Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr1
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: 96304692
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2448173 characters in sequence are not A, C, G, or T
File 156 of 313
Found at i:49279171 original size:6 final size:6
Alignment explanation
Indices: 49279161--49279202 Score: 75
Period size: 6 Copynumber: 7.0 Consensus size: 6
49279151 CTTATGCTTT
*
49279161 ATATAT ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC
1 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC
49279203 TCTTTTGCAT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.50, C:0.14, G:0.00, T:0.36
Consensus pattern (6 bp):
ATATAC
Found at i:49280759 original size:15 final size:15
Alignment explanation
Indices: 49280739--49280792 Score: 54
Period size: 15 Copynumber: 3.3 Consensus size: 15
49280729 ATACTATAAA
49280739 ATATTTATTATTAAT
1 ATATTTATTATTAAT
*
49280754 ATATTTATAAATGTAAT
1 ATATTTAT-TAT-TAAT
*
49280771 AAATATTTATTATTAAA
1 --ATATTTATTATTAAT
49280788 ATATT
1 ATATT
49280793 AATATTGAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
15 13 0.41
16 2 0.06
17 7 0.22
18 2 0.06
19 8 0.25
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (15 bp):
ATATTTATTATTAAT
Found at i:49280856 original size:16 final size:16
Alignment explanation
Indices: 49280825--49280861 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
49280815 ATGTGTATAA
49280825 TATTATTTAAAATTAT
1 TATTATTTAAAATTAT
49280841 TATT-TTTAAAATTTAT
1 TATTATTTAAAA-TTAT
49280857 TATTA
1 TATTA
49280862 CAATAAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 7 0.37
16 12 0.63
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TATTATTTAAAATTAT
Found at i:49280911 original size:22 final size:22
Alignment explanation
Indices: 49280885--49280928 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
49280875 TTATTAAATA
49280885 ATTTATTAAAATAATAAATTAT
1 ATTTATTAAAATAATAAATTAT
* * *
49280907 ATTTATTATATTAATAATTTAT
1 ATTTATTAAAATAATAAATTAT
49280929 TATATGACTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (22 bp):
ATTTATTAAAATAATAAATTAT
Found at i:49286436 original size:16 final size:16
Alignment explanation
Indices: 49286415--49286463 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 16
49286405 AATTACCTTA
49286415 ATTAATTAACTTAATC
1 ATTAATTAACTTAATC
*
49286431 ATTAATTAATTTAAT-
1 ATTAATTAACTTAATC
*
49286446 -TTAATTATCATTAATC
1 ATTAATTAAC-TTAATC
49286462 AT
1 AT
49286464 ATTAGTGGAG
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
14 7 0.26
15 5 0.19
16 14 0.52
17 1 0.04
ACGTcount: A:0.43, C:0.08, G:0.00, T:0.49
Consensus pattern (16 bp):
ATTAATTAACTTAATC
Found at i:49286440 original size:24 final size:24
Alignment explanation
Indices: 49286412--49286460 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 24
49286402 TTTAATTACC
49286412 TTAA-TTAA-TTAACTTAATCATTAA
1 TTAATTTAATTTAA-TT-ATCATTAA
49286436 TTAATTTAATTTAATTATCATTAA
1 TTAATTTAATTTAATTATCATTAA
49286460 T
1 T
49286461 CATATTAGTG
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
24 13 0.57
25 6 0.26
26 4 0.17
ACGTcount: A:0.43, C:0.06, G:0.00, T:0.51
Consensus pattern (24 bp):
TTAATTTAATTTAATTATCATTAA
Found at i:49290216 original size:30 final size:30
Alignment explanation
Indices: 49290182--49290244 Score: 117
Period size: 30 Copynumber: 2.1 Consensus size: 30
49290172 AACTTATTTC
49290182 TTGTTAATTTTGTTATTATTTTAAAGGCAT
1 TTGTTAATTTTGTTATTATTTTAAAGGCAT
*
49290212 TTGTTAATTTTGTTATTATTTTAGAGGCAT
1 TTGTTAATTTTGTTATTATTTTAAAGGCAT
49290242 TTG
1 TTG
49290245 CTTGTTAAGT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.24, C:0.03, G:0.16, T:0.57
Consensus pattern (30 bp):
TTGTTAATTTTGTTATTATTTTAAAGGCAT
Found at i:49290420 original size:10 final size:10
Alignment explanation
Indices: 49290401--49290430 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
49290391 AAAATTAATA
49290401 CGGG-CGGGC
1 CGGGTCGGGC
49290410 CGGGTCGGGC
1 CGGGTCGGGC
49290420 CGGGTCGGGC
1 CGGGTCGGGC
49290430 C
1 C
49290431 CGAGTTTTAG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 4 0.20
10 16 0.80
ACGTcount: A:0.00, C:0.33, G:0.60, T:0.07
Consensus pattern (10 bp):
CGGGTCGGGC
Found at i:49296015 original size:18 final size:17
Alignment explanation
Indices: 49295979--49296026 Score: 51
Period size: 17 Copynumber: 2.7 Consensus size: 17
49295969 CATATATGTA
**
49295979 TATATAAAGCAAAAAAG
1 TATATAAAAAAAAAAAG
49295996 TATATAAAAAAAAGAAAG
1 TATATAAAAAAAA-AAAG
*
49296014 TAAAATAAAAAAA
1 T-ATATAAAAAAA
49296027 TGTAGGTATA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
17 11 0.42
18 5 0.19
19 10 0.38
ACGTcount: A:0.73, C:0.02, G:0.08, T:0.17
Consensus pattern (17 bp):
TATATAAAAAAAAAAAG
Found at i:49296039 original size:19 final size:19
Alignment explanation
Indices: 49295992--49296047 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 19
49295982 ATAAAGCAAA
*
49295992 AAAGTAT-ATAAAAAAAAG
1 AAAGTATAATAAAAAAATG
*
49296010 AAAGTAAAATAAAAAAATG
1 AAAGTATAATAAAAAAATG
* *
49296029 TAGGTATAATAATAAAAAT
1 AAAGTATAATAA-AAAAAT
49296048 ATGTAATATT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
18 6 0.19
19 19 0.61
20 6 0.19
ACGTcount: A:0.68, C:0.00, G:0.11, T:0.21
Consensus pattern (19 bp):
AAAGTATAATAAAAAAATG
Found at i:49300977 original size:19 final size:20
Alignment explanation
Indices: 49300935--49300977 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
49300925 TCATGCTTTC
*
49300935 TATTCACATTTTCATATTCA
1 TATTCACATTTTCAAATTCA
49300955 -ATTCACATTTTCAAATT-A
1 TATTCACATTTTCAAATTCA
49300973 TATTC
1 TATTC
49300978 TACAATCACG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 1 0.05
19 20 0.95
ACGTcount: A:0.33, C:0.19, G:0.00, T:0.49
Consensus pattern (20 bp):
TATTCACATTTTCAAATTCA
Found at i:49301230 original size:45 final size:45
Alignment explanation
Indices: 49301166--49301362 Score: 304
Period size: 45 Copynumber: 4.4 Consensus size: 45
49301156 GTAGCAGTAT
* * * * *
49301166 CAGTAACAGTAACAATATTCAACACACAAAGTGCTGAATTTGTAA
1 CAGTAACGGTAACAGTATTCGACACACAAAGTGCCGAATTGGTAA
49301211 CAGTAACGGTAACAGTATTCGACACACAAAGTGCCGAATTGGTAA
1 CAGTAACGGTAACAGTATTCGACACACAAAGTGCCGAATTGGTAA
* * * *
49301256 CAGTAACGATAATAGTATTCGACACACAAAGTACCGAATTGATAA
1 CAGTAACGGTAACAGTATTCGACACACAAAGTGCCGAATTGGTAA
*
49301301 CAGTAACGGTAACAGTATTCGACACACAAAGTGTCGAATTGGTAA
1 CAGTAACGGTAACAGTATTCGACACACAAAGTGCCGAATTGGTAA
49301346 CAGTAACGGTAACAGTA
1 CAGTAACGGTAACAGTA
49301363 ACAGTAGTCA
Statistics
Matches: 138, Mismatches: 14, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 138 1.00
ACGTcount: A:0.41, C:0.18, G:0.19, T:0.22
Consensus pattern (45 bp):
CAGTAACGGTAACAGTATTCGACACACAAAGTGCCGAATTGGTAA
Found at i:49302539 original size:13 final size:13
Alignment explanation
Indices: 49302523--49302549 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
49302513 ATTAAAATAC
49302523 ATAAGTAATTACA
1 ATAAGTAATTACA
49302536 ATAAGTAATTACA
1 ATAAGTAATTACA
49302549 A
1 A
49302550 CTTCAACTCG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.56, C:0.07, G:0.07, T:0.30
Consensus pattern (13 bp):
ATAAGTAATTACA
Found at i:49303598 original size:26 final size:26
Alignment explanation
Indices: 49303569--49303637 Score: 93
Period size: 26 Copynumber: 2.6 Consensus size: 26
49303559 TTATTATGCT
*
49303569 ACAAAAGCTTTCTTTCATATTACACC
1 ACAAAGGCTTTCTTTCATATTACACC
* * *
49303595 ACAAAGGCTTTATTTCATGTTACGCC
1 ACAAAGGCTTTCTTTCATATTACACC
49303621 ACAAAGGCTTTTCTTTC
1 ACAAAGGC-TTTCTTTC
49303638 CTAAAATTTA
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
26 30 0.81
27 7 0.19
ACGTcount: A:0.29, C:0.25, G:0.10, T:0.36
Consensus pattern (26 bp):
ACAAAGGCTTTCTTTCATATTACACC
Found at i:49307099 original size:26 final size:25
Alignment explanation
Indices: 49307063--49307111 Score: 80
Period size: 26 Copynumber: 1.9 Consensus size: 25
49307053 AAGAATTTTC
*
49307063 TCAAAATTTTATCGGAGGTAAAATCA
1 TCAAAATTTTACCGGA-GTAAAATCA
49307089 TCAAAATTTTACCGGAGTAAAAT
1 TCAAAATTTTACCGGAGTAAAAT
