score: 107
Period size: 43 Copynumber: 2.0 Consensus size: 43
45708343 CAGGTTATCA
* * * * *
45708353 CATATTGATGCCACTGTCTCGGACAGGGTCTTAAACGTAATCT
1 CATATCGATGCCAATGTCCCAGACAGGGTCTTAAACGAAATCT
* *
45708396 CATATCGATGCCAATGTCCCAGACATGGTCTTACACGAAATC
1 CATATCGATGCCAATGTCCCAGACAGGGTCTTAAACGAAATC
45708438 ACACATCGGG
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
43 35 1.00
ACGTcount: A:0.28, C:0.26, G:0.19, T:0.27
Consensus pattern (43 bp):
CATATCGATGCCAATGTCCCAGACAGGGTCTTAAACGAAATCT
Found at i:45712228 original size:49 final size:49
Alignment explanation
Indices: 45712171--45712300 Score: 167
Period size: 49 Copynumber: 2.7 Consensus size: 49
45712161 GTTGCATATA
*
45712171 TATTTAAAACTCGTTTAAATAATAATTTAAATT-T-TATTTAATTA-TATTT
1 TATTTAAAACTCATTTAAATAATAA-TTAAATTATGT-TTTAATTATTA-TT
*
45712220 TATTTAAAACTCATTTAAATAATAAATAAATTATGTTTTAATTATTATT
1 TATTTAAAACTCATTTAAATAATAATTAAATTATGTTTTAATTATTATT
* * *
45712269 TATCTAAAACTCTTTTGAATAATAATTAAATT
1 TATTTAAAACTCATTTAAATAATAATTAAATT
45712301 CTTTTTCCTT
Statistics
Matches: 72, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
48 6 0.08
49 63 0.88
50 3 0.04
ACGTcount: A:0.43, C:0.05, G:0.02, T:0.49
Consensus pattern (49 bp):
TATTTAAAACTCATTTAAATAATAATTAAATTATGTTTTAATTATTATT
Found at i:45712360 original size:94 final size:94
Alignment explanation
Indices: 45712255--45712429 Score: 289
Period size: 94 Copynumber: 1.9 Consensus size: 94
45712245 ATAAATTATG
* *
45712255 TTTTAATTATTATTTATCTAAAACTCTTTTGAATAATAATTAAATTCTTTTTCCTTATCT-GATA
1 TTTTAATTATTATTTATCTAAAACTCTTTTAAATAATAATTAAATTCTATTTCCTTATCTAG-TA
*
45712319 AGGAATATATCTAATCCTTTTGATTTTGAA
65 AGGAATATATCAAATCCTTTTGATTTTGAA
* *
45712349 TTTTAATTATTATTTATCTAAAACTCTTTTAAATAATTATTAAATTCTATTTGCTTATCTAGTAA
1 TTTTAATTATTATTTATCTAAAACTCTTTTAAATAATAATTAAATTCTATTTCCTTATCTAGTAA
45712414 GGAATATATCAAATCC
66 GGAATATATCAAATCC
45712430 CCTTTTTATC
Statistics
Matches: 75, Mismatches: 5, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
94 74 0.99
95 1 0.01
ACGTcount: A:0.35, C:0.11, G:0.06, T:0.49
Consensus pattern (94 bp):
TTTTAATTATTATTTATCTAAAACTCTTTTAAATAATAATTAAATTCTATTTCCTTATCTAGTAA
GGAATATATCAAATCCTTTTGATTTTGAA
Found at i:45730179 original size:22 final size:23
Alignment explanation
Indices: 45730146--45730189 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
45730136 TCTATCGAAA
45730146 ATTATCAAAATTAATCAAAATTT
1 ATTATCAAAATTAATCAAAATTT
*
45730169 ATTAT-AAAATTAATTAAAATT
1 ATTATCAAAATTAATCAAAATT
45730190 AAACATGTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.41
Consensus pattern (23 bp):
ATTATCAAAATTAATCAAAATTT
Found at i:45734350 original size:11 final size:12
Alignment explanation
Indices: 45734333--45734361 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
45734323 TAGGTAAGGT
45734333 TTGATTTTGAGC
1 TTGATTTTGAGC
45734345 -TGATTTTGAGC
1 TTGATTTTGAGC
45734356 TTGATT
1 TTGATT
45734362 GAATGTCGAC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.69
12 5 0.31
ACGTcount: A:0.17, C:0.07, G:0.24, T:0.52
Consensus pattern (12 bp):
TTGATTTTGAGC
Found at i:45736563 original size:29 final size:29
Alignment explanation
Indices: 45736532--45736586 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
45736522 AAAGCCCTTT
45736532 TTTTTAA-AATTTACCGAAATGGGCCACA
1 TTTTTAATAATTTACCGAAATGGGCCACA
* *
45736560 TTTTTAATTATTTACCGGAATGGGCCA
1 TTTTTAATAATTTACCGAAATGGGCCA
45736587 TTTCCGCGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 7 0.29
29 17 0.71
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.36
Consensus pattern (29 bp):
TTTTTAATAATTTACCGAAATGGGCCACA
Found at i:45737575 original size:27 final size:27
Alignment explanation
Indices: 45737520--45737577 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 27
45737510 GATTTCGCGG
*
45737520 AAAATGGCCCATTCCGGTGAATATCAA
1 AAAATGGCCCATTCCGGTAAATATCAA
* *
45737547 AAAATCGGCCCATTTCGGTAAAT-TTAA
1 AAAAT-GGCCCATTCCGGTAAATATCAA
45737574 AAAA
1 AAAA
45737578 GAAATGGCTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
27 12 0.44
28 15 0.56
ACGTcount: A:0.41, C:0.19, G:0.16, T:0.24
Consensus pattern (27 bp):
AAAATGGCCCATTCCGGTAAATATCAA
Found at i:45738094 original size:10 final size:10
Alignment explanation
Indices: 45738010--45738101 Score: 52
Period size: 10 Copynumber: 9.4 Consensus size: 10
45738000 TCTCCCGCTC
45738010 TTATTAAAAA
1 TTATTAAAAA
**
45738020 TTAGAAAAAA
1 TTATTAAAAA
*
45738030 TAATATAAAAA
1 TTAT-TAAAAA
45738041 --A-TAATAAA
1 TTATTAA-AAA
45738049 TT-TTAAAAA
1 TTATTAAAAA
**
45738058 TTTTATTAAATT
1 --TTATTAAAAA
*
45738070 TTAATAAAAA
1 TTATTAAAAA
45738080 -T-TTAAAAA
1 TTATTAAAAA
45738088 TTATTAAAAA
1 TTATTAAAAA
45738098 TTAT
1 TTAT
45738102 ATTTTTTTAT
Statistics
Matches: 61, Mismatches: 11, Indels: 20
0.66 0.12 0.22
Matches are distributed among these distances:
7 3 0.05
8 9 0.15
9 6 0.10
10 31 0.51
11 7 0.11
12 5 0.08
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.39
Consensus pattern (10 bp):
TTATTAAAAA
Found at i:45738099 original size:30 final size:32
Alignment explanation
Indices: 45738040--45738099 Score: 81
Period size: 30 Copynumber: 1.9 Consensus size: 32
45738030 TAATATAAAA
*
45738040 AATAATAAATTTTAAAAATTTTATTAAATTTT
1 AATAATAAATTTTAAAAATTTTATAAAATTTT
45738072 AATAA-AAA-TTTAAAAATTATTA-AAAATT
1 AATAATAAATTTTAAAAATT-TTATAAAATT
45738100 ATATTTTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
30 15 0.58
31 6 0.23
32 5 0.19
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (32 bp):
AATAATAAATTTTAAAAATTTTATAAAATTTT
Found at i:45738124 original size:38 final size:37
Alignment explanation
Indices: 45738033--45738125 Score: 100
Period size: 40 Copynumber: 2.4 Consensus size: 37
45738023 GAAAAAATAA
*
45738033 TATAAAAA-ATAATAAATTTTAAAAATTTTATTAAATTTT
1 TATAAAAATATAA-AAATTTTAAAAATTATATT--ATTTT
* *
45738072 AATAAAAATTTAAAAATTATTAAAAATTATATT-TTTT
1 TATAAAAATATAAAAATT-TTAAAAATTATATTATTTT
45738109 TATAAAAATAGTAAAAA
1 TATAAAAATA-TAAAAA
45738126 AATGTAAAAT
Statistics
Matches: 46, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
37 12 0.26
38 6 0.13
39 12 0.26
40 16 0.35
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (37 bp):
TATAAAAATATAAAAATTTTAAAAATTATATTATTTT
Found at i:45738125 original size:29 final size:29
Alignment explanation
Indices: 45738082--45738158 Score: 75
Period size: 29 Copynumber: 2.7 Consensus size: 29
45738072 AATAAAAATT
* * ***
45738082 TAAAAATTATTAAAAATTATATTTTTTTA
1 TAAAAATCATAAAAAATTATAAAATTTTA
* *
45738111 TAAAAAT-AGTAAAAAAATGTAAAATTTTA
1 TAAAAATCA-TAAAAAATTATAAAATTTTA
45738140 TAAAAATCATAAAAAATTA
1 TAAAAATCATAAAAAATTA
45738159 ACGACCCTTA
Statistics
Matches: 38, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
28 1 0.03
29 36 0.95
30 1 0.03
ACGTcount: A:0.58, C:0.01, G:0.03, T:0.38
Consensus pattern (29 bp):
TAAAAATCATAAAAAATTATAAAATTTTA
Found at i:45738409 original size:28 final size:28
Alignment explanation
Indices: 45738351--45738407 Score: 82
Period size: 28 Copynumber: 2.1 Consensus size: 28
45738341 TTCTTACGAC
*
45738351 TTTATAAAATTTTATAAGTATTACTATT
1 TTTATAAAATTTTACAAGTATTACTATT
*
45738379 TTTATAAAATTTTACAA-TATT-TTATT
1 TTTATAAAATTTTACAAGTATTACTATT
45738405 TTT
1 TTT
45738408 TTTACAATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
26 7 0.26
27 4 0.15
28 16 0.59
ACGTcount: A:0.37, C:0.04, G:0.02, T:0.58
Consensus pattern (28 bp):
TTTATAAAATTTTACAAGTATTACTATT
Found at i:45738419 original size:18 final size:20
Alignment explanation
Indices: 45738388--45738428 Score: 68
Period size: 19 Copynumber: 2.1 Consensus size: 20
45738378 TTTTATAAAA
45738388 TTTTACAATATTTTAT-TTT
1 TTTTACAATATTTTATATTT
45738407 TTTTACAAT-TTTTATATTT
1 TTTTACAATATTTTATATTT
45738426 TTT
1 TTT
