Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr4
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: 30015117
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1306243 characters in sequence are not A, C, G, or T
File 84 of 85
Found at i:29556572 original size:23 final size:23
Alignment explanation
Indices: 29556551--29556597 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
29556541 TAAGATTTTT
29556551 TTTATCAATTTTATATTTTTTTATG
1 TTTAT-AATTTTA-ATTTTTTTATG
*
29556576 TTTATATTTTTAATTTTTTTAT
1 TTTATAATTTTAATTTTTTTAT
29556598 AAGATAAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 10 0.48
24 6 0.29
25 5 0.24
ACGTcount: A:0.23, C:0.02, G:0.02, T:0.72
Consensus pattern (23 bp):
TTTATAATTTTAATTTTTTTATG
Found at i:29556624 original size:74 final size:74
Alignment explanation
Indices: 29556513--29556659 Score: 287
Period size: 73 Copynumber: 2.0 Consensus size: 74
29556503 AAATATTTCA
29556513 TAATTTTTTTATAAGATAAATAATTTTTTAAGATTTTTTTTATCAATTTTATATTTTTTTAT-GT
1 TAATTTTTTTATAAGATAAATAATTTTTTAAGATTTTTTTTATCAATTTTATATTTTTTTATGGT
29556577 TTATATTTT
66 TTATATTTT
29556586 TAATTTTTTTATAAGATAAATAATTTTTTAAGATTTTTTTTATCAATTTTATATTTTTTTATGGT
1 TAATTTTTTTATAAGATAAATAATTTTTTAAGATTTTTTTTATCAATTTTATATTTTTTTATGGT
29556651 TTATATTTT
66 TTATATTTT
29556660 AACAATTAAA
Statistics
Matches: 73, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
73 62 0.85
74 11 0.15
ACGTcount: A:0.30, C:0.01, G:0.05, T:0.64
Consensus pattern (74 bp):
TAATTTTTTTATAAGATAAATAATTTTTTAAGATTTTTTTTATCAATTTTATATTTTTTTATGGT
TTATATTTT
Found at i:29559683 original size:6 final size:6
Alignment explanation
Indices: 29559672--29559699 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
29559662 TAGGGAAACT
29559672 ATGCCC ATGCCC ATGCCC ATGCCC ATGC
1 ATGCCC ATGCCC ATGCCC ATGCCC ATGC
29559700 TATATATATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.18, C:0.46, G:0.18, T:0.18
Consensus pattern (6 bp):
ATGCCC
Found at i:29562639 original size:35 final size:33
Alignment explanation
Indices: 29562592--29562661 Score: 88
Period size: 35 Copynumber: 2.1 Consensus size: 33
29562582 GTGATAATTG
29562592 GACACATGTTTTGTATTAACTTAATTACA-ACAT
1 GACACATGTTTTGTATTAACTTAATTA-AGACAT
* *
29562625 GACACAATGGTTTTGTGTTAAGTTAATTAAGACAT
1 GACAC-AT-GTTTTGTATTAACTTAATTAAGACAT
29562660 GA
1 GA
29562662 TTTGACATTG
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
33 5 0.16
34 3 0.09
35 24 0.75
ACGTcount: A:0.36, C:0.11, G:0.16, T:0.37
Consensus pattern (33 bp):
GACACATGTTTTGTATTAACTTAATTAAGACAT
Found at i:29563678 original size:2 final size:2
Alignment explanation
Indices: 29563673--29563708 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
29563663 TTCACACACT
*
29563673 GA GA GA GA GA CA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
29563709 AGGGGGGGGC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.03, G:0.47, T:0.00
Consensus pattern (2 bp):
GA
Found at i:29565830 original size:7 final size:8
Alignment explanation
Indices: 29565811--29565835 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
29565801 CAAATAATAC
29565811 AAAAAATT
1 AAAAAATT
29565819 AAAAAATT
1 AAAAAATT
29565827 AAAAAATT
1 AAAAAATT
29565835 A
1 A
29565836 TCAAAATAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (8 bp):
AAAAAATT
Found at i:29565936 original size:27 final size:27
Alignment explanation
Indices: 29565897--29565964 Score: 91
Period size: 27 Copynumber: 2.5 Consensus size: 27
29565887 CGAGGGACTA
* * *
29565897 CCACAGACGGCACTAAAGGTGCCAGTG
1 CCACAGGCGGCACCAAAGGTGCCACTG
* *
29565924 GCAGAGGCGGCACCAAAGGTGCCACTG
1 CCACAGGCGGCACCAAAGGTGCCACTG
29565951 CCACAGGCGGCACC
1 CCACAGGCGGCACC
29565965 CCCCTTATAT
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.26, C:0.34, G:0.32, T:0.07
Consensus pattern (27 bp):
CCACAGGCGGCACCAAAGGTGCCACTG
Found at i:29567894 original size:3 final size:3
Alignment explanation
Indices: 29567888--29567926 Score: 53
Period size: 3 Copynumber: 13.3 Consensus size: 3
29567878 AAGGAAAAAA
* *
29567888 AAG AAG AAG AAG -AG AAG AAG AAG ATG ATG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
29567927 GAGATAACAG
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
2 2 0.06
3 31 0.94
ACGTcount: A:0.62, C:0.00, G:0.33, T:0.05
Consensus pattern (3 bp):
AAG
Found at i:29567905 original size:11 final size:11
Alignment explanation
Indices: 29567889--29567923 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
29567879 AGGAAAAAAA
29567889 AGAAGAAGAAG
1 AGAAGAAGAAG
29567900 AGAAGAAGAAG
1 AGAAGAAGAAG
*
29567911 ATGATGAAGAAG
1 A-GAAGAAGAAG
29567923 A
1 A
29567924 AGAGAGATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 12 0.55
12 10 0.45
ACGTcount: A:0.60, C:0.00, G:0.34, T:0.06
Consensus pattern (11 bp):
AGAAGAAGAAG
Found at i:29567943 original size:23 final size:21
Alignment explanation
Indices: 29567917--29567968 Score: 59
Period size: 23 Copynumber: 2.4 Consensus size: 21
29567907 GAAGATGATG
29567917 AAGAAGAAGAGAGATAACAGAAA
1 AAGAAGAAGAGAGATAA-AG-AA
* *
29567940 AAGAATAATAGAGATAAAGAA
1 AAGAAGAAGAGAGATAAAGAA
*
29567961 CAGAAGAA
1 AAGAAGAA
29567969 AACAGGAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
21 8 0.32
22 2 0.08
23 15 0.60
ACGTcount: A:0.65, C:0.04, G:0.23, T:0.08
Consensus pattern (21 bp):
AAGAAGAAGAGAGATAAAGAA
Found at i:29568270 original size:14 final size:14
Alignment explanation
Indices: 29568253--29568285 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
29568243 AATATATACA
29568253 TATATGTATGTGTG
1 TATATGTATGTGTG
*
29568267 TATATGTGTGTGTG
1 TATATGTATGTGTG
29568281 TATAT
1 TATAT
29568286 ATATAAACAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.21, C:0.00, G:0.27, T:0.52
Consensus pattern (14 bp):
TATATGTATGTGTG
Found at i:29568837 original size:15 final size:15
Alignment explanation
Indices: 29568817--29568845 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
29568807 GCTTCTTTTA
29568817 ACCATCATCATCATC
1 ACCATCATCATCATC
29568832 ACCATCATCATCAT
1 ACCATCATCATCAT
29568846 ACTCAAGATC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.34, C:0.38, G:0.00, T:0.28
Consensus pattern (15 bp):
ACCATCATCATCATC
Found at i:29578375 original size:28 final size:29
Alignment explanation
Indices: 29578335--29578389 Score: 85
Period size: 28 Copynumber: 1.9 Consensus size: 29
29578325 TAAATATATA
29578335 TTTTTTAATTTTTTTAATTTTAAAATACT
1 TTTTTTAATTTTTTTAATTTTAAAATACT
* *
29578364 TTTTTTTA-TTTTTTATTTTTAAAATA
1 TTTTTTAATTTTTTTAATTTTAAAATA
29578390 AATTTTTGGT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 17 0.71
29 7 0.29
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (29 bp):
TTTTTTAATTTTTTTAATTTTAAAATACT
Found at i:29578395 original size:29 final size:30
Alignment explanation
Indices: 29578326--29578396 Score: 83
Period size: 28 Copynumber: 2.4 Consensus size: 30
29578316 CGAATATAAT
*
29578326 AAATATATATTTTTTAATTTTTTTAATTTTA
1 AAATAAAT-TTTTTTAATTTTTTTAATTTTA
* * *
29578357 AAAT-ACTTTTTTTTA-TTTTTTATTTTTA
1 AAATAAATTTTTTTAATTTTTTTAATTTTA
29578385 AAATAAATTTTT
1 AAATAAATTTTT
29578397 GGTGTTTATT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
28 16 0.47
29 13 0.38
30 1 0.03
31 4 0.12
ACGTcount: A:0.34, C:0.01, G:0.00, T:0.65
Consensus pattern (30 bp):
AAATAAATTTTTTTAATTTTTTTAATTTTA
Found at i:29580438 original size:4 final size:4
Alignment explanation
Indices: 29580429--29580485 Score: 96
Period size: 4 Copynumber: 14.2 Consensus size: 4
29580419 ATTGAAAAGC
*
29580429 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA GGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
*
29580477 GGTA TGTA T
1 TGTA TGTA T
29580486 TTGTATATTT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
4 51 1.00
ACGTcount: A:0.25, C:0.00, G:0.28, T:0.47
Consensus pattern (4 bp):
TGTA
Found at i:29584480 original size:30 final size:30
Alignment explanation
Indices: 29584445--29584547 Score: 98
Period size: 31 Copynumber: 3.4 Consensus size: 30
29584435 TAACTAGGTC
*
29584445 CCTTCAAAATTTTTAAAAATTCTAAATAAA
1 CCTTCAAAATTTTTAAAAATTCTAATTAAA
* * *
29584475 CCTTCAAATAGTTTTAAAAATTTTAATTAGA
1 CCTTCAAA-ATTTTTAAAAATTCTAATTAAA
* * * * * *
29584506 CCCTCAAATTTTTTGAAAAGTCTCATTAAT
1 CCTTCAAAATTTTTAAAAATTCTAATTAAA
29584536 CCTCTCAAAATT
1 CCT-TCAAAATT
29584548 GTAACATTTT
Statistics
Matches: 56, Mismatches: 15, Indels: 3
0.76 0.20 0.04
Matches are distributed among these distances:
30 24 0.43
31 32 0.57
ACGTcount: A:0.41, C:0.17, G:0.04, T:0.39
Consensus pattern (30 bp):
CCTTCAAAATTTTTAAAAATTCTAATTAAA
Found at i:29584893 original size:3 final size:3
Alignment explanation
Indices: 29584885--29584914 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
29584875 CAATGACCTG
*
29584885 CAA CAA CAA CAA CAA CAA CAA CAA GAA CAA
1 CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA
29584915 TTTCATGGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.67, C:0.30, G:0.03, T:0.00
Consensus pattern (3 bp):
CAA
Found at i:29589078 original size:57 final size:58
Alignment explanation
Indices: 29588978--29589092 Score: 162
Period size: 57 Copynumber: 2.0 Consensus size: 58
29588968 ATAGAAATGG
* *
29588978 TGAAAATGGAGAAATGAGAAAATTTTGGAAATGATGATGATTTTCTCCAAAATGAAAA
1 TGAAAATGGAGAAATGAGAAAATTTTGGAAATGATGATAATTTTCTCCAAAAAGAAAA
* * *
29589036 TGAAAATGGAGAAATGA-AATCA-TTTGGAAATGATTATAATTTTCTCTAAAAAGAAAA
1 TGAAAATGGAGAAATGAGAA-AATTTTGGAAATGATGATAATTTTCTCCAAAAAGAAAA
29589093 AAATGAAAAA
Statistics
Matches: 51, Mismatches: 5, Indels: 3
0.86 0.08 0.05
Matches are distributed among these distances:
57 33 0.65
58 18 0.35
ACGTcount: A:0.48, C:0.05, G:0.18, T:0.29
Consensus pattern (58 bp):
TGAAAATGGAGAAATGAGAAAATTTTGGAAATGATGATAATTTTCTCCAAAAAGAAAA
Found at i:29590436 original size:16 final size:16
Alignment explanation
Indices: 29590415--29590445 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
29590405 TGTGCAATTG
29590415 AATTTGATTCAATTTA
1 AATTTGATTCAATTTA
29590431 AATTTGATTCAATTT
1 AATTTGATTCAATTT
29590446 TCACAAACCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.35, C:0.06, G:0.06, T:0.52
Consensus pattern (16 bp):
AATTTGATTCAATTTA
Found at i:29594799 original size:26 final size:25
Alignment explanation
Indices: 29594735--29594785 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
29594725 AATGTGAAAA
29594735 TATGTCCTAAATTTCTTTTTTACTT
1 TATGTCCTAAATTTCTTTTTTACTT
29594760 TATGTCCTAAATTTCTTTTTTACTT
1 TATGTCCTAAATTTCTTTTTTACTT
29594785 T
1 T
29594786 CCAGTGTAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.20, C:0.16, G:0.04, T:0.61
Consensus pattern (25 bp):
TATGTCCTAAATTTCTTTTTTACTT
Found at i:29597239 original size:60 final size:61
Alignment explanation
Indices: 29597166--29597280 Score: 146
Period size: 62 Copynumber: 1.9 Consensus size: 61
29597156 GAATTTGATA
* *
29597166 TTTTTTTTAAATTTGATA-TCTAAG-TTTTTTTGA-TCCAATTTGGTACTTGAACTTAATAT
1 TTTTTTTTAAATTTGATACT-TAAGTTTTTTTTAAGTCCAATTTGGTACTTAAACTTAATAT
* * *
29597225 TTTTTTTCTTAATTTGGTACTTAAGTTTTTTTTAAGTTCAATTTGGTACTTAAACT
1 TTTTTTT-TAAATTTGATACTTAAGTTTTTTTTAAGTCCAATTTGGTACTTAAACT
29597281 AATCACATGT
Statistics
Matches: 47, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
59 7 0.15
60 13 0.28
61 9 0.19
62 18 0.38
ACGTcount: A:0.25, C:0.09, G:0.10, T:0.56
Consensus pattern (61 bp):
TTTTTTTTAAATTTGATACTTAAGTTTTTTTTAAGTCCAATTTGGTACTTAAACTTAATAT
Found at i:29597254 original size:27 final size:29
Alignment explanation
Indices: 29597216--29597277 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