49307112 TAGGATGAGA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 7 0.32
26 15 0.68
ACGTcount: A:0.43, C:0.12, G:0.14, T:0.31
Consensus pattern (25 bp):
TCAAAATTTTACCGGAGTAAAATCA
Found at i:49310360 original size:86 final size:86
Alignment explanation
Indices: 49310215--49310385 Score: 261
Period size: 86 Copynumber: 2.0 Consensus size: 86
49310205 TTTAAGATCA
* *
49310215 ATTAAATGATCTCTTACGAATCTTGTCAATATTTCCCAATAATCTTGATAAATCTTGAAAACAAT
1 ATTAAAAGACCTCTTACGAATCTTGTCAATATTTCCCAATAATCTTGATAAATCTTGAAAACAAT
*
49310280 ATCTAATTCTTGCGCAAATCG
66 ATCTAATTCTTGCACAAATCG
* *** *
49310301 ATTAAAAGACCTCTTACGAATCTTGTCGATATTTCCTGGTAATCTTGATAAATCTTGAAAATAAT
1 ATTAAAAGACCTCTTACGAATCTTGTCAATATTTCCCAATAATCTTGATAAATCTTGAAAACAAT
*
49310366 ATCTAGTTCTTGCACAAATC
66 ATCTAATTCTTGCACAAATC
49310386 TTGTTTGAAT
Statistics
Matches: 76, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
86 76 1.00
ACGTcount: A:0.35, C:0.18, G:0.11, T:0.36
Consensus pattern (86 bp):
ATTAAAAGACCTCTTACGAATCTTGTCAATATTTCCCAATAATCTTGATAAATCTTGAAAACAAT
ATCTAATTCTTGCACAAATCG
Found at i:49329700 original size:14 final size:14
Alignment explanation
Indices: 49329683--49329709 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
49329673 CTTGAAAACA
49329683 ATTTTTAAAAAATG
1 ATTTTTAAAAAATG
49329697 ATTTTTAAAAAAT
1 ATTTTTAAAAAAT
49329710 AAATTAATTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.44
Consensus pattern (14 bp):
ATTTTTAAAAAATG
Found at i:49330754 original size:19 final size:19
Alignment explanation
Indices: 49330709--49330763 Score: 60
Period size: 19 Copynumber: 3.0 Consensus size: 19
49330699 AAAAACTATG
*
49330709 AAAAAAT-ATATTATTTA-
1 AAAAAATAATATTTTTTAT
**
49330726 AATCAATAATATTTTTTAT
1 AAAAAATAATATTTTTTAT
*
49330745 AAAAAATAATAGTTTTTAT
1 AAAAAATAATATTTTTTAT
49330764 TTAACTTTTA
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
17 5 0.17
18 9 0.30
19 16 0.53
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (19 bp):
AAAAAATAATATTTTTTAT
Found at i:49334534 original size:17 final size:18
Alignment explanation
Indices: 49334512--49334549 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
49334502 CAAATTGAAC
*
49334512 AATAAAAACAAAGGA-AA
1 AATAAAAAAAAAGGAGAA
49334529 AATAAAAAAAAAGGAGAA
1 AATAAAAAAAAAGGAGAA
49334547 AAT
1 AAT
49334550 TACTTGAAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 14 0.74
18 5 0.26
ACGTcount: A:0.76, C:0.03, G:0.13, T:0.08
Consensus pattern (18 bp):
AATAAAAAAAAAGGAGAA
Found at i:49347596 original size:29 final size:30
Alignment explanation
Indices: 49347549--49347607 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 30
49347539 TATGGTTTAA
* *
49347549 TGTGCAATTGTGTATATG-AACTTTGATTT
1 TGTGCAATTGTATACATGAAACTTTGATTT
* *
49347578 TGTGCAATTTTATACATGAAATTTTGATTT
1 TGTGCAATTGTATACATGAAACTTTGATTT
49347608 GATCCAATCC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
29 15 0.60
30 10 0.40
ACGTcount: A:0.27, C:0.07, G:0.17, T:0.49
Consensus pattern (30 bp):
TGTGCAATTGTATACATGAAACTTTGATTT
Found at i:49348379 original size:11 final size:11
Alignment explanation
Indices: 49348363--49348387 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
49348353 TTTTGAAAGC
49348363 AAAAAAGAAAT
1 AAAAAAGAAAT
49348374 AAAAAAGAAAT
1 AAAAAAGAAAT
49348385 AAA
1 AAA
49348388 TACATATAGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.84, C:0.00, G:0.08, T:0.08
Consensus pattern (11 bp):
AAAAAAGAAAT
Found at i:49353669 original size:7 final size:7
Alignment explanation
Indices: 49353657--49353682 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
49353647 ATTTATATAT
49353657 AAATTTA
1 AAATTTA
49353664 AAATTTA
1 AAATTTA
49353671 AAATTTA
1 AAATTTA
49353678 AAATT
1 AAATT
49353683 ACTAATTAAA
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:0.00, G:0.00, T:0.42
Consensus pattern (7 bp):
AAATTTA
Found at i:49364650 original size:6 final size:6
Alignment explanation
Indices: 49364641--49364679 Score: 69
Period size: 6 Copynumber: 6.5 Consensus size: 6
49364631 CCCCAAAAAG
*
49364641 AAAACC AAAACC AAAACC AAAACC AAAACC AAAATC AAA
1 AAAACC AAAACC AAAACC AAAACC AAAACC AAAACC AAA
49364680 CCTAATCTTA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.69, C:0.28, G:0.00, T:0.03
Consensus pattern (6 bp):
AAAACC
Found at i:49364654 original size:18 final size:18
Alignment explanation
Indices: 49364633--49364679 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
49364623 TCCCTAACCC
*
49364633 CCAAAAAGAAAACCAAAA
1 CCAAAAACAAAACCAAAA
*
49364651 CCAAAACCAAAACCAAAA
1 CCAAAAACAAAACCAAAA
*
49364669 CCAAAATCAAA
1 CCAAAAACAAA
49364680 CCTAATCTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.68, C:0.28, G:0.02, T:0.02
Consensus pattern (18 bp):
CCAAAAACAAAACCAAAA
Found at i:49375353 original size:103 final size:103
Alignment explanation
Indices: 49375174--49375376 Score: 352
Period size: 103 Copynumber: 2.0 Consensus size: 103
49375164 AAGAGGCTCT
* *
49375174 TGAATCAGCTGAGTGGAGACAAGCCGTGATGGAAGAAATGAAGGCCCTCAAAAACAATGAAACAT
1 TGAATCAGCTGAGTGGAGACAAGCCCTGATAGAAGAAATGAAGGCCCTCAAAAACAATGAAACAT
49375239 GAGAAGTCTCGAATCTACCTAAAGGGAAAAAAACTTCA
66 GAGAAGTCTCGAATCTACCTAAAGGGAAAAAAACTTCA
* *
49375277 TGAATCAGCTGAGTGGAGACAAGCCCTGATAGAATAAATGAAGGCCCTCAAAAATAATGAAACAT
1 TGAATCAGCTGAGTGGAGACAAGCCCTGATAGAAGAAATGAAGGCCCTCAAAAACAATGAAACAT
* *
49375342 GGGAAGTCTCGAATCTACCTAAAGGGAGAAAAACT
66 GAGAAGTCTCGAATCTACCTAAAGGGAAAAAAACT
49375377 GTAGGGTGCA
Statistics
Matches: 94, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
103 94 1.00
ACGTcount: A:0.42, C:0.17, G:0.23, T:0.17
Consensus pattern (103 bp):
TGAATCAGCTGAGTGGAGACAAGCCCTGATAGAAGAAATGAAGGCCCTCAAAAACAATGAAACAT
GAGAAGTCTCGAATCTACCTAAAGGGAAAAAAACTTCA
Found at i:49376834 original size:32 final size:32
Alignment explanation
Indices: 49376793--49376857 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
49376783 TTGAGGGGAG
49376793 TGTTGGAATCCCTATAATTAAGGATAGAAATC
1 TGTTGGAATCCCTATAATTAAGGATAGAAATC
49376825 TGTTGGAATCCCTATAATTAAGGATAGAAATC
1 TGTTGGAATCCCTATAATTAAGGATAGAAATC
49376857 T
1 T
49376858 TACCTTATTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.37, C:0.12, G:0.18, T:0.32
Consensus pattern (32 bp):
TGTTGGAATCCCTATAATTAAGGATAGAAATC
Found at i:49387531 original size:33 final size:32
Alignment explanation
Indices: 49387493--49387611 Score: 118
Period size: 33 Copynumber: 3.7 Consensus size: 32
49387483 AGATTAATTT
49387493 ATATTTTATGTATTATTACATTAAATTATTTAA
1 ATATTTTATGTATTATTA-ATTAAATTATTTAA
* *
49387526 ATATTTCATGTATCATTATATTAAATTATTTAA
1 ATATTTTATGTATTATTA-ATTAAATTATTTAA
* * *
49387559 ATATAATTTAT-TACTA-TATTTAAGTT-TTTAAA
1 ATAT--TTTATGTATTATTAATTAAATTATTT-AA
*
49387591 ATATTTTAAGTATTATTAATT
1 ATATTTTATGTATTATTAATT
49387612 TTATAAATAA
Statistics
Matches: 70, Mismatches: 11, Indels: 11
0.76 0.12 0.12
Matches are distributed among these distances:
30 4 0.06
31 7 0.10
32 16 0.23
33 36 0.51
34 3 0.04
35 4 0.06
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.54
Consensus pattern (32 bp):
ATATTTTATGTATTATTAATTAAATTATTTAA
Found at i:49387613 original size:26 final size:26
Alignment explanation
Indices: 49387584--49387637 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 26
49387574 ATATTTAAGT
*
49387584 TTTTA-AAATATTTTAAGTATT-ATTAA
1 TTTTATAAATAATTT-A-TATTAATTAA
49387610 TTTTATAAATAATTTATATTAATTAA
1 TTTTATAAATAATTTATATTAATTAA
49387636 TT
1 TT
49387638 AAAAGGTATT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
25 4 0.16
26 13 0.52
27 8 0.32
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.56
Consensus pattern (26 bp):
TTTTATAAATAATTTATATTAATTAA
Found at i:49390929 original size:17 final size:17
Alignment explanation
Indices: 49390906--49390946 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
49390896 TTTCGAAAAT
49390906 ATTATTTATTTAATCAA
1 ATTATTTATTTAATCAA
* *
49390923 TTTATTTATTTAATTAA
1 ATTATTTATTTAATCAA
49390940 ATTATTT
1 ATTATTT
49390947 TCTAAACCCA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (17 bp):