45738429 CTAATTGTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 6 0.29
19 15 0.71
ACGTcount: A:0.24, C:0.05, G:0.00, T:0.71
Consensus pattern (20 bp):
TTTTACAATATTTTATATTT
Found at i:45738434 original size:18 final size:18
Alignment explanation
Indices: 45738388--45738428 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 18
45738378 TTTTATAAAA
*
45738388 TTTTACAATATTTTATTTT
1 TTTTACAAT-TTTTATATT
45738407 TTTTACAATTTTTATATT
1 TTTTACAATTTTTATATT
45738425 TTTT
1 TTTT
45738429 CTAATTGTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
18 12 0.57
19 9 0.43
ACGTcount: A:0.24, C:0.05, G:0.00, T:0.71
Consensus pattern (18 bp):
TTTTACAATTTTTATATT
Found at i:45738688 original size:87 final size:87
Alignment explanation
Indices: 45738532--45738699 Score: 232
Period size: 87 Copynumber: 1.9 Consensus size: 87
45738522 AAGCAGGGGT
* ** * * *
45738532 TTAATTGCTTTTTTTTTTAAGTTTGAGGGTCTTTTTGATGCATTTTGAAAGTTTAAGTACGCAAT
1 TTAATTGCTTTTCTTTAAAAGTTTGAGGGTCTTTTTGATGCATTTTGAAAGTTCAAATACGCAAA
**
45738597 TGAGTGCAAAAAAAAATAGGGC
66 TGAGTAAAAAAAAAAATAGGGC
45738619 TTAATTGCTTTTCTTTAAAAGATTTGAGGGTC-TTTTGATGCATTTTGAAAGTTCAAATAC-CTA
1 TTAATTGCTTTTCTTTAAAAG-TTTGAGGGTCTTTTTGATGCATTTTGAAAGTTCAAATACGC-A
45738682 AATGAGTAAAAAAAAAAA
64 AATGAGTAAAAAAAAAAA
45738700 GCAAGGGCTT
Statistics
Matches: 71, Mismatches: 8, Indels: 4
0.86 0.10 0.05
Matches are distributed among these distances:
86 1 0.01
87 60 0.85
88 10 0.14
ACGTcount: A:0.35, C:0.08, G:0.18, T:0.39
Consensus pattern (87 bp):
TTAATTGCTTTTCTTTAAAAGTTTGAGGGTCTTTTTGATGCATTTTGAAAGTTCAAATACGCAAA
TGAGTAAAAAAAAAAATAGGGC
Found at i:45741659 original size:43 final size:43
Alignment explanation
Indices: 45741605--45741790 Score: 210
Period size: 43 Copynumber: 4.3 Consensus size: 43
45741595 TTTTGGAAAC
* * * *
45741605 AAACGTCGCTAAAGAGCGGGACCTTTAGCGGTGCTTTTTCCAA
1 AAACGCCGCTAAAGAGCCGGACCTTTAGCGGCGCTTTTCCCAA
* *
45741648 AAATGCCGCTAAAGAGCCGGACCTTTAGCGGCGCTTTTCCCAC
1 AAACGCCGCTAAAGAGCCGGACCTTTAGCGGCGCTTTTCCCAA
* * * * *
45741691 AAACGTCGCTAAAGAGCCGGACTTTTGGCGACGCTTTTCCCAT
1 AAACGCCGCTAAAGAGCCGGACCTTTAGCGGCGCTTTTCCCAA
* * * * * *
45741734 AAACACCGCTAAAGAGCAGGACCTTTAGCGGCACTTTTTCGAC
1 AAACGCCGCTAAAGAGCCGGACCTTTAGCGGCGCTTTTCCCAA
*
45741777 AAACGCCACTAAAG
1 AAACGCCGCTAAAG
45741791 GTCATGAAAA
Statistics
Matches: 119, Mismatches: 24, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
43 119 1.00
ACGTcount: A:0.27, C:0.28, G:0.23, T:0.22
Consensus pattern (43 bp):
AAACGCCGCTAAAGAGCCGGACCTTTAGCGGCGCTTTTCCCAA
Found at i:45741703 original size:86 final size:86
Alignment explanation
Indices: 45741603--45741790 Score: 241
Period size: 86 Copynumber: 2.2 Consensus size: 86
45741593 GTTTTTGGAA
* ** * ** *
45741603 ACAAACGTCGCTAAAGAGCGGGACCTTTAGCGGTGCTTTTTCCAAAAATGCCGCTAAAGAGCCGG
1 ACAAACGTCGCTAAAGAGCCGGACCTTTAGCGACGCTTTTCCCAAAAACACCGCTAAAGAGCAGG
*
45741668 ACCTTTAGCGGCGCTTTTCCC
66 ACCTTTAGCGGCACTTTTCCC
* * *
45741689 ACAAACGTCGCTAAAGAGCCGGACTTTTGGCGACGCTTTTCCCATAAACACCGCTAAAGAGCAGG
1 ACAAACGTCGCTAAAGAGCCGGACCTTTAGCGACGCTTTTCCCAAAAACACCGCTAAAGAGCAGG
* *
45741754 ACCTTTAGCGGCACTTTTTCG
66 ACCTTTAGCGGCACTTTTCCC
* *
45741775 ACAAACGCCACTAAAG
1 ACAAACGTCGCTAAAG
45741791 GTCATGAAAA
Statistics
Matches: 87, Mismatches: 15, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
86 87 1.00
ACGTcount: A:0.28, C:0.28, G:0.22, T:0.22
Consensus pattern (86 bp):
ACAAACGTCGCTAAAGAGCCGGACCTTTAGCGACGCTTTTCCCAAAAACACCGCTAAAGAGCAGG
ACCTTTAGCGGCACTTTTCCC
Found at i:45743941 original size:27 final size:25
Alignment explanation
Indices: 45743898--45743950 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 25
45743888 CATGTATAAA
45743898 TTTTAGTTTTTTATTTCATTTATATTT
1 TTTTAGTTTTTTATTTC--TTATATTT
*
45743925 TTTTA-TTTTATTTTTTCTTATATTT
1 TTTTAGTTTT-TTATTTCTTATATTT
45743950 T
1 T
45743951 GGTCCTATCC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
25 9 0.38
26 4 0.17
27 11 0.46
ACGTcount: A:0.17, C:0.04, G:0.02, T:0.77
Consensus pattern (25 bp):
TTTTAGTTTTTTATTTCTTATATTT
Found at i:45743990 original size:2 final size:2
Alignment explanation
Indices: 45743983--45744026 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
45743973 TAATTACCTG
45743983 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
45744025 TA
1 TA
45744027 NNNNNNNNNN
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:45744356 original size:71 final size:72
Alignment explanation
Indices: 45744226--45744394 Score: 187
Period size: 71 Copynumber: 2.3 Consensus size: 72
45744216 AGACTTATTA
* * * * * *
45744226 GCGCTTTCTAAAAAAGGCCGCAAAATTCCTGAAAGCTCAAAAAACGGCATTGTTGGGCTTAGG-T
1 GCGCTTTCTCAAAAACGCCGCTAAATCCCCGAAAGCTCAAAAAACGGCATCGTTGGGCTTAGGTT
45744290 TTTTACG
66 TTTTACG
** * ** *
45744297 GCGCTTTCTCAAAAACGCCGCTAAATCCCCGAAAGCTCAGCAAATGGTGTCGTTTGGCTTAGGTT
1 GCGCTTTCTCAAAAACGCCGCTAAATCCCCGAAAGCTCAAAAAACGGCATCGTTGGGCTTAGG-T
*
45744362 TTTTTGCG
65 TTTTTACG
* *
45744370 GCGCTTCCCCAAAAACGCCGCTAAA
1 GCGCTTTCTCAAAAACGCCGCTAAA
45744395 GCCTTGAGCA
Statistics
Matches: 81, Mismatches: 15, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
71 51 0.63
73 30 0.37
ACGTcount: A:0.27, C:0.25, G:0.22, T:0.26
Consensus pattern (72 bp):
GCGCTTTCTCAAAAACGCCGCTAAATCCCCGAAAGCTCAAAAAACGGCATCGTTGGGCTTAGGTT
TTTTACG
Found at i:45744425 original size:114 final size:114
Alignment explanation
Indices: 45744295--45744622 Score: 485
Period size: 114 Copynumber: 2.9 Consensus size: 114
45744285 TAGGTTTTTA
* * *
45744295 CGGCGCTTTCTCAAAAACGCCGCTAAATCCCCGAAAGCTCAGCAAATGGTGTCGTTTGGCTTAGG
1 CGGCGCTTTCTAAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGGTGTCGTTTGGCTTAGG
* * *
45744360 TTTTTTTGCGGCGCTTCCCCAAAAACGCCGCTAAAGCCTTGAGCATTAG
66 TTTTTTTGCGGCGCTTTCTCAAAAACGCCGCTAAAGCCCTGAGCATTAG
* * **
45744409 CGGCGCTTTCTAAAAAACGCTGCTAAATCCCCGAAAGCTTAGAAAACGGCATCGTTTGGCTTAGG
1 CGGCGCTTTCTAAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGGTGTCGTTTGGCTTAGG
* * * *
45744474 TTTTTTTGTGACGCTTTCTCAAAAACGCCGTTAAATCCCTGAGCATTAG
66 TTTTTTTGCGGCGCTTTCTCAAAAACGCCGCTAAAGCCCTGAGCATTAG
* * * *
45744523 CGACACTTTCTTAAAAACGCCGCTAAATCCCCGAAAACTCAGAAAACGGTGTCGTTTGGCTTAGG
1 CGGCGCTTTCTAAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGGTGTCGTTTGGCTTAGG
*
45744588 TTTTTTTGCGGCGCTTTATCAAAAACGCCGCTAAA
66 TTTTTTTGCGGCGCTTTCTCAAAAACGCCGCTAAA
45744623 TCCCCGAAAG
Statistics
Matches: 188, Mismatches: 26, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
114 188 1.00
ACGTcount: A:0.27, C:0.26, G:0.21, T:0.27
Consensus pattern (114 bp):
CGGCGCTTTCTAAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGGTGTCGTTTGGCTTAGG
TTTTTTTGCGGCGCTTTCTCAAAAACGCCGCTAAAGCCCTGAGCATTAG
Found at i:45744614 original size:187 final size:187
Alignment explanation
Indices: 45744408--45744813 Score: 607
Period size: 187 Copynumber: 2.2 Consensus size: 187
45744398 TTGAGCATTA
* * * *
45744408 GCGGCGCTTTCTAAAAAACGCTGCTAAATCCCCGAAAGCTTAGAAAACGGCATCGTTTGGCTTAG
1 GCGGCGCTTTATCAAAAACGCTGCTAAATCCCCGAAAGCTCAAAAAACGGCATCGTTTGGCTTAG
* * * *
45744473 GTTTTTTTGTGACGCTTTCTCAAAAACGCCGTTAAATCCCTGAGCATTAGCGACACTTTCTTAAA
66 GTTTTTTTGCGACGATTTATCAAAAACGCCGCTAAATCCCTGAGCATTAGCGACACTTTCTTAAA
* * *
45744538 AACGCCGCTAAATCCCCGAAAACTCAGAAAACGGTGTCGTTTGGCTTAGGTTTTTTT
131 AACGCCGCTAAATCCCCGAAAACTCAAAAAACGGCGTCGTTTGGCTTAGGGTTTTTT
* * *
45744595 GCGGCGCTTTATCAAAAACGCCGCTAAATCCCCGAAAGCTCAAAAAATGGCGTCGTTTGGCTTAG
1 GCGGCGCTTTATCAAAAACGCTGCTAAATCCCCGAAAGCTCAAAAAACGGCATCGTTTGGCTTAG
* * *
45744660 GTTTTTTTGCGGCGATTTATCAAAAACGCCGCTAAATCCCTGAGCATTAGCGGCGCTTTCTTAAA
66 GTTTTTTTGCGACGATTTATCAAAAACGCCGCTAAATCCCTGAGCATTAGCGACACTTTCTTAAA
* * *
45744725 AACGCCGCTAAATCTCCGAAAGCTCAAAAAACGGCGTTGTTTGGCTTAGGGTTTTTT
131 AACGCCGCTAAATCCCCGAAAACTCAAAAAACGGCGTCGTTTGGCTTAGGGTTTTTT
*
45744782 GCAGCGCTTTATCAAAAACG-TCGCTAAATCCC