29597206 TGGTACTTGA
*
29597216 ACTTAATATTTTTTT-TCTT-AATTTGGT
1 ACTTAATATTTTTTTAACTTCAATTTGGT
*
29597243 ACTTAAGT-TTTTTTTAAGTTCAATTTGGT
1 ACTTAA-TATTTTTTTAACTTCAATTTGGT
29597272 ACTTAA
1 ACTTAA
29597278 ACTAATCACA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
27 13 0.43
28 3 0.10
29 14 0.47
ACGTcount: A:0.26, C:0.08, G:0.10, T:0.56
Consensus pattern (29 bp):
ACTTAATATTTTTTTAACTTCAATTTGGT
Found at i:29598618 original size:19 final size:17
Alignment explanation
Indices: 29598594--29598628 Score: 52
Period size: 19 Copynumber: 1.9 Consensus size: 17
29598584 TTTTTTTGGA
29598594 TATTGTATAACTCTTGTTT
1 TATTGT-TAACT-TTGTTT
29598613 TATTGTTAACTTTGTT
1 TATTGTTAACTTTGTT
29598629 ACTATTTTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.31
18 5 0.31
19 6 0.38
ACGTcount: A:0.20, C:0.09, G:0.11, T:0.60
Consensus pattern (17 bp):
TATTGTTAACTTTGTTT
Found at i:29598634 original size:18 final size:19
Alignment explanation
Indices: 29598594--29598634 Score: 50
Period size: 18 Copynumber: 2.2 Consensus size: 19
29598584 TTTTTTTGGA
*
29598594 TATTGTATAACTCTTGTTT
1 TATTGTATAACTCTTGTTC
29598613 TATTGT-TAACT-TTGTTAC
1 TATTGTATAACTCTTGTT-C
29598631 TATT
1 TATT
29598635 TTAGAGACAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
17 5 0.25
18 9 0.45
19 6 0.30
ACGTcount: A:0.22, C:0.10, G:0.10, T:0.59
Consensus pattern (19 bp):
TATTGTATAACTCTTGTTC
Found at i:29598853 original size:19 final size:17
Alignment explanation
Indices: 29598829--29598863 Score: 52
Period size: 19 Copynumber: 1.9 Consensus size: 17
29598819 TTTTTTTGGA
29598829 TATTGTATAACTCTTGTTT
1 TATTGT-TAACT-TTGTTT
29598848 TATTGTTAACTTTGTT
1 TATTGTTAACTTTGTT
29598864 ACTATTTTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.31
18 5 0.31
19 6 0.38
ACGTcount: A:0.20, C:0.09, G:0.11, T:0.60
Consensus pattern (17 bp):
TATTGTTAACTTTGTTT
Found at i:29598869 original size:18 final size:19
Alignment explanation
Indices: 29598829--29598869 Score: 50
Period size: 18 Copynumber: 2.2 Consensus size: 19
29598819 TTTTTTTGGA
*
29598829 TATTGTATAACTCTTGTTT
1 TATTGTATAACTCTTGTTC
29598848 TATTGT-TAACT-TTGTTAC
1 TATTGTATAACTCTTGTT-C
29598866 TATT
1 TATT
29598870 TTAGAGACAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
17 5 0.25
18 9 0.45
19 6 0.30
ACGTcount: A:0.22, C:0.10, G:0.10, T:0.59
Consensus pattern (19 bp):
TATTGTATAACTCTTGTTC
Found at i:29598878 original size:235 final size:236
Alignment explanation
Indices: 29598467--29598937 Score: 935
Period size: 235 Copynumber: 2.0 Consensus size: 236
29598457 AGGCTTTTTG
29598467 GCCTGGGCCCCGACCCTAAATTGCCAAAAAAACCCTATTGTTTTGATGTTGTTTTCCTACTATTT
1 GCCTGGGCCCCGACCCTAAATTGCCAAAAAAACCCTATTGTTTTGATGTTGTTTTCCTACTATTT
29598532 TGCTCTTGTTTTGTTGTCATTTCAATATTATGTTGCTATTATTTTGTTATTATTTTTTTGGATAT
66 TGCTCTTGTTTTGTTGTCATTTCAATATTATGTTGCTATTATTTTGTTATTATTTTTTTGGATAT
29598597 TGTATAACTCTTGTTTTATTGTTAACTTTGTTACTATTTTAGAGACATTTGCTTGTTAAGTTTCA
131 TGTATAACTCTTGTTTTATTGTTAACTTTGTTACTATTTTAGAGACATTTGCTTGTTAAGTTTCA
29598662 ACTATCTTAGTGTTATTTAAGTATAAATA-TTTTTAAATTT
196 ACTATCTTAGTGTTATTTAAGTATAAATATTTTTTAAATTT
29598702 GCCTGGGCCCCGACCCTAAATTGCCAAAAAAACCCTATTGTTTTGATGTTGTTTTCCTACTATTT
1 GCCTGGGCCCCGACCCTAAATTGCCAAAAAAACCCTATTGTTTTGATGTTGTTTTCCTACTATTT
29598767 TGCTCTTGTTTTGTTGTCATTTCAATATTATGTTGCTATTATTTTGTTATTATTTTTTTGGATAT
66 TGCTCTTGTTTTGTTGTCATTTCAATATTATGTTGCTATTATTTTGTTATTATTTTTTTGGATAT
29598832 TGTATAACTCTTGTTTTATTGTTAACTTTGTTACTATTTTAGAGACATTTGCTTGTTAAGTTTCA
131 TGTATAACTCTTGTTTTATTGTTAACTTTGTTACTATTTTAGAGACATTTGCTTGTTAAGTTTCA
29598897 ACTATCTTAGTGTTATTTAAGTATAAATATTTTTTAAATTT
196 ACTATCTTAGTGTTATTTAAGTATAAATATTTTTTAAATTT
29598938 ATTTTCAATT
Statistics
Matches: 235, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
235 224 0.95
236 11 0.05
ACGTcount: A:0.23, C:0.13, G:0.13, T:0.50
Consensus pattern (236 bp):
GCCTGGGCCCCGACCCTAAATTGCCAAAAAAACCCTATTGTTTTGATGTTGTTTTCCTACTATTT
TGCTCTTGTTTTGTTGTCATTTCAATATTATGTTGCTATTATTTTGTTATTATTTTTTTGGATAT
TGTATAACTCTTGTTTTATTGTTAACTTTGTTACTATTTTAGAGACATTTGCTTGTTAAGTTTCA
ACTATCTTAGTGTTATTTAAGTATAAATATTTTTTAAATTT
Found at i:29600232 original size:16 final size:17
Alignment explanation
Indices: 29600211--29600243 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
29600201 AAATTTTATA
29600211 TAAATAT-TTATAATTT
1 TAAATATATTATAATTT
29600227 TAAATATGATTATAATT
1 TAAATAT-ATTATAATT
29600244 AGATGAGGGT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
18 8 0.53
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (17 bp):
TAAATATATTATAATTT
Found at i:29600793 original size:19 final size:21
Alignment explanation
Indices: 29600755--29600795 Score: 59
Period size: 19 Copynumber: 2.0 Consensus size: 21
29600745 TCACTCTTAG
29600755 GATTCGAGGTTTGAGGTTCAA
1 GATTCGAGGTTTGAGGTTCAA
*
29600776 GATTC-AGGTTT-TGGTTCAA
1 GATTCGAGGTTTGAGGTTCAA
29600795 G
1 G
29600796 CTGATTCGGG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 8 0.42
20 6 0.32
21 5 0.26
ACGTcount: A:0.22, C:0.10, G:0.32, T:0.37
Consensus pattern (21 bp):
GATTCGAGGTTTGAGGTTCAA
Found at i:29603165 original size:21 final size:22
Alignment explanation
Indices: 29603141--29603201 Score: 65
Period size: 20 Copynumber: 2.9 Consensus size: 22
29603131 AAATAGCAGC
* *
29603141 AAAATAGTAA-AAAATAATAAG
1 AAAATAGCAACAAAATAACAAG
29603162 AAAATAGCAACAAAATAACAAG
1 AAAATAGCAACAAAATAACAAG
* *
29603184 --AATAGGAAAAAAATAACA
1 AAAATAGCAACAAAATAACA
29603202 TTGTTTTTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
20 16 0.46
21 9 0.26
22 10 0.29
ACGTcount: A:0.70, C:0.07, G:0.10, T:0.13
Consensus pattern (22 bp):
AAAATAGCAACAAAATAACAAG
Found at i:29608601 original size:231 final size:231
Alignment explanation
Indices: 29608198--29608659 Score: 924
Period size: 231 Copynumber: 2.0 Consensus size: 231
29608188 AGTTATTTTT
29608198 GGGCAAATTACCAATAAAAGCCCATTTATTTTCAAAACTACCGAAATGGGCCAGGTCCTAAATTA
1 GGGCAAATTACCAATAAAAGCCCATTTATTTTCAAAACTACCGAAATGGGCCAGGTCCTAAATTA
29608263 ATTACCGGAATGGGTCAATTTTCCCCAAAACGCGTCCACGTCAGCGCGTTGTCAGGGGATAAAGC
66 ATTACCGGAATGGGTCAATTTTCCCCAAAACGCGTCCACGTCAGCGCGTTGTCAGGGGATAAAGC
29608328 AGGAAAACGCTTACTCAAGGAAAGGCATGCTTCGTGTCCACGTGGACAAAGCGCTTCCTTGAGGA
131 AGGAAAACGCTTACTCAAGGAAAGGCATGCTTCGTGTCCACGTGGACAAAGCGCTTCCTTGAGGA
29608393 AGCATTTTTCCCGTTTTTTAGGGTTAGGATTTTCTA
196 AGCATTTTTCCCGTTTTTTAGGGTTAGGATTTTCTA
29608429 GGGCAAATTACCAATAAAAGCCCATTTATTTTCAAAACTACCGAAATGGGCCAGGTCCTAAATTA
1 GGGCAAATTACCAATAAAAGCCCATTTATTTTCAAAACTACCGAAATGGGCCAGGTCCTAAATTA
29608494 ATTACCGGAATGGGTCAATTTTCCCCAAAACGCGTCCACGTCAGCGCGTTGTCAGGGGATAAAGC
66 ATTACCGGAATGGGTCAATTTTCCCCAAAACGCGTCCACGTCAGCGCGTTGTCAGGGGATAAAGC
29608559 AGGAAAACGCTTACTCAAGGAAAGGCATGCTTCGTGTCCACGTGGACAAAGCGCTTCCTTGAGGA
131 AGGAAAACGCTTACTCAAGGAAAGGCATGCTTCGTGTCCACGTGGACAAAGCGCTTCCTTGAGGA
29608624 AGCATTTTTCCCGTTTTTTAGGGTTAGGATTTTCTA
196 AGCATTTTTCCCGTTTTTTAGGGTTAGGATTTTCTA
29608660 CAATTAGGGT
Statistics
Matches: 231, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
231 231 1.00
ACGTcount: A:0.29, C:0.22, G:0.23, T:0.26
Consensus pattern (231 bp):
GGGCAAATTACCAATAAAAGCCCATTTATTTTCAAAACTACCGAAATGGGCCAGGTCCTAAATTA
ATTACCGGAATGGGTCAATTTTCCCCAAAACGCGTCCACGTCAGCGCGTTGTCAGGGGATAAAGC
AGGAAAACGCTTACTCAAGGAAAGGCATGCTTCGTGTCCACGTGGACAAAGCGCTTCCTTGAGGA
AGCATTTTTCCCGTTTTTTAGGGTTAGGATTTTCTA
Found at i:29608885 original size:7 final size:7
Alignment explanation
Indices: 29608870--29608899 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
29608860 AAAAATTAGA
29608870 TTAGGGT
1 TTAGGGT
*
29608877 TTAGTGT
1 TTAGGGT
29608884 TTAGGGT
1 TTAGGGT
29608891 TTAGGGT
1 TTAGGGT
29608898 TT
1 TT
29608900 TTAAGAAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.13, C:0.00, G:0.37, T:0.50
Consensus pattern (7 bp):
TTAGGGT
Found at i:29609009 original size:97 final size:97
Alignment explanation
Indices: 29608692--29609741 Score: 1775
Period size: 97 Copynumber: 10.8 Consensus size: 97
29608682 GTTTTTAGAT
* ** *
29608692 TTTAGGG-TTTTAAGGAAAAAATCAAATAAATTAGTGTTTAAGGTTTCTTGAGTAAATTAATTAT
1 TTTAGGGTTTTTAAGGAAAAAATCAAATAAATTAGAGTTTGGGGTTACTTGAGTAAATTAATTAT
29608756 AAATTTTAAAAAA-TTAGATTAGGGTTTAGTG
66 AAATTTTAAAAAATTTAGATTAGGGTTTAGTG
* * * *
29608787 TTTAAGGTTTTTAAGAAAAAAAT-AAATAAATTAGGGTTTAGGGTTACTTGAGTAAATTAATTAT
1 TTTAGGGTTTTTAAGGAAAAAATCAAATAAATTAGAGTTTGGGGTTACTTGAGTAAATTAATTAT
*
29608851 AAATTTTAAAAAAATTAGATTAGGGTTTAGTGTTTAGGG
66 AAATTTTAAAAAATTTAGATTAGGGTTTA--G--T---G
* * * * *
29608890 TTTAGGGTTTTTAAGAAAAAAATTAAATAAATTAGGGTTTAGGATTACTTGAGTAAATTAATTAT
1 TTTAGGGTTTTTAAGGAAAAAATCAAATAAATTAGAGTTTGGGGTTACTTGAGTAAATTAATTAT
29608955 AAATTTTAAAAAATTTAGATTAGGGTTTAGTG
66 AAATTTTAAAAAATTTAGATTAGGGTTTAGTG
29608987 TTTAGGGTTTTTAAGGAAAAAATCAAATAAATTAGAGTTTGGGGTTACTTGAGTAAATTAATTAT
1 TTTAGGGTTTTTAAGGAAAAAATCAAATAAATTAGAGTTTGGGGTTACTTGAGTAAATTAATTAT
29609052 AAATTTTAAAAAATTTAGATTAGGGTTTAGTG
66 AAATTTTAAAAAATTTAGATTAGGGTTTAGTG
29609084 TTTAGGGTTTTTAAGGAAAAAATCAAATAAATTAGAGTTTGGGGTTACTTGAGTAAATTAATTAT
1 TTTAGGGTTTTTAAGGAAAAAATCAAATAAATTAGAGTTTGGGGTTACTTGAGTAAATTAATTAT
29609149 AAATTTTAAAAAATTTAGATTAGGGTTTAGTG
66 AAATTTTAAAAAATTTAGATTAGGGTTTAGTG
29609181 TTTAGGGTTTTTAAGGAAAAAATCAAATAAATTAGAGTTTGGGGTTACTTGAGTAAATTAATTAT
1 TTTAGGGTTTTTAAGGAAAAAATCAAATAAATTAGAGTTTGGGGTTACTTGAGTAAATTAATTAT
29609246 AAATTTTAAAAAATTTAGATTAGGGTTTAGTG
66 AAATTTTAAAAAATTTAGATTAGGGTTTAGTG
29609278 TTTAGGGTTTTTAAGGAAAAAATCAAATAAATTAGAGTTTGGGGTTACTTGAGTAAATTAATTAT
1 TTTAGGGTTTTTAAGGAAAAAATCAAATAAATTAGAGTTTGGGGTTACTTGAGTAAATTAATTAT
29609343 AAATTTTAAAAAATTTAGATTAGGGTTTAGTG
66 AAATTTTAAAAAATTTAGATTAGGGTTTAGTG
29609375 TTTAGGGTTTTTAAGGAAAAAATCAAATAAATTAGAGTTTGGGGTTACTTGAGTAAATTAATTAT
1 TTTAGGGTTTTTAAGGAAAAAATCAAATAAATTAGAGTTTGGGGTTACTTGAGTAAATTAATTAT
29609440 AAATTTTAAAAAATTTAGATTAGGGTTTAGTG
66 AAATTTTAAAAAATTTAGATTAGGGTTTAGTG
* * *
29609472 TTTAGGGTTTTTAAGGAAAAAATCAAATAAATTAGGGTTTAGGATTACTTGAGTAAATTAATTAT
1 TTTAGGGTTTTTAAGGAAAAAATCAAATAAATTAGAGTTTGGGGTTACTTGAGTAAATTAATTAT
29609537 AAATTTTAAAAAATTTAGATTAGGGTTTAGTG
66 AAATTTTAAAAAATTTAGATTAGGGTTTAGTG
29609569 TTTAGGGTTTTTAAGGAAAAAATCAAATAAATTAGAGTTTGGGGTTACTTGAGTAAATTAATTAT
1 TTTAGGGTTTTTAAGGAAAAAATCAAATAAATTAGAGTTTGGGGTTACTTGAGTAAATTAATTAT
*
29609634 AAATTTTAAAAAATTTAGATTAAGGTTTAGTG
66 AAATTTTAAAAAATTTAGATTAGGGTTTAGTG
* * * * * * *
29609666 TTTAGGGGTTTTAAGG-AAAAATCAAATAAATTAGGGTTTAGGGTTACTTAATTAAATTATTTGT
1 TTTAGGGTTTTTAAGGAAAAAATCAAATAAATTAGAGTTTGGGGTTACTTGAGTAAATTAATTAT
*
29609730 TAATTTTAAAAA
66 AAATTTTAAAAA
29609742 GCTCCTACGT
Statistics
Matches: 917, Mismatches: 28, Indels: 19
0.95 0.03 0.02
Matches are distributed among these distances:
95 57 0.06
96 82 0.09
97 683 0.74
98 1 0.00
100 2 0.00
102 1 0.00
103 23 0.03
104 68 0.07
ACGTcount: A:0.40, C:0.02, G:0.19, T:0.39
Consensus pattern (97 bp):
TTTAGGGTTTTTAAGGAAAAAATCAAATAAATTAGAGTTTGGGGTTACTTGAGTAAATTAATTAT
AAATTTTAAAAAATTTAGATTAGGGTTTAGTG
Found at i:29609965 original size:126 final size:126
Alignment explanation
Indices: 29609740--29610156 Score: 676
Period size: 126 Copynumber: 3.3 Consensus size: 126
29609730 TAATTTTAAA
* * *
29609740 AAGCTCCTACGTGGACGCTCTTTTGCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGTTT
1 AAGCTCCCACGTGAACGCTCTTTTGCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGATGTTT
* * * * * **
29609805 CTGAGCAAATAGTG-CAAAAAATGCTTTAAGCAGGATGCATTGTTTGCAAAAGTACTGAAAG
66 CTGAGTAACTAGTGTC-AAAAACGCTTCAAGCAGGATGCAATGTCAGCAAAAGTACTGAAAG
* * * *