ATTATTTATTTAATCAA
Found at i:49401235 original size:21 final size:21
Alignment explanation
Indices: 49401209--49401256 Score: 64
Period size: 19 Copynumber: 2.3 Consensus size: 21
49401199 AGAGCACTTT
*
49401209 TTATAAAGTTTTTTATACAA-A
1 TTATAAA-TTTTTTATAAAACA
49401230 TTAT-AATTTTTTATAAAACA
1 TTATAAATTTTTTATAAAACA
49401250 TTATAAA
1 TTATAAA
49401257 AATTATTTCA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
19 11 0.46
20 7 0.29
21 6 0.25
ACGTcount: A:0.46, C:0.04, G:0.02, T:0.48
Consensus pattern (21 bp):
TTATAAATTTTTTATAAAACA
Found at i:49404553 original size:18 final size:17
Alignment explanation
Indices: 49404509--49404559 Score: 59
Period size: 17 Copynumber: 2.9 Consensus size: 17
49404499 TAAAAATATA
49404509 TATTTAAAAATCTAAAAT
1 TATTTAAAAA-CTAAAAT
**
49404527 TATGAAAAAACTAAAAT
1 TATTTAAAAACTAAAAT
49404544 TATTTCAAAAA-TAAAA
1 TATTT-AAAAACTAAAA
49404560 AATCATTTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
17 15 0.54
18 13 0.46
ACGTcount: A:0.61, C:0.06, G:0.02, T:0.31
Consensus pattern (17 bp):
TATTTAAAAACTAAAAT
Found at i:49404579 original size:18 final size:19
Alignment explanation
Indices: 49404538--49404579 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 19
49404528 ATGAAAAAAC
*
49404538 TAAAATTATTTCAAAAATA
1 TAAAATCATTTCAAAAATA
* *
49404557 AAAAATCATTT-AAATATA
1 TAAAATCATTTCAAAAATA
49404575 TAAAA
1 TAAAA
49404580 AAATTAAAAT
Statistics
Matches: 19, Mismatches: 4, Indels: 1
0.79 0.17 0.04
Matches are distributed among these distances:
18 10 0.53
19 9 0.47
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (19 bp):
TAAAATCATTTCAAAAATA
Found at i:49407497 original size:49 final size:50
Alignment explanation
Indices: 49407431--49407572 Score: 214
Period size: 49 Copynumber: 2.9 Consensus size: 50
49407421 TTCTGTACTA
* * * **
49407431 CCAATGCCATATCCCAGATATGGTCTTACATGGGAGTTCTCATCTCGGTG
1 CCAACGCCATGTCCCAGACATGGTCTTACATGGGACATCTCATCTCGGTG
49407481 CCAACGCCATGT-CCAGACATGGTCTTACATGGGACATCTCATCTCGGTG
1 CCAACGCCATGTCCCAGACATGGTCTTACATGGGACATCTCATCTCGGTG
* *
49407530 CCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCAT
1 CCAACGCCATGTCCCAGACATGGTCTTACATGGGACATCTCAT
49407573 AATCTCAATG
Statistics
Matches: 84, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
49 45 0.54
50 39 0.46
ACGTcount: A:0.23, C:0.30, G:0.21, T:0.27
Consensus pattern (50 bp):
CCAACGCCATGTCCCAGACATGGTCTTACATGGGACATCTCATCTCGGTG
Found at i:49411472 original size:74 final size:75
Alignment explanation
Indices: 49411351--49411570 Score: 354
Period size: 75 Copynumber: 2.9 Consensus size: 75
49411341 CAAAATTGGT
* * * *
49411351 AAGTATATCATTTTTATTTGATAAATGGTAAGTATATTATCAGTTAACTATTTATGGTTATAATA
1 AAGTATATCATTTTTATTTGATAAATGGTAAGTATATCATTAGTTAACTATTTATAGTTTTAATA
49411416 TTAGGT-GGA
66 TTAGGTGGGA
* *
49411425 AAGTATATCATTTTTATCTGATAAATGGTAAGTATATGATTAGTTAACTATTTATTA-TTTTAAT
1 AAGTATATCATTTTTATTTGATAAATGGTAAGTATATCATTAGTTAACTATTTA-TAGTTTTAAT
49411489 ATTAGGTGGGA
65 ATTAGGTGGGA
*
49411500 AAGTATATCATTTTTATTTGATAAATGGTAAGTGTATCATTAGTTAACTATTTATAGTTTTAATA
1 AAGTATATCATTTTTATTTGATAAATGGTAAGTATATCATTAGTTAACTATTTATAGTTTTAATA
49411565 TTAGGT
66 TTAGGT
49411571 TAGTAAAACT
Statistics
Matches: 135, Mismatches: 8, Indels: 5
0.91 0.05 0.03
Matches are distributed among these distances:
74 66 0.49
75 69 0.51
ACGTcount: A:0.35, C:0.04, G:0.15, T:0.46
Consensus pattern (75 bp):
AAGTATATCATTTTTATTTGATAAATGGTAAGTATATCATTAGTTAACTATTTATAGTTTTAATA
TTAGGTGGGA
Found at i:49415345 original size:19 final size:20
Alignment explanation
Indices: 49415320--49415368 Score: 66
Period size: 19 Copynumber: 2.5 Consensus size: 20
49415310 CACCAACGCA
49415320 AAGAAAAAGCAACTCAAAAG
1 AAGAAAAAGCAACTCAAAAG
*
49415340 -AGAAAAAG-AACTCGAAAG
1 AAGAAAAAGCAACTCAAAAG
49415358 AAGAGAAAAGC
1 AAGA-AAAAGC
49415369 CAAAAAAAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
18 9 0.36
19 11 0.44
20 5 0.20
ACGTcount: A:0.63, C:0.12, G:0.20, T:0.04
Consensus pattern (20 bp):
AAGAAAAAGCAACTCAAAAG
Found at i:49416244 original size:3 final size:3
Alignment explanation
Indices: 49416236--49416260 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
49416226 TCTAACTTGC
49416236 ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
49416261 GAGAAAATCG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:49416970 original size:20 final size:20
Alignment explanation
Indices: 49416934--49416971 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
49416924 AAAAGGCCCT
**
49416934 TTGACCATTAATTTTAACAG
1 TTGACCATTAAAGTTAACAG
49416954 TTGACCATTAAAGTTAAC
1 TTGACCATTAAAGTTAAC
49416972 TGTCTCTAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.37, C:0.16, G:0.11, T:0.37
Consensus pattern (20 bp):
TTGACCATTAAAGTTAACAG
Found at i:49417071 original size:10 final size:10
Alignment explanation
Indices: 49417058--49417160 Score: 61
Period size: 10 Copynumber: 10.2 Consensus size: 10
49417048 ATAAAAAAAT
49417058 AAAATTTATA
1 AAAATTTATA
*
49417068 AAAA-TTATT
1 AAAATTTATA
*
49417077 AAATTTTAATA
1 AAAATTT-ATA
* *
49417088 AAAATATAAA
1 AAAATTTATA
49417098 AACAATATT-T-
1 AA-AAT-TTATA
*
49417108 AAATTTTATTA
1 AAAATTTA-TA
49417119 AAAA-TTATA
1 AAAATTTATA
* *
49417128 AAAATCGTAAA
1 AAAAT-TTATA
49417139 AAAATTTATA
1 AAAATTTATA
*
49417149 AAATTTTATA
1 AAAATTTATA
49417159 AA
1 AA
49417161 GTCGTAAACA
Statistics
Matches: 69, Mismatches: 15, Indels: 18
0.68 0.15 0.18
Matches are distributed among these distances:
8 2 0.03
9 15 0.22
10 30 0.43
11 21 0.30
12 1 0.01
ACGTcount: A:0.59, C:0.02, G:0.01, T:0.38
Consensus pattern (10 bp):
AAAATTTATA
Found at i:49417147 original size:31 final size:32
Alignment explanation
Indices: 49417112--49417183 Score: 80
Period size: 30 Copynumber: 2.4 Consensus size: 32
49417102 ATATTTAAAT
49417112 TTTATTAAAAATTATA-AAAATCGTAAAAAAA
1 TTTATTAAAAATTATATAAAATCGTAAAAAAA
* * *
49417143 TTTA-T-AAAATTTTATAAAGTCGTAAACAAA
1 TTTATTAAAAATTATATAAAATCGTAAAAAAA
*
49417173 -TTATAAAAAAT
1 TTTATTAAAAAT
49417184 GTAAAGAAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
29 11 0.32
30 14 0.41
31 9 0.26
ACGTcount: A:0.57, C:0.04, G:0.04, T:0.35
Consensus pattern (32 bp):
TTTATTAAAAATTATATAAAATCGTAAAAAAA
Found at i:49417176 original size:29 final size:28
Alignment explanation
Indices: 49417115--49417180 Score: 80
Period size: 29 Copynumber: 2.3 Consensus size: 28
49417105 TTTAAATTTT
49417115 ATTA-AAAATTATAAAAATCGTAAAAAA
1 ATTATAAAATTATAAAAATCGTAAAAAA
* * *
49417142 ATTTATAAAATTTTATAAAGTCGTAAACAA
1 A-TTATAAAATTATA-AAAATCGTAAAAAA
49417172 ATTATAAAA
1 ATTATAAAA
49417181 AATGTAAAGA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
27 1 0.03
28 3 0.09
29 16 0.48
30 13 0.39
ACGTcount: A:0.59, C:0.05, G:0.05, T:0.32
Consensus pattern (28 bp):
ATTATAAAATTATAAAAATCGTAAAAAA
Found at i:49417422 original size:10 final size:10
Alignment explanation
Indices: 49417409--49417555 Score: 58
Period size: 10 Copynumber: 14.4 Consensus size: 10
49417399 TTTTGATGCA
49417409 TTTTATATAT
1 TTTTATATAT
49417419 TTTT-TATGAT
1 TTTTATAT-AT
* *
49417429 TTTTATAAAA
1 TTTTATATAT
*
49417439 TTTTACA-AT
1 TTTTATATAT
49417448 TTTT-TATAAT
1 TTTTATAT-AT
* *
49417458 TTCTTTTACGAT
1 TT-TTATA-TAT
*
49417470 TTTTATCATTT
1 TTTTAT-ATAT
*
49417481 TTTTCTA-AT
1 TTTTATATAT
49417490 TTTTA-ATAT
1 TTTTATATAT
*
49417499 ATTTTATA-AC
1 -TTTTATATAT
49417509 TTTTA-ATAAT
1 TTTTATAT-AT
49417519 TTTTATA-ACT
1 TTTTATATA-T
*
49417529 TTTTATTTTGATT
1 TTTTA-TAT-A-T
49417542 TTTTATATAT
1 TTTTATATAT
49417552 TTTT
1 TTTT
49417556 TGCCACATGT
Statistics
Matches: 102, Mismatches: 17, Indels: 36
0.66 0.11 0.23
Matches are distributed among these distances:
8 3 0.03
9 21 0.21
10 45 0.44
11 17 0.17
12 9 0.09
13 7 0.07
ACGTcount: A:0.28, C:0.05, G:0.02, T:0.65
Consensus pattern (10 bp):
TTTTATATAT
Found at i:49417472 original size:21 final size:21
Alignment explanation
Indices: 49417439--49417503 Score: 62
Period size: 21 Copynumber: 3.0 Consensus size: 21
49417429 TTTTATAAAA