1 GCGGCGCTTTATCAAAAACGCT-GCTAAATCCC
45744814 TGAGCATTAG
Statistics
Matches: 196, Mismatches: 22, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
187 196 1.00
ACGTcount: A:0.27, C:0.24, G:0.20, T:0.28
Consensus pattern (187 bp):
GCGGCGCTTTATCAAAAACGCTGCTAAATCCCCGAAAGCTCAAAAAACGGCATCGTTTGGCTTAG
GTTTTTTTGCGACGATTTATCAAAAACGCCGCTAAATCCCTGAGCATTAGCGACACTTTCTTAAA
AACGCCGCTAAATCCCCGAAAACTCAAAAAACGGCGTCGTTTGGCTTAGGGTTTTTT
Found at i:45744626 original size:73 final size:73
Alignment explanation
Indices: 45744535--45744699 Score: 285
Period size: 73 Copynumber: 2.3 Consensus size: 73
45744525 ACACTTTCTT
* *
45744535 AAAAACGCCGCTAAATCCCCGAAAACTCAGAAAACGGTGTCGTTTGGCTTAGGTTTTTTTGCGGC
1 AAAAACGCCGCTAAATCCCCGAAAACTCAAAAAACGGCGTCGTTTGGCTTAGGTTTTTTTGCGGC
*
45744600 GCTTTATC
66 GATTTATC
* *
45744608 AAAAACGCCGCTAAATCCCCGAAAGCTCAAAAAATGGCGTCGTTTGGCTTAGGTTTTTTTGCGGC
1 AAAAACGCCGCTAAATCCCCGAAAACTCAAAAAACGGCGTCGTTTGGCTTAGGTTTTTTTGCGGC
45744673 GATTTATC
66 GATTTATC
45744681 AAAAACGCCGCTAAATCCC
1 AAAAACGCCGCTAAATCCC
45744700 TGAGCATTAG
Statistics
Matches: 87, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
73 87 1.00
ACGTcount: A:0.28, C:0.24, G:0.21, T:0.27
Consensus pattern (73 bp):
AAAAACGCCGCTAAATCCCCGAAAACTCAAAAAACGGCGTCGTTTGGCTTAGGTTTTTTTGCGGC
GATTTATC
Found at i:45744795 original size:114 final size:114
Alignment explanation
Indices: 45744595--45744904 Score: 451
Period size: 114 Copynumber: 2.7 Consensus size: 114
45744585 AGGTTTTTTT
* * * *
45744595 GCGGCGCTTTATCAAAAACGCCGCTAAATCCCCGAAAGCTCAAAAAATGGCGTCGTTTGGCTTAG
1 GCGGCGCTTTCTTAAAAACGCCGCTAAATCTCCGAAAGCTCAAAAAACGGCGTCGTTTGGCTTAG
* *
45744660 GTTTTTTTGCGGCGATTTATCAAAAACGCCGCTAAATCCCTGAGCATTA
66 GGTTTTTTGCGGCGCTTTATCAAAAACGCCGCTAAATCCCTGAGCATTA
*
45744709 GCGGCGCTTTCTTAAAAACGCCGCTAAATCTCCGAAAGCTCAAAAAACGGCGTTGTTTGGCTTAG
1 GCGGCGCTTTCTTAAAAACGCCGCTAAATCTCCGAAAGCTCAAAAAACGGCGTCGTTTGGCTTAG
* *
45744774 GGTTTTTTGCAGCGCTTTATCAAAAACGTCGCTAAATCCCTGAGCATTA
66 GGTTTTTTGCGGCGCTTTATCAAAAACGCCGCTAAATCCCTGAGCATTA
* * * * *** * *
45744823 GCAGCGCTTTCTTAAAAACACCGCTAAATCTTCGAAAACTCGGTAAACGGCATCGTTGGGCTTA-
1 GCGGCGCTTTCTTAAAAACGCCGCTAAATCTCCGAAAGCTCAAAAAACGGCGTCGTTTGGCTTAG
45744887 GGTTTTTTGCGGCGCTTT
66 GGTTTTTTGCGGCGCTTT
45744905 CTAGAAAATG
Statistics
Matches: 176, Mismatches: 20, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
113 17 0.10
114 159 0.90
ACGTcount: A:0.26, C:0.24, G:0.22, T:0.28
Consensus pattern (114 bp):
GCGGCGCTTTCTTAAAAACGCCGCTAAATCTCCGAAAGCTCAAAAAACGGCGTCGTTTGGCTTAG
GGTTTTTTGCGGCGCTTTATCAAAAACGCCGCTAAATCCCTGAGCATTA
Found at i:45744837 original size:301 final size:300
Alignment explanation
Indices: 45744225--45744904 Score: 952
Period size: 301 Copynumber: 2.3 Consensus size: 300
45744215 AAGACTTATT
* * * * * * * *
45744225 AGCGCTTTCTAAAAAAGGCCGCAAAATTCCTGAAAGCTCAAAAAACGGCATTGTTGGGCTTAGG-
1 AGCGCTTTCTTAAAAACGCCGCTAAATCCCCGAAAACTCAGAAAACGGCATCGTTGGGCTTAGGT
* * ** *
45744289 TTTTTACGGCGCTTTCTCAAAAACGCCGCTAAATCCCCGAAAGCTCAGCAAATGGTGTCGTTTGG
66 TTTTTGCGGCGCTTTATCAAAAACGCCGCTAAATCCCCGAAAGCTCAAAAAATGGCGTCGTTTGG
* * *
45744354 CTTAGGTTTTTTTGCGGCGCTTCCCCAAAAACGCCGCTAAAGCCTTGAGCATTAGCGGCGCTTTC
131 CTTAGGTTTTTTTGCGGCGATTCACCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTC
* * * * *
45744419 TAAAAAACGCTGCTAAATCCCCGAAAGCTTAGAAAACGGCATCGTTTGGCTTAGGTTTTTTTGTG
196 TAAAAAACGCCGCTAAATCCCCGAAAGCTCAAAAAACGGCATCGTTTGGCTTAGGGTTTTTTGAG
* *
45744484 ACGCTTTCTCAAAAACGCCGTTAAATCCCTGAGCATTAGC
261 ACGCTTTATCAAAAACGCCGCTAAATCCCTGAGCATTAGC
* ** *
45744524 -GACACTTTCTTAAAAACGCCGCTAAATCCCCGAAAACTCAGAAAACGGTGTCGTTTGGCTTAGG
1 AG-CGCTTTCTTAAAAACGCCGCTAAATCCCCGAAAACTCAGAAAACGGCATCGTTGGGCTTAGG
45744588 TTTTTTTGCGGCGCTTTATCAAAAACGCCGCTAAATCCCCGAAAGCTCAAAAAATGGCGTCGTTT
65 -TTTTTTGCGGCGCTTTATCAAAAACGCCGCTAAATCCCCGAAAGCTCAAAAAATGGCGTCGTTT
* * *
45744653 GGCTTAGGTTTTTTTGCGGCGATTTATCAAAAACGCCGCTAAATCCCTGAGCATTAGCGGCGCTT
129 GGCTTAGGTTTTTTTGCGGCGATTCACCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTT
* * * *
45744718 TCTTAAAAACGCCGCTAAATCTCCGAAAGCTCAAAAAACGGCGTTGTTTGGCTTAGGGTTTTTTG
194 TCTAAAAAACGCCGCTAAATCCCCGAAAGCTCAAAAAACGGCATCGTTTGGCTTAGGGTTTTTTG
*
45744783 CAG-CGCTTTATCAAAAACGTCGCTAAATCCCTGAGCATTAGC
259 -AGACGCTTTATCAAAAACGCCGCTAAATCCCTGAGCATTAGC
* ** * *
45744825 AGCGCTTTCTTAAAAACACCGCTAAATCTTCGAAAACTCGGTAAACGGCATCGTTGGGCTTAGGT
1 AGCGCTTTCTTAAAAACGCCGCTAAATCCCCGAAAACTCAGAAAACGGCATCGTTGGGCTTAGGT
45744890 TTTTTGCGGCGCTTT
66 TTTTTGCGGCGCTTT
45744905 CTAGAAAATG
Statistics
Matches: 332, Mismatches: 44, Indels: 9
0.86 0.11 0.02
Matches are distributed among these distances:
298 1 0.00
299 50 0.15
300 16 0.05
301 263 0.79
302 2 0.01
ACGTcount: A:0.27, C:0.24, G:0.21, T:0.28
Consensus pattern (300 bp):
AGCGCTTTCTTAAAAACGCCGCTAAATCCCCGAAAACTCAGAAAACGGCATCGTTGGGCTTAGGT
TTTTTGCGGCGCTTTATCAAAAACGCCGCTAAATCCCCGAAAGCTCAAAAAATGGCGTCGTTTGG
CTTAGGTTTTTTTGCGGCGATTCACCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTC
TAAAAAACGCCGCTAAATCCCCGAAAGCTCAAAAAACGGCATCGTTTGGCTTAGGGTTTTTTGAG
ACGCTTTATCAAAAACGCCGCTAAATCCCTGAGCATTAGC
Found at i:45753127 original size:20 final size:20
Alignment explanation
Indices: 45753093--45753134 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
45753083 TACTATTTAA
** *
45753093 ATAATATTATTTGAATAGTT
1 ATAATATTAAATGAATAATT
45753113 ATAATATTAAATGAATAATT
1 ATAATATTAAATGAATAATT
45753133 AT
1 AT
45753135 GTGTTTATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.45
Consensus pattern (20 bp):
ATAATATTAAATGAATAATT
Found at i:45754114 original size:32 final size:32
Alignment explanation
Indices: 45754073--45754144 Score: 110
Period size: 32 Copynumber: 2.2 Consensus size: 32
45754063 CAGCTATTTT
*
45754073 TGTTCACACCCAATGGACCGTCCAACTCC-TGA
1 TGTTCACACCCAAGGGACCGTCCAACTCCAT-A
*
45754105 TGTTCACACCCAAGGGACCGTCCAAGTCCATA
1 TGTTCACACCCAAGGGACCGTCCAACTCCATA
45754137 TGTTCACA
1 TGTTCACA
45754145 TCAAGGACTT
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
32 36 0.97
33 1 0.03
ACGTcount: A:0.26, C:0.35, G:0.17, T:0.22
Consensus pattern (32 bp):
TGTTCACACCCAAGGGACCGTCCAACTCCATA
Found at i:45754182 original size:13 final size:13
Alignment explanation
Indices: 45754164--45754188 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
45754154 TTTTAGACGC
45754164 CACAAGATGCATT
1 CACAAGATGCATT
45754177 CACAAGATGCAT
1 CACAAGATGCAT
45754189 GTATATTCGG
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:0.40, C:0.24, G:0.16, T:0.20
Consensus pattern (13 bp):
CACAAGATGCATT
Found at i:45761166 original size:4 final size:5
Alignment explanation
Indices: 45761145--45761186 Score: 59
Period size: 5 Copynumber: 8.6 Consensus size: 5
45761135 CTCTTCTTCC
* *
45761145 TCTTT TATTT TCCTT TC-TT TCTTT TCTTT TCTTT TCTTT TCT
1 TCTTT TCTTT TCTTT TCTTT TCTTT TCTTT TCTTT TCTTT TCT
45761187 GTCTTTTACT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
4 4 0.12
5 29 0.88
ACGTcount: A:0.02, C:0.21, G:0.00, T:0.76
Consensus pattern (5 bp):
TCTTT
Found at i:45761169 original size:19 final size:19
Alignment explanation
Indices: 45761145--45761183 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
45761135 CTCTTCTTCC
45761145 TCTTTTATTTTCCTTTCTT
1 TCTTTTATTTTCCTTTCTT
* *
45761164 TCTTTTCTTTTCTTTTCTT
1 TCTTTTATTTTCCTTTCTT
45761183 T
1 T
45761184 TCTGTCTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.03, C:0.21, G:0.00, T:0.77
Consensus pattern (19 bp):
TCTTTTATTTTCCTTTCTT
Found at i:45761172 original size:24 final size:24
Alignment explanation
Indices: 45761145--45761193 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
45761135 CTCTTCTTCC
*
45761145 TCTTTTATTTTCCTTTCTTTCTTT
1 TCTTTTATTTTCCTTTCTGTCTTT
* *
45761169 TCTTTTCTTTTCTTTTCTGTCTTT
1 TCTTTTATTTTCCTTTCTGTCTTT