29609866 AAGCTCTCACGTTGAA-GCTTTTTTGCTACAATAGTTTCTGAAAAAATAATTTTGAGAAGATGTT
1 AAGCTCCCACG-TGAACGCTCTTTTGCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGATGTT
29609930 TCTGAGTAACTAGTGTCAAAAACGCTTCAAGCAGGATGCAATGTCAGCAAAAGTACTGAAAG
65 TCTGAGTAACTAGTGTCAAAAACGCTTCAAGCAGGATGCAATGTCAGCAAAAGTACTGAAAG
29609992 AAGCTCCCACGTGAACGCTCTTTTGCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGATGTTT
1 AAGCTCCCACGTGAACGCTCTTTTGCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGATGTTT
29610057 CTGAGTAACTAGTGTCAAAAACGCTTCAAGCAGGATGCAATGTCAGCAAAAGTACTGAAAG
66 CTGAGTAACTAGTGTCAAAAACGCTTCAAGCAGGATGCAATGTCAGCAAAAGTACTGAAAG
29610118 AAGCTCCCACGTGAACGCTCTTTTGCTACAGTAGTTCCT
1 AAGCTCCCACGTGAACGCTCTTTTGCTACAGTAGTTCCT
29610157 ATTTGGCCTG
Statistics
Matches: 270, Mismatches: 18, Indels: 6
0.92 0.06 0.02
Matches are distributed among these distances:
125 4 0.01
126 262 0.97
127 4 0.01
ACGTcount: A:0.34, C:0.18, G:0.20, T:0.28
Consensus pattern (126 bp):
AAGCTCCCACGTGAACGCTCTTTTGCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGATGTTT
CTGAGTAACTAGTGTCAAAAACGCTTCAAGCAGGATGCAATGTCAGCAAAAGTACTGAAAG
Found at i:29611056 original size:7 final size:7
Alignment explanation
Indices: 29611046--29611071 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
29611036 TTATATACAT
29611046 AATACTA
1 AATACTA
29611053 AATACTA
1 AATACTA
29611060 AATACTA
1 AATACTA
29611067 AATAC
1 AATAC
29611072 GAATCGACTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.58, C:0.15, G:0.00, T:0.27
Consensus pattern (7 bp):
AATACTA
Found at i:29619309 original size:162 final size:162
Alignment explanation
Indices: 29619124--29619488 Score: 522
Period size: 162 Copynumber: 2.3 Consensus size: 162
29619114 AAGGTGAAGA
* ** *
29619124 AAATGGTGAAGATGCATATTTTGATGATTGGAGGTCTAAGCTTAGTA-GCAACCAAGGATTTGTT
1 AAATGGTGAAGATGAATATTTTGATGATTGGAGGTCTAAGCTTAG-AGGCAACCAAGGAAATGGT
* *
29619188 GAAGAT-AATTATGTTGATGATTGGAGGTCTAAGCTTAGTAGCAACCATGGAAATGAAGAATTTG
65 GAAGATGAA-TATGTTGATGACTGGAGGTCTAAGCTTAGTAGCAACCATGGAAAGGAAGAATTTG
*
29619252 ATGATTGG-GACCATGATTTTAGTGGCAGCCATGG
129 ATGATTGGAG-CCATGATTTTAGTGGCAGCCAGGG
** *
29619286 AAATGGTGAAGATTTATATTTTGATGATTGGAGGTCTAAGCTTAGAGGCAACCATGGAAATGGTG
1 AAATGGTGAAGATGAATATTTTGATGATTGGAGGTCTAAGCTTAGAGGCAACCAAGGAAATGGTG
* * * *
29619351 AAGATGCATATTTTGATGACTGGAGGTCTAAGCTTAGTGGCAACCATGGAGAGGAAGAATTTGAT
66 AAGATGAATATGTTGATGACTGGAGGTCTAAGCTTAGTAGCAACCATGGAAAGGAAGAATTTGAT
29619416 GATTGGAGCCATGATTTTAGTGGCAGCCAGGG
131 GATTGGAGCCATGATTTTAGTGGCAGCCAGGG
* *
29619448 AAATAGTGAAGATGAATATTTTGAT-ACTTGGAGATCTAAGC
1 AAATGGTGAAGATGAATATTTTGATGA-TTGGAGGTCTAAGC
29619489 CCAGTTCCAA
Statistics
Matches: 182, Mismatches: 17, Indels: 8
0.88 0.08 0.04
Matches are distributed among these distances:
161 2 0.01
162 178 0.98
163 2 0.01
ACGTcount: A:0.32, C:0.10, G:0.28, T:0.30
Consensus pattern (162 bp):
AAATGGTGAAGATGAATATTTTGATGATTGGAGGTCTAAGCTTAGAGGCAACCAAGGAAATGGTG
AAGATGAATATGTTGATGACTGGAGGTCTAAGCTTAGTAGCAACCATGGAAAGGAAGAATTTGAT
GATTGGAGCCATGATTTTAGTGGCAGCCAGGG
Found at i:29619316 original size:57 final size:56
Alignment explanation
Indices: 29619248--29619488 Score: 180
Period size: 57 Copynumber: 4.4 Consensus size: 56
29619238 AAATGAAGAA
* ** * *
29619248 TTTGATGATTGG-GACCATGATTTTAGTGGCAGCCATGGAAATGGTGAAGATTTATAT
1 TTTGATGATTGGAGACC-TAAGCTTAGTGGCAACCATGGAAATGGTGAAGA-TGATAT
** *
29619305 TTTGATGATTGGAGGTCTAAGCTTAGAGGCAACCATGGAAATGGTGAAGATGCATAT
1 TTTGATGATTGGAGACCTAAGCTTAGTGGCAACCATGGAAATGGTGAAGATG-ATAT
* ** *
29619362 TTTGATGACTGGAGGTCTAAGCTTAGTGGCAACCATGGAGA--G-G-A-A-GA-A-
1 TTTGATGATTGGAGACCTAAGCTTAGTGGCAACCATGGAAATGGTGAAGATGATAT
* ** * * *
29619410 TTTGATGATTGGAG-CCATGATTTTAGTGGCAGCCAGGGAAATAGTGAAGATGAATAT
1 TTTGATGATTGGAGACC-TAAGCTTAGTGGCAACCATGGAAATGGTGAAGATG-ATAT
*
29619467 TTTGAT-ACTTGGAGATCTAAGC
1 TTTGATGA-TTGGAGACCTAAGC
29619489 CCAGTTCCAA
Statistics
Matches: 147, Mismatches: 23, Indels: 28
0.74 0.12 0.14
Matches are distributed among these distances:
47 1 0.01
48 31 0.21
49 1 0.01
50 2 0.01
51 2 0.01
52 2 0.01
53 2 0.01
54 2 0.01
55 2 0.01
56 3 0.02
57 96 0.65
58 3 0.02
ACGTcount: A:0.30, C:0.10, G:0.29, T:0.30
Consensus pattern (56 bp):
TTTGATGATTGGAGACCTAAGCTTAGTGGCAACCATGGAAATGGTGAAGATGATAT
Found at i:29619414 original size:105 final size:105
Alignment explanation
Indices: 29619305--29619523 Score: 253
Period size: 105 Copynumber: 2.1 Consensus size: 105
29619295 AGATTTATAT
* * * *
29619305 TTTGATGATTGGAGGTC-TAAGCTTAGAGGCAACCATGGAAATGGTGAAGATGCATATTTTGATG
1 TTTGATGATTGGA-GCCATAAGCTTAGAGGCAACCAGGGAAATAGTGAAGATGAATATTTTGAT-
* ** * * * *
29619369 AC-TGGAGGTCTAAGCTTAGTGGCAACCATGGAGAGGAAGAA
64 ACTTGGAGATCTAAGCCCAGTGCCAACAATGGAAACGAAGAA
* ** * *
29619410 TTTGATGATTGGAGCCATGATTTTAGTGGCAGCCAGGGAAATAGTGAAGATGAATATTTTGATAC
1 TTTGATGATTGGAGCCATAAGCTTAGAGGCAACCAGGGAAATAGTGAAGATGAATATTTTGATAC
*
29619475 TTGGAGATCTAAGCCCAGTTCCAACAATGGAAACGAAGAA
66 TTGGAGATCTAAGCCCAGTGCCAACAATGGAAACGAAGAA
29619515 TTTGATGAT
1 TTTGATGAT
29619524 CGGGACCATG
Statistics
Matches: 95, Mismatches: 17, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
104 4 0.04
105 91 0.96
ACGTcount: A:0.32, C:0.12, G:0.28, T:0.27
Consensus pattern (105 bp):
TTTGATGATTGGAGCCATAAGCTTAGAGGCAACCAGGGAAATAGTGAAGATGAATATTTTGATAC
TTGGAGATCTAAGCCCAGTGCCAACAATGGAAACGAAGAA
Found at i:29619533 original size:105 final size:105
Alignment explanation
Indices: 29619327--29619542 Score: 274
Period size: 105 Copynumber: 2.1 Consensus size: 105
29619317 AGGTCTAAGC
* * * * * ** *
29619327 TTAGAGGCAACCATGGAAATGGTGAAGATGCATATTTTGATGACTGGAGGTCTAAGCTTAGTGGC
1 TTAGTGGCAACCAGGGAAATAGTGAAGATGAATATTTTGATGACTGGAGATCTAAGCCCAGTGCC
* * * *
29619392 AACCATGGAGAGGAAGAATTTGATGATTGGAGCCATGATT
66 AACAATGGAAACGAAGAATTTGATGATGGGAGCCATGATT
* *
29619432 TTAGTGGCAGCCAGGGAAATAGTGAAGATGAATATTTTGAT-ACTTGGAGATCTAAGCCCAGTTC
1 TTAGTGGCAACCAGGGAAATAGTGAAGATGAATATTTTGATGAC-TGGAGATCTAAGCCCAGTGC
29619496 CAACAATGGAAACGAAGAATTTGATGATCGGGA-CCATGATT
65 CAACAATGGAAACGAAGAATTTGATGAT-GGGAGCCATGATT
29619537 TTAGTG
1 TTAGTG
29619543 CCCGTCATGG
Statistics
Matches: 95, Mismatches: 14, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
104 2 0.02
105 90 0.95
106 3 0.03
ACGTcount: A:0.32, C:0.12, G:0.28, T:0.27
Consensus pattern (105 bp):
TTAGTGGCAACCAGGGAAATAGTGAAGATGAATATTTTGATGACTGGAGATCTAAGCCCAGTGCC
AACAATGGAAACGAAGAATTTGATGATGGGAGCCATGATT
Found at i:29626510 original size:230 final size:226
Alignment explanation
Indices: 29625998--29626733 Score: 1080
Period size: 227 Copynumber: 3.2 Consensus size: 226
29625988 CCAATGCTGG
* * *
29625998 CTACGAGGCAGGAAGTTATGGAAATGAACAATCAATCCAAGGTAAATCATTTTATTTCCATTATA
1 CTACCAGGCTGGAAGTTATGGAAATGAACAATCAATCCAAGGTAAATCATTTGATTTCCATTATA
* * *
29626063 TGTATATATGTTAATGTTTAGGTTTTTGAGAACAGAACTCAACTGTTTAAGCCAAATTAACTAAA
66 TGTATATATGTTAATGTTTAGGTTTTCGAGAATAAAACTCAACTG-TTAAGCCAAATTAAC-AAA
* * *
29626128 -CTTTAACATTTAAAATTTGGGTTTAAATGTTTTCAGACTATTCAGGTAATGGTACTGGACCATC
129 GCTTTAACATTTAAATTTTGGGTCTAAATGTTTTCAGACTATTCAGGTAATAGTACTGGACCATC
* *
29626192 TAAGGAATTTAGTGCTCCAACCTCTCTAGGAGC
194 TAAGGAATTTAGTGCTCCAAGCTCTCTAGGTGC
*
29626225 CTACCAGGCTGGAAGTTATGGAAATGAACAATCAATCCAAGGTAAATCATTTGATTTCTATTATA
1 CTACCAGGCTGGAAGTTATGGAAATGAACAATCAATCCAAGGTAAATCATTTGATTTCCATTATA
* *
29626290 TGTATATATGTTAATGTTTAGGTTTTCGAGAATAAAACTCAATTGTTCGAGCCAAATTAACAAAG
66 TGTATATATGTTAATGTTTAGGTTTTCGAGAATAAAACTCAACTGTT-AAGCCAAATTAACAAAG
* *
29626355 TTTTAACATTTAAATTTTGGGTCTAAATGTTTTGATCAGACTATTCAGGTAATAATACTGGACCA
130 CTTTAACATTTAAATTTTGGGTCTAAATG-TTT--TCAGACTATTCAGGTAATAGTACTGGACCA
29626420 TCTAAGGAATTTAGTGCTCCAAGCTCTCTAGGTGC
192 TCTAAGGAATTTAGTGCTCCAAGCTCTCTAGGTGC
* *
29626455 CTACCAGGCTGGAAGTTATGGAAATGAACAATCAATCCAAGGTAAATCGTTTGATTTCCATTACA
1 CTACCAGGCTGGAAGTTATGGAAATGAACAATCAATCCAAGGTAAATCATTTGATTTCCATTATA
* * * * *
29626520 TGTATATATATGTTAATGTTTAGATTTTCGAAAATAAAACTCAACCGTATAAGCTAAATTAACTA
66 TG--TATATATGTTAATGTTTAGGTTTTCGAGAATAAAACTCAACTGT-TAAGCCAAATTAACAA
* **
29626585 AGCTTTAACA-TTAAATTTTGGGTCTAAATGTTTTCAGGCTATTCAGGTAATAGTACTACACCAT
128 AGCTTTAACATTTAAATTTTGGGTCTAAATGTTTTCAGACTATTCAGGTAATAGTACTGGACCAT
* * *
29626649 CTAAAGAATTTAGTACTCCAAGCTCTCTAGGTAC
193 CTAAGGAATTTAGTGCTCCAAGCTCTCTAGGTGC
* * * *
29626683 CTACCAAGCCGGAAGTTATGGAAATAAACAATCAATCCCAGGTAAATCATT
1 CTACCAGGCTGGAAGTTATGGAAATGAACAATCAATCCAAGGTAAATCATT
29626734 ATGCCTACAT
Statistics
Matches: 462, Mismatches: 39, Indels: 15
0.90 0.08 0.03
Matches are distributed among these distances:
226 5 0.01
227 140 0.30
228 107 0.23
230 128 0.28
231 20 0.04
232 61 0.13
233 1 0.00
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Consensus pattern (226 bp):
CTACCAGGCTGGAAGTTATGGAAATGAACAATCAATCCAAGGTAAATCATTTGATTTCCATTATA
TGTATATATGTTAATGTTTAGGTTTTCGAGAATAAAACTCAACTGTTAAGCCAAATTAACAAAGC
TTTAACATTTAAATTTTGGGTCTAAATGTTTTCAGACTATTCAGGTAATAGTACTGGACCATCTA
AGGAATTTAGTGCTCCAAGCTCTCTAGGTGC
Found at i:29638598 original size:23 final size:22
Alignment explanation
Indices: 29638558--29638601 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 22
29638548 ATTTTTACTA
29638558 ATTATAAATTTATGATTTATAC
1 ATTATAAATTTATGATTTATAC
29638580 ATTATAAAATATTAT-ATTTATA
1 ATTAT-AAAT-TTATGATTTATA
29638602 TTTTTTTTCC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 5 0.25
23 11 0.55
24 4 0.20
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.50
Consensus pattern (22 bp):
ATTATAAATTTATGATTTATAC
Found at i:29656576 original size:93 final size:93
Alignment explanation
Indices: 29656389--29656589 Score: 217
Period size: 93 Copynumber: 2.2 Consensus size: 93
29656379 GGTTCTGACC
* * ** *
29656389 ACCGAATCGTTGGTTTTAGTAACAGGATTGGGTGCTAAAGCAGGGGACATTGCCGGAGCTGGTGA
1 ACCGAATCATTGGTTTTAGTAACAGGATTGGGTGCTAAAGCAGGGGACATAGCCGGAGCCAGCGA
*** ** *
29656454 AGATTTGCTTTCTTCACCGGATTTAACA
66 AGAACCGAATCCTTCACCGGATTTAACA
* *
29656482 ACCGAATCATTGGTTTTAGTAACCGGATTGGGTGCTACAA-CAGGGGACATAGCTGGAGCCAGCG
1 ACCGAATCATTGGTTTTAGTAACAGGATTGGGTGCTA-AAGCAGGGGACATAGCCGGAGCCAGCG
* * *
29656546 AAGAAACCGAATCCTT-ACTGGTTTTTACA
65 AAG-AACCGAATCCTTCACCGGATTTAACA
*
29656575 ACAGAATCATTGGTT
1 ACCGAATCATTGGTT
29656590 GCTAAAACAG
Statistics
Matches: 89, Mismatches: 17, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
93 81 0.91
94 8 0.09
ACGTcount: A:0.27, C:0.18, G:0.27, T:0.27
Consensus pattern (93 bp):
ACCGAATCATTGGTTTTAGTAACAGGATTGGGTGCTAAAGCAGGGGACATAGCCGGAGCCAGCGA
AGAACCGAATCCTTCACCGGATTTAACA
Found at i:29656599 original size:75 final size:75
Alignment explanation
Indices: 29656508--29656739 Score: 313
Period size: 75 Copynumber: 3.1 Consensus size: 75
29656498 TAGTAACCGG
* * * * * * * *
29656508 ATTGGGTGCTACAACA-GGGGACATAGCTGGAGCCAGCGAAGAAACCGAATCCTTACTGGTTTTT
1 ATTGGTTGCTAAAACAGGGGGA-ATTGCCGGAGCCGGCGAAGAAACAGAATCCTCACCGGTTTTT
*
29656572 ACAACAGAATC
65 ACAACGGAATC
29656583 ATTGGTTGCTAAAACAGGGGGAATTGCCGGAGCCGGCGAAGAAACAGAATCCTCACCGGTTTTTA
1 ATTGGTTGCTAAAACAGGGGGAATTGCCGGAGCCGGCGAAGAAACAGAATCCTCACCGGTTTTTA
29656648 CAACGGAATC
66 CAACGGAATC
** * *
29656658 ATTGGTTGCTAATGCAGGGGGAATTGCCGGAGCCGGCGAAGAAATAGAATCCTCACCGGTTTTAA
1 ATTGGTTGCTAAAACAGGGGGAATTGCCGGAGCCGGCGAAGAAACAGAATCCTCACCGGTTTTTA
*
29656723 CAATGGAATC
66 CAACGGAATC
*
29656733 ATCGGTT
1 ATTGGTT
29656740 TCAGTAATGG
Statistics
Matches: 141, Mismatches: 15, Indels: 2
0.89 0.09 0.01
Matches are distributed among these distances:
75 136 0.96
76 5 0.04
ACGTcount: A:0.30, C:0.20, G:0.28, T:0.22
Consensus pattern (75 bp):
ATTGGTTGCTAAAACAGGGGGAATTGCCGGAGCCGGCGAAGAAACAGAATCCTCACCGGTTTTTA
CAACGGAATC