49417439 TTTTACAATTTTTTATAATTT
1 TTTTACAATTTTTTATAATTT
* *
49417460 CTTTTACGA-TTTTTATCATTT
1 -TTTTACAATTTTTTATAATTT
*
49417481 TTTT-CTAATTTTTAATATATTT
1 TTTTAC-AATTTTTTATA-ATTT
49417503 T
1 T
49417504 ATAACTTTTA
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
19 1 0.03
20 5 0.14
21 17 0.49
22 12 0.34
ACGTcount: A:0.25, C:0.08, G:0.02, T:0.66
Consensus pattern (21 bp):
TTTTACAATTTTTTATAATTT
Found at i:49417503 original size:19 final size:18
Alignment explanation
Indices: 49417490--49417531 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 18
49417480 TTTTTCTAAT
49417490 TTTTAATATATTTTATAAC
1 TTTTAATA-ATTTTATAAC
49417509 TTTTAATAATTTTTATAAC
1 TTTTAATAA-TTTTATAAC
49417528 TTTT
1 TTTT
49417532 TATTTTGATT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 1 0.05
19 21 0.95
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (18 bp):
TTTTAATAATTTTATAAC
Found at i:49417824 original size:89 final size:87
Alignment explanation
Indices: 49417715--49417936 Score: 259
Period size: 90 Copynumber: 2.5 Consensus size: 87
49417705 AAAAGAAGAA
* *
49417715 GAAAAAGAAGCAAGGG-CTTAATTGCTTTTTTTTTAAAAGTTTGAGGACCGTTTTGGTGCATTTT
1 GAAAAAGAAGC-AGGGACTTAATTG-TTTTTTTTAAAAAGTTTGAGGACCGTTTTGATGCATTTT
49417779 GAAAGTAAAAGTAC-CTAATTGAGT
64 GAAAGTAAAAGTACTC-AATTGAGT
* * *
49417803 GAAAAAGGAAGCAGGGACTTAATTATTTTTCTTTGAAAAAGTTTGAGGGCCTTTTTGATGCATTT
1 GAAAAA-GAAGCAGGGACTTAATTGTTTTT-TTT-AAAAAGTTTGAGGACCGTTTTGATGCATTT
**
49417868 TGAAAGTTCAAGTACTCAATTGAGT
63 TGAAAGTAAAAGTACTCAATTGAGT
* * ** *
49417893 TAAAAAAAAGCAATGACTTAATTGTGTTGTTTTAAAAAGTTTGA
1 GAAAAAGAAGCAGGGACTTAATTGT-TTTTTTTAAAAAGTTTGA
49417937 AGACTTTTTA
Statistics
Matches: 115, Mismatches: 13, Indels: 12
0.82 0.09 0.09
Matches are distributed among these distances:
88 26 0.23
89 33 0.29
90 55 0.48
91 1 0.01
ACGTcount: A:0.35, C:0.09, G:0.21, T:0.36
Consensus pattern (87 bp):
GAAAAAGAAGCAGGGACTTAATTGTTTTTTTTAAAAAGTTTGAGGACCGTTTTGATGCATTTTGA
AAGTAAAAGTACTCAATTGAGT
Found at i:49423387 original size:49 final size:49
Alignment explanation
Indices: 49423332--49423427 Score: 131
Period size: 49 Copynumber: 2.0 Consensus size: 49
49423322 AACTAATTTA
* *
49423332 ACAATTCT-ATTCAGGATTTTTATTCCTGCCGTTCAACAGGATTTATTCC
1 ACAATTCTGATTCAGGA-TTCTATTCCTGCCGTTCAACAGAATTTATTCC
* * *
49423381 ACAATTCTGTTTCATGATTCTATTCCTGCCGTTCAATAGAATTTATT
1 ACAATTCTGATTCAGGATTCTATTCCTGCCGTTCAACAGAATTTATT
49423428 TGATTTCTAT
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
49 35 0.85
50 6 0.15
ACGTcount: A:0.25, C:0.21, G:0.11, T:0.43
Consensus pattern (49 bp):
ACAATTCTGATTCAGGATTCTATTCCTGCCGTTCAACAGAATTTATTCC
Found at i:49426179 original size:33 final size:33
Alignment explanation
Indices: 49426127--49426192 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
49426117 TAGATGTTAA
*
49426127 ATTACAAGCTGAACAAACTTACCTGGACTGAAT
1 ATTACAAGCCGAACAAACTTACCTGGACTGAAT
* *
49426160 ATTACAATCCGAACGAACTTACCTGGACTGAAT
1 ATTACAAGCCGAACAAACTTACCTGGACTGAAT
49426193 TGTAGTAGTT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.38, C:0.23, G:0.15, T:0.24
Consensus pattern (33 bp):
ATTACAAGCCGAACAAACTTACCTGGACTGAAT
Found at i:49428489 original size:25 final size:25
Alignment explanation
Indices: 49428454--49428540 Score: 138
Period size: 25 Copynumber: 3.5 Consensus size: 25
49428444 AACCAAACCG
49428454 AAGCCTTTGTGGCAAGTTATTTGTA
1 AAGCCTTTGTGGCAAGTTATTTGTA
*
49428479 AAGTCTTTGTGGCAAGTTATTTGTA
1 AAGCCTTTGTGGCAAGTTATTTGTA
* * *
49428504 AAGCCTTTGTGACAAGTTATCTATA
1 AAGCCTTTGTGGCAAGTTATTTGTA
49428529 AAGCCTTTGTGG
1 AAGCCTTTGTGG
49428541 TGAATTATCT
Statistics
Matches: 56, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 56 1.00
ACGTcount: A:0.25, C:0.13, G:0.23, T:0.39
Consensus pattern (25 bp):
AAGCCTTTGTGGCAAGTTATTTGTA
Found at i:49428556 original size:25 final size:25
Alignment explanation
Indices: 49428454--49428559 Score: 117
Period size: 25 Copynumber: 4.2 Consensus size: 25
49428444 AACCAAACCG
* *
49428454 AAGCCTTTGTGGCAAGTTATTTGTA
1 AAGCCTTTGTGGCAAGTTATCTGAA
* * *
49428479 AAGTCTTTGTGGCAAGTTATTTGTA
1 AAGCCTTTGTGGCAAGTTATCTGAA
*
49428504 AAGCCTTTGTGACAAGTTATCT-ATA
1 AAGCCTTTGTGGCAAGTTATCTGA-A
*
49428529 AAGCCTTTGTGGTGAA-TTATCTGAA
1 AAGCCTTTGTGG-CAAGTTATCTGAA
49428554 AAGCCT
1 AAGCCT
49428560 ATGTAGTGTA
Statistics
Matches: 71, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
25 68 0.96
26 3 0.04
ACGTcount: A:0.27, C:0.13, G:0.22, T:0.38
Consensus pattern (25 bp):
AAGCCTTTGTGGCAAGTTATCTGAA
Found at i:49428557 original size:50 final size:50
Alignment explanation
Indices: 49428454--49428559 Score: 133
Period size: 50 Copynumber: 2.1 Consensus size: 50
49428444 AACCAAACCG
* * * * * *
49428454 AAGCCTTTGTGGCAAGTTATTTGTAAAGTCTTTGTGGCAAGTTATTTGTA
1 AAGCCTTTGTGACAAGTTATCTATAAAGCCTTTGTGGCAAGTTATCTGAA
*
49428504 AAGCCTTTGTGACAAGTTATCTATAAAGCCTTTGTGGTGAA-TTATCTGAA
1 AAGCCTTTGTGACAAGTTATCTATAAAGCCTTTGTGG-CAAGTTATCTGAA
49428554 AAGCCT
1 AAGCCT
49428560 ATGTAGTGTA
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
50 46 0.96
51 2 0.04
ACGTcount: A:0.27, C:0.13, G:0.22, T:0.38
Consensus pattern (50 bp):
AAGCCTTTGTGACAAGTTATCTATAAAGCCTTTGTGGCAAGTTATCTGAA
Found at i:49428572 original size:25 final size:25
Alignment explanation
Indices: 49428520--49428573 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 25
49428510 TTGTGACAAG
* *
49428520 TTATCTATAAAGCCTTTGTGGTGAA
1 TTATCTATAAAGCCTATGTAGTGAA
*
49428545 TTATCTGA-AAAGCCTATGTAGTGTA
1 TTATCT-ATAAAGCCTATGTAGTGAA
49428570 TTAT
1 TTAT
49428574 TTGGGAAGCC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 24 0.96
26 1 0.04
ACGTcount: A:0.30, C:0.11, G:0.19, T:0.41
Consensus pattern (25 bp):
TTATCTATAAAGCCTATGTAGTGAA
Found at i:49434368 original size:9 final size:9
Alignment explanation
Indices: 49434318--49434369 Score: 50
Period size: 9 Copynumber: 5.4 Consensus size: 9
49434308 TGTTCTTGCG
*
49434318 TTTTTGTAT
1 TTTTTTTAT
*
49434327 TTTCTTTAT
1 TTTTTTTAT
49434336 TTTCCTTTTAT
1 TTT--TTTTAT
49434347 TTTATTTTAT
1 TTT-TTTTAT
*
49434357 TTTTTTTGT
1 TTTTTTTAT
49434366 TTTT
1 TTTT
49434370 ATACAATCTT
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
9 19 0.53
10 9 0.25
11 8 0.22
ACGTcount: A:0.10, C:0.06, G:0.04, T:0.81
Consensus pattern (9 bp):
TTTTTTTAT
Found at i:49435427 original size:198 final size:198
Alignment explanation
Indices: 49435190--49435591 Score: 772
Period size: 198 Copynumber: 2.0 Consensus size: 198
49435180 ATGTGTCTTA
49435190 TTATAT-TAATATTATTATTATATTTTGCTTATATATGTATATATGTTTATGTATTTGTTTCTAA
1 TTATATATAATATTATTATTATATTTTGCTTATATATGTATATATGTTTATGTATTTGTTTCTAA
49435254 CTTATTTAATATATACATAAATGCTTTTTTCTTTTATATATGTATATCTATATACTTTTCTTTTT
66 CTTATTTAATATATACATAAATGCTTTTTTCTTTTATATATGTATATCTATATACTTTTCTTTTT
49435319 TCCTCACGAATATACGTATACATATTTATATGTTTTTTTATACGGTTTTTTTATCTTACTTTATT
131 TCCTCACGAATATACGTATACATATTTATATGTTTTTTTATACGGTTTTTTTATCTTACTTTATT
49435384 TTT
196 TTT
49435387 TTATATAT-ATATTATTATTATATATTTGCTTATATATGTATATATGTTTATGTATTTGTTTCTA
1 TTATATATAATATTATTATTATAT-TTTGCTTATATATGTATATATGTTTATGTATTTGTTTCTA
49435451 ACTTATTTAATATATACATAAATGCTTTTTTCTTTTATATATGTATATCTATATACTTTTCTTTT
65 ACTTATTTAATATATACATAAATGCTTTTTTCTTTTATATATGTATATCTATATACTTTTCTTTT
49435516 TTCCTCACGAATATACGTATACATATTTATATGTTTTTTTATACGGTTTTTTTATCTTACTTTAT
130 TTCCTCACGAATATACGTATACATATTTATATGTTTTTTTATACGGTTTTTTTATCTTACTTTAT
49435581 TTTT
195 TTTT
*
49435585 ATATATA
1 TTATATA
49435592 CCTCACATGC
Statistics
Matches: 202, Mismatches: 1, Indels: 3
0.98 0.00 0.01
Matches are distributed among these distances:
197 21 0.10
198 181 0.90
ACGTcount: A:0.28, C:0.09, G:0.06, T:0.57
Consensus pattern (198 bp):
TTATATATAATATTATTATTATATTTTGCTTATATATGTATATATGTTTATGTATTTGTTTCTAA
CTTATTTAATATATACATAAATGCTTTTTTCTTTTATATATGTATATCTATATACTTTTCTTTTT
TCCTCACGAATATACGTATACATATTTATATGTTTTTTTATACGGTTTTTTTATCTTACTTTATT
TTT
Found at i:49435629 original size:198 final size:197
Alignment explanation
Indices: 49435206--49435635 Score: 697
Period size: 198 Copynumber: 2.2 Consensus size: 197