45761193 T
1 T
45761194 ACTTCCTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.02, C:0.20, G:0.02, T:0.76
Consensus pattern (24 bp):
TCTTTTATTTTCCTTTCTGTCTTT
Found at i:45767777 original size:9 final size:9
Alignment explanation
Indices: 45767765--45767795 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
45767755 TTTTCCTTAC
45767765 TTTCTTTCT
1 TTTCTTTCT
45767774 TTTCTTTTCT
1 TTTC-TTTCT
45767784 TTTCTTTCT
1 TTTCTTTCT
45767793 TTT
1 TTT
45767796 ACTTCCTTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 12 0.57
10 9 0.43
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (9 bp):
TTTCTTTCT
Found at i:45767779 original size:23 final size:23
Alignment explanation
Indices: 45767748--45767794 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
45767738 CTCTTCTTCC
45767748 TCTTCTCTTTTCCTTACTTTCTT
1 TCTTCTCTTTTCCTTACTTTCTT
* * *
45767771 TCTTTTCTTTTCTTTTCTTTCTT
1 TCTTCTCTTTTCCTTACTTTCTT
45767794 T
1 T
45767795 TACTTCCTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.02, C:0.26, G:0.00, T:0.72
Consensus pattern (23 bp):
TCTTCTCTTTTCCTTACTTTCTT
Found at i:45768458 original size:29 final size:29
Alignment explanation
Indices: 45768423--45768480 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
45768413 GACACAACTG
45768423 TGTGCTCAGGCTGTGTGGGACACAAGAGT
1 TGTGCTCAGGCTGTGTGGGACACAAGAGT
45768452 TGTGCTCAGGCTGTGTGGGACACAAGAGT
1 TGTGCTCAGGCTGTGTGGGACACAAGAGT
45768481 AGACACATAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.21, C:0.17, G:0.38, T:0.24
Consensus pattern (29 bp):
TGTGCTCAGGCTGTGTGGGACACAAGAGT
Found at i:45770523 original size:3 final size:3
Alignment explanation
Indices: 45770510--45770600 Score: 96
Period size: 3 Copynumber: 30.7 Consensus size: 3
45770500 TTAGTAATTC
45770510 TAT TAT T-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
** * * * * *
45770557 TAT CCT TAC TA- TATT TGT TAG TAT TAT TAC TAA TAT TAT TAT TA
1 TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
45770601 CTAATTTATA
Statistics
Matches: 73, Mismatches: 12, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
2 4 0.05
3 68 0.93
4 1 0.01
ACGTcount: A:0.32, C:0.04, G:0.02, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:45770601 original size:15 final size:14
Alignment explanation
Indices: 45770578--45770609 Score: 55
Period size: 15 Copynumber: 2.2 Consensus size: 14
45770568 TATTTGTTAG
45770578 TATTATTACTAATAT
1 TATTATTACTAAT-T
45770593 TATTATTACTAATT
1 TATTATTACTAATT
45770607 TAT
1 TAT
45770610 ATTTACACTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.24
15 13 0.76
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.56
Consensus pattern (14 bp):
TATTATTACTAATT
Found at i:45771690 original size:110 final size:110
Alignment explanation
Indices: 45771539--45771847 Score: 446
Period size: 110 Copynumber: 2.8 Consensus size: 110
45771529 TTTTTTCTAA
* * **
45771539 AAAAATTTTCAAAATAAGGCAATATTTTACGTTTAGG-AATTCGAGAAAACATGTCCTAAGGTGC
1 AAAAA-TTTCAAAATAAGGCAATGTTTTGCGTTT-GGAAATTCGAGAAAACATACCCTAAGGTGC
*
45771603 TGGGTATCGATTTTTCTCGTTCAACCAAATGGCTTAATATCTTTTTT
64 TGGGTATCGATTTTTCTCGTTCAACCAAATGGCTTAATATCCTTTTT
* *
45771650 AAAAATTTCAAAATATGGCAATGTTTTGCATTTGGAAATTCGAGAAAACATACCCTAAGGTGCTG
1 AAAAATTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATACCCTAAGGTGCTG
*
45771715 GGTATCGATTTTTCTCGTTCAACCAAATGGCTTAATGTCCTTTTT
66 GGTATCGATTTTTCTCGTTCAACCAAATGGCTTAATATCCTTTTT
* * * *
45771760 AAAATTTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAG-GAACGTACCCTAAGGTACTG
1 AAAAATTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATACCCTAAGGTGCTG
* *
45771824 GGTTTCGA--TTTCTCGTTTAACCAA
66 GGTATCGATTTTTCTCGTTCAACCAA
45771848 GTTGCCAAAT
Statistics
Matches: 181, Mismatches: 16, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
107 15 0.08
109 26 0.14
110 135 0.75
111 5 0.03
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.35
Consensus pattern (110 bp):
AAAAATTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATACCCTAAGGTGCTG
GGTATCGATTTTTCTCGTTCAACCAAATGGCTTAATATCCTTTTT
Found at i:45773228 original size:19 final size:20
Alignment explanation
Indices: 45773188--45773231 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
45773178 GTCTCTTTAG
* *
45773188 GCATT-CATTTCATACATTT
1 GCATTACATTGCATACATAT
45773207 GCATTACATTGCAT-CATAT
1 GCATTACATTGCATACATAT
45773226 GCATTA
1 GCATTA
45773232 GATTTTCACG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 15 0.68
20 7 0.32
ACGTcount: A:0.30, C:0.20, G:0.09, T:0.41
Consensus pattern (20 bp):
GCATTACATTGCATACATAT
Found at i:45775346 original size:6 final size:6
Alignment explanation
Indices: 45775337--45775374 Score: 58
Period size: 6 Copynumber: 6.0 Consensus size: 6
45775327 CAAAAATAGG
45775337 AGAAAA AGAAAGA AGAAAAA AGAAAA AGAAAA AGAAAA
1 AGAAAA AGAAA-A AG-AAAA AGAAAA AGAAAA AGAAAA
45775375 GGAGAGGTCA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
6 21 0.70
7 6 0.20
8 3 0.10
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (6 bp):
AGAAAA
Found at i:45777674 original size:88 final size:88
Alignment explanation
Indices: 45777501--45777670 Score: 211
Period size: 88 Copynumber: 1.9 Consensus size: 88
45777491 TCAAAGACAA
* * * * * *
45777501 CAGATCTTGCCTTCCTGCCTTGACAGTGAAGCAGATCGAAGATACAAGCTTTGTCTCCATCGGTT
1 CAGATCTGGCCTTCCTGCATTAACAGCGAAGCAGATCGAAGATACAAGCCTTGCCTCCATCGGTT
* *
45777566 GCGGTGGAACTGTTTGAAGATAG
66 GCAGTGGAACTGATTGAAGATAG
* *
45777589 CAGATCTGGCCTTCCTGCATTAACGGCGAAGCAGATTGAA-A-ACAAAGCCTTGCCTCCATCGGT
1 CAGATCTGGCCTTCCTGCATTAACAGCGAAGCAGATCGAAGATAC-AAGCCTTGCCTCCATCGGT
45777652 TGCAGT-GAAGCTGATTGAA
65 TGCAGTGGAA-CTGATTGAA
45777671 AGATTTCAAA
Statistics
Matches: 70, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
86 5 0.07
87 31 0.44
88 34 0.49
ACGTcount: A:0.26, C:0.23, G:0.25, T:0.26
Consensus pattern (88 bp):
CAGATCTGGCCTTCCTGCATTAACAGCGAAGCAGATCGAAGATACAAGCCTTGCCTCCATCGGTT
GCAGTGGAACTGATTGAAGATAG
Found at i:45777878 original size:87 final size:86
Alignment explanation
Indices: 45777728--45778100 Score: 296
Period size: 87 Copynumber: 4.3 Consensus size: 86
45777718 ATTGTAATCC
* ** ** *
45777728 TATCTCCCTGAGATTACAGTGGAGCGGA-GTAA-AA-TAAAGGATCTTATCTCTCTGAAGTTACA
1 TATCTCCCTGAGATTACAGTGGAGCAGACCAAAGAATTTCA-GATCTTATCTCCCTGAAGTTACA
45777790 GCAGAGTAGATCGCGTCAGGTCT
65 GCAGAGTAGATCGCGT-AGGTCT
* * * *
45777813 TATTTCCCTGAGATTATAGTGGAACAAACCAAAGAATTTCAGATCTTATCTCCCTG-AGATTACA
1 TATCTCCCTGAGATTACAGTGGAGCAGACCAAAGAATTTCAGATCTTATCTCCCTGAAG-TTACA
* * * *
45777877 GCGGAGCAGATTGAAGATA-GTCAT
65 GCAGAGTAGATCG-CG-TAGGTC-T
* ** ** * *
45777901 CCTATCTCCCTGAGATTACAGTGGAGCGGA-TTAA-AA-TAAAGGATCTCATCTCTCTGAAGTTA
1 --TATCTCCCTGAGATTACAGTGGAGCAGACCAAAGAATTTCA-GATCTTATCTCCCTGAAGTTA
* *
45777963 CAGCAGAGTAGATCACATTAGGTCT
63 CAGCAGAGTAGATCGC-GTAGGTCT
45777988 TATCTCCCTGAGATTACAGTGGAGCAGACCAAAGAATTTCAGATCTTATCTCCCTG-AGATTACA
1 TATCTCCCTGAGATTACAGTGGAGCAGACCAAAGAATTTCAGATCTTATCTCCCTGAAG-TTACA
* * * * *
45778052 GCGGAGTAGATTGAAGCTAGTAATCC
65 GCAGAGTAGATCG-CG-TAG--GTCT
45778078 TATCTCCCTGAGATTACAGTGGA
1 TATCTCCCTGAGATTACAGTGGA
45778101 ATGGATTAAA
Statistics
Matches: 222, Mismatches: 45, Indels: 37
0.73 0.15 0.12
Matches are distributed among these distances:
85 50 0.23
86 8 0.04
87 69 0.31
88 42 0.19
89 5 0.02
90 48 0.22
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.28
Consensus pattern (86 bp):
TATCTCCCTGAGATTACAGTGGAGCAGACCAAAGAATTTCAGATCTTATCTCCCTGAAGTTACAG
CAGAGTAGATCGCGTAGGTCT
Found at i:45777971 original size:175 final size:175
Alignment explanation
Indices: 45777669--45778170 Score: 781
Period size: 175 Copynumber: 2.9 Consensus size: 175
45777659 AAGCTGATTG
* * *
45777669 AAAG-ATTTCAAATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGATTGTAATCCTATCT
1 AAAGAATTTCAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGATAGTAATCCTATCT
*
45777733 CCCTGAGATTACAGTGGAGCGGAGTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGCAGAGTA
66 CCCTGAGATTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGCAGAGTA
* *
45777798 GATCGCGTCAGGTCTTATTTCCCTGAGATTATAGTGGAACAAACC
131 GATCGCATCAGGTCTTATTTCCCTGAGATTACAGTGGAACAAACC
*
45777843 AAAGAATTTCAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGATAGTCATCCTATCT
1 AAAGAATTTCAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGATAGTAATCCTATCT
*
45777908 CCCTGAGATTACAGTGGAGCGGATTAAAATAAAGGATCTCATCTCTCTGAAGTTACAGCAGAGTA
66 CCCTGAGATTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGCAGAGTA
* * * * *
45777973 GATCACATTAGGTCTTATCTCCCTGAGATTACAGTGGAGCAGACC
131 GATCGCATCAGGTCTTATTTCCCTGAGATTACAGTGGAACAAACC
* *
45778018 AAAGAATTTCAGATCTTATCTCCCTGAGATTACAGCGGAGTAGATTGAAGCTAGTAATCCTATCT
1 AAAGAATTTCAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGATAGTAATCCTATCT
** * * *
45778083 CCCTGAGATTACAGTGGAATGGATTAAAATAAAGGATCTTATCTCTTTGAGGTTACAGTAGAGTA
66 CCCTGAGATTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGCAGAGTA
** *
45778148 GATCGTTTCAGATCTTATCTTCC
131 GATCGCATCAGGTCTTAT-TTCC
45778171 GAAGTAGAGC
Statistics
Matches: 298, Mismatches: 28, Indels: 2
0.91 0.09 0.01
Matches are distributed among these distances:
174 4 0.01
175 291 0.98
176 3 0.01
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.29
Consensus pattern (175 bp):
AAAGAATTTCAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGATAGTAATCCTATCT
CCCTGAGATTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGCAGAGTA
GATCGCATCAGGTCTTATTTCCCTGAGATTACAGTGGAACAAACC
Found at i:45778126 original size:44 final size:42
Alignment explanation
Indices: 45777680--45778150 Score: 227
Period size: 44 Copynumber: 10.8 Consensus size: 42
45777670 AAGATTTCAA
* * *
45777680 ATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGATTGTA
1 ATCTTATCTCCCTGAGATTACAGTGGAGCAGATT-AAAATAG-G
* * *
45777724 ATCCTATCTCCCTGAGATTACAGTGGAGCGGAGTAAAATAAAGG
1 ATCTTATCTCCCTGAGATTACAGTGGAGCAGATTAAAAT--AGG
* ** * ****
45777768 ATCTTATCTCTCTGA-AGTTACAGCAGAGTAGA-TCGCGTCAGG
1 ATCTTATCTCCCTGAGA-TTACAGTGGAGCAGATTAAAAT-AGG
* * * * **
45777810 -TCTTATTTCCCTGAGATTATAGTGGAACAAACCAAAGAATTTCA-G
1 ATCTTATCTCCCTGAGATTACAGTGGAGCAGA-TTAA-AA--T-AGG
* * *
45777855 ATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGATAGTC
1 ATCTTATCTCCCTGAGATTACAGTGGAGCAGATT-AAAATAG-G
* *
45777899 ATCCTATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAGG
1 ATCTTATCTCCCTGAGATTACAGTGGAGCAGATTAAAAT--AGG
* * ** * * * *
45777943 ATCTCATCTCTCTGA-AGTTACAGCAGAGTAGATCACATTAGG
1 ATCTTATCTCCCTGAGA-TTACAGTGGAGCAGATTAAAATAGG
**
45777985 -TCTTATCTCCCTGAGATTACAGTGGAGCAGACCAAAGAATTTCA-G
1 ATCTTATCTCCCTGAGATTACAGTGGAGCAGA-TTAA-AA--T-AGG
* * ** *
45778030 ATCTTATCTCCCTGAGATTACAGCGGAGTAGATTGAAGCTAGTA
1 ATCTTATCTCCCTGAGATTACAGTGGAGCAGATT-AAAATAG-G
* ***
45778074 ATCCTATCTCCCTGAGATTACAGTGGAATGGATTAAAATAAAGG
1 ATCTTATCTCCCTGAGATTACAGTGGAGCAGATTAAAAT--AGG
** * * *
45778118 ATCTTATCTCTTTGAGGTTACAGTAGAGTAGAT
1 ATCTTATCTCCCTGAGATTACAGTGGAGCAGAT
45778151 CGTTTCAGAT
Statistics
Matches: 315, Mismatches: 84, Indels: 56
0.69 0.18 0.12
Matches are distributed among these distances:
41 45 0.14
42 11 0.03
43 18 0.06
44 169 0.54
45 9 0.03
46 63 0.20
ACGTcount: A:0.31, C:0.18, G:0.21, T:0.29
Consensus pattern (42 bp):
ATCTTATCTCCCTGAGATTACAGTGGAGCAGATTAAAATAGG
Found at i:45779879 original size:3 final size:3
Alignment explanation
Indices: 45779866--45779936 Score: 135
Period size: 3 Copynumber: 24.0 Consensus size: 3
45779856 TTAGTAATTC
45779866 TAT TAT T-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
45779913 TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT
45779937 CTTTACTATA
Statistics
Matches: 67, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 2 0.03
3 65 0.97
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:45780525 original size:61 final size:64
Alignment explanation
Indices: 45780460--45780586 Score: 188
Period size: 67 Copynumber: 2.0 Consensus size: 64
45780450 TTTGTTAGTC
*
45780460 TTGTTCGTTTATTTATGTACA-TG-T-TTGTTTTTCTTGCTTTAGTTTTTATCTGTTTATCATT
1 TTGTTCGTTTATTTATGTACATTGTTATTGTTTTTCTTGCTTTAGTTTTTACCTGTTTATCATT
*
45780521 TTGTTCGTTTATTTATGTACATGTTTGTTATTGTTTTTCTTGCTTTAGTTTTTGCCTGTTTATCA
1 TTGTTCGTTTATTTATGTACA---TTGTTATTGTTTTTCTTGCTTTAGTTTTTACCTGTTTATCA
45780586 T
63 T
45780587 CTGTCATGAT
Statistics
Matches: 58, Mismatches: 2, Indels: 6
0.88 0.03 0.09
Matches are distributed among these distances:
61 21 0.36
65 2 0.03
66 1 0.02
67 34 0.59
ACGTcount: A:0.13, C:0.10, G:0.14, T:0.63
Consensus pattern (64 bp):
TTGTTCGTTTATTTATGTACATTGTTATTGTTTTTCTTGCTTTAGTTTTTACCTGTTTATCATT
Found at i:45781053 original size:110 final size:109
Alignment explanation
Indices: 45780933--45781240 Score: 449
Period size: 110 Copynumber: 2.8 Consensus size: 109
45780923 TTTTCTAAAA
* * * **
45780933 AAAAAATTCAAAATAAGGCAATATTTTGCGTTTAGAAATTCGACAAAACATGTCCTAAGGTGCTG
1 AAAAATTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGA-AAAACATACCCTAAGGTGCTG
*
45780998 GGTATCGATTTTTCTCGTTCAACCAAATGGCTTAATATCTTTTTT
65 GGTATCGATTTTTCTCGTTCAACCAAATGGCTTAATATCCTTTTT
* *
45781043 AAAAATTTCAAAATATGGCAATGTTTTGCATTTGGAAATTCGAGAAAACATACCCTAAGGTGCTG
1 AAAAATTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGA-AAAACATACCCTAAGGTGCTG
*
45781108 GGTATCGATTTTTCTCGTTCAACCAAATGGCTTAATGTCCTTTTT
65 GGTATCGATTTTTCTCGTTCAACCAAATGGCTTAATATCCTTTTT
* ** *
45781153 AAAATTTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGGAACGTACCCTAAGGTGCTGG
1 AAAAATTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAAAAACATACCCTAAGGTGCTGG
* *
45781218 GTTTCGA--TTTCTCGTTTAACCAA
66 GTATCGATTTTTCTCGTTCAACCAA
45781241 GTTGCCAAAT
Statistics
Matches: 180, Mismatches: 18, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
107 15 0.08
109 25 0.14
110 140 0.78
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.35
Consensus pattern (109 bp):
AAAAATTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAAAAACATACCCTAAGGTGCTGG
GTATCGATTTTTCTCGTTCAACCAAATGGCTTAATATCCTTTTT
Found at i:45787072 original size:27 final size:27
Alignment explanation
Indices: 45787042--45787106 Score: 80
Period size: 27 Copynumber: 2.4 Consensus size: 27
45787032 GACGACACAT
*
45787042 TAAACATGGGATAGT-CTCTTAGGACAC
1 TAAACATGGGATAGTCCTCTT-GGACAA
*
45787069 TAAAC-TCGGGGTAGTCCTCTTGGACAA
1 TAAACAT-GGGATAGTCCTCTTGGACAA
45787096 TAAACATGGGA
1 TAAACATGGGA
45787107 GATTATGAGG
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
26 1 0.03
27 25 0.78
28 6 0.19
ACGTcount: A:0.32, C:0.18, G:0.25, T:0.25
Consensus pattern (27 bp):
TAAACATGGGATAGTCCTCTTGGACAA
Found at i:45789697 original size:2 final size:2
Alignment explanation
Indices: 45789690--45789731 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
45789680 ATTATGGTGG
45789690 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
45789731 T
1 T
45789732 TTCTTTAATT
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:45797861 original size:175 final size:173
Alignment explanation
Indices: 45797504--45797863 Score: 513
Period size: 175 Copynumber: 2.1 Consensus size: 173
45797494 TACATTATAT
*
45797504 GGGAGATAAGGTCTGAAATTCTTCGGTCTATTCCACTCTAATCTCAGGGAGATAAGACCTGATAC
1 GGGAGATAAGATCTGAAATTCTTCGGTCTATTCCACTCTAATCTCAGGGAGATAAGACCTGATAC
* * *
45797569 GATCTGCTCTACTGTAACTTCAGAGATAAGATCCTTTATTTTAATCCACTCCACTGTAATCTAAA
66 GATCTACTCTACTGTAACTTCAGAGATAAAATCCTTTAGTTTAATCCACTCCACTGTAATCTAAA
* * * *
45797634 TGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTGA
131 GGAAATAAGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCA
* * * * *
45797677 GGAAGATAAGATCTGAAATTCTTCTGTTTATTCCACTGTAATCTCAGGGAGATAAGACCTGATGC
1 GGGAGATAAGATCTGAAATTCTTCGGTCTATTCCACTCTAATCTCAGGGAGATAAGACCTGATAC
* ** * *
45797742 GATCTACTCTACTGTAACTTCAGAGAGATAAAATCCTTTGGTTTAATCCGTTCCATTGTAATCTC
66 GATCTACTCTACTGTAACTTC--AGAGATAAAATCCTTTAGTTTAATCCACTCCACTGTAATCTA
* * *
45797807 AGGGAAATAAGATTACTGGCTTCAATCTGCTCTGCTGTAATCTCA
129 AAGGAAATAAGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCA
45797852 GGGAGATAAGAT
1 GGGAGATAAGAT
45797864 TCACCATCTT
Statistics
Matches: 163, Mismatches: 22, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
173 79 0.48
175 84 0.52
ACGTcount: A:0.29, C:0.20, G:0.19, T:0.32
Consensus pattern (173 bp):
GGGAGATAAGATCTGAAATTCTTCGGTCTATTCCACTCTAATCTCAGGGAGATAAGACCTGATAC
GATCTACTCTACTGTAACTTCAGAGATAAAATCCTTTAGTTTAATCCACTCCACTGTAATCTAAA
GGAAATAAGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCA
Found at i:45797901 original size:173 final size:172
Alignment explanation
Indices: 45797507--45797906 Score: 441
Period size: 173 Copynumber: 2.3 Consensus size: 172
45797497 ATTATATGGG
* * * * *
45797507 AGATAAGGTCTGAAATTCTTC-GGTCTATTCCACTCTAATCTCAGGGAGATAAGACCTGATACGA
1 AGATAAGATCTCAAATTCTTCTGAT-TACTCCAC-GTAATCTCAGGGAGATAAGACCTGATACGA
* * * *
45797571 TCTGCTCTACTGTAACTTCAGAGATAAGATCCTTTATTTTAATCCACTCCACTGTAATCTAAATG
64 TCTACTCTACTGTAACTTCAGAGATAAAATCCTTTAGTTTAATCCACTCCACTGTAATCTAAAGG
* * *
45797636 AGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTGAGGA
129 AAATAAGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAGGA
* * * *
45797680 AGATAAGATCTGAAATTCTTCTGTTTATTCCACTGTAATCTCAGGGAGATAAGACCTGATGCGAT
1 AGATAAGATCTCAAATTCTTCTGATTACTCCAC-GTAATCTCAGGGAGATAAGACCTGATACGAT
* ** * * *
45797745 CTACTCTACTGTAACTTCAGAGAGATAAAATCCTTTGGTTTAATCCGTTCCATTGTAATCTCAGG
65 CTACTCTACTGTAACTTC--AGAGATAAAATCCTTTAGTTTAATCCACTCCACTGTAATCTAAAG
* * *
45797810 GAAATAAGATTACTGGCTTCAATCTGCTCTGCTGTAATCTCAGGG
128 GAAATAAGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAGGA
* * *
45797855 AGATAAGAT-TCACCA-TCTTC-GATTAGCTCCAC-TATTGCTTAGGGAGATAAGA
1 AGATAAGATCTCA-AATTCTTCTGATTA-CTCCACGTAAT-CTCAGGGAGATAAGA
45797907 TCTGGAATTC
Statistics
Matches: 195, Mismatches: 26, Indels: 12
0.84 0.11 0.05
Matches are distributed among these distances:
172 3 0.02
173 93 0.48
174 14 0.07
175 85 0.44
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.32
Consensus pattern (172 bp):
AGATAAGATCTCAAATTCTTCTGATTACTCCACGTAATCTCAGGGAGATAAGACCTGATACGATC
TACTCTACTGTAACTTCAGAGATAAAATCCTTTAGTTTAATCCACTCCACTGTAATCTAAAGGAA
ATAAGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAGGA
Found at i:45797935 original size:219 final size:219
Alignment explanation
Indices: 45797680--45798129 Score: 749
Period size: 219 Copynumber: 2.1 Consensus size: 219
45797670 AATCTGAGGA
* *
45797680 AGATAAGATCTGAAATTCTTCTGTTTATTCCACTGTAATCTCAGGGAGATAAGACCTGATGCGAT
1 AGATAAGATCTGAAATTCTTCGGTCTATTCCACTGTAATCTCAGGGAGATAAGACCTGATGCGAT
* * *
45797745 CTACTCTACTGTAACTTCAGAGAGATAAAATCCTTTGGTTTAATCCGTTCCATTGTAATCTCAGG
66 CTACTCTACTGTAACTTCAGAGAGATAAAATCCTTTAGTTTAATCCGCTCCACTGTAATCTCAGG
* *
45797810 GAAATAAGATTACTGGCTTCAATCTGCTCTGCTGTAATCTCAGGGAGATAAGATTCACCATCTTC
131 GAAATAAGATTACTGGCTTCAATCTGCTCCGCTATAATCTCAGGGAGATAAGATTCACCATCTTC
*
45797875 GAT-TAGCTCCACTATTGCTTAGGG
196 GATCT-GCTCCACTATTGCTCAGGG
*
45797899 AGATAAGATCTGGAATTCTTCGGTCTATTCCACTGTAATCTCAGGGAGATAAGACCTGATGCGAT
1 AGATAAGATCTGAAATTCTTCGGTCTATTCCACTGTAATCTCAGGGAGATAAGACCTGATGCGAT
* *
45797964 CTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAATCTCAGG
66 CTACTCTACTGTAACTTCAGAGAGATAAAATCCTTTAGTTTAATCCGCTCCACTGTAATCTCAGG
*
45798029 GAAATAGGATTACTGGCTTCAATCTGCTCCGCTATAATCTCAGGGAGATAAGATTCACCATCTTC
131 GAAATAAGATTACTGGCTTCAATCTGCTCCGCTATAATCTCAGGGAGATAAGATTCACCATCTTC
*
45798094 GATCTGCTCCGCTATTGCTCAGGG
196 GATCTGCTCCACTATTGCTCAGGG
* *
45798118 AGACAGGATCTG
1 AGATAAGATCTG
45798130 TTATATTCAC
Statistics
Matches: 215, Mismatches: 15, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
219 214 1.00
220 1 0.00
ACGTcount: A:0.28, C:0.21, G:0.20, T:0.31
Consensus pattern (219 bp):
AGATAAGATCTGAAATTCTTCGGTCTATTCCACTGTAATCTCAGGGAGATAAGACCTGATGCGAT
CTACTCTACTGTAACTTCAGAGAGATAAAATCCTTTAGTTTAATCCGCTCCACTGTAATCTCAGG
GAAATAAGATTACTGGCTTCAATCTGCTCCGCTATAATCTCAGGGAGATAAGATTCACCATCTTC
GATCTGCTCCACTATTGCTCAGGG
Found at i:45810412 original size:22 final size:22
Alignment explanation
Indices: 45810370--45810436 Score: 68
Period size: 20 Copynumber: 3.0 Consensus size: 22
45810360 AATCGAAATG
45810370 AATA-AAAATTTTA-AAACATA
1 AATATAAAATTTTATAAACATA
*
45810390 AA-ATAAAATTTTATAAATTATA
1 AATATAAAATTTTATAAA-CATA
45810412 AATTATAATACATTTTATAAACATA
1 AA-TATAA-A-ATTTTATAAACATA
45810437 TACATATATT
Statistics
Matches: 38, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
19 1 0.03
20 11 0.29
21 3 0.08
22 5 0.13
24 4 0.11
25 4 0.11
26 10 0.26
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.37
Consensus pattern (22 bp):
AATATAAAATTTTATAAACATA
Found at i:45811957 original size:15 final size:15
Alignment explanation
Indices: 45811925--45811961 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
45811915 AGTATTGGAC
45811925 TTTTAT-TATATTTA
1 TTTTATATATATTTA
45811939 TTTTATATATATATT-
1 TTTTATATATAT-TTA
45811954 TTTTATAT
1 TTTTATAT
45811962 TTGGGTTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 6 0.29
15 13 0.62
16 2 0.10
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (15 bp):
TTTTATATATATTTA
Found at i:45812443 original size:13 final size:15
Alignment explanation
Indices: 45812417--45812448 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
45812407 CATTGTACGC
45812417 ATTTCCCGCCATC-T
1 ATTTCCCGCCATCTT
45812431 ATTTCCC-CCATCTT
1 ATTTCCCGCCATCTT
45812445 ATTT
1 ATTT
45812449 GGTTCAAAGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 5 0.29
14 12 0.71
ACGTcount: A:0.16, C:0.38, G:0.03, T:0.44
Consensus pattern (15 bp):
ATTTCCCGCCATCTT
Found at i:45814679 original size:29 final size:30
Alignment explanation
Indices: 45814637--45814708 Score: 85
Period size: 30 Copynumber: 2.5 Consensus size: 30
45814627 AAAAAGTATT
** *
45814637 AATTAAG-TATTAATTGAATATT-GCAATC
1 AATTAAGCTATTAATCAAATATTAGCAATA
*
45814665 AATTAAGCTATTAATCAAATGTTAGCAATA
1 AATTAAGCTATTAATCAAATATTAGCAATA
*
45814695 AATTAAGCTTTTAA
1 AATTAAGCTATTAA
45814709 AATATAGTTT
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
28 7 0.19
29 12 0.32
30 18 0.49
ACGTcount: A:0.44, C:0.08, G:0.10, T:0.38
Consensus pattern (30 bp):
AATTAAGCTATTAATCAAATATTAGCAATA
Found at i:45814897 original size:10 final size:10
Alignment explanation
Indices: 45814869--45814942 Score: 55
Period size: 10 Copynumber: 7.4 Consensus size: 10
45814859 TTTTTAAATT
45814869 TTATAAAAAA
1 TTATAAAAAA
* *
45814879 TCAT-TAAAA
1 TTATAAAAAA
45814888 TTATAAAAAAA
1 TTAT-AAAAAA
45814899 GTTA-AATAAAA
1 -TTATAA-AAAA
*
45814910 TTATATAAAA
1 TTATAAAAAA
*
45814920 TTAT-TAAAA
1 TTATAAAAAA
*
45814929 TGATAAAAAA
1 TTATAAAAAA
45814939 TTAT
1 TTAT
45814943 TGCAATTAAT
Statistics
Matches: 50, Mismatches: 8, Indels: 12
0.71 0.11 0.17
Matches are distributed among these distances:
9 15 0.30
10 23 0.46
11 9 0.18
12 3 0.06
ACGTcount: A:0.62, C:0.01, G:0.03, T:0.34
Consensus pattern (10 bp):
TTATAAAAAA
Found at i:45814940 original size:19 final size:19
Alignment explanation
Indices: 45814869--45814973 Score: 93
Period size: 19 Copynumber: 5.3 Consensus size: 19
45814859 TTTTTAAATT
*
45814869 TTATAAAAAATCATTAAAA
1 TTATAAAAAATTATTAAAA
*
45814888 TTATAAAAAAAGTTAAATAAAA
1 TTAT-AAAAAA-TT-ATTAAAA
*
45814910 TTATATAAAATTATTAAAA
1 TTATAAAAAATTATTAAAA
* **
45814929 TGATAAAAAATTATTGCAA
1 TTATAAAAAATTATTAAAA
* *
45814948 TTAATAAAAATTTATAAAAA
1 TT-ATAAAAAATTATTAAAA