Found at i:29663387 original size:2 final size:2
Alignment explanation
Indices: 29663380--29663411 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
29663370 NATTTAGCCC
29663380 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
29663412 TTGTAAATGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:29665816 original size:20 final size:21
Alignment explanation
Indices: 29665791--29665839 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 21
29665781 GCTTGGCTCG
29665791 GATACCCTTAAC-AAAGTATC
1 GATACCCTTAACAAAAGTATC
* **
29665811 GATACCTTTTTCAAAAGTATC
1 GATACCCTTAACAAAAGTATC
*
29665832 GACACCCT
1 GATACCCT
29665840 GCTTGAGAAT
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
20 9 0.39
21 14 0.61
ACGTcount: A:0.35, C:0.27, G:0.10, T:0.29
Consensus pattern (21 bp):
GATACCCTTAACAAAAGTATC
Found at i:29667995 original size:29 final size:29
Alignment explanation
Indices: 29667953--29668019 Score: 82
Period size: 29 Copynumber: 2.3 Consensus size: 29
29667943 ATAGGGATTT
*
29667953 GATCAAATTAGT-CCTTCAACTATTAAATA
1 GATCAAATTAGTCCCTT-AACTATTAAAAA
* *
29667982 GATCAATTTAGTCCCTTTACTATTAAAAA
1 GATCAAATTAGTCCCTTAACTATTAAAAA
29668011 GAATCAAAT
1 G-ATCAAAT
29668020 AAGACCAAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
29 22 0.69
30 10 0.31
ACGTcount: A:0.42, C:0.16, G:0.07, T:0.34
Consensus pattern (29 bp):
GATCAAATTAGTCCCTTAACTATTAAAAA
Found at i:29676150 original size:7 final size:7
Alignment explanation
Indices: 29676140--29676167 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
29676130 AAATGGAAAA
29676140 TTGGGTG
1 TTGGGTG
29676147 TTGGGTG
1 TTGGGTG
29676154 TTGGGTG
1 TTGGGTG
29676161 TTGGGTG
1 TTGGGTG
29676168 GATTCTTGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.00, C:0.00, G:0.57, T:0.43
Consensus pattern (7 bp):
TTGGGTG
Found at i:29678103 original size:4 final size:4
Alignment explanation
Indices: 29678088--29678123 Score: 58
Period size: 4 Copynumber: 9.5 Consensus size: 4
29678078 TTTTTGTGTC
29678088 TAAT TAA- T-AT TAAT TAAT TAAT TAAT TAAT TAAT TA
1 TAAT TAAT TAAT TAAT TAAT TAAT TAAT TAAT TAAT TA
29678124 TAAGCTTAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 1 0.03
3 2 0.07
4 27 0.90
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (4 bp):
TAAT
Found at i:29678642 original size:10 final size:10
Alignment explanation
Indices: 29678627--29678653 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
29678617 CAATGTCAAG
29678627 GGGGCAAGTA
1 GGGGCAAGTA
29678637 GGGGCAAGTA
1 GGGGCAAGTA
29678647 GGGGCAA
1 GGGGCAA
29678654 TCTTGTTAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.30, C:0.11, G:0.52, T:0.07
Consensus pattern (10 bp):
GGGGCAAGTA
Found at i:29680901 original size:16 final size:17
Alignment explanation
Indices: 29680876--29680908 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
29680866 GTAATTTTAC
*
29680876 TTTTATAAA-TTTAAAA
1 TTTTAAAAATTTTAAAA
29680892 TTTTAAAAATTTTAAAA
1 TTTTAAAAATTTTAAAA
29680909 GGCTTAAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
TTTTAAAAATTTTAAAA
Found at i:29688671 original size:22 final size:24
Alignment explanation
Indices: 29688595--29688807 Score: 133
Period size: 26 Copynumber: 8.2 Consensus size: 24
29688585 AAACGAAACA
** *
29688595 AAATAATATATGAAACAATTTGGAGT
1 AAATAATATA--AAACAATTTAAAAT
* * **
29688621 AAATAGTATAAAACAACTTAAAGC
1 AAATAATATAAAACAATTTAAAAT
*
29688645 AAATAATATGTAAAACAAATTAAAAT
1 AAATAATA--TAAAACAATTTAAAAT
29688671 AAATAATATACAAAGCAATTTAAAAT
1 AAATAATATA-AAA-CAATTTAAAAT
*
29688697 AAATAACATATAAGACAATTTAAAAT
1 AAAT-A-ATATAAAACAATTTAAAAT
*
29688723 AATATGTAAT-TAAAA-AGTTTAAAAT
1 AA-A--TAATATAAAACAATTTAAAAT
* *
29688748 AAATAATATGTAAAAAGAAGTTTCAAAT
1 AAATAATA--T-AAAACAA-TTTAAAAT
* *
29688776 AAATAATATACAAAACAGTTAAAAAT
1 AAATAATAT--AAAACAATTTAAAAT
29688802 AAATAA
1 AAATAA
29688808 ATGATGTGTA
Statistics
Matches: 151, Mismatches: 20, Indels: 32
0.74 0.10 0.16
Matches are distributed among these distances:
22 4 0.03
24 20 0.13
25 15 0.10
26 78 0.52
27 12 0.08
28 21 0.14
29 1 0.01
ACGTcount: A:0.60, C:0.06, G:0.07, T:0.27
Consensus pattern (24 bp):
AAATAATATAAAACAATTTAAAAT
Found at i:29688777 original size:28 final size:28
Alignment explanation
Indices: 29688719--29688784 Score: 98
Period size: 28 Copynumber: 2.3 Consensus size: 28
29688709 AGACAATTTA
29688719 AAATAATATGTAATTAAAAAGTTTAAAAT
1 AAATAATATGTAA-TAAAAAGTTTAAAAT
*
29688748 AAATAATATGTAA-AAAGAAGTTTCAAAT
1 AAATAATATGTAATAAA-AAGTTTAAAAT
29688776 AAATAATAT
1 AAATAATAT
29688785 ACAAAACAGT
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
27 3 0.09
28 19 0.54
29 13 0.37
ACGTcount: A:0.59, C:0.02, G:0.08, T:0.32
Consensus pattern (28 bp):
AAATAATATGTAATAAAAAGTTTAAAAT
Found at i:29692260 original size:17 final size:17
Alignment explanation
Indices: 29692238--29692273 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
29692228 TTTTTTTTTT
29692238 TAATTTCCCATGAAGAA
1 TAATTTCCCATGAAGAA
29692255 TAATTTCCCATGAAGAA
1 TAATTTCCCATGAAGAA
29692272 TA
1 TA
29692274 TTAAGTGAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.42, C:0.17, G:0.11, T:0.31
Consensus pattern (17 bp):
TAATTTCCCATGAAGAA
Found at i:29694787 original size:104 final size:105
Alignment explanation
Indices: 29694504--29694836 Score: 379
Period size: 97 Copynumber: 3.3 Consensus size: 105
29694494 ATCTTTAGAT
* * * * * *
29694504 TTTAGGG-TTTTAA-GAAAAAATTAAATAAATAAGGGTTTA-AAGTTTAGGGTTTCTTAATTAAA
1 TTTAGGGTTTTTAAGGAAAAAATCAAATAAATTAGGGTTTAGGA-TTTAAGGTTACTTAAGTAAA
* *
29694566 TTAATTATAAA--TTTTAAAAAATTAAATTAGAGTTTAGTA
65 TTAATTATAAATTTTTTAAAAAATTAGATTAGGGTTTAGTA
* * * * *
29694605 TTTATGGTTTTTAAGAAAAAAAGCAAATAAATTAGGGTTCAGG-----A--TTACTTTAGTAAAT
1 TTTAGGGTTTTTAAGGAAAAAATCAAATAAATTAGGGTTTAGGATTTAAGGTTACTTAAGTAAAT
* * * *
29694663 TAATTATAAA-TTTTAAAAAAAATAGATTAGGGTTTAATC
66 TAATTATAAATTTTTTAAAAAATTAGATTAGGGTTTAGTA
* *
29694702 TTTAGGGTTTTTAAGGAAAAAATTAAATAAATTAGGGTTTAGGATTTAAGGTTACTTGAGTAAAT
1 TTTAGGGTTTTTAAGGAAAAAATCAAATAAATTAGGGTTTAGGATTTAAGGTTACTTAAGTAAAT
*
29694767 TAATTATAAATTTTTTAAAAAATTAGATTGGGGTTTAGTA
66 TAATTATAAATTTTTTAAAAAATTAGATTAGGGTTTAGTA
29694807 TTTAGGGTTTTTAAGG-AAAAATCAAATAAA
1 TTTAGGGTTTTTAAGGAAAAAATCAAATAAA
29694837 GCTAATTTTA
Statistics
Matches: 191, Mismatches: 29, Indels: 21
0.79 0.12 0.09
Matches are distributed among these distances:
96 21 0.11
97 60 0.31
101 6 0.03
102 7 0.04
103 21 0.11
104 36 0.19
105 40 0.21
ACGTcount: A:0.43, C:0.02, G:0.16, T:0.39
Consensus pattern (105 bp):
TTTAGGGTTTTTAAGGAAAAAATCAAATAAATTAGGGTTTAGGATTTAAGGTTACTTAAGTAAAT
TAATTATAAATTTTTTAAAAAATTAGATTAGGGTTTAGTA
Found at i:29696179 original size:154 final size:152
Alignment explanation
Indices: 29695935--29696300 Score: 462
Period size: 154 Copynumber: 2.4 Consensus size: 152
29695925 TATAATGTAT
* * *
29695935 TAAAATAATAAAATTAGAAAATAGTATATTTTTTTAAAGTAATAAAATTCGGAAAAAAATATGAA
1 TAAAATAATAAAATTAGAAAATAATAAATTTTTTTAAAATAATAAAATTCGGAAAAAAATATGAA
* * * * *
29696000 TAAAGGGCTGAAATAAGGGCTTTTTTTAAATTTATTTAAAAAATACAGTAAATTAATATATTTCA
66 TAAAGGGCCGAAATAAGGGCTTTTTTAAAATTTATTTAAAAAATACACTAAATGAATACATTTCA
29696065 AACATAAAATACTAAAATAATG
131 AACATAAAATACTAAAATAATG
*
29696087 TAAAATAATAAAA-TACGAAAATAATAAATTTTTATTGAAAATAATAAAA-TCTGGGAAAAAATA
1 TAAAATAATAAAATTA-GAAAATAATAAATTTTT-TT-AAAATAATAAAATTC-GGAAAAAAATA
*
29696150 TGAATAAA-GGCCGAAATAAGGAGTTTTTTTAAAATTTATTTAAAAAATACACTAAATGAATACA
62 TGAATAAAGGGCCGAAATAAGG-GCTTTTTTAAAATTTATTTAAAAAATACACTAAATGAATACA
* **
29696214 TTTCAAATATAATGTACTAAAATAATG
126 TTTCAAACATAAAATACTAAAATAATG
* * * *
29696241 TAAAATTAGAAAATTAGAAAATAGT--A-TTTTTT-AAATAAATAAAA-TC-TAAAAAAATATGA
1 TAAAATAATAAAATTAGAAAATAATAAATTTTTTTAAAAT-AATAAAATTCGGAAAAAAATATGA
29696300 A
65 A
29696301 CAAAAGATCG
Statistics
Matches: 189, Mismatches: 18, Indels: 19
0.84 0.08 0.08
Matches are distributed among these distances:
147 12 0.06
148 4 0.02
149 9 0.05
150 2 0.01
151 6 0.03
152 29 0.15
153 16 0.08
154 109 0.58
155 2 0.01
ACGTcount: A:0.54, C:0.05, G:0.09, T:0.32
Consensus pattern (152 bp):
TAAAATAATAAAATTAGAAAATAATAAATTTTTTTAAAATAATAAAATTCGGAAAAAAATATGAA
TAAAGGGCCGAAATAAGGGCTTTTTTAAAATTTATTTAAAAAATACACTAAATGAATACATTTCA
AACATAAAATACTAAAATAATG
Found at i:29697406 original size:11 final size:12
Alignment explanation
Indices: 29697407--29697480 Score: 73
Period size: 11 Copynumber: 6.2 Consensus size: 12
29697397 TTTTAAAAAA
29697407 TAAAAAAGTATTT
1 TAAAAAA-TATTT
29697420 T-AAAAATATTT
1 TAAAAAATATTT
29697431 T-AAAAATATTT
1 TAAAAAATATTT
* ***
29697442 TAAAAATAAAAAA
1 TAAAAA-ATATTT
29697455 TAAAAAATATTT
1 TAAAAAATATTT
29697467 T-AAAAATATTT
1 TAAAAAATATTT
29697478 TAA
1 TAA
29697481 CATTAAAAAA
Statistics
Matches: 50, Mismatches: 8, Indels: 7
0.77 0.12 0.11
Matches are distributed among these distances:
11 28 0.56
12 13 0.26
13 9 0.18
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.38
Consensus pattern (12 bp):
TAAAAAATATTT
Found at i:29697468 original size:36 final size:36
Alignment explanation
Indices: 29697421--29697490 Score: 122
Period size: 36 Copynumber: 1.9 Consensus size: 36
29697411 AAAGTATTTT
29697421 AAAAATATTTTAAAAATATTTTAAAAATAAAAAATA
1 AAAAATATTTTAAAAATATTTTAAAAATAAAAAATA
* *
29697457 AAAAATATTTTAAAAATATTTTAACATTAAAAAA
1 AAAAATATTTTAAAAATATTTTAAAAATAAAAAA
29697491 ATATTTATTA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.64, C:0.01, G:0.00, T:0.34
Consensus pattern (36 bp):
AAAAATATTTTAAAAATATTTTAAAAATAAAAAATA
Found at i:29697794 original size:18 final size:17
Alignment explanation
Indices: 29697763--29697798 Score: 63
Period size: 18 Copynumber: 2.1 Consensus size: 17
29697753 AGGCCTTCCT
29697763 TTTATATAATAGTAGTA
1 TTTATATAATAGTAGTA
29697780 TTTATATATATAGTAGTA
1 TTTATATA-ATAGTAGTA
29697798 T
1 T
29697799 AGATACTGGG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 8 0.44
18 10 0.56
ACGTcount: A:0.39, C:0.00, G:0.11, T:0.50
Consensus pattern (17 bp):
TTTATATAATAGTAGTA
Found at i:29698669 original size:11 final size:10
Alignment explanation
Indices: 29698635--29698691 Score: 53
Period size: 10 Copynumber: 5.5 Consensus size: 10
29698625 CGAACTCGCC
29698635 AAAAAATTTT
1 AAAAAATTTT
* **
29698645 TAAAAATTAA
1 AAAAAATTTT
29698655 AAAAGAATTTT
1 AAAA-AATTTT
29698666 AAAATAA-TTT
1 AAAA-AATTTT
29698676 AAAAATATTTT
1 AAAAA-ATTTT
29698687 AAAAA
1 AAAAA
29698692 TAAAAAATAA
Statistics
Matches: 37, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
9 1 0.03
10 18 0.49
11 18 0.49
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (10 bp):
AAAAAATTTT
Found at i:29698692 original size:11 final size:11
Alignment explanation
Indices: 29698661--29698693 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
29698651 TTAAAAAAGA
29698661 ATTTT-AAAAT
1 ATTTTAAAAAT
*
29698671 AATTTAAAAAT
1 ATTTTAAAAAT
29698682 ATTTTAAAAAT
1 ATTTTAAAAAT
29698693 A
1 A
29698694 AAAAATAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
10 4 0.20
11 16 0.80
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (11 bp):
ATTTTAAAAAT
Found at i:29698697 original size:17 final size:18
Alignment explanation
Indices: 29698635--29698700 Score: 62
Period size: 18 Copynumber: 3.4 Consensus size: 18
29698625 CGAACTCGCC
29698635 AAAAAAT-TTTTAAAAATT
1 AAAAAATATTTTAAAAA-T
*
29698653 AAAAAAGAATTTTAAAATAATT
1 AAAAAA-TATTTT-AAA-AA-T
*
29698675 TAAAAATATTTTAAAAAT
1 AAAAAATATTTTAAAAAT
29698693 AAAAAATA
1 AAAAAATA
29698701 AAAAATATTT
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
18 14 0.35
19 2 0.05
20 7 0.17