49435196 TAATATTATT
*
49435206 ATTATAT-TTTGCTTATATATGTATATATGTTTATGTATTTGTTTCTAACTTATTTAATATATAC
1 ATTATATATATGC-TATATATGTATATATGTTTATGTATTTGTTTCTAACTTATTTAATATATAC
49435270 ATAAATGCTTTTTTCTTTTATATATGTATATCTATATACTTTTCTTTTTTCCTCACGAATATACG
65 ATAAATGCTTTTTTCTTTTATATATGTATATCTATATACTTTTCTTTTTTCCTCACGAATATACG
* * *
49435335 TATACATATTTATATGTTTTTTTATACGGTTTTTTTATCTTACTTTATTTTTTTATATATATATT
130 TATACATATTTATATGTTTTTTTATACGGTTTTTTTATCTTACTTTATTTTTATATATATACATC
*
49435400 ATT
195 ATC
*
49435403 ATTATATATTTGCTTATATATGTATATATGTTTATGTATTTGTTTCTAACTTATTTAATATATAC
1 ATTATATATATGC-TATATATGTATATATGTTTATGTATTTGTTTCTAACTTATTTAATATATAC
49435468 ATAAATGCTTTTTTCTTTTATATATGTATATCTATATACTTTTCTTTTTTCCTCACGAATATACG
65 ATAAATGCTTTTTTCTTTTATATATGTATATCTATATACTTTTCTTTTTTCCTCACGAATATACG
49435533 TATACATATTTATATGTTTTTTTATACGGTTTTTTTATCTTACTTTATTTTTATATATACCTCAC
130 TATACATATTTATATGTTTTTTTATACGGTTTTTTTATCTTACTTTATTTTTATATATA--T-AC
49435598 ATGCA-C
192 AT-CATC
* * *
49435604 ATTTTTTATATG-TATATAT-TATATATATTTAT
1 ATTATATATATGCTATATATGTATATATGTTTAT
49435636 ATAATATTTA
Statistics
Matches: 220, Mismatches: 8, Indels: 9
0.93 0.03 0.04
Matches are distributed among these distances:
197 7 0.03
198 192 0.87
199 7 0.03
200 1 0.00
201 12 0.05
202 1 0.00
ACGTcount: A:0.28, C:0.10, G:0.06, T:0.57
Consensus pattern (197 bp):
ATTATATATATGCTATATATGTATATATGTTTATGTATTTGTTTCTAACTTATTTAATATATACA
TAAATGCTTTTTTCTTTTATATATGTATATCTATATACTTTTCTTTTTTCCTCACGAATATACGT
ATACATATTTATATGTTTTTTTATACGGTTTTTTTATCTTACTTTATTTTTATATATATACATCA
TC
Found at i:49435647 original size:17 final size:17
Alignment explanation
Indices: 49435608--49435647 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
49435598 ATGCACATTT
*
49435608 TTTATATGTATATATTA
1 TTTATATGTATATAATA
* *
49435625 TATATATTTATATAATA
1 TTTATATGTATATAATA
49435642 TTTATA
1 TTTATA
49435648 CGCATTTGCG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (17 bp):
TTTATATGTATATAATA
Found at i:49444132 original size:42 final size:42
Alignment explanation
Indices: 49443925--49444127 Score: 280
Period size: 42 Copynumber: 4.8 Consensus size: 42
49443915 GCGTTTTAAA
* *
49443925 AAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGAA
1 AAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTTGAT
*
49443967 AAAAACGCCGCTAAAGACCATGTTCTTTAGAGGCGCTTTGAT
1 AAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTTGAT
*
49444009 AAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTTGGT
1 AAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTTGAT
* * * * *
49444051 AAAAATGCCACGAAAGACCATGTTCTTTAGCGGCGTTTTTAT
1 AAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTTGAT
* * * * *
49444093 CAAAGCGCCGCTAAAGAACATGGTCTTTAGAGGCG
1 AAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCG
49444128 TTTTTTTCTA
Statistics
Matches: 142, Mismatches: 19, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 142 1.00
ACGTcount: A:0.31, C:0.22, G:0.23, T:0.25
Consensus pattern (42 bp):
AAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTTGAT
Found at i:49444739 original size:334 final size:334
Alignment explanation
Indices: 49444130--49444798 Score: 1338
Period size: 334 Copynumber: 2.0 Consensus size: 334
49444120 TAGAGGCGTT
49444130 TTTTTCTAAGCGCCGCTAAAGAACATGCAAAAACTCCACTATTTTTGGGATTTTTTTATTAAATT
1 TTTTTCTAAGCGCCGCTAAAGAACATGCAAAAACTCCACTATTTTTGGGATTTTTTTATTAAATT
49444195 TTTTTATTTTTCAGCCCTCCTGTAACAACAAATCAAAAGCAACCAAATCTAAAACAGCCAAAAGC
66 TTTTTATTTTTCAGCCCTCCTGTAACAACAAATCAAAAGCAACCAAATCTAAAACAGCCAAAAGC
49444260 AATAAATTTATATAATATTTCAAATTAAACGAATAAAATAATATTAATATCAATAAATAAAAGTG
131 AATAAATTTATATAATATTTCAAATTAAACGAATAAAATAATATTAATATCAATAAATAAAAGTG
49444325 AATTCATATTATTTTTGCAAAAATGTTAAATGTTAAAATGATAAAAATATTTATGCCATACACTA
196 AATTCATATTATTTTTGCAAAAATGTTAAATGTTAAAATGATAAAAATATTTATGCCATACACTA
49444390 TGAAGGCGGAAGTTGCGACTGAAACATCTTTATCATAATCTGAAGCTGCTGCTGGAGTTCGTCAT
261 TGAAGGCGGAAGTTGCGACTGAAACATCTTTATCATAATCTGAAGCTGCTGCTGGAGTTCGTCAT
49444455 ACTTTTTGG
326 ACTTTTTGG
49444464 TTTTTCTAAGCGCCGCTAAAGAACATGCAAAAACTCCACTATTTTTGGGATTTTTTTATTAAATT
1 TTTTTCTAAGCGCCGCTAAAGAACATGCAAAAACTCCACTATTTTTGGGATTTTTTTATTAAATT
49444529 TTTTTATTTTTCAGCCCTCCTGTAACAACAAATCAAAAGCAACCAAATCTAAAACAGCCAAAAGC
66 TTTTTATTTTTCAGCCCTCCTGTAACAACAAATCAAAAGCAACCAAATCTAAAACAGCCAAAAGC
49444594 AATAAATTTATATAATATTTCAAATTAAACGAATAAAATAATATTAATATCAATAAATAAAAGTG
131 AATAAATTTATATAATATTTCAAATTAAACGAATAAAATAATATTAATATCAATAAATAAAAGTG
49444659 AATTCATATTATTTTTGCAAAAATGTTAAATGTTAAAATGATAAAAATATTTATGCCATACACTA
196 AATTCATATTATTTTTGCAAAAATGTTAAATGTTAAAATGATAAAAATATTTATGCCATACACTA
49444724 TGAAGGCGGAAGTTGCGACTGAAACATCTTTATCATAATCTGAAGCTGCTGCTGGAGTTCGTCAT
261 TGAAGGCGGAAGTTGCGACTGAAACATCTTTATCATAATCTGAAGCTGCTGCTGGAGTTCGTCAT
49444789 ACTTTTTGG
326 ACTTTTTGG
49444798 T
1 T
49444799 CTGCTCTGCT
Statistics
Matches: 335, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
334 335 1.00
ACGTcount: A:0.39, C:0.15, G:0.12, T:0.34
Consensus pattern (334 bp):
TTTTTCTAAGCGCCGCTAAAGAACATGCAAAAACTCCACTATTTTTGGGATTTTTTTATTAAATT
TTTTTATTTTTCAGCCCTCCTGTAACAACAAATCAAAAGCAACCAAATCTAAAACAGCCAAAAGC
AATAAATTTATATAATATTTCAAATTAAACGAATAAAATAATATTAATATCAATAAATAAAAGTG
AATTCATATTATTTTTGCAAAAATGTTAAATGTTAAAATGATAAAAATATTTATGCCATACACTA
TGAAGGCGGAAGTTGCGACTGAAACATCTTTATCATAATCTGAAGCTGCTGCTGGAGTTCGTCAT
ACTTTTTGG
Found at i:49444836 original size:21 final size:21
Alignment explanation
Indices: 49444802--49444872 Score: 106
Period size: 21 Copynumber: 3.4 Consensus size: 21
49444792 TTTTGGTCTG
*
49444802 CTCTGCTTCTCTCGCTGCAGC
1 CTCTGCTTCCCTCGCTGCAGC
*
49444823 CTCCGCTTCCCTCGCTGCAGC
1 CTCTGCTTCCCTCGCTGCAGC
* *
49444844 CGCTGCTTCCCTCGCTGCCGC
1 CTCTGCTTCCCTCGCTGCAGC
49444865 CTCTGCTT
1 CTCTGCTT
49444873 TAAGTTGTAG
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 44 1.00
ACGTcount: A:0.03, C:0.48, G:0.20, T:0.30
Consensus pattern (21 bp):
CTCTGCTTCCCTCGCTGCAGC
Found at i:49448315 original size:7 final size:7
Alignment explanation
Indices: 49448303--49448338 Score: 54
Period size: 7 Copynumber: 5.0 Consensus size: 7
49448293 TCATATTATT
49448303 AACCCTA
1 AACCCTA
49448310 AACCCTA
1 AACCCTA
*
49448317 AACTCTA
1 AACCCTA
49448324 AACCCTAA
1 AACCCT-A
49448332 AACCCTA
1 AACCCTA
49448339 TATTAACTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
7 19 0.73
8 7 0.27
ACGTcount: A:0.44, C:0.39, G:0.00, T:0.17
Consensus pattern (7 bp):
AACCCTA
Found at i:49448689 original size:40 final size:41
Alignment explanation
Indices: 49448643--49448740 Score: 126
Period size: 41 Copynumber: 2.4 Consensus size: 41
49448633 CGGCGCATAA
*
49448643 ACAAAAAACGCCGCTAAAACACCTAG-ATTAGCGGCGATTT
1 ACAAAAAACGCCACTAAAACACCTAGCATTAGCGGCGATTT
* ** * * *
49448683 TCAAAAAACGCCACTAAAAGTCTTAGCCTTAGCGGCGCTTT
1 ACAAAAAACGCCACTAAAACACCTAGCATTAGCGGCGATTT
49448724 ACAAAAAACGCCACTAA
1 ACAAAAAACGCCACTAA
49448741 TTCCCCCGAA
Statistics
Matches: 49, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
40 21 0.43
41 28 0.57
ACGTcount: A:0.40, C:0.27, G:0.15, T:0.18
Consensus pattern (41 bp):
ACAAAAAACGCCACTAAAACACCTAGCATTAGCGGCGATTT
Found at i:49448829 original size:39 final size:38
Alignment explanation
Indices: 49448786--49448875 Score: 126
Period size: 40 Copynumber: 2.3 Consensus size: 38
49448776 TGTATTATTT
49448786 GCGGCGTTTTTTATAAACGCCGCTAACGCTCACTCTTTA
1 GCGGCGTTTTTT-TAAACGCCGCTAACGCTCACTCTTTA
* *
49448825 GCGGCGCTTTTCCTTAAACGCCGCTAATGCTCACTCTTTA
1 GCGGCG-TTTT-TTTAAACGCCGCTAACGCTCACTCTTTA
*
49448865 GCGGCGCTTTT
1 GCGGCGTTTTT
49448876 CCTAAAACGC
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
39 9 0.20
40 35 0.78
41 1 0.02
ACGTcount: A:0.17, C:0.30, G:0.20, T:0.33
Consensus pattern (38 bp):
GCGGCGTTTTTTTAAACGCCGCTAACGCTCACTCTTTA
Found at i:49448844 original size:40 final size:40
Alignment explanation
Indices: 49448799--49448890 Score: 157
Period size: 40 Copynumber: 2.3 Consensus size: 40
49448789 GCGTTTTTTA
49448799 TAAACGCCGCTAACGCTCACTCTTTAGCGGCGCTTTTCCT
1 TAAACGCCGCTAACGCTCACTCTTTAGCGGCGCTTTTCCT