45814968 TATATA
1 T-TATA
45814974 TATAAATTTA
Statistics
Matches: 68, Mismatches: 13, Indels: 9
0.76 0.14 0.10
Matches are distributed among these distances:
19 26 0.38
20 25 0.37
21 7 0.10
22 10 0.15
ACGTcount: A:0.61, C:0.02, G:0.03, T:0.34
Consensus pattern (19 bp):
TTATAAAAAATTATTAAAA
Found at i:45816321 original size:17 final size:18
Alignment explanation
Indices: 45816296--45816329 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
45816286 GAAAGAGTAG
*
45816296 TAATTTTTAAT-TTTTTA
1 TAATATTTAATATTTTTA
45816313 TAATATTTAATATTTTT
1 TAATATTTAATATTTTT
45816330 TAAAAAATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (18 bp):
TAATATTTAATATTTTTA
Found at i:45819528 original size:18 final size:18
Alignment explanation
Indices: 45819495--45819535 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
45819485 GTTCGCATTC
*
45819495 AGTTCGTATTCATATAAG
1 AGTTCGCATTCATATAAG
45819513 -GTTCGCATTGCATATAAG
1 AGTTCGCATT-CATATAAG
45819531 AGTTC
1 AGTTC
45819536 TCATACCTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
17 8 0.40
18 8 0.40
19 4 0.20
ACGTcount: A:0.29, C:0.15, G:0.20, T:0.37
Consensus pattern (18 bp):
AGTTCGCATTCATATAAG
Found at i:45822043 original size:58 final size:60
Alignment explanation
Indices: 45821972--45822102 Score: 180
Period size: 58 Copynumber: 2.2 Consensus size: 60
45821962 TAATTCATAT
* *
45821972 TTTAATAATAATTAAATTAAGAATGTTATTAAATTA-TA-TATTA-TT-TTATTAAATTGTA
1 TTTAATAATAATTAAATTAA-AATATGATTAAATTATTATTATTATTTATTATTAAATT-TA
*
45822030 TTTAATAATAATTATATTAAAATATGATTAAATTATTTATTATTATTTATTATTAAATTTA
1 TTTAATAATAATTAAATTAAAATATGATTAAATTA-TTATTATTATTTATTATTAAATTTA
45822091 TTTAATAATAAT
1 TTTAATAATAAT
45822103 CCTATTAAAA
Statistics
Matches: 65, Mismatches: 3, Indels: 7
0.87 0.04 0.09
Matches are distributed among these distances:
57 13 0.20
58 19 0.29
59 2 0.03
60 5 0.08
61 16 0.25
62 10 0.15
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (60 bp):
TTTAATAATAATTAAATTAAAATATGATTAAATTATTATTATTATTTATTATTAAATTTA
Found at i:45822101 original size:61 final size:57
Alignment explanation
Indices: 45821972--45822113 Score: 178
Period size: 61 Copynumber: 2.4 Consensus size: 57
45821962 TAATTCATAT
* * *
45821972 TTTAATAATAATTAAATTAAGAATGTTATTAAATTATATATTATTTTATTAAATTGTA
1 TTTAATAATAATTATATTAA-AATATGATTAAATTATATATTATTTTATTAAATTGTA
45822030 TTTAATAATAATTATATTAAAATATGATTAAATTATTTATTATTATTTATTATTAAATT-TA
1 TTTAATAATAATTATATTAAAATATGATTAAATTA--TA-TATTA-TT-TTATTAAATTGTA
**
45822091 TTTAATAATAATCCTATTAAAAT
1 TTTAATAATAATTATATTAAAAT
45822114 TTAATAACAA
Statistics
Matches: 74, Mismatches: 5, Indels: 7
0.86 0.06 0.08
Matches are distributed among these distances:
57 13 0.18
58 19 0.26
59 2 0.03
60 5 0.07
61 25 0.34
62 10 0.14
ACGTcount: A:0.45, C:0.01, G:0.03, T:0.51
Consensus pattern (57 bp):
TTTAATAATAATTATATTAAAATATGATTAAATTATATATTATTTTATTAAATTGTA
Found at i:45826624 original size:117 final size:114
Alignment explanation
Indices: 45826394--45826628 Score: 382
Period size: 117 Copynumber: 2.0 Consensus size: 114
45826384 TCGTAAGTCT
45826394 CTAAGGGCTCCTTTAGATGGGTGTTTACCTCTAGTGCGGTGCATTTAGCTTTTTTTTGTCTCACG
1 CTAAGGGCTCCTTTAGATGGGTGTTTACCTCTAGTGCGGTGCATTTAGCTTTTTTTTGTCTCACG
*
45826459 CTACAGTATGGTTATAGTATCTAATCTCATCGCCACAACAGTTTTTACA
66 CTACAGTATGGCTATAGTATCTAATCTCATCGCCACAACAGTTTTTACA
*
45826508 CTAAGGGCTCCTTTAGATGGGTGTTTACCTCTAGTGCGGTGCGTTTAGCTTTTTTTTTTTGTCTC
1 CTAAGGGCTCCTTTAGATGGGTGTTTACCTCTAGTGCGGTGCATTTAGC---TTTTTTTTGTCTC
* * *
45826573 ACTCTACAGTATGGCTATAGTGTCTAATCTCATCGCCATAACTA-TTTTTACA
63 ACGCTACAGTATGGCTATAGTATCTAATCTCATCGCCACAAC-AGTTTTTACA
45826625 CTAA
1 CTAA
45826629 CCGCAGGTAA
Statistics
Matches: 112, Mismatches: 5, Indels: 5
0.92 0.04 0.04
Matches are distributed among these distances:
114 48 0.43
117 63 0.56
118 1 0.01
ACGTcount: A:0.20, C:0.21, G:0.19, T:0.40
Consensus pattern (114 bp):
CTAAGGGCTCCTTTAGATGGGTGTTTACCTCTAGTGCGGTGCATTTAGCTTTTTTTTGTCTCACG
CTACAGTATGGCTATAGTATCTAATCTCATCGCCACAACAGTTTTTACA
Found at i:45828462 original size:12 final size:12
Alignment explanation
Indices: 45828445--45828470 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
45828435 CTTTTCCCTT
45828445 CCATCGGTTCTG
1 CCATCGGTTCTG
45828457 CCATCGGTTCTG
1 CCATCGGTTCTG
45828469 CC
1 CC
45828471 GTCGCTTAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.08, C:0.38, G:0.23, T:0.31
Consensus pattern (12 bp):
CCATCGGTTCTG
Found at i:45831354 original size:15 final size:17
Alignment explanation
Indices: 45831320--45831452 Score: 91
Period size: 18 Copynumber: 8.0 Consensus size: 17
45831310 AATACTAAGA
45831320 ATTTTATTAAATTATAT
1 ATTTTATTAAATTATAT
*
45831337 ATTTTGTTAAA-T-TAT
1 ATTTTATTAAATTATAT
* *
45831352 A-TTTAAT-AATAAT-T
1 ATTTTATTAAATTATAT
* * *
45831366 ATTTAAATTATATTTTAT
1 ATTT-TATTAAATTATAT
* * *
45831384 AGTATTA-TATATTAT-G
1 A-TTTTATTAAATTATAT
*
45831400 ATTTTAGTAAATTCATAT
1 ATTTTATTAAATT-ATAT
45831418 ATTTTATTAAATTATATT
1 ATTTTATTAAATTATA-T
45831436 ATTTTATTAAATTATAT
1 ATTTTATTAAATTATAT
45831453 TTAATAATAA
Statistics
Matches: 88, Mismatches: 17, Indels: 22
0.69 0.13 0.17
Matches are distributed among these distances:
13 2 0.02
14 6 0.07
15 11 0.12
16 9 0.10
17 26 0.30
18 32 0.36
19 2 0.02
ACGTcount: A:0.40, C:0.01, G:0.03, T:0.56
Consensus pattern (17 bp):
ATTTTATTAAATTATAT
Found at i:45831516 original size:44 final size:49
Alignment explanation
Indices: 45831428--45831517 Score: 118
Period size: 47 Copynumber: 1.9 Consensus size: 49
45831418 ATTTTATTAA
*
45831428 ATTATATTATTTTATTAAATTATATTTAATAATAATTATGTTAAAATATG
1 ATTAAATTATTTTATTAAATTATATTTAATAATAATTA-GTTAAAATATG
*
45831478 ATTAAATTA-TTTATT-ATTTATA-TTAATAAT-ATTA-TTAAAA
1 ATTAAATTATTTTATTAAATTATATTTAATAATAATTAGTTAAAA
45831518 ATTAATAACA
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
44 6 0.16
46 4 0.11
47 8 0.21
48 6 0.16
49 6 0.16
50 8 0.21
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (49 bp):
ATTAAATTATTTTATTAAATTATATTTAATAATAATTAGTTAAAATATG
Found at i:45831678 original size:44 final size:46
Alignment explanation
Indices: 45831611--45831703 Score: 145
Period size: 44 Copynumber: 2.1 Consensus size: 46
45831601 TTACACTTCT
* * *
45831611 ATTCCATTCAGCCAAACACAAGAA-TATC-ATTACGCCTCTATTCC
1 ATTCCATTCAACCAAACAAAAGAATTACCTATTACGCCTCTATTCC
45831655 ATTCCATTCAACCAAACAAAAGAATTACCTATTACGCCTCTATTCC
1 ATTCCATTCAACCAAACAAAAGAATTACCTATTACGCCTCTATTCC
45831701 ATT
1 ATT
45831704 ACGCATCTAT
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
44 22 0.50
45 3 0.07
46 19 0.43
ACGTcount: A:0.35, C:0.30, G:0.05, T:0.29
Consensus pattern (46 bp):
ATTCCATTCAACCAAACAAAAGAATTACCTATTACGCCTCTATTCC
Found at i:45831706 original size:16 final size:16
Alignment explanation
Indices: 45831685--45831721 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
45831675 AGAATTACCT
*
45831685 ATTACGCCTCTATTCC
1 ATTACGCATCTATTCC
45831701 ATTACGCATCTATTCC
1 ATTACGCATCTATTCC
45831717 ATTAC
1 ATTAC
45831722 AGCGAACCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.24, C:0.32, G:0.05, T:0.38
Consensus pattern (16 bp):
ATTACGCATCTATTCC
Found at i:45832676 original size:115 final size:113
Alignment explanation
Indices: 45832450--45832729 Score: 314
Period size: 115 Copynumber: 2.4 Consensus size: 113
45832440 TTTTTTATAA
* * *
45832450 TTTTTTTAGATTTAAGTTTGTATTAAATGTATGGTTAATTTGTTTTATTAATGTTATTGTTGTAT
1 TTTTTTTAGATTTAAGTTTGTATT-AAGGTATGATTAATTT-TTTTATTAATGTTATTGTGGTAT
*
45832515 CTTATATCAGTTTTTTTCGTATTCAAGGGAAATGATATTTTTTTGTTGTG
64 CTTATATCAGATTTTTTCGTATTCAAGGGAAATGATATTTTTTTGTTGTG
* *
45832565 TTTTTTTAGTTTTATA-TTTGTATTGAAGGTATGATTAATTTATTTTATTAATGTTTTTGTGGTA
1 TTTTTTTAGATTTA-AGTTTGTATT-AAGGTATGATTAATTT-TTTTATTAATGTTATTGTGGTA
* ***** *
45832629 TCTTATATTA-ATTTTTT-GTATTTTCTTGAAATGTTATTTTTTGTTGTTGTG