21 8 0.20
22 9 0.22
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (18 bp):
AAAAAATATTTTAAAAAT
Found at i:29713875 original size:19 final size:21
Alignment explanation
Indices: 29713834--29713872 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
29713824 TTTTTTATGT
29713834 TTATATATTTTTTAAAATTTA
1 TTATATATTTTTTAAAATTTA
29713855 TTAT-TATTTTTTAAAATT
1 TTATATATTTTTTAAAATT
29713873 ATTTATGCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (21 bp):
TTATATATTTTTTAAAATTTA
Found at i:29713878 original size:20 final size:20
Alignment explanation
Indices: 29713833--29713878 Score: 67
Period size: 20 Copynumber: 2.2 Consensus size: 20
29713823 ATTTTTTATG
29713833 TTTATATATTTTTTAAAATT
1 TTTATATATTTTTTAAAATT
29713853 TATTAT-TATTTTTTAAAATT
1 T-TTATATATTTTTTAAAATT
29713873 ATTTAT
1 -TTTAT
29713879 GCATTTTTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
20 19 0.79
21 5 0.21
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (20 bp):
TTTATATATTTTTTAAAATT
Found at i:29714736 original size:16 final size:16
Alignment explanation
Indices: 29714706--29714758 Score: 63
Period size: 15 Copynumber: 3.3 Consensus size: 16
29714696 AAATAAAAAT
29714706 AAAATTAAAATTTTTAA
1 AAAATTAAAA-TTTTAA
29714723 AAAATTAAAATTTT-A
1 AAAATTAAAATTTTAA
* * *
29714738 AATATTTAAATATTAA
1 AAAATTAAAATTTTAA
29714754 AAAAT
1 AAAAT
29714759 ACATTTGACT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
15 12 0.39
16 9 0.29
17 10 0.32
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
AAAATTAAAATTTTAA
Found at i:29714897 original size:7 final size:7
Alignment explanation
Indices: 29714887--29714911 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
29714877 TGTAAAAATC
29714887 ATATATA
1 ATATATA
29714894 ATATATA
1 ATATATA
29714901 ATATATA
1 ATATATA
29714908 ATAT
1 ATAT
29714912 NNNNNNNNNN
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (7 bp):
ATATATA
Found at i:29716237 original size:2 final size:2
Alignment explanation
Indices: 29716230--29716261 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
29716220 ATAAATGTGA
29716230 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
29716262 TTTGTTTGGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:29721734 original size:44 final size:45
Alignment explanation
Indices: 29721628--29722398 Score: 309
Period size: 44 Copynumber: 17.8 Consensus size: 45
29721618 TCGGCTTTAA
* * * * **
29721628 TCTGCTCCTCTGCAACTTTA-AAGAGATAAGATTTGCCATCTTCAG
1 TCTGCTCCACTGCAACTTCAGGAGAGATAAGACTTGCTTTCTT-AG
* * *
29721673 TCTAC-CTTACTGCAACTTCAGGAG-GATAAGACTTGTTTTCTTAG
1 TCTGCTC-CACTGCAACTTCAGGAGAGATAAGACTTGCTTTCTTAG
** * *
29721717 TCTGCTCCACTGCAACTTCAGG-GAGATAAGAC-T-CGATGTGA-
1 TCTGCTCCACTGCAACTTCAGGAGAGATAAGACTTGCTTTCTTAG
* * * *
29721758 TCTGCT-CTCTGCAACTTCA-GAGAGATAAGATCTGAGGTTT-TTAA
1 TCTGCTCCACTGCAACTTCAGGAGAGATAAGA-CT-TGCTTTCTTAG
* * * * * *** *
29721802 TCCGC-CCACTGAAACTTCAGCA-AGATAGGA-TTACCGACTTTAA
1 TCTGCTCCACTGCAACTTCAGGAGAGATAAGACTTGCTTTC-TTAG
* * * **
29721845 TCTGCTCCACTACAATTTCAGG-GAGATAAGATTTGCCATCTTCAG
1 TCTGCTCCACTGCAACTTCAGGAGAGATAAGACTTGCTTTCTT-AG
*
29721890 TCTGC-CTCACTGCAACTTCAGGAG-GATAAGACTTGCTTACTTAG
1 TCTGCTC-CACTGCAACTTCAGGAGAGATAAGACTTGCTTTCTTAG
* * * * * *
29721934 TCCGCTCCACTACAACTTCAGG-GAGATAAGACTAG-ATGC-GA-
1 TCTGCTCCACTGCAACTTCAGGAGAGATAAGACTTGCTTTCTTAG
* * * * * * *
29721975 TCTACT-CTCTGCCATTTCA-GAGAGATAAGATCTAAG-GTT-TTAA
1 TCTGCTCCACTGCAACTTCAGGAGAGATAAGA-CT-TGCTTTCTTAG
* * * * *** *
29722018 TCCGC-CCACTGCAACTTTAGCGA-A-ATAGGA-TTACCGGCTTTAA
1 TCTGCTCCACTGCAACTTCAG-GAGAGATAAGACTTGCTTTC-TTAG
* **
29722061 TCTGCTCCACTGCAACTTCAGG-GAGATAAGATTTGCCATCTTCAG
1 TCTGCTCCACTGCAACTTCAGGAGAGATAAGACTTGCTTTCTT-AG
* * *
29722106 TTTGCTTCACTGCAACTTCAGGAG-GATAAGACTTGCTTACTTAG
1 TCTGCTCCACTGCAACTTCAGGAGAGATAAGACTTGCTTTCTTAG
* * * * *
29722150 TCCGCTCCACTGCAACTTCAGG-GAGATAAGACTAG-ATGC-GA-
1 TCTGCTCCACTGCAACTTCAGGAGAGATAAGACTTGCTTTCTTAG
* * * * * *
29722191 TCTGAT-CTCTGCAATTTCA-GAGAGATAAGATCTAAG-GTT-TTAA
1 TCTGCTCCACTGCAACTTCAGGAGAGATAAGA-CT-TGCTTTCTTAG
* * * *** *
29722234 TCTGC-CCACTGCAACTTCAGCA-AGATAGGA-TTACCGGCTTTAA
1 TCTGCTCCACTGCAACTTCAGGAGAGATAAGACTTGCTTTC-TTAG
* * * **
29722277 TCTGCTCCACTGTAACTTCAGG-GAGATAAGATTTTCCATCTTCAG
1 TCTGCTCCACTGCAACTTCAGGAGAGATAAGACTTGCTTTCTT-AG
* *
29722322 TCTGC-CTCACTGCAACTTCTGGAG-GATAAGACTTGCTTACTTAG
1 TCTGCTC-CACTGCAACTTCAGGAGAGATAAGACTTGCTTTCTTAG
*
29722366 TCCGCTCCACTGCAACTTCAGG-GAGATAAGACT
1 TCTGCTCCACTGCAACTTCAGGAGAGATAAGACT
29722399 CGATCTGTTA
Statistics
Matches: 539, Mismatches: 129, Indels: 117
0.69 0.16 0.15
Matches are distributed among these distances:
39 3 0.01
40 59 0.11
41 21 0.04
42 14 0.03
43 77 0.14
44 211 0.39
45 149 0.28
46 5 0.01
ACGTcount: A:0.27, C:0.24, G:0.19, T:0.29
Consensus pattern (45 bp):
TCTGCTCCACTGCAACTTCAGGAGAGATAAGACTTGCTTTCTTAG
Found at i:29721941 original size:89 final size:90
Alignment explanation
Indices: 29721848--29722396 Score: 292
Period size: 89 Copynumber: 6.3 Consensus size: 90
29721838 ACTTTAATCT
* *
29721848 GCTCCACTACAATTTCAGGGAGATAAGATTTGCCATCTTCAGTCTGCCTCACTGCAACTTCAGGA
1 GCTCCACTGCAACTTCAGGGAGATAAGATTTGCCATCTTCAGTCTGCCTCACTGCAACTTCAGGA
29721913 G-GATAAGACTTGCTTACTTAGTCC
66 GAGATAAGACTTGCTTACTTAGTCC
* * * * * * * *
29721937 GCTCCACTACAACTTCAGGGAGATAAGACTAG--A--TGC-GATCT-ACTCTCTGCCATTTCA-G
1 GCTCCACTGCAACTTCAGGGAGATAAGATTTGCCATCTTCAG-TCTGCCTCACTGCAACTTCAGG
* * *
29721995 AGAGATAAGATCTAAGGTT--TTAATCC
65 AGAGATAAGA-CT-TGCTTACTTAGTCC
* * * * * ** * *
29722021 GC-CCACTGCAACTTTAGCGAAATAGGA-TTACCGGCTTTAATCTG-CTCCACTGCAACTTCAGG
1 GCTCCACTGCAACTTCAGGGAGATAAGATTTGCCATCTTCAGTCTGCCT-CACTGCAACTTCAGG
* * **
29722083 -GAGATAAGATTTGC-CATCTTCAGTTT
65 AGAGATAAGACTTGCTTA-CTT-AGTCC
* * * *
29722109 GCTTCACTGCAACTTCA-GGAGGATAAGACTTG-CTTACTT-AGTCCG-CTCCACTGCAACTTCA
1 GCTCCACTGCAACTTCAGGGA-GATAAGATTTGCCAT-CTTCAGTCTGCCT-CACTGCAACTTCA
* * * * *
29722170 GG-GAGATAAGACTAG-ATGC-GA-TCT
63 GGAGAGATAAGACTTGCTTACTTAGTCC
* * * * * **** * * *
29722194 GAT-CTCTGCAATTTCAGAGAGATAAGATCTAAGGT-TTTAATCTGCC-CACTGCAACTTCAGCA
1 GCTCCACTGCAACTTCAGGGAGATAAGATTTGCCATCTTCAGTCTGCCTCACTGCAACTTCAGGA
* * *** * *
29722256 -AGATAGGA-TTACCGGCTTTAATCT
66 GAGATAAGACTTGCTTAC-TTAGTCC
* * *
29722280 GCTCCACTGTAACTTCAGGGAGATAAGATTTTCCATCTTCAGTCTGCCTCACTGCAACTTCTGGA
1 GCTCCACTGCAACTTCAGGGAGATAAGATTTGCCATCTTCAGTCTGCCTCACTGCAACTTCAGGA
29722345 G-GATAAGACTTGCTTACTTAGTCC
66 GAGATAAGACTTGCTTACTTAGTCC
29722369 GCTCCACTGCAACTTCAGGGAGATAAGA
1 GCTCCACTGCAACTTCAGGGAGATAAGA
29722397 CTCGATCTGT
Statistics
Matches: 337, Mismatches: 88, Indels: 70
0.68 0.18 0.14
Matches are distributed among these distances:
82 2 0.01
83 48 0.14
84 51 0.15
85 17 0.05
86 16 0.05
87 45 0.13
88 17 0.05
89 132 0.39
90 9 0.03
ACGTcount: A:0.28, C:0.24, G:0.20, T:0.28
Consensus pattern (90 bp):
GCTCCACTGCAACTTCAGGGAGATAAGATTTGCCATCTTCAGTCTGCCTCACTGCAACTTCAGGA
GAGATAAGACTTGCTTACTTAGTCC
Found at i:29722131 original size:216 final size:216
Alignment explanation
Indices: 29721510--29722398 Score: 1388
Period size: 216 Copynumber: 4.1 Consensus size: 216
29721500 CTGCTTCTGG
* * * *
29721510 TGCAACTTCAAGGAGATAAGACTAAATGCGATCTGCTCTCTGCAACTTT-AGAGAGATAAGATCC
1 TGCAACTTCAGGGAGATAAGACTAGATGCGATCTACTCTCTGCAA-TTTCAGAGAGATAAGATCT
* * * * * *
29721574 AAGGTTTTAATCCACTCTACTACAACTTCAGGAAGATAGGATTATCGGCTTTAATCTGCTCCTCT
65 AAGGTTTTAATCCGC-CCACTGCAACTTCAGCAAGATAGGATTACCGGCTTTAATCTGCTCCACT
* ** * *
29721639 GCAACTTTAAAGAGATAAGATTTGCCATCTTCAGTCTACCTTACTGCAACTTCAGGAGGATAAGA
129 GCAACTTCAGGGAGATAAGATTTGCCATCTTCAGTCTGCCTCACTGCAACTTCAGGAGGATAAGA
* * *
29721704 CTTGTTTTCTTAGTCTGCTCCAC
194 CTTGCTTACTTAGTCCGCTCCAC
* * * * *
29721727 TGCAACTTCAGGGAGATAAGACTCGATGTGATCTGCTCTCTGCAACTTCAGAGAGATAAGATCTG
1 TGCAACTTCAGGGAGATAAGACTAGATGCGATCTACTCTCTGCAATTTCAGAGAGATAAGATCTA
* * *
29721792 AGGTTTTTAATCCGCCCACTGAAACTTCAGCAAGATAGGATTACCGACTTTAATCTGCTCCACTA
66 AGG-TTTTAATCCGCCCACTGCAACTTCAGCAAGATAGGATTACCGGCTTTAATCTGCTCCACTG
*
29721857 CAATTTCAGGGAGATAAGATTTGCCATCTTCAGTCTGCCTCACTGCAACTTCAGGAGGATAAGAC
130 CAACTTCAGGGAGATAAGATTTGCCATCTTCAGTCTGCCTCACTGCAACTTCAGGAGGATAAGAC
29721922 TTGCTTACTTAGTCCGCTCCAC
195 TTGCTTACTTAGTCCGCTCCAC
* *
29721944 TACAACTTCAGGGAGATAAGACTAGATGCGATCTACTCTCTGCCATTTCAGAGAGATAAGATCTA
1 TGCAACTTCAGGGAGATAAGACTAGATGCGATCTACTCTCTGCAATTTCAGAGAGATAAGATCTA
*
29722009 AGGTTTTAATCCGCCCACTGCAACTTTAGCGAA-ATAGGATTACCGGCTTTAATCTGCTCCACTG
66 AGGTTTTAATCCGCCCACTGCAACTTCAGC-AAGATAGGATTACCGGCTTTAATCTGCTCCACTG
* *
29722073 CAACTTCAGGGAGATAAGATTTGCCATCTTCAGTTTGCTTCACTGCAACTTCAGGAGGATAAGAC
130 CAACTTCAGGGAGATAAGATTTGCCATCTTCAGTCTGCCTCACTGCAACTTCAGGAGGATAAGAC
29722138 TTGCTTACTTAGTCCGCTCCAC
195 TTGCTTACTTAGTCCGCTCCAC
29722160 TGCAACTTCAGGGAGATAAGACTAGATGCGATCTGA-TCTCTGCAATTTCAGAGAGATAAGATCT
1 TGCAACTTCAGGGAGATAAGACTAGATGCGATCT-ACTCTCTGCAATTTCAGAGAGATAAGATCT
*
29722224 AAGGTTTTAATCTGCCCACTGCAACTTCAGCAAGATAGGATTACCGGCTTTAATCTGCTCCACTG
65 AAGGTTTTAATCCGCCCACTGCAACTTCAGCAAGATAGGATTACCGGCTTTAATCTGCTCCACTG
* * *
29722289 TAACTTCAGGGAGATAAGATTTTCCATCTTCAGTCTGCCTCACTGCAACTTCTGGAGGATAAGAC
130 CAACTTCAGGGAGATAAGATTTGCCATCTTCAGTCTGCCTCACTGCAACTTCAGGAGGATAAGAC
29722354 TTGCTTACTTAGTCCGCTCCAC
195 TTGCTTACTTAGTCCGCTCCAC
29722376 TGCAACTTCAGGGAGATAAGACT
1 TGCAACTTCAGGGAGATAAGACT
29722399 CGATCTGTTA
Statistics
Matches: 619, Mismatches: 48, Indels: 11
0.91 0.07 0.02
Matches are distributed among these distances:
215 2 0.00
216 365 0.59
217 242 0.39
218 10 0.02
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.29
Consensus pattern (216 bp):
TGCAACTTCAGGGAGATAAGACTAGATGCGATCTACTCTCTGCAATTTCAGAGAGATAAGATCTA
AGGTTTTAATCCGCCCACTGCAACTTCAGCAAGATAGGATTACCGGCTTTAATCTGCTCCACTGC
AACTTCAGGGAGATAAGATTTGCCATCTTCAGTCTGCCTCACTGCAACTTCAGGAGGATAAGACT
TGCTTACTTAGTCCGCTCCAC
Found at i:29734213 original size:35 final size:33
Alignment explanation
Indices: 29734158--29734229 Score: 83
Period size: 35 Copynumber: 2.1 Consensus size: 33
29734148 TATGAATAAA
*
29734158 CAAATAAATAAATAAAATAATGACATGAAAAATAT-
1 CAAATAAATAAACAAAATAAT-A-AT-AAAAATATG
* *
29734193 CAAATAAATAGACAAGATAATAATAAAAATATG
1 CAAATAAATAAACAAAATAATAATAAAAATATG
29734226 CAAA
1 CAAA
29734230 CATAAATTAA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
32 8 0.24
33 6 0.18
34 1 0.03
35 18 0.55
ACGTcount: A:0.65, C:0.07, G:0.07, T:0.21
Consensus pattern (33 bp):
CAAATAAATAAACAAAATAATAATAAAAATATG
Found at i:29734606 original size:222 final size:223
Alignment explanation
Indices: 29734220--29734665 Score: 885
Period size: 222 Copynumber: 2.0 Consensus size: 223
29734210 TAATAATAAA
29734220 AATATGCAAACATAAATTAATAAACAAATGATAAACAACAAAAAAAATATACATGTACACATAAA
1 AATATGCAAACATAAATTAATAAACAAATGATAAACAACAAAAAAAATATACATGTACACATAAA
29734285 AAATACATAAGTTTAAAACAATTAAAATAATATCAAAATTAATTAAATAAAATAAACATGTGTAT
66 AAATACATAAGTTTAAAACAATTAAAATAATATCAAAATTAATTAAATAAAATAAACATGTGTAT
29734350 AAAATATATGAAAAACATTGGTTTTTTCAAACGTATAAGTACATACATAAAAAACCTATATATAT
131 AAAATATATGAAAAACATTGGTTTTTTCAAACGTATAAGTACATACATAAAAAACCTATATATAT
29734415 AAAATAATAATAATTAC-TATGAAAATT
196 AAAATAATAATAATTACTTATGAAAATT
29734442 AATATGCAAACATAAATTAATAAACAAATGATAAACAACAAAAAAAATATACATGTACACATAAA
1 AATATGCAAACATAAATTAATAAACAAATGATAAACAACAAAAAAAATATACATGTACACATAAA
29734507 AAATACATAAGTTTAAAACAATTAAAATAATATCAAAATTAATTAAATAAAATAAACATGTGTAT
66 AAATACATAAGTTTAAAACAATTAAAATAATATCAAAATTAATTAAATAAAATAAACATGTGTAT
29734572 AAAATATATGAAAAACATTGGTTTTTTCAAACGTATAAGTACATACATAAAAAACCTATATATAT
131 AAAATATATGAAAAACATTGGTTTTTTCAAACGTATAAGTACATACATAAAAAACCTATATATAT