*
49448839 TAAACGCCGCTAATGCTCACTCTTTAGCGGCGCTTTTCCT
1 TAAACGCCGCTAACGCTCACTCTTTAGCGGCGCTTTTCCT
* *
49448879 AAAACGCTGCTA
1 TAAACGCCGCTA
49448891 TTTCTCGATT
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 49 1.00
ACGTcount: A:0.21, C:0.33, G:0.17, T:0.29
Consensus pattern (40 bp):
TAAACGCCGCTAACGCTCACTCTTTAGCGGCGCTTTTCCT
Found at i:49458343 original size:27 final size:25
Alignment explanation
Indices: 49458313--49458364 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 25
49458303 TCGAAATGGT
*
49458313 GATTTCTTATTTTTATTCAATTATTTA
1 GATTTCTTATTTTAATT-AATT-TTTA
*
49458340 GATTTTTTATTTTAATTAATTTTTA
1 GATTTCTTATTTTAATTAATTTTTA
49458365 AATATGCAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 4 0.17
26 4 0.17
27 15 0.65
ACGTcount: A:0.27, C:0.04, G:0.04, T:0.65
Consensus pattern (25 bp):
GATTTCTTATTTTAATTAATTTTTA
Found at i:49460013 original size:32 final size:32
Alignment explanation
Indices: 49459976--49460038 Score: 90
Period size: 32 Copynumber: 2.0 Consensus size: 32
49459966 TTATAATCTT
* *
49459976 ATAAATTTATTACTTGAATTTAATAACTCATG
1 ATAAATTAATTAATTGAATTTAATAACTCATG
* *
49460008 ATAAATTAATTAATTTAATTTGATAACTCAT
1 ATAAATTAATTAATTGAATTTAATAACTCAT
49460039 ACTGATTAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.43, C:0.08, G:0.05, T:0.44
Consensus pattern (32 bp):
ATAAATTAATTAATTGAATTTAATAACTCATG
Found at i:49466841 original size:5 final size:5
Alignment explanation
Indices: 49466831--49466856 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
49466821 TTTGTTTTTT
49466831 TAATA TAATA TAATA TAATA TAATA T
1 TAATA TAATA TAATA TAATA TAATA T
49466857 CATTCCATTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (5 bp):
TAATA
Found at i:49475108 original size:21 final size:21
Alignment explanation
Indices: 49475069--49475118 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
49475059 CAGCCTGTTG
*
49475069 AGTTGGGGTACTCTCTTGCTG
1 AGTTGGGGTACTCTCTTGCTA
* *
49475090 ATTTGGGGTAGC-CTGTTGCTA
1 AGTTGGGGTA-CTCTCTTGCTA
49475111 AGTTGGGG
1 AGTTGGGG
49475119 CAACCACTTG
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
21 23 0.96
22 1 0.04
ACGTcount: A:0.12, C:0.14, G:0.38, T:0.36
Consensus pattern (21 bp):
AGTTGGGGTACTCTCTTGCTA
Found at i:49480455 original size:15 final size:15
Alignment explanation
Indices: 49480423--49480473 Score: 57
Period size: 15 Copynumber: 3.4 Consensus size: 15
49480413 TTATCCTATT
**
49480423 AGACACATCACTTTC
1 AGACACATCACTACC
**
49480438 AGATGCATCACTACC
1 AGACACATCACTACC
*
49480453 AGACACATCACTATC
1 AGACACATCACTACC
49480468 AGACAC
1 AGACAC
49480474 GGTTGTCTGA
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
15 29 1.00
ACGTcount: A:0.37, C:0.33, G:0.10, T:0.20
Consensus pattern (15 bp):
AGACACATCACTACC
Found at i:49481406 original size:18 final size:17
Alignment explanation
Indices: 49481368--49481406 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
49481358 GTTGTACGTT
* *
49481368 TGGGCCACACAGGCGTG
1 TGGGCCACACAGGCCTA
49481385 TGGGCCCACACAGGCCTA
1 TGGG-CCACACAGGCCTA
49481403 TGGG
1 TGGG
49481407 TTTTGGGCCA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 4 0.21
18 15 0.79
ACGTcount: A:0.18, C:0.31, G:0.38, T:0.13
Consensus pattern (17 bp):
TGGGCCACACAGGCCTA
Found at i:49481718 original size:13 final size:13
Alignment explanation
Indices: 49481700--49481724 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
49481690 TATTTGTTTT
49481700 TTCTGTATCTGTA
1 TTCTGTATCTGTA
49481713 TTCTGTATCTGT
1 TTCTGTATCTGT
49481725 GATTGGGGTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.12, C:0.16, G:0.16, T:0.56
Consensus pattern (13 bp):
TTCTGTATCTGTA
Found at i:49490402 original size:70 final size:71
Alignment explanation
Indices: 49490311--49490483 Score: 208
Period size: 70 Copynumber: 2.5 Consensus size: 71
49490301 GGCCGTATGG
* * * *
49490311 GCCACATGGGCTAGGCTAAGTTGGGCGTGTGGGGC-ACAAGGGCGTGTGGGTTTTGGGCCAGGCG
1 GCCACACGGGCTAGGCCAAGTTGGGCGTGTGGGGCTACAAGGGCGTGTGGCTTTTGGGCCAGGCC
49490375 GTGTAA
66 GTGTAA
* * * * *
49490381 GCCACACGGGTTAGGCCAAGTTGGGCATGT-GGGCTACACGGGCGTGTGTCTTTTTGGCCAGGCC
1 GCCACACGGGCTAGGCCAAGTTGGGCGTGTGGGGCTACAAGGGCGTGTGGCTTTTGGGCCAGGCC
*
49490445 GTGTAG
66 GTGTAA
* *
49490451 GCCACACGGGCAAGGCCAA-TCTAGGCGTGTGGG
1 GCCACACGGGCTAGGCCAAGT-TGGGCGTGTGGG
49490484 CCCACACGGG
Statistics
Matches: 86, Mismatches: 14, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
69 5 0.06
70 79 0.92
71 2 0.02
ACGTcount: A:0.16, C:0.21, G:0.42, T:0.21
Consensus pattern (71 bp):
GCCACACGGGCTAGGCCAAGTTGGGCGTGTGGGGCTACAAGGGCGTGTGGCTTTTGGGCCAGGCC
GTGTAA
Found at i:49495184 original size:9 final size:9
Alignment explanation
Indices: 49495166--49495230 Score: 78
Period size: 9 Copynumber: 7.2 Consensus size: 9
49495156 TCGGGTATTT
49495166 TTCGGTTAA
1 TTCGGTTAA
*
49495175 TTCTGTTAA
1 TTCGGTTAA
49495184 TTCGGTTAA
1 TTCGGTTAA
49495193 TTCAGG-TAA
1 TTC-GGTTAA
*
49495202 TTCGGGTAA
1 TTCGGTTAA
*
49495211 TTCGGGTAA
1 TTCGGTTAA
*
49495220 TTCGGGTAA
1 TTCGGTTAA
49495229 TT
1 TT
49495231 TTTAACCAAA
Statistics
Matches: 52, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
8 2 0.04
9 48 0.92
10 2 0.04
ACGTcount: A:0.23, C:0.11, G:0.25, T:0.42
Consensus pattern (9 bp):
TTCGGTTAA
Found at i:49498068 original size:27 final size:26
Alignment explanation
Indices: 49498036--49498090 Score: 67
Period size: 27 Copynumber: 2.1 Consensus size: 26
49498026 GAAATTTAGC
49498036 GTGCCCAT-TGTCCTATTAAGCACTATG
1 GTGCCC-TCTGTCCTATT-AGCACTATG
* *
49498063 GTGCCCTCTGTTCTATTAGCACTTTG
1 GTGCCCTCTGTCCTATTAGCACTATG
49498089 GT
1 GT
49498091 TCATTCCGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 11 0.44
27 14 0.56
ACGTcount: A:0.16, C:0.25, G:0.20, T:0.38
Consensus pattern (26 bp):
GTGCCCTCTGTCCTATTAGCACTATG
Found at i:49504149 original size:28 final size:28
Alignment explanation
Indices: 49504118--49504173 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 28
49504108 AATTAGGGAT
49504118 TAAAT-TGAGAAA-TGTGAAAATTGTATGG
1 TAAATGTGAGAAATTGTG-AAA-TGTATGG
*
49504146 TAAATGTGTGAAATTGTGAAATGTATGG
1 TAAATGTGAGAAATTGTGAAATGTATGG
49504174 GCTGCTATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
28 12 0.48
29 9 0.36
30 4 0.16
ACGTcount: A:0.39, C:0.00, G:0.27, T:0.34
Consensus pattern (28 bp):
TAAATGTGAGAAATTGTGAAATGTATGG
Found at i:49504944 original size:17 final size:17
Alignment explanation
Indices: 49504922--49504985 Score: 67
Period size: 17 Copynumber: 3.6 Consensus size: 17
49504912 AATCTTAGAG
49504922 TTCTAATTGTATACAGC
1 TTCTAATTGTATACAGC
* *
49504939 TTCTAATTGTGT-CTTAGAG
1 TTCTAATTGTATAC--AG-C
49504958 TTCTAATTGTATACAGC
1 TTCTAATTGTATACAGC
*
49504975 TTTTAATTGTA
1 TTCTAATTGTA
49504986 GCCTATGATG
Statistics
Matches: 38, Mismatches: 5, Indels: 8
0.75 0.10 0.16
Matches are distributed among these distances:
16 1 0.03
17 21 0.55
18 4 0.11
19 11 0.29
20 1 0.03
ACGTcount: A:0.27, C:0.12, G:0.14, T:0.47
Consensus pattern (17 bp):
TTCTAATTGTATACAGC
Found at i:49504961 original size:36 final size:36
Alignment explanation
Indices: 49504914--49504984 Score: 133
Period size: 36 Copynumber: 2.0 Consensus size: 36
49504904 GATTATGTAA
49504914 TCTTAGAGTTCTAATTGTATACAGCTTCTAATTGTG
1 TCTTAGAGTTCTAATTGTATACAGCTTCTAATTGTG
*
49504950 TCTTAGAGTTCTAATTGTATACAGCTTTTAATTGT
1 TCTTAGAGTTCTAATTGTATACAGCTTCTAATTGT
49504985 AGCCTATGAT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.25, C:0.13, G:0.15, T:0.46
Consensus pattern (36 bp):
TCTTAGAGTTCTAATTGTATACAGCTTCTAATTGTG
Found at i:49504963 original size:19 final size:19
Alignment explanation
Indices: 49504913--49504969 Score: 66
Period size: 19 Copynumber: 3.1 Consensus size: 19
49504903 TGATTATGTA
49504913 ATCTTAGAGTTCTAATTGT
1 ATCTTAGAGTTCTAATTGT
*
49504932 ATAC--AG-CTTCTAATTGT
1 AT-CTTAGAGTTCTAATTGT
*
49504949 GTCTTAGAGTTCTAATTGT
1 ATCTTAGAGTTCTAATTGT
49504968 AT
1 AT
49504970 ACAGCTTTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 8
0.71 0.10 0.19
Matches are distributed among these distances:
16 1 0.03
17 11 0.37
18 4 0.13
19 13 0.43
20 1 0.03
ACGTcount: A:0.26, C:0.12, G:0.16, T:0.46
Consensus pattern (19 bp):
ATCTTAGAGTTCTAATTGT
Found at i:49510084 original size:17 final size:17
Alignment explanation
Indices: 49510062--49510125 Score: 58
Period size: 17 Copynumber: 3.6 Consensus size: 17
49510052 AATCTTAGAG
49510062 TTCTAATTGTATACAGC
1 TTCTAATTGTATACAGC
* *
49510079 TTCTAATTGTGT-CTTAGAG
1 TTCTAATTGTATAC--AG-C
*
49510098 TTCTAATTGTATACAAC
1 TTCTAATTGTATACAGC
*
49510115 TTTTAATTGTA
1 TTCTAATTGTA
49510126 GCCTTTGATG
Statistics
Matches: 37, Mismatches: 6, Indels: 8
0.73 0.12 0.16
Matches are distributed among these distances:
16 1 0.03
17 21 0.57
18 3 0.08
19 11 0.30
20 1 0.03
ACGTcount: A:0.28, C:0.12, G:0.12, T:0.47
Consensus pattern (17 bp):
TTCTAATTGTATACAGC
Found at i:49510101 original size:36 final size:36
Alignment explanation
Indices: 49510054--49510124 Score: 124
Period size: 36 Copynumber: 2.0 Consensus size: 36
49510044 GATTATGTAA
*
49510054 TCTTAGAGTTCTAATTGTATACAGCTTCTAATTGTG
1 TCTTAGAGTTCTAATTGTATACAACTTCTAATTGTG
*
49510090 TCTTAGAGTTCTAATTGTATACAACTTTTAATTGT
1 TCTTAGAGTTCTAATTGTATACAACTTCTAATTGT
49510125 AGCCTTTGAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.27, C:0.13, G:0.14, T:0.46
Consensus pattern (36 bp):
TCTTAGAGTTCTAATTGTATACAACTTCTAATTGTG
Found at i:49510103 original size:19 final size:19
Alignment explanation
Indices: 49510053--49510109 Score: 66
Period size: 19 Copynumber: 3.1 Consensus size: 19
49510043 TGATTATGTA
49510053 ATCTTAGAGTTCTAATTGT
1 ATCTTAGAGTTCTAATTGT
*
49510072 ATAC--AG-CTTCTAATTGT
1 AT-CTTAGAGTTCTAATTGT
*
49510089 GTCTTAGAGTTCTAATTGT
1 ATCTTAGAGTTCTAATTGT
49510108 AT
1 AT
49510110 ACAACTTTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 8
0.71 0.10 0.19
Matches are distributed among these distances:
16 1 0.03
17 11 0.37
18 4 0.13
19 13 0.43
20 1 0.03
ACGTcount: A:0.26, C:0.12, G:0.16, T:0.46
Consensus pattern (19 bp):
ATCTTAGAGTTCTAATTGT
Found at i:49510385 original size:48 final size:48
Alignment explanation
Indices: 49510329--49510423 Score: 172
Period size: 48 Copynumber: 2.0 Consensus size: 48
49510319 TGAAGGAATT
*
49510329 CTGTTGAATTCTTTATCATTGCAAGTTAGGCTGACTTAGGCGTTTTTG
1 CTGTTGAATCCTTTATCATTGCAAGTTAGGCTGACTTAGGCGTTTTTG
*
49510377 CTGTTGAATCCTTTATCATTGCGAGTTAGGCTGACTTAGGCGTTTTT
1 CTGTTGAATCCTTTATCATTGCAAGTTAGGCTGACTTAGGCGTTTTT
49510424 AAGCAAAGAA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 45 1.00
ACGTcount: A:0.18, C:0.16, G:0.23, T:0.43
Consensus pattern (48 bp):
CTGTTGAATCCTTTATCATTGCAAGTTAGGCTGACTTAGGCGTTTTTG
Found at i:49513041 original size:29 final size:30
Alignment explanation
Indices: 49513009--49513065 Score: 73
Period size: 29 Copynumber: 1.9 Consensus size: 30
49512999 ATGTCCGCTC
*
49513009 ATTATTTG-TAATATTACAA-ATGTTATAAA
1 ATTA-TTGCTAATATTACAATATCTTATAAA
*
49513038 ATTATTGCTAATGTTACAATATCTTATA
1 ATTATTGCTAATATTACAATATCTTATA
49513066 GGGTCATACC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 3 0.12
29 14 0.58
30 7 0.29
ACGTcount: A:0.40, C:0.07, G:0.07, T:0.46
Consensus pattern (30 bp):
ATTATTGCTAATATTACAATATCTTATAAA
Found at i:49519224 original size:13 final size:13
Alignment explanation
Indices: 49519206--49519232 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
49519196 CCTCCAGGCT
49519206 CTAAGCCCAAGAA
1 CTAAGCCCAAGAA
49519219 CTAAGCCCAAGAA
1 CTAAGCCCAAGAA
49519232 C
1 C
49519233 AATTCATGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.44, C:0.33, G:0.15, T:0.07
Consensus pattern (13 bp):
CTAAGCCCAAGAA
Found at i:49519247 original size:7 final size:7
Alignment explanation
Indices: 49519235--49519293 Score: 73
Period size: 7 Copynumber: 8.3 Consensus size: 7
49519225 CCAAGAACAA
49519235 TTCATGT
1 TTCATGT
49519242 TTCATGT
1 TTCATGT
49519249 TTCATGT
1 TTCATGT
*
49519256 TTCACGAT
1 TTCATG-T
49519264 TTCATGT
1 TTCATGT
**
49519271 TTCATAC
1 TTCATGT
*
49519278 TGCATGT
1 TTCATGT
49519285 TTCATGT
1 TTCATGT
49519292 TT
1 TT
49519294 TCTTCTGTAC
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
7 37 0.86
8 6 0.14
ACGTcount: A:0.17, C:0.17, G:0.14, T:0.53
Consensus pattern (7 bp):
TTCATGT
Found at i:49519583 original size:37 final size:37
Alignment explanation
Indices: 49519540--49519645 Score: 158
Period size: 37 Copynumber: 2.9 Consensus size: 37
49519530 TGTGTTAAAG
*
49519540 ACTTATGTAATGTTTTTAATTATTTAGTGATTCAAAA
1 ACTTATGTAATGTTTTTAATTATATAGTGATTCAAAA
* * * *
49519577 ATTTATGTAATGTTTTTAGTTATGTAGTGATTCAAAG
1 ACTTATGTAATGTTTTTAATTATATAGTGATTCAAAA
*
49519614 ACTTATGTAATTTTTTTAATTATATAGTGATT
1 ACTTATGTAATGTTTTTAATTATATAGTGATT
49519646 TAAATCGGTT
Statistics
Matches: 61, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 61 1.00
ACGTcount: A:0.32, C:0.04, G:0.13, T:0.51
Consensus pattern (37 bp):
ACTTATGTAATGTTTTTAATTATATAGTGATTCAAAA
Found at i:49519664 original size:9 final size:9
Alignment explanation
Indices: 49519645--49519728 Score: 125
Period size: 9 Copynumber: 9.4 Consensus size: 9
49519635 ATATAGTGAT
49519645 TTAAATCGG
1 TTAAATCGG
* *
49519654 TTAAGTTGG
1 TTAAATCGG
49519663 TTAAATCGG
1 TTAAATCGG
49519672 TTAAATCGG
1 TTAAATCGG
49519681 TTAAATCGG
1 TTAAATCGG
*
49519690 TTAAGTCGG
1 TTAAATCGG
49519699 TT-AATCGG
1 TTAAATCGG
*
49519707 TTAAATAGG
1 TTAAATCGG
49519716 TTAAATCGG
1 TTAAATCGG
49519725 TTAA
1 TTAA
49519729 TTTTTAACCA
Statistics
Matches: 66, Mismatches: 8, Indels: 2
0.87 0.11 0.03
Matches are distributed among these distances:
8 7 0.11
9 59 0.89
ACGTcount: A:0.32, C:0.08, G:0.24, T:0.36
Consensus pattern (9 bp):
TTAAATCGG
Found at i:49519712 original size:35 final size:36
Alignment explanation
Indices: 49519645--49519728 Score: 143
Period size: 35 Copynumber: 2.4 Consensus size: 36
49519635 ATATAGTGAT
* *
49519645 TTAAATCGGTTAAGTTGGTTAAATCGGTTAAATCGG
1 TTAAATCGGTTAAGTCGGTTAAATCGGTTAAATAGG
49519681 TTAAATCGGTTAAGTCGGTT-AATCGGTTAAATAGG
1 TTAAATCGGTTAAGTCGGTTAAATCGGTTAAATAGG
49519716 TTAAATCGGTTAA
1 TTAAATCGGTTAA
49519729 TTTTTAACCA
Statistics
Matches: 46, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
35 27 0.59
36 19 0.41
ACGTcount: A:0.32, C:0.08, G:0.24, T:0.36
Consensus pattern (36 bp):
TTAAATCGGTTAAGTCGGTTAAATCGGTTAAATAGG
Found at i:49525764 original size:36 final size:37
Alignment explanation
Indices: 49525705--49525778 Score: 105
Period size: 36 Copynumber: 2.0 Consensus size: 37
49525695 TATAGTTTCT
*
49525705 GCATTGCATTTTACTCGCTTTTTAATACTTTTATCTA
1 GCATTGCATTTTACTCGCATTTTAATACTTTTATCTA
* **
49525742 GCATTGCA-TTTACTCGCATTTTAGTGGTTTTATCTA
1 GCATTGCATTTTACTCGCATTTTAATACTTTTATCTA
49525778 G
1 G
49525779 TCTGCAGGAT
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
36 25 0.76
37 8 0.24
ACGTcount: A:0.20, C:0.18, G:0.14, T:0.49
Consensus pattern (37 bp):
GCATTGCATTTTACTCGCATTTTAATACTTTTATCTA
Found at i:49529202 original size:3 final size:3
Alignment explanation
Indices: 49529194--49529241 Score: 60
Period size: 3 Copynumber: 15.3 Consensus size: 3
49529184 AAGTGAGACC
* *
49529194 TCT TCT TCTT TCT TCT TTT TCT TCT TTT TCTT TCT TCT TCT TCT TCT
1 TCT TCT TC-T TCT TCT TCT TCT TCT TCT TC-T TCT TCT TCT TCT TCT
49529241 T
1 T
49529242 TTTTTTTTTT
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
3 33 0.85
4 6 0.15
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (3 bp):
TCT
Found at i:49529217 original size:16 final size:16
Alignment explanation
Indices: 49529196--49529244 Score: 75
Period size: 16 Copynumber: 3.1 Consensus size: 16
49529186 GTGAGACCTC
49529196 TTCTTCTTTCTTCTTT
1 TTCTTCTTTCTTCTTT
49529212 TTCTTCTTT-TTCTTT
1 TTCTTCTTTCTTCTTT
49529227 CTTCTTC-TTCTTCTTT
1 -TTCTTCTTTCTTCTTT
49529243 TT
1 TT
49529245 TTTTTTTTGC
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
15 10 0.32
16 21 0.68
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (16 bp):
TTCTTCTTTCTTCTTT
Found at i:49529224 original size:22 final size:22
Alignment explanation
Indices: 49529194--49529244 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