63 TCTTATATCAGATTTTTTCGTATTCAAGGGAAATGATA-TTTTT-TTGTTGTG
* * * * *
45832680 TTTTATTAGCTTTAAGCTTGTATTTAGGTTTGATTAATTTTTTTATTAAT
1 TTTTTTTAGATTTAAGTTTGTATTAAGGTATGATTAATTTTTTTATTAAT
45832730 ATGGGTAAGA
Statistics
Matches: 141, Mismatches: 20, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
113 23 0.16
114 26 0.18
115 91 0.65
116 1 0.01
ACGTcount: A:0.23, C:0.03, G:0.15, T:0.60
Consensus pattern (113 bp):
TTTTTTTAGATTTAAGTTTGTATTAAGGTATGATTAATTTTTTTATTAATGTTATTGTGGTATCT
TATATCAGATTTTTTCGTATTCAAGGGAAATGATATTTTTTTGTTGTG
Found at i:45832881 original size:22 final size:22
Alignment explanation
Indices: 45832827--45832881 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 22
45832817 ATTTGGGGAA
45832827 TTGTGTTTATTAATATAATTAAT
1 TTGT-TTTATTAATATAATTAAT
* *
45832850 TTGTTATATTAAT-TAATTTAT
1 TTGTTTTATTAATATAATTAAT
*
45832871 TATTTTTTATT
1 T-TGTTTTATT
45832882 CAAGTTTTAT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
21 8 0.30
22 15 0.56
23 4 0.15
ACGTcount: A:0.31, C:0.00, G:0.05, T:0.64
Consensus pattern (22 bp):
TTGTTTTATTAATATAATTAAT
Found at i:45837715 original size:16 final size:17
Alignment explanation
Indices: 45837682--45837716 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
45837672 TTCATTATTC
*
45837682 AATTTTTAATTATTTAT
1 AATTTTTAATTATATAT
45837699 AATTTTTAA-TATATAT
1 AATTTTTAATTATATAT
45837715 AA
1 AA
45837717 AACTACGAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
AATTTTTAATTATATAT
Found at i:45842128 original size:18 final size:17
Alignment explanation
Indices: 45842107--45842207 Score: 123
Period size: 17 Copynumber: 5.8 Consensus size: 17
45842097 AAAAACAAAA
45842107 TTTTAAAACACGAGAATT
1 TTTTAAAACACGA-AATT
*
45842125 TTTTGAAAACATGAAATT
1 TTTT-AAAACACGAAATT
* *
45842143 TTTTGAAACACGAAAAT
1 TTTTAAAACACGAAATT
45842160 TTTT-AAACACGAGAATT
1 TTTTAAAACACGA-AATT
45842177 TTTTGAAAACACGAAATT
1 TTTT-AAAACACGAAATT
*
45842195 TTTTTAAACACGA
1 TTTTAAAACACGA
45842208 GAAAGTTTTT
Statistics
Matches: 73, Mismatches: 6, Indels: 9
0.83 0.07 0.10
Matches are distributed among these distances:
16 8 0.11
17 29 0.40
18 20 0.27
19 16 0.22
ACGTcount: A:0.44, C:0.11, G:0.11, T:0.35
Consensus pattern (17 bp):
TTTTAAAACACGAAATT
Found at i:45842168 original size:52 final size:52
Alignment explanation
Indices: 45842103--45842217 Score: 185
Period size: 52 Copynumber: 2.2 Consensus size: 52
45842093 GTAAAAAAAC
* *
45842103 AAAATTTTAAAACACGAGAATTTTTTGAAAACATGAAATTTTTTGAAACACG
1 AAAATTTTTAAACACGAGAATTTTTTGAAAACACGAAATTTTTTGAAACACG
*
45842155 AAAATTTTTAAACACGAGAATTTTTTGAAAACACGAAATTTTTTTAAACACG
1 AAAATTTTTAAACACGAGAATTTTTTGAAAACACGAAATTTTTTGAAACACG
45842207 AGAAAGTTTTT
1 A-AAA-TTTTT
45842218 TTTTAAAAAC
Statistics
Matches: 58, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
52 50 0.86
53 3 0.05
54 5 0.09
ACGTcount: A:0.44, C:0.10, G:0.11, T:0.35
Consensus pattern (52 bp):
AAAATTTTTAAACACGAGAATTTTTTGAAAACACGAAATTTTTTGAAACACG
Found at i:45842216 original size:17 final size:17
Alignment explanation
Indices: 45842103--45842217 Score: 99
Period size: 17 Copynumber: 6.5 Consensus size: 17
45842093 GTAAAAAAAC
*
45842103 AAAA-TTTTAAAACACG
1 AAAATTTTTGAAACACG
* *
45842119 AGAATTTTTTGAAAACATG
1 A-AAATTTTTG-AAACACG
*
45842138 AAATTTTTTGAAACACG
1 AAAATTTTTGAAACACG
45842155 AAAATTTTT-AAACACG
1 AAAATTTTTGAAACACG
*
45842171 AGAATTTTTTGAAAACACG
1 A-AAATTTTTG-AAACACG
* *
45842190 AAATTTTTTTAAACACG
1 AAAATTTTTGAAACACG
45842207 AGAAAGTTTTT
1 A-AAA-TTTTT
45842218 TTTTAAAAAC
Statistics
Matches: 83, Mismatches: 8, Indels: 13
0.80 0.08 0.12
Matches are distributed among these distances:
16 9 0.11
17 31 0.37
18 23 0.28
19 20 0.24
ACGTcount: A:0.44, C:0.10, G:0.11, T:0.35
Consensus pattern (17 bp):
AAAATTTTTGAAACACG
Found at i:45842216 original size:18 final size:19
Alignment explanation
Indices: 45842107--45842218 Score: 116
Period size: 18 Copynumber: 6.2 Consensus size: 19
45842097 AAAAACAAAA
*
45842107 TTTTAAAACACGAG-AATT
1 TTTTGAAACACGAGAAATT
45842125 TTTTGAAA-AC-ATGAAATT
1 TTTTGAAACACGA-GAAATT
45842143 TTTTGAAACACGA-AAA-T
1 TTTTGAAACACGAGAAATT
45842160 TTTT-AAACACGAG-AATT
1 TTTTGAAACACGAGAAATT
45842177 TTTTGAAA-AC-ACGAAATT
1 TTTTGAAACACGA-GAAATT
*
45842195 TTTTTAAACACGAGAAAGTT
1 TTTTGAAACACGAGAAA-TT
45842215 TTTT
1 TTTT
45842219 TTTAAAAACG
Statistics
Matches: 80, Mismatches: 2, Indels: 22
0.77 0.02 0.21
Matches are distributed among these distances:
16 12 0.15
17 16 0.20
18 36 0.45
19 8 0.10
20 8 0.10
ACGTcount: A:0.42, C:0.10, G:0.12, T:0.37
Consensus pattern (19 bp):
TTTTGAAACACGAGAAATT
Found at i:45842234 original size:17 final size:17
Alignment explanation
Indices: 45842107--45842236 Score: 84
Period size: 18 Copynumber: 7.2 Consensus size: 17
45842097 AAAAACAAAA
45842107 TTTTAAAACACGAGAATTT
1 TTTTAAAA-ACGA-AATTT
* *
45842126 TTTGAAAACATGAAATTT
1 TTTTAAAA-ACGAAATTT
* * *
45842144 TTTGAAACACGAAA-AT
1 TTTTAAAAACGAAATTT
*
45842160 TTTTAAACACGAGAATTT
1 TTTTAAAAACGA-AATTT
*
45842178 TTTGAAAACACGAAATTT
1 TTTTAAAA-ACGAAATTT
*
45842196 TTTTAAACACGAGAAAGTTTTT
1 TTTTAAAAAC--GAAA---TTT
45842218 TTTTAAAAACG-AATTT
1 TTTTAAAAACGAAATTT
45842234 TTT
1 TTT
45842237 CAATTTTTTT
Statistics
Matches: 91, Mismatches: 12, Indels: 19
0.75 0.10 0.16
Matches are distributed among these distances:
16 18 0.20
17 9 0.10
18 30 0.33
19 21 0.23
20 1 0.01
22 12 0.13
ACGTcount: A:0.42, C:0.09, G:0.11, T:0.38
Consensus pattern (17 bp):
TTTTAAAAACGAAATTT
Found at i:45843013 original size:12 final size:11
Alignment explanation
Indices: 45842988--45843050 Score: 54
Period size: 11 Copynumber: 5.5 Consensus size: 11
45842978 GACTGTTTTA
45842988 TTTTTTTTCCT
1 TTTTTTTTCCT
* *
45842999 TTTTTTCTCTT
1 TTTTTTTTCCT
45843010 TTTTTTTTCCCT
1 TTTTTTTT-CCT
*
45843022 TTCTTCTTTCCT
1 TT-TTTTTTCCT
* * *
45843034 TCTTTCTTCCC
1 TTTTTTTTCCT
45843045 TTTTTT
1 TTTTTT
45843051 CTTTTTTTCT
Statistics
Matches: 39, Mismatches: 11, Indels: 4
0.72 0.20 0.07
Matches are distributed among these distances:
11 26 0.67
12 8 0.21
13 5 0.13
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (11 bp):
TTTTTTTTCCT
Found at i:45843044 original size:24 final size:24
Alignment explanation
Indices: 45843016--45843066 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
45843006 TCTTTTTTTT
45843016 TTCCCTTTCTTCTTTCCTTCTTTC
1 TTCCCTTTCTTCTTTCCTTCTTTC
* **
45843040 TTCCCTTTTTTCTTTTTTTCTTTC
1 TTCCCTTTCTTCTTTCCTTCTTTC
45843064 TTC
1 TTC
45843067 TCCGTTCATC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (24 bp):
TTCCCTTTCTTCTTTCCTTCTTTC
Found at i:45843051 original size:12 final size:12
Alignment explanation
Indices: 45842988--45843053 Score: 57
Period size: 12 Copynumber: 5.8 Consensus size: 12
45842978 GACTGTTTTA
*
45842988 TTTTTT-TTCCT
1 TTTTTTCTTCCC
*
45842999 TTTTTTC-T-CT
1 TTTTTTCTTCCC
*
45843009 TTTTTTTTTCCC
1 TTTTTTCTTCCC
* *
45843021 TTTCTTCTTTCC
1 TTTTTTCTTCCC
*
45843033 TTCTTTCTTCCC
1 TTTTTTCTTCCC
45843045 TTTTTTCTT
1 TTTTTTCTT
45843054 TTTTTCTTTC
Statistics
Matches: 43, Mismatches: 9, Indels: 5
0.75 0.16 0.09
Matches are distributed among these distances:
10 8 0.19
11 8 0.19
12 27 0.63
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (12 bp):
TTTTTTCTTCCC
Found at i:45843192 original size:19 final size:18
Alignment explanation
Indices: 45843167--45843211 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
45843157 CTCTCATTTT
* *
45843167 CTTTTTTTTCTTC-TTTG
1 CTTTTTTTTTTTCGCTTG
45843184 CTTTCTTTTTTTTCGCTTG
1 CTTT-TTTTTTTTCGCTTG
45843203 CTTTTTTTT
1 CTTTTTTTT
45843212 ATTTTTTACT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 4 0.17
18 13 0.54
19 7 0.29
ACGTcount: A:0.00, C:0.18, G:0.07, T:0.76
Consensus pattern (18 bp):
CTTTTTTTTTTTCGCTTG
Done.