29734637 AAAATAATAATAATTACTTATGAAAATT
196 AAAATAATAATAATTACTTATGAAAATT
29734665 A
1 A
29734666 TAAAATAAAA
Statistics
Matches: 223, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
222 212 0.95
223 11 0.05
ACGTcount: A:0.57, C:0.09, G:0.05, T:0.28
Consensus pattern (223 bp):
AATATGCAAACATAAATTAATAAACAAATGATAAACAACAAAAAAAATATACATGTACACATAAA
AAATACATAAGTTTAAAACAATTAAAATAATATCAAAATTAATTAAATAAAATAAACATGTGTAT
AAAATATATGAAAAACATTGGTTTTTTCAAACGTATAAGTACATACATAAAAAACCTATATATAT
AAAATAATAATAATTACTTATGAAAATT
Found at i:29736865 original size:51 final size:49
Alignment explanation
Indices: 29736803--29736966 Score: 171
Period size: 51 Copynumber: 3.3 Consensus size: 49
29736793 GATGTGTAAT
29736803 ATGAGAATGGATTGAAACATGTTATATTATATGAAATATTTGTGTGTTG
1 ATGAGAATGGATTGAAACATGTTATATTATATGAAATATTTGTGTGTTG
* * **
29736852 ATGATGAATTGGATTG--A-AT-TGA-ATTGAAATG-AGCATTTGATGTGTAAT-
1 ATGA-GAA-TGGATTGAAACATGTTATATT-ATATGAAATATTTG-TGTGT--TG
29736900 ATGAGAATGGATTGAAACATGTTATATTATATGAAATATTTGTGTGTTG
1 ATGAGAATGGATTGAAACATGTTATATTATATGAAATATTTGTGTGTTG
29736949 ATGATGAATTGGATTGAA
1 ATGA-GAA-TGGATTGAA
29736967 TTGAATTGAA
Statistics
Matches: 92, Mismatches: 8, Indels: 28
0.72 0.06 0.22
Matches are distributed among these distances:
46 16 0.17
47 14 0.15
48 8 0.09
49 12 0.13
50 17 0.18
51 25 0.27
ACGTcount: A:0.35, C:0.02, G:0.24, T:0.39
Consensus pattern (49 bp):
ATGAGAATGGATTGAAACATGTTATATTATATGAAATATTTGTGTGTTG
Found at i:29736911 original size:46 final size:48
Alignment explanation
Indices: 29736787--29736915 Score: 117
Period size: 46 Copynumber: 2.7 Consensus size: 48
29736777 TATTTAGTGG
* *
29736787 GCATTTGATGTGTAATATGAGAATGGATTGAAACATGTTATATTATATGAA
1 GCATTTGATGTGTAATATGAGAATGGATTG--A-ATGTGATATTAAATGAA
**
29736838 ATATTTG-TGTGT--TGATGATGAATTGGATTGAAT-TGA-ATTGAAATG-A
1 GCATTTGATGTGTAAT-ATGA-GAA-TGGATTGAATGTGATATT-AAATGAA
29736884 GCATTTGATGTGTAATATGAGAATGGATTGAA
1 GCATTTGATGTGTAATATGAGAATGGATTGAA
29736916 ACATGTTATA
Statistics
Matches: 65, Mismatches: 6, Indels: 19
0.72 0.07 0.21
Matches are distributed among these distances:
46 18 0.28
47 14 0.22
48 7 0.11
49 6 0.09
50 8 0.12
51 12 0.18
ACGTcount: A:0.35, C:0.02, G:0.25, T:0.38
Consensus pattern (48 bp):
GCATTTGATGTGTAATATGAGAATGGATTGAATGTGATATTAAATGAA
Found at i:29736953 original size:97 final size:97
Alignment explanation
Indices: 29736787--29736980 Score: 388
Period size: 97 Copynumber: 2.0 Consensus size: 97
29736777 TATTTAGTGG
29736787 GCATTTGATGTGTAATATGAGAATGGATTGAAACATGTTATATTATATGAAATATTTGTGTGTTG
1 GCATTTGATGTGTAATATGAGAATGGATTGAAACATGTTATATTATATGAAATATTTGTGTGTTG
29736852 ATGATGAATTGGATTGAATTGAATTGAAATGA
66 ATGATGAATTGGATTGAATTGAATTGAAATGA
29736884 GCATTTGATGTGTAATATGAGAATGGATTGAAACATGTTATATTATATGAAATATTTGTGTGTTG
1 GCATTTGATGTGTAATATGAGAATGGATTGAAACATGTTATATTATATGAAATATTTGTGTGTTG
29736949 ATGATGAATTGGATTGAATTGAATTGAAATGA
66 ATGATGAATTGGATTGAATTGAATTGAAATGA
29736981 AATGAGATAA
Statistics
Matches: 97, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
97 97 1.00
ACGTcount: A:0.35, C:0.02, G:0.24, T:0.39
Consensus pattern (97 bp):
GCATTTGATGTGTAATATGAGAATGGATTGAAACATGTTATATTATATGAAATATTTGTGTGTTG
ATGATGAATTGGATTGAATTGAATTGAAATGA
Found at i:29739548 original size:15 final size:15
Alignment explanation
Indices: 29739528--29739558 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
29739518 ATGAGGGGCT
*
29739528 TTTGGGCCTGTTCCA
1 TTTGGGCCTCTTCCA
29739543 TTTGGGCCTCTTCCA
1 TTTGGGCCTCTTCCA
29739558 T
1 T
29739559 ATCGGGTTCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.06, C:0.29, G:0.23, T:0.42
Consensus pattern (15 bp):
TTTGGGCCTCTTCCA
Found at i:29739968 original size:45 final size:45
Alignment explanation
Indices: 29739891--29739994 Score: 115
Period size: 45 Copynumber: 2.4 Consensus size: 45
29739881 CATTTCTCAT
*
29739891 TTTCATTTC-C-ATTTTGAAAAAACCACATTCATTTCCAAAT-AA
1 TTTCATTTCTCTATTTTGAAAAAACCACAATCATTTCCAAATGAA
* * ** **
29739933 TTTCATTTCTCTATTTTGGAGAAAACCATAATCATTTCTGAATGTT
1 TTTCATTTCTCTATTTT-GAAAAAACCACAATCATTTCCAAATGAA
29739979 TTTCATTTCTCTATTT
1 TTTCATTTCTCTATTT
29739995 CTATCCATTC
Statistics
Matches: 51, Mismatches: 7, Indels: 4
0.82 0.11 0.06
Matches are distributed among these distances:
42 9 0.18
43 1 0.02
44 5 0.10
45 20 0.39
46 16 0.31
ACGTcount: A:0.30, C:0.18, G:0.06, T:0.46
Consensus pattern (45 bp):
TTTCATTTCTCTATTTTGAAAAAACCACAATCATTTCCAAATGAA
Found at i:29743658 original size:59 final size:61
Alignment explanation
Indices: 29743587--29743721 Score: 186
Period size: 62 Copynumber: 2.2 Consensus size: 61
29743577 AATCACTTTA
* * *
29743587 ATATTAAATTAATATAATA-TT-TCT-TAAGATGAATATTAGATTAAATTTAATATTAAAT
1 ATATTAAATTAATATAATATTTGTCTATAAGATAAAAATTAAATTAAATTTAATATTAAAT
* *
29743645 CTTATTAAATTAATAGAATATTTGTCTATAAGATAAAAATTAAATTAAATTTAATATTAAAT
1 -ATATTAAATTAATATAATATTTGTCTATAAGATAAAAATTAAATTAAATTTAATATTAAAT
*
29743707 ATATTAAAATAATAT
1 ATATTAAATTAATAT
29743722 TATTTTTGGA
Statistics
Matches: 65, Mismatches: 8, Indels: 4
0.84 0.10 0.05
Matches are distributed among these distances:
59 17 0.26
60 2 0.03
61 15 0.23
62 31 0.48
ACGTcount: A:0.50, C:0.02, G:0.04, T:0.43
Consensus pattern (61 bp):
ATATTAAATTAATATAATATTTGTCTATAAGATAAAAATTAAATTAAATTTAATATTAAAT
Found at i:29751878 original size:31 final size:31
Alignment explanation
Indices: 29751842--29751905 Score: 94
Period size: 31 Copynumber: 2.1 Consensus size: 31
29751832 GGCAAATTAC
* *
29751842 AAGAGTAATTGAAT-TTATTAAAAACTCTTTA
1 AAGAGTAATTGAATCCTAAT-AAAACTCTTTA
29751873 AAGAGTAATTGAATCCTAATAAAACTCTTTA
1 AAGAGTAATTGAATCCTAATAAAACTCTTTA
29751904 AA
1 AA
29751906 ATCATCTAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 27 0.90
32 3 0.10
ACGTcount: A:0.47, C:0.09, G:0.09, T:0.34
Consensus pattern (31 bp):
AAGAGTAATTGAATCCTAATAAAACTCTTTA
Found at i:29752299 original size:58 final size:59
Alignment explanation
Indices: 29752209--29752327 Score: 231
Period size: 58 Copynumber: 2.0 Consensus size: 59
29752199 TGACCTCGTC
29752209 ATGTGTGTGTTACCCTCATATAATATCCTTGATTCCTTTGAGTGAAATT-GTTCACTCA
1 ATGTGTGTGTTACCCTCATATAATATCCTTGATTCCTTTGAGTGAAATTCGTTCACTCA
29752267 ATGTGTGTGTTACCCTCATATAATATCCTTGATTCCTTTGAGTGAAATTCGTTCACTCA
1 ATGTGTGTGTTACCCTCATATAATATCCTTGATTCCTTTGAGTGAAATTCGTTCACTCA
29752326 AT
1 AT
29752328 ACAATTATAT
Statistics
Matches: 60, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
58 49 0.82
59 11 0.18
ACGTcount: A:0.24, C:0.19, G:0.15, T:0.41
Consensus pattern (59 bp):
ATGTGTGTGTTACCCTCATATAATATCCTTGATTCCTTTGAGTGAAATTCGTTCACTCA
Found at i:29757652 original size:10 final size:10
Alignment explanation
Indices: 29757637--29757665 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
29757627 AAGTTTTTTT
29757637 TAAGGATTTC
1 TAAGGATTTC
29757647 TAAGGATTTC
1 TAAGGATTTC
29757657 TAAGGATTT
1 TAAGGATTT
29757666 AATGAATTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.31, C:0.07, G:0.21, T:0.41
Consensus pattern (10 bp):
TAAGGATTTC
Found at i:29759053 original size:66 final size:66
Alignment explanation
Indices: 29758943--29759091 Score: 255
Period size: 66 Copynumber: 2.3 Consensus size: 66
29758933 ATGAGATTAT
* *
29758943 ATGA-TATGTGGTTGCTATGCAAATTATCTTAAAATGTATATATGTGTAATGTGATGTATGCCTA
1 ATGAGTATGTGGTTGCTATGCAAATTATCTTAAAATGTATATATGTGTAAGGTAATGTATGCCTA
29759007 A
66 A
*
29759008 ATGAGTATGTGGTTGCTATTCAAATTATCTTAAAATGTATATATGTGTAAGGTAATGTATGCCTA
1 ATGAGTATGTGGTTGCTATGCAAATTATCTTAAAATGTATATATGTGTAAGGTAATGTATGCCTA
29759073 A
66 A
*
29759074 ATGAGTATGTCGTTGCTA
1 ATGAGTATGTGGTTGCTA
29759092 ACACCTCCTT
Statistics
Matches: 79, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
65 4 0.05
66 75 0.95
ACGTcount: A:0.32, C:0.08, G:0.21, T:0.40
Consensus pattern (66 bp):
ATGAGTATGTGGTTGCTATGCAAATTATCTTAAAATGTATATATGTGTAAGGTAATGTATGCCTA
A
Found at i:29766806 original size:51 final size:52
Alignment explanation
Indices: 29766690--29766819 Score: 192
Period size: 51 Copynumber: 2.5 Consensus size: 52
29766680 ACTAGTGACT
29766690 CAAGTGTGGTACTATGTGAAGGCCACTTTGTGAAGAAAGATAGCTTTGGTCA
1 CAAGTGTGGTACTATGTGAAGGCCACTTTGTGAAGAAAGATAGCTTTGGTCA
* * *
29766742 CAAGTGTGGTACTATGTGAAGGTCAGTTTGTGAAG-AAGGTAGCTTTGG-CTA
1 CAAGTGTGGTACTATGTGAAGGCCACTTTGTGAAGAAAGATAGCTTTGGTC-A
* *
29766793 CAAGGGTGGTACTATGTGCAGGCCACT
1 CAAGTGTGGTACTATGTGAAGGCCACT
29766820 GGGTATCCGT
Statistics
Matches: 70, Mismatches: 7, Indels: 3
0.88 0.09 0.04
Matches are distributed among these distances:
50 1 0.01
51 36 0.51
52 33 0.47
ACGTcount: A:0.26, C:0.14, G:0.32, T:0.28
Consensus pattern (52 bp):
CAAGTGTGGTACTATGTGAAGGCCACTTTGTGAAGAAAGATAGCTTTGGTCA
Found at i:29773644 original size:24 final size:25
Alignment explanation
Indices: 29773612--29773660 Score: 73
Period size: 26 Copynumber: 2.0 Consensus size: 25
29773602 CAAAGTTTAA
*
29773612 ATTTTTTTC-AAGTATGTTTTAATC
1 ATTTCTTTCAAAGTATGTTTTAATC
29773636 ATTTCTTTCATAAGTATGTTTTAAT
1 ATTTCTTTCA-AAGTATGTTTTAAT
29773661 AAATGAATGT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 8 0.36
26 14 0.64
ACGTcount: A:0.27, C:0.08, G:0.08, T:0.57
Consensus pattern (25 bp):
ATTTCTTTCAAAGTATGTTTTAATC
Found at i:29774500 original size:39 final size:39
Alignment explanation
Indices: 29774446--29774530 Score: 134
Period size: 39 Copynumber: 2.2 Consensus size: 39
29774436 TCAACCTTGT
29774446 GATTGTTTGCTTGATTGATAGGAAATTATGTTGAATAAA
1 GATTGTTTGCTTGATTGATAGGAAATTATGTTGAATAAA
* * *
29774485 GATTGTTTTCTTGATTGATAGGAAATTCTGTTGATTAAA
1 GATTGTTTGCTTGATTGATAGGAAATTATGTTGAATAAA
*
29774524 GAATGTT
1 GATTGTT
29774531 ATTTATGGCT
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
39 42 1.00
ACGTcount: A:0.31, C:0.04, G:0.22, T:0.44
Consensus pattern (39 bp):
GATTGTTTGCTTGATTGATAGGAAATTATGTTGAATAAA
Found at i:29781836 original size:51 final size:52
Alignment explanation
Indices: 29781720--29781838 Score: 195
Period size: 52 Copynumber: 2.3 Consensus size: 52
29781710 ACTAGTGACT
*
29781720 CAAGTGTGGTACTATGTGAAGGCCACTTTGTGAAGAAAGATAGCTTTGGTTA
1 CAAGTGTGGTACTATGTGAAGGCCACTTTGTGAAGAAAGATAGCTTTGGCTA
* *
29781772 CAAGTGTGGTACTATGTGAAGGTCACTTTGTGAAG-AAGGTAGCTTTGGCTA
1 CAAGTGTGGTACTATGTGAAGGCCACTTTGTGAAGAAAGATAGCTTTGGCTA
*
29781823 CAAGGGTGGTACTATG
1 CAAGTGTGGTACTATG
29781839 CGTGGGCCAC
Statistics
Matches: 63, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
51 29 0.46
52 34 0.54
ACGTcount: A:0.27, C:0.12, G:0.31, T:0.30
Consensus pattern (52 bp):
CAAGTGTGGTACTATGTGAAGGCCACTTTGTGAAGAAAGATAGCTTTGGCTA
Found at i:29792861 original size:17 final size:17
Alignment explanation
Indices: 29792839--29792872 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
29792829 CTGGTTGATT
29792839 GAGCTTA-TAAAGCAGAA
1 GAGCTTAGTAAAG-AGAA
29792856 GAGCTTAGTAAAGAGAA
1 GAGCTTAGTAAAGAGAA
29792873 AAGACAAGCT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.47, C:0.09, G:0.26, T:0.18
Consensus pattern (17 bp):
GAGCTTAGTAAAGAGAA
Found at i:29793796 original size:179 final size:179
Alignment explanation
Indices: 29793491--29793854 Score: 615
Period size: 179 Copynumber: 2.0 Consensus size: 179
29793481 TTGAGTCCAC
*
29793491 TAAATTCGTAGTTAAATTATCAAACCCCCTAGGCAGGTACGTGATGGTGGATAAAATTTGTAAGA
1 TAAATTCGTAGTTAAAGTATCAAACCCCCTAGGCAGGTACGTGATGGTGGATAAAATTTGTAAGA
*
29793556 ATTGTCCGTTAATGATACGGGGTTATTGTTTCCCGGTTGATTTAATATTATTACAATTTAATGAA
66 ATTGTCCGTTAATGATACGGGGTTATTGTTTCCCAGTTGATTTAATATTATTACAATTTAATGAA
*
29793621 TTTGATATGATTCTAGGTATGGACTAGTTAACTCAACATGATGT-TGTGG
131 TTTGATATGATTCTAGGTATGGACTAGTTAACTCAACATGAT-TCTGTAG
* * *
29793670 TAAATTCGTGGTTAAAGTATCAAATCCTCTAGGCCA-GTACGTGATGGTGGATAAAATTTGTAAG
1 TAAATTCGTAGTTAAAGTATCAAACCCCCTAGG-CAGGTACGTGATGGTGGATAAAATTTGTAAG
*
29793734 AATTGTCCGTTAATGATACGGGGTTATTGTTTCCCAGTTGATTTAATATTATTACCATTTAATGA
65 AATTGTCCGTTAATGATACGGGGTTATTGTTTCCCAGTTGATTTAATATTATTACAATTTAATGA
* *
29793799 ATTTGATGTGATTCTGGGTATGGACTAGTTAACTCAACATGATTCTGTAG
130 ATTTGATATGATTCTAGGTATGGACTAGTTAACTCAACATGATTCTGTAG
29793849 TAAATT
1 TAAATT
29793855 GTAAGCAAAA
Statistics
Matches: 174, Mismatches: 9, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
178 1 0.01
179 171 0.98
180 2 0.01
ACGTcount: A:0.30, C:0.12, G:0.21, T:0.37
Consensus pattern (179 bp):
TAAATTCGTAGTTAAAGTATCAAACCCCCTAGGCAGGTACGTGATGGTGGATAAAATTTGTAAGA
ATTGTCCGTTAATGATACGGGGTTATTGTTTCCCAGTTGATTTAATATTATTACAATTTAATGAA
TTTGATATGATTCTAGGTATGGACTAGTTAACTCAACATGATTCTGTAG
Found at i:29796671 original size:16 final size:16
Alignment explanation
Indices: 29796637--29796671 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
29796627 GTTTCCAAAG
*
29796637 TTTTCATTAAGGGGGT
1 TTTTCATTAAGGGGAT
*
29796653 TTTTCATTAAGGGTAT
1 TTTTCATTAAGGGGAT
29796669 TTT
1 TTT
29796672 GGTCATTTAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.20, C:0.06, G:0.23, T:0.51
Consensus pattern (16 bp):
TTTTCATTAAGGGGAT
Found at i:29797666 original size:45 final size:45
Alignment explanation
Indices: 29797584--29797703 Score: 109
Period size: 45 Copynumber: 2.7 Consensus size: 45
29797574 ATTAATGAAA
* * * * *
29797584 ATAAAGGTAGTTGCTATGTACTGATTTCAC-CAGATACCAATG-GTT
1 ATAAAGGTGGTTCCTATGTGCTAATTTCACTC-TATACCAATGAG-T
* *
29797629 ATATAGGTGGTTCCTATGTGCTAATTTCACTCTATACCATTGAGT
1 ATAAAGGTGGTTCCTATGTGCTAATTTCACTCTATACCAATGAGT
** * *
29797674 ATAAAGGTGGTTGTTATGTGTTGATTTCAC
1 ATAAAGGTGGTTCCTATGTGCTAATTTCAC
29797704 CGATAGTACT
Statistics
Matches: 61, Mismatches: 12, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
45 59 0.97
46 2 0.03
ACGTcount: A:0.27, C:0.14, G:0.21, T:0.38
Consensus pattern (45 bp):
ATAAAGGTGGTTCCTATGTGCTAATTTCACTCTATACCAATGAGT
Found at i:29800232 original size:24 final size:25
Alignment explanation
Indices: 29800192--29800246 Score: 67
Period size: 24 Copynumber: 2.2 Consensus size: 25
29800182 CACAGCTCGA
* *
29800192 ATGAGCATCTCGTTA-TTAGCTCTC
1 ATGAGCATCCCGATATTTAGCTCTC
*
29800216 ATGAGCATCCCGATATTTGGCTCTC
1 ATGAGCATCCCGATATTTAGCTCTC
*
29800241 ACGAGC
1 ATGAGC
29800247 TTTCCGTTAT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
24 13 0.50
25 13 0.50
ACGTcount: A:0.22, C:0.27, G:0.20, T:0.31
Consensus pattern (25 bp):
ATGAGCATCCCGATATTTAGCTCTC
Found at i:29805245 original size:17 final size:17
Alignment explanation
Indices: 29805182--29805296 Score: 78
Period size: 17 Copynumber: 6.9 Consensus size: 17
29805172 CCATCCATGC
29805182 AAACTGCGAGCT--CCA
1 AAACTGCGAGCTCACCA
29805197 AATA-TGCGAGCTCTA-CA
1 AA-ACTGCGAGCTC-ACCA
* *
29805214 AAACTGTGAGTTCACCA
1 AAACTGCGAGCTCACCA
* *
29805231 AAAGTGCGAGCTCACCC
1 AAACTGCGAGCTCACCA
* *
29805248 AGACTGCAAGCTCACCA
1 AAACTGCGAGCTCACCA
**
29805265 AATA-TATGAGCTCACCA
1 AA-ACTGCGAGCTCACCA
* *
29805282 AGACTACGAGCTCAC
1 AAACTGCGAGCTCAC
29805297 TAAACTTGAC
Statistics
Matches: 76, Mismatches: 16, Indels: 14
0.72 0.15 0.13
Matches are distributed among these distances:
15 10 0.13
16 4 0.05
17 61 0.80
18 1 0.01
ACGTcount: A:0.35, C:0.30, G:0.18, T:0.17
Consensus pattern (17 bp):
AAACTGCGAGCTCACCA
Found at i:29809037 original size:2 final size:2
Alignment explanation
Indices: 29809030--29809058 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
29809020 GACACTCAGG
29809030 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
29809059 TATGTACTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:29815789 original size:21 final size:21
Alignment explanation
Indices: 29815764--29815837 Score: 71
Period size: 21 Copynumber: 3.5 Consensus size: 21
29815754 ATAGATTTTA
*
29815764 CAAATGCTTTAACAACGATTT
1 CAAATGTTTTAACAACGATTT
* * *
29815785 CAAATTTTTTTA-TA-GATTTT
1 CAAATGTTTTAACAACGA-TTT
29815805 ACAAATGTTTTAACAACGATTT
1 -CAAATGTTTTAACAACGATTT
*
29815827 CAAATTTTTTA
1 CAAATGTTTTA
29815838 TTAGCATTAT
Statistics
Matches: 41, Mismatches: 8, Indels: 8
0.72 0.14 0.14
Matches are distributed among these distances:
19 2 0.05
20 4 0.10
21 29 0.71
22 4 0.10
23 2 0.05
ACGTcount: A:0.36, C:0.12, G:0.07, T:0.45
Consensus pattern (21 bp):
CAAATGTTTTAACAACGATTT
Found at i:29815801 original size:42 final size:42
Alignment explanation
Indices: 29815741--29815836 Score: 174
Period size: 42 Copynumber: 2.3 Consensus size: 42
29815731 CTAATTTATA
29815741 TCAAATTTTTTTTATAGATTTTACAAATGCTTTAACAACGATT
1 TCAAA-TTTTTTTATAGATTTTACAAATGCTTTAACAACGATT
*
29815784 TCAAATTTTTTTATAGATTTTACAAATGTTTTAACAACGATT
1 TCAAATTTTTTTATAGATTTTACAAATGCTTTAACAACGATT
29815826 TCAAATTTTTT
1 TCAAATTTTTT
29815837 ATTAGCATTA
Statistics
Matches: 52, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
42 47 0.90
43 5 0.10
ACGTcount: A:0.34, C:0.10, G:0.06, T:0.49
Consensus pattern (42 bp):
TCAAATTTTTTTATAGATTTTACAAATGCTTTAACAACGATT
Found at i:29818244 original size:11 final size:11
Alignment explanation
Indices: 29818230--29818255 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
29818220 GCAAAAGAGG
29818230 AAAATTAAATC
1 AAAATTAAATC
29818241 AAAATTAAATC
1 AAAATTAAATC
29818252 AAAA
1 AAAA
29818256 GCATAGGCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.69, C:0.08, G:0.00, T:0.23
Consensus pattern (11 bp):
AAAATTAAATC
Found at i:29820195 original size:41 final size:41
Alignment explanation
Indices: 29820138--29820219 Score: 164
Period size: 41 Copynumber: 2.0 Consensus size: 41
29820128 AAAGCCACAA
29820138 GATATGAAATCAAAGTGTGTTTTGGTATACTAGAAAATGTC
1 GATATGAAATCAAAGTGTGTTTTGGTATACTAGAAAATGTC
29820179 GATATGAAATCAAAGTGTGTTTTGGTATACTAGAAAATGTC
1 GATATGAAATCAAAGTGTGTTTTGGTATACTAGAAAATGTC
29820220 TTTTTCCGTT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.37, C:0.07, G:0.22, T:0.34
Consensus pattern (41 bp):
GATATGAAATCAAAGTGTGTTTTGGTATACTAGAAAATGTC
Found at i:29822144 original size:62 final size:62
Alignment explanation
Indices: 29822062--29822189 Score: 238
Period size: 62 Copynumber: 2.1 Consensus size: 62
29822052 TCAATTTTTC
29822062 AATTAGAAATAGTGATTTCCCCATGTTGTGTAAAATCCGCACTGAAAAAATAGAAAAAAGAA
1 AATTAGAAATAGTGATTTCCCCATGTTGTGTAAAATCCGCACTGAAAAAATAGAAAAAAGAA
* *
29822124 AATTAGAAATAGTGATTTCCCTATGTTGTGTAAAATCCGCACTGAAAAAATAGAAAAAATAA
1 AATTAGAAATAGTGATTTCCCCATGTTGTGTAAAATCCGCACTGAAAAAATAGAAAAAAGAA
29822186 AATT
1 AATT
29822190 TTCTCCTATC
Statistics
Matches: 64, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
62 64 1.00
ACGTcount: A:0.47, C:0.12, G:0.15, T:0.27
Consensus pattern (62 bp):
AATTAGAAATAGTGATTTCCCCATGTTGTGTAAAATCCGCACTGAAAAAATAGAAAAAAGAA
Found at i:29822774 original size:16 final size:16
Alignment explanation
Indices: 29822753--29822804 Score: 68
Period size: 16 Copynumber: 3.2 Consensus size: 16
29822743 TGAATTACTG
* *
29822753 ATTACAGCTTTATTTC
1 ATTACAGCTCTATTTA
*
29822769 ATTACAACTCTATTTA
1 ATTACAGCTCTATTTA
*
29822785 ATTACAGCTCTATTCA
1 ATTACAGCTCTATTTA
29822801 ATTA
1 ATTA
29822805 TAGTGAACCA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 31 1.00
ACGTcount: A:0.33, C:0.19, G:0.04, T:0.44
Consensus pattern (16 bp):
ATTACAGCTCTATTTA
Found at i:29835279 original size:15 final size:15
Alignment explanation
Indices: 29835259--29835288 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
29835249 TTCTTGTTAC
29835259 TTGATTCAATTTGAT
1 TTGATTCAATTTGAT
29835274 TTGATTCAATTTGAT
1 TTGATTCAATTTGAT
29835289 CCAATCTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.07, G:0.13, T:0.53
Consensus pattern (15 bp):
TTGATTCAATTTGAT
Found at i:29842185 original size:42 final size:42
Alignment explanation
Indices: 29842113--29842193 Score: 103
Period size: 42 Copynumber: 1.9 Consensus size: 42
29842103 ACGGCCTAAT
*
29842113 ACACGATCGTGTGTATCAAGTCAGTGAGTTACACGGTCTAGC
1 ACACGATCGTGTGTATCAAGTCAATGAGTTACACGGTCTAGC
* *
29842155 ACACGGTCGTGTGTCA-CAAGTCAAAT-AGTTACATGGTCT
1 ACACGATCGTGTGT-ATCAAGTC-AATGAGTTACACGGTCT
29842194 GTCACAGGGC
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
42 31 0.91
43 3 0.09
ACGTcount: A:0.27, C:0.21, G:0.25, T:0.27
Consensus pattern (42 bp):
ACACGATCGTGTGTATCAAGTCAATGAGTTACACGGTCTAGC
Found at i:29853076 original size:2 final size:2
Alignment explanation
Indices: 29853069--29853125 Score: 58
Period size: 2 Copynumber: 32.5 Consensus size: 2
29853059 CTTTCTTTTG
29853069 AT AT AT AT AT AT AT AT AT AT AT A- AT AT A- AT AT A- 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
29853108 -T A- AT A- AT A- AT AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT A
29853126 AAAACATAAT
Statistics
Matches: 47, Mismatches: 0, Indels: 16
0.75 0.00 0.25
Matches are distributed among these distances:
1 8 0.17
2 39 0.83
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:29853082 original size:8 final size:8
Alignment explanation
Indices: 29853069--29853125 Score: 58
Period size: 7 Copynumber: 8.1 Consensus size: 8
29853059 CTTTCTTTTG
29853069 ATATATAT
1 ATATATAT
29853077 ATATATAT
1 ATATATAT
29853085 ATATATA-
1 ATATATAT
29853092 ATATA-AT
1 ATATATAT
29853099 ATA-ATAT
1 ATATATAT
29853106 AT-TA-AT
1 ATATATAT
29853112 A-ATA-AT
1 ATATATAT
29853118 ATA-ATAT
1 ATATATAT
29853125 A
1 A
29853126 AAAACATAAT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
6 11 0.26
7 17 0.40
8 15 0.35
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (8 bp):
ATATATAT
Found at i:29853084 original size:10 final size:9
Alignment explanation
Indices: 29853069--29853125 Score: 66
Period size: 8 Copynumber: 6.3 Consensus size: 9
29853059 CTTTCTTTTG
29853069 ATATAT-AT
1 ATATATAAT
29853077 ATATAT-AT
1 ATATATAAT
29853085 ATATATAAT
1 ATATATAAT
29853094 ATAATATAAT
1 AT-ATATAAT
29853104 ATAT-TAAT
1 ATATATAAT
29853112 AATAATATAAT
1 -AT-ATATAAT
29853123 ATA
1 ATA
29853126 AAAACATAAT
Statistics
Matches: 44, Mismatches: 0, Indels: 9
0.83 0.00 0.17
Matches are distributed among these distances:
8 18 0.41
9 9 0.20
10 13 0.30
11 4 0.09
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (9 bp):
ATATATAAT
Found at i:29853135 original size:24 final size:25
Alignment explanation
Indices: 29853089--29853154 Score: 64
Period size: 24 Copynumber: 2.7 Consensus size: 25
29853079 ATATATATAT
* *
29853089 ATAATATAATATAATATATTAAT-A
1 ATAATATAATATAATAAAATAATCA
29853113 ATAATATAATATAA-AAACATAATCA
1 ATAATATAATATAATAAA-ATAATCA
* * *
29853138 TTACTATAATATTATAA
1 ATAATATAATATAATAA
29853155 TATTTTTTTA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
23 2 0.06
24 18 0.53
25 12 0.35
26 2 0.06
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.38
Consensus pattern (25 bp):
ATAATATAATATAATAAAATAATCA
Found at i:29857641 original size:27 final size:26
Alignment explanation
Indices: 29857611--29857677 Score: 71
Period size: 27 Copynumber: 2.5 Consensus size: 26
29857601 TGTCCTGGCA
* *
29857611 GACTCTCCCATGTTTATTGTCCCAATG
1 GACTC-CCCATGTTTACTATCCCAATG
* *
29857638 GACTACCCCGTGTTTACTATCCCGATG
1 GACT-CCCCATGTTTACTATCCCAATG
*
29857665 GACTCCCTATGTT
1 GACTCCCCATGTT
29857678 GCGATAGCCA
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
26 7 0.21
27 25 0.76
28 1 0.03
ACGTcount: A:0.18, C:0.31, G:0.16, T:0.34
Consensus pattern (26 bp):
GACTCCCCATGTTTACTATCCCAATG
Found at i:29857646 original size:121 final size:120
Alignment explanation
Indices: 29857449--29857703 Score: 352
Period size: 121 Copynumber: 2.1 Consensus size: 120
29857439 CATAGCATAA
* *
29857449 CTATGGTCTTACACTTGTAACCCATGTTTAATATCCTAGCGAACTCTCCAATGTTTATTGTCTCA
1 CTATGGTCTTACACATGTAACCCATGTTTAATATCCTAGCGAACTCTCCAATGTTTATTGTCCCA
* * * *
29857514 GCAGACTACCCCGTGTTTACTGTCCCGATAGG-CTCTCTATGTTGCCACAGTCAAG
66 ACAGACTACCCCGTGTTTACTATCCCGAT-GGACTCCCTATGTTGCCACAGCCAAG
* * *
29857569 CTATGGTCTTACACATGTAACCCCATGTTTAATGTCCTGGC-AGACTCTCCCATGTTTATTGTCC
1 CTATGGTCTTACACATGTAA-CCCATGTTTAATATCCTAGCGA-ACTCTCCAATGTTTATTGTCC
** * *
29857633 CAATGGACTACCCCGTGTTTACTATCCCGATGGACTCCCTATGTTGCGATAGCCAAG
64 CAACAGACTACCCCGTGTTTACTATCCCGATGGACTCCCTATGTTGCCACAGCCAAG
29857690 CTATGGTCTTACAC
1 CTATGGTCTTACAC
29857704 CTTAAACCTC
Statistics
Matches: 119, Mismatches: 13, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
120 22 0.18
121 97 0.82
ACGTcount: A:0.22, C:0.28, G:0.17, T:0.33
Consensus pattern (120 bp):
CTATGGTCTTACACATGTAACCCATGTTTAATATCCTAGCGAACTCTCCAATGTTTATTGTCCCA
ACAGACTACCCCGTGTTTACTATCCCGATGGACTCCCTATGTTGCCACAGCCAAG
Found at i:29859257 original size:31 final size:31
Alignment explanation
Indices: 29859217--29859629 Score: 477
Period size: 31 Copynumber: 13.3 Consensus size: 31
29859207 CAACCTTTTG
* * * *
29859217 AACCTTTTCATTTGACATCCGTTTTGGATAT
1 AACCTTTTCATTTAATATTCGTTTCGGATAT
* * ** *
29859248 AACTTTTTCATTTGATACCCGTTTTGGATAT
1 AACCTTTTCATTTAATATTCGTTTCGGATAT
29859279 AACCTTTTCATTTAATATTCGTTTCGGATAT
1 AACCTTTTCATTTAATATTCGTTTCGGATAT
* ** * *
29859310 AACATTTTCATTTGGTATTTGTTTCAGATAT
1 AACCTTTTCATTTAATATTCGTTTCGGATAT
* *
29859341 AACCTTTTCAATTAATATTCATTTCGGATAT
1 AACCTTTTCATTTAATATTCGTTTCGGATAT
* *
29859372 AACCTTTTCTTTTGATATTCGTTTCGGATAT
1 AACCTTTTCATTTAATATTCGTTTCGGATAT
* * *
29859403 AATCTTTTCAATTAATATTTGTTTCGGATAT
1 AACCTTTTCATTTAATATTCGTTTCGGATAT
29859434 AACCTTTTCATTTAATATTCGTTTCGGATAT
1 AACCTTTTCATTTAATATTCGTTTCGGATAT
* * ** *
29859465 ATCATTTTCATTTGGTA-TCTGTTTCAGATAT
1 AACCTTTTCATTTAATATTC-GTTTCGGATAT
* * *
29859496 AACCTTTTCAATTAATATTCATTTTGGATAT
1 AACCTTTTCATTTAATATTCGTTTCGGATAT
* *
29859527 AACCTTTTCTTTTGATATTCGTTTCGGATAT
1 AACCTTTTCATTTAATATTCGTTTCGGATAT
* * *
29859558 AATCTTTTCAATTAATATTTGTTTCGGATAT
1 AACCTTTTCATTTAATATTCGTTTCGGATAT
* * *
29859589 AACCTTTTCATTTTATATACATTTCGGATAT
1 AACCTTTTCATTTAATATTCGTTTCGGATAT
29859620 AACCTTTTCA
1 AACCTTTTCA
29859630 AGAATTCAGT
Statistics
Matches: 319, Mismatches: 61, Indels: 4
0.83 0.16 0.01
Matches are distributed among these distances:
30 2 0.01
31 315 0.99
32 2 0.01
ACGTcount: A:0.26, C:0.15, G:0.10, T:0.49
Consensus pattern (31 bp):
AACCTTTTCATTTAATATTCGTTTCGGATAT
Found at i:29861790 original size:27 final size:27
Alignment explanation
Indices: 29861744--29862002 Score: 199
Period size: 27 Copynumber: 9.5 Consensus size: 27
29861734 GTATGCCATC
29861744 AAGGCATTCCTTT-AAAGTCTGCCACA
1 AAGGCATTCCTTTCAAAGTCTGCCACA
29861770 AAGGCATTCCCTTT-AAAGTCTGCCACA
1 AAGGCATT-CCTTTCAAAGTCTGCCACA
* *
29861797 AAGGCATTCCTTTCAGAGT-TCGCCATA
1 AAGGCATTCCTTTCAAAGTCT-GCCACA
*
29861824 AAGGCATTTCTTTCAAAGTCTGCCACA
1 AAGGCATTCCTTTCAAAGTCTGCCACA
* * *
29861851 AAGACATTCCTTTCAGAGTTTGCCACA
1 AAGGCATTCCTTTCAAAGTCTGCCACA
*
29861878 AAGGCATTTCTATTCATATA-T-TGCCACA
1 AAGGCATTCCT-TTCA-A-AGTCTGCCACA
* * **
29861906 AAGGCATTCTTTTTTATATA-T-TGCCATG
1 AAGGCATTC-CTTTCA-A-AGTCTGCCACA
* * * * *
29861934 AAGGCATTCATTTTCATATTTTTCCACA
1 AAGGCATTC-CTTTCAAAGTCTGCCACA
* * * *
29861962 AAGGCATTCATTTTAATATTTTGCCACA
1 AAGGCATTCCTTTCAA-AGTCTGCCACA
29861990 AAGGCATTCCTTT
1 AAGGCATTCCTTT
29862003 TTATATATTG
Statistics
Matches: 194, Mismatches: 28, Indels: 20
0.80 0.12 0.08
Matches are distributed among these distances:
26 15 0.08
27 94 0.48
28 82 0.42
29 2 0.01
30 1 0.01
ACGTcount: A:0.29, C:0.23, G:0.14, T:0.34
Consensus pattern (27 bp):
AAGGCATTCCTTTCAAAGTCTGCCACA
Found at i:29861902 original size:28 final size:28
Alignment explanation
Indices: 29861790--29862016 Score: 168
Period size: 28 Copynumber: 8.2 Consensus size: 28
29861780 CTTTAAAGTC
* *
29861790 TGCCACAAAGGCA-TTCCTTTCAGAGT-T
1 TGCCACAAAGGCATTTCTTTTCATA-TAT
* *
29861817 CGCCATAAAGGCATTTC-TTTCA-A-AGT
1 TGCCACAAAGGCATTTCTTTTCATATA-T
* * *
29861843 CTGCCACAAAGACA-TTCCTTTCAGAGT-T
1 -TGCCACAAAGGCATTTCTTTTCATA-TAT
*
29861871 TGCCACAAAGGCATTTCTATTCATATAT
1 TGCCACAAAGGCATTTCTTTTCATATAT
*
29861899 TGCCACAAAGGCA-TTCTTTTTTATATAT
1 TGCCACAAAGGCATTTC-TTTTCATATAT
** *
29861927 TGCCATGAAGGCA-TTCATTTTCATATTT
1 TGCCACAAAGGCATTTC-TTTTCATATAT
* * *
29861955 TTCCACAAAGGCA-TTCATTTTAATATTT
1 TGCCACAAAGGCATTTC-TTTTCATATAT
* *
29861983 TGCCACAAAGGCATTCCTTTTTATATAT
1 TGCCACAAAGGCATTTCTTTTCATATAT
29862011 TGCCAC
1 TGCCAC
29862017 GAAAATATTC
Statistics
Matches: 164, Mismatches: 24, Indels: 23
0.78 0.11 0.11
Matches are distributed among these distances:
26 5 0.03
27 47 0.29
28 110 0.67
29 2 0.01
ACGTcount: A:0.29, C:0.22, G:0.13, T:0.36
Consensus pattern (28 bp):
TGCCACAAAGGCATTTCTTTTCATATAT
Found at i:29861950 original size:56 final size:56
Alignment explanation
Indices: 29861870--29862016 Score: 188
Period size: 56 Copynumber: 2.6 Consensus size: 56
29861860 CTTTCAGAGT
* * *
29861870 TTGCCACAAAGGCATTTC-TATTCATATATTGCCACAAAGGCATTCTTTTTTATATA
1 TTGCCACAAAGGCA-TTCATTTTCATATATTGCCACAAAGGCATTCATTTTAATATA
** * * *
29861926 TTGCCATGAAGGCATTCATTTTCATATTTTTCCACAAAGGCATTCATTTTAATATT
1 TTGCCACAAAGGCATTCATTTTCATATATTGCCACAAAGGCATTCATTTTAATATA
* *
29861982 TTGCCACAAAGGCATTCCTTTTTATATATTGCCAC
1 TTGCCACAAAGGCATTCATTTTCATATATTGCCAC
29862017 GAAAATATTC
Statistics
Matches: 76, Mismatches: 14, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
55 3 0.04
56 73 0.96
ACGTcount: A:0.29, C:0.20, G:0.11, T:0.40
Consensus pattern (56 bp):
TTGCCACAAAGGCATTCATTTTCATATATTGCCACAAAGGCATTCATTTTAATATA
Found at i:29872684 original size:43 final size:42
Alignment explanation
Indices: 29872614--29872785 Score: 150
Period size: 43 Copynumber: 4.0 Consensus size: 42
29872604 CACATAGTAC
* * * *
29872614 CGTAACAATGCCATATCCCAGATATGGTCTTACATGTAATCT
1 CGTATCAATGCCATAGCCCAGACATGGTCTTACACGTAATCT
* * *
29872656 CGTATCAATGCCAATAGCCCAGCCATGGTCTTACACGAAATCA
1 CGTATCAATGCC-ATAGCCCAGACATGGTCTTACACGTAATCT
* * * *
29872699 CATACCGATGCCA-ATGTCCCAAACATGGTCTTACACG-AAGTCT
1 CGTATCAATGCCATA-G-CCCAGACATGGTCTTACACGTAA-TCT
* ** * *
29872742 CATATTGATGCCATATCCCAGATATGGTCTTACACGTAATCT
1 CGTATCAATGCCATAGCCCAGACATGGTCTTACACGTAATCT
29872784 CG
1 CG
29872786 GTAACCCTAT
Statistics
Matches: 105, Mismatches: 19, Indels: 12
0.77 0.14 0.09
Matches are distributed among these distances:
41 1 0.01
42 37 0.35
43 66 0.63
44 1 0.01
ACGTcount: A:0.30, C:0.27, G:0.16, T:0.27
Consensus pattern (42 bp):
CGTATCAATGCCATAGCCCAGACATGGTCTTACACGTAATCT
Found at i:29875299 original size:30 final size:30
Alignment explanation
Indices: 29875265--29875327 Score: 126
Period size: 30 Copynumber: 2.1 Consensus size: 30
29875255 TTAGACACTT
29875265 AAGACCATCTAGTTTAAGTACCTTCCTATG
1 AAGACCATCTAGTTTAAGTACCTTCCTATG
29875295 AAGACCATCTAGTTTAAGTACCTTCCTATG
1 AAGACCATCTAGTTTAAGTACCTTCCTATG
29875325 AAG
1 AAG
29875328 CTCTACTCAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.32, C:0.22, G:0.14, T:0.32
Consensus pattern (30 bp):
AAGACCATCTAGTTTAAGTACCTTCCTATG
Found at i:29877703 original size:20 final size:20
Alignment explanation
Indices: 29877666--29877702 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
29877656 ATTTATTTCA
29877666 TTTATTTATTATTGTTTTAT
1 TTTATTTATTATTGTTTTAT
*
29877686 TTTATTTTTTATT-TTTT
1 TTTATTTATTATTGTTTT
29877703 TTGGGGGGGG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 4 0.25
20 12 0.75
ACGTcount: A:0.16, C:0.00, G:0.03, T:0.81
Consensus pattern (20 bp):
TTTATTTATTATTGTTTTAT
Found at i:29880338 original size:15 final size:15
Alignment explanation
Indices: 29880315--29880357 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
29880305 AATTCAACAA
*
29880315 TTAAATTTTCAGTAC
1 TTAATTTTTCAGTAC
* **
29880330 TTATTTTTTCAACAC
1 TTAATTTTTCAGTAC
29880345 TTAATTTTTCAGT
1 TTAATTTTTCAGT
29880358 TTATCAAACA
Statistics
Matches: 21, Mismatches: 7, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.28, C:0.14, G:0.05, T:0.53
Consensus pattern (15 bp):
TTAATTTTTCAGTAC
Found at i:29895173 original size:16 final size:16
Alignment explanation
Indices: 29895152--29895184 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
29895142 CTGATTTGCT
29895152 ATTACGCCTCTATTCC
1 ATTACGCCTCTATTCC
29895168 ATTACGCCTCTATTCC
1 ATTACGCCTCTATTCC
29895184 A
1 A
29895185 ATACAGCGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.21, C:0.36, G:0.06, T:0.36
Consensus pattern (16 bp):
ATTACGCCTCTATTCC
Found at i:29895598 original size:24 final size:25
Alignment explanation
Indices: 29895544--29895600 Score: 62
Period size: 29 Copynumber: 2.2 Consensus size: 25
29895534 TTTTTAACCG
*
29895544 TTAACCGAACCGAAATTTTTTCAAAAAAA
1 TTAACCGAACCAAAATTTTTTC----AAA
29895573 TTAACCGAACCAAAATTTTTTC-AA
1 TTAACCGAACCAAAATTTTTTCAAA
29895597 TTAA
1 TTAA
29895601 TTCGGTCGGT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
24 6 0.22
29 21 0.78
ACGTcount: A:0.46, C:0.18, G:0.05, T:0.32
Consensus pattern (25 bp):
TTAACCGAACCAAAATTTTTTCAAA
Found at i:29895670 original size:9 final size:9
Alignment explanation
Indices: 29895656--29895731 Score: 82
Period size: 9 Copynumber: 8.4 Consensus size: 9
29895646 TTTAGTTAAA
29895656 AATTAACCG
1 AATTAACCG
*
29895665 AATTAACTG
1 AATTAACCG
29895674 AATT-ACCTG
1 AATTAACC-G
*
29895683 AATTAACTG
1 AATTAACCG
*
29895692 TATTAACCG
1 AATTAACCG
*
29895701 AATTACCCG
1 AATTAACCG
*
29895710 AATTAACCA
1 AATTAACCG
*
29895719 AATTAACCA
1 AATTAACCG
29895728 AATT
1 AATT
29895732 GAATCACTAC
Statistics
Matches: 56, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
8 2 0.04
9 52 0.93
10 2 0.04
ACGTcount: A:0.43, C:0.20, G:0.08, T:0.29
Consensus pattern (9 bp):
AATTAACCG
Found at i:29895696 original size:27 final size:27
Alignment explanation
Indices: 29895656--29895731 Score: 98
Period size: 27 Copynumber: 2.8 Consensus size: 27
29895646 TTTAGTTAAA
* *
29895656 AATTAACCGAATTAACTGAATTACCTG
1 AATTAACCGAATTAACCGAATTACCCG
* *
29895683 AATTAACTGTATTAACCGAATTACCCG
1 AATTAACCGAATTAACCGAATTACCCG
* *
29895710 AATTAACCAAATTAACCAAATT
1 AATTAACCGAATTAACCGAATT
29895732 GAATCACTAC
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 41 1.00
ACGTcount: A:0.43, C:0.20, G:0.08, T:0.29
Consensus pattern (27 bp):
AATTAACCGAATTAACCGAATTACCCG
Found at i:29895833 original size:18 final size:18
Alignment explanation
Indices: 29895810--29895853 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 18
29895800 AATTTTTATG
29895810 ATTGGGTTGGGTTAGG-TA
1 ATTGGGTTGGGTT-GGATA
29895828 ATTGGGTTGGGTTGGATA
1 ATTGGGTTGGGTTGGATA
*
29895846 CTTGGGTT
1 ATTGGGTT
29895854 TGGATTGAGT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 2 0.08
18 22 0.92
ACGTcount: A:0.14, C:0.02, G:0.43, T:0.41
Consensus pattern (18 bp):
ATTGGGTTGGGTTGGATA
Found at i:29907978 original size:31 final size:31
Alignment explanation
Indices: 29907943--29908007 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 31
29907933 ACAGCCCAAG
*
29907943 GACTTAAGTAAAAACTTTT-GAATAGTTCAGT
1 GACTTAAATAAAAA-TTTTCGAATAGTTCAGT
* *
29907974 GACTTAAATGAAAATTTTCGAATAGTTTAGT
1 GACTTAAATAAAAATTTTCGAATAGTTCAGT
29908005 GAC
1 GAC
29908008 CAAAATGTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
30 4 0.13
31 26 0.87
ACGTcount: A:0.38, C:0.09, G:0.17, T:0.35
Consensus pattern (31 bp):
GACTTAAATAAAAATTTTCGAATAGTTCAGT
Done.