49529184 AAGTGAGACC
* *
49529194 TCTTCTTCTTTCTTCTTTTTCT
1 TCTTTTTCTTTCTTCTTCTTCT
49529216 TCTTTTTCTTTCTTCTTCTTCT
1 TCTTTTTCTTTCTTCTTCTTCT
49529238 TCTTTTT
1 TCTTTTT
49529245 TTTTTTTTGC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (22 bp):
TCTTTTTCTTTCTTCTTCTTCT
Found at i:49542991 original size:30 final size:29
Alignment explanation
Indices: 49542955--49543013 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 29
49542945 AATAATTATA
49542955 TACATATATATAGATTATAAAA-AAGATAAT
1 TACATATATATAGA-TATAAAACAA-ATAAT
*
49542985 TACATATATATATATATAAAACAAATAAT
1 TACATATATATAGATATAAAACAAATAAT
49543014 AATAATTACA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 12 0.44
30 15 0.56
ACGTcount: A:0.58, C:0.05, G:0.03, T:0.34
Consensus pattern (29 bp):
TACATATATATAGATATAAAACAAATAAT
Found at i:49545472 original size:36 final size:36
Alignment explanation
Indices: 49545432--49545509 Score: 113
Period size: 36 Copynumber: 2.2 Consensus size: 36
49545422 ATAAAACAAC
49545432 ATAAA-AAACAAGTTAGTACAAAGTAAAAGAAAATGA
1 ATAAAGAAACAA-TTAGTACAAAGTAAAAGAAAATGA
* * *
49545468 ATAAAGTACCTATTAGTACAAAGTAAAAGAAAATGA
1 ATAAAGAAACAATTAGTACAAAGTAAAAGAAAATGA
49545504 ATAAAG
1 ATAAAG
49545510 TACCTACTCG
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
36 35 0.92
37 3 0.08
ACGTcount: A:0.60, C:0.06, G:0.14, T:0.19
Consensus pattern (36 bp):
ATAAAGAAACAATTAGTACAAAGTAAAAGAAAATGA
Found at i:49545510 original size:36 final size:36
Alignment explanation
Indices: 49545444--49545515 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
49545434 AAAAAACAAG
49545444 TTAGTACAAAGTAAAAGAAAATGAATAAAGTACCTA
1 TTAGTACAAAGTAAAAGAAAATGAATAAAGTACCTA
49545480 TTAGTACAAAGTAAAAGAAAATGAATAAAGTACCTA
1 TTAGTACAAAGTAAAAGAAAATGAATAAAGTACCTA
49545516 CTCGGGTGAC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.56, C:0.08, G:0.14, T:0.22
Consensus pattern (36 bp):
TTAGTACAAAGTAAAAGAAAATGAATAAAGTACCTA
Found at i:49568317 original size:8 final size:9
Alignment explanation
Indices: 49568301--49568328 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
49568291 TATAGTAAAA
49568301 TATTTTTTT
1 TATTTTTTT
49568310 TATTTTTTT
1 TATTTTTTT
49568319 TATTTTTTT
1 TATTTTTTT
49568328 T
1 T
49568329 CTTAACAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.11, C:0.00, G:0.00, T:0.89
Consensus pattern (9 bp):
TATTTTTTT
Found at i:49568365 original size:20 final size:20
Alignment explanation
Indices: 49568332--49568373 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
49568322 TTTTTTTCTT
* * *
49568332 AACAATAATTTTAAAAACTA
1 AACAAAAATCTTAAAAAATA
49568352 AACAAAAATCTTAAAAAATA
1 AACAAAAATCTTAAAAAATA
49568372 AA
1 AA
49568374 TATAAACTAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.67, C:0.10, G:0.00, T:0.24
Consensus pattern (20 bp):
AACAAAAATCTTAAAAAATA
Found at i:49571173 original size:22 final size:22
Alignment explanation
Indices: 49571121--49571179 Score: 66
Period size: 22 Copynumber: 2.7 Consensus size: 22
49571111 TGCACTATTG
49571121 AACAGAGAGCACTAAAGTGCTA
1 AACAGAGAGCACTAAAGTGCTA
* *
49571143 TACAAAGAGCAC-AAATGTGCTA
1 AACAGAGAGCACTAAA-GTGCTA
* *
49571165 AACGGAGAGTACTAA
1 AACAGAGAGCACTAA
49571180 GGTGATAATA
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
21 3 0.10
22 24 0.83
23 2 0.07
ACGTcount: A:0.46, C:0.17, G:0.22, T:0.15
Consensus pattern (22 bp):
AACAGAGAGCACTAAAGTGCTA
Found at i:49577056 original size:45 final size:45
Alignment explanation
Indices: 49576992--49577416 Score: 379
Period size: 45 Copynumber: 9.5 Consensus size: 45
49576982 ATCCGTTTCA
* * * *
49576992 CTGCCAGTACAGGAAGACAAAATCTACTATCTTCAGTCTACTTTG
1 CTGCCAATACAGGAAGACAAGATCTGCTATCTTCAGTCTACTTCG
* *
49577037 CTGCCAATACAGGAAGACAAGA-CTTGCTATCTTC-GATCTACTCCA
1 CTGCCAATACAGGAAGACAAGATC-TGCTATCTTCAG-TCTACTTCG
*** * * *
49577082 CTGCTGCT-CAGGGAGACAAGATCTGGTATCTTC-GATCTACTTTG
1 CTGCCAATACAGGAAGACAAGATCTGCTATCTTCAG-TCTACTTCG
* * *
49577126 CTGCCAATACAGGAAGACAAGATCTGCAATCTTCAGTCCACTTTG
1 CTGCCAATACAGGAAGACAAGATCTGCTATCTTCAGTCTACTTCG
* * **
49577171 CTTCCAATACAGGAAGAAAAGA-CTTATTATCTTCAGTCTACTTCG
1 CTGCCAATACAGGAAGACAAGATC-TGCTATCTTCAGTCTACTTCG
* *
49577216 CTGCCAATACAGGAAGACAAGA-CTTGAC-ATATTCAGTTTACTTCG
1 CTGCCAATACAGGAAGACAAGATC-TG-CTATCTTCAGTCTACTTCG
* *
49577261 CTGCCAATACAGGAAGACAAGA-CTTGCTATCTTC-GATCTACTCCA
1 CTGCCAATACAGGAAGACAAGATC-TGCTATCTTCAG-TCTACTTCG
*** *
49577306 CTGCTGCT-CAAGG-AGACAAGATCTGCTATC-TCCGATCTACTTCG
1 CTGCCAATAC-AGGAAGACAAGATCTGCTATCTTCAG-TCTACTTCG
* * * *
49577350 CTGCCAATACAGGAAGACAAGATCTGCAATCTTCAATCCATTTCG
1 CTGCCAATACAGGAAGACAAGATCTGCTATCTTCAGTCTACTTCG
* *
49577395 CTCCCAATATAGGAAGACAAGA
1 CTGCCAATACAGGAAGACAAGA
49577417 CTTGACATGA
Statistics
Matches: 312, Mismatches: 53, Indels: 30
0.79 0.13 0.08
Matches are distributed among these distances:
43 2 0.01
44 72 0.23
45 235 0.75
46 3 0.01
ACGTcount: A:0.31, C:0.26, G:0.17, T:0.26
Consensus pattern (45 bp):
CTGCCAATACAGGAAGACAAGATCTGCTATCTTCAGTCTACTTCG
Found at i:49577325 original size:179 final size:180
Alignment explanation
Indices: 49576992--49577424 Score: 447
Period size: 179 Copynumber: 2.4 Consensus size: 180
49576982 ATCCGTTTCA
* * *
49576992 CTGCCAGTACAGGAAGACAAA-ATCTAC-TATCTTCAGTCTACTTTGCTGCCAATACAGGAAGAC
1 CTGCCAATACAGGAAGA-AAAGATCTGCATATCTTCAGTCTACTTCGCTGCCAATACAGGAAGAC
* *** * *
49577055 AAGACTTG-CTATCTTCGATCTACTCCACTGCTGCTCAGGGAGACAAGATCTGGTATCTTCGATC
65 AAGACTTGAC-ATATTCGATCTACTCCACTGCCAATCAGGAAGACAAGATCTGCTATCTTCGATC
*** *
49577119 TACTTTGCTGCCAATACAGGAAGACAAGATCTGCAATCTTCAG-TCCACTTTG
129 TACTCCACTGCCAATACAGGAAGACAAGATCTGCAATC-TCAGATCCACTTCG
* *
49577171 CTTCCAATACAGGAAGAAAAGA-CT-TATTATCTTCAGTCTACTTCGCTGCCAATACAGGAAGAC
1 CTGCCAATACAGGAAGAAAAGATCTGCA-TATCTTCAGTCTACTTCGCTGCCAATACAGGAAGAC
* * *
49577234 AAGACTTGACATATTC-AGTTTACTTCGCTGCCAATACAGGAAGACAAGA-CTTGCTATCTTCGA
65 AAGACTTGACATATTCGA-TCTACTCCACTGCCAAT-CAGGAAGACAAGATC-TGCTATCTTCGA
*** * * *
49577297 TCTACTCCACTGCTGCT-CAAGG-AGACAAGATCTGCTATCTCCGATCTACTTCG
127 TCTACTCCACTGCCAATAC-AGGAAGACAAGATCTGCAATCTCAGATCCACTTCG
* * * * * *
49577350 CTGCCAATACAGGAAGACAAGATCTGCA-ATCTTCAATCCATTTCGCTCCCAATATAGGAAGACA
1 CTGCCAATACAGGAAGAAAAGATCTGCATATCTTCAGTCTACTTCGCTGCCAATACAGGAAGACA
49577414 AGACTTGACAT
66 AGACTTGACAT
49577425 GATGACTTCA
Statistics
Matches: 212, Mismatches: 31, Indels: 22
0.80 0.12 0.08
Matches are distributed among these distances:
178 9 0.04
179 162 0.76
180 40 0.19
181 1 0.00
ACGTcount: A:0.30, C:0.26, G:0.17, T:0.27
Consensus pattern (180 bp):
CTGCCAATACAGGAAGAAAAGATCTGCATATCTTCAGTCTACTTCGCTGCCAATACAGGAAGACA
AGACTTGACATATTCGATCTACTCCACTGCCAATCAGGAAGACAAGATCTGCTATCTTCGATCTA
CTCCACTGCCAATACAGGAAGACAAGATCTGCAATCTCAGATCCACTTCG
Found at i:49577411 original size:224 final size:224
Alignment explanation
Indices: 49576992--49577419 Score: 691
Period size: 224 Copynumber: 1.9 Consensus size: 224
49576982 ATCCGTTTCA
* * *
49576992 CTGCCAGTACAGGAAGACAAAATCTACTATCTTCAGTCTACTTTGCTGCCAATACAGGAAGACAA
1 CTGCCAATACAGGAAGACAAAATCTACTATATTCAGTCTACTTCGCTGCCAATACAGGAAGACAA
* * *
49577057 GACTTGCTATCTTCGATCTACTCCACTGCTGCTCAGGGAGACAAGATCTGGTATCTTCGATCTAC
66 GACTTGCTATCTTCGATCTACTCCACTGCTGCTCAAGGAGACAAGATCTGCTATCTCCGATCTAC
* * *
49577122 TTTGCTGCCAATACAGGAAGACAAGATCTGCAATCTTCAGTCCACTTTGCTTCCAATACAGGAAG
131 TTCGCTGCCAATACAGGAAGACAAGATCTGCAATCTTCAATCCACTTTGCTCCCAATACAGGAAG
49577187 AAAAGACTTATTATCTTCAGTCTACTTCG
196 AAAAGACTTATTATCTTCAGTCTACTTCG
* *
49577216 CTGCCAATACAGGAAGACAAGA-CTTGAC-ATATTCAGTTTACTTCGCTGCCAATACAGGAAGAC
1 CTGCCAATACAGGAAGACAAAATC-T-ACTATATTCAGTCTACTTCGCTGCCAATACAGGAAGAC
49577279 AAGACTTGCTATCTTCGATCTACTCCACTGCTGCTCAAGGAGACAAGATCTGCTATCTCCGATCT
64 AAGACTTGCTATCTTCGATCTACTCCACTGCTGCTCAAGGAGACAAGATCTGCTATCTCCGATCT
*
49577344 ACTTCGCTGCCAATACAGGAAGACAAGATCTGCAATCTTCAATCCA-TTTCGCTCCCAATATAGG
129 ACTTCGCTGCCAATACAGGAAGACAAGATCTGCAATCTTCAATCCACTTT-GCTCCCAATACAGG
*
49577408 AAGACAAGACTT
193 AAGAAAAGACTT
49577420 GACATGATGA
Statistics
Matches: 188, Mismatches: 13, Indels: 6
0.91 0.06 0.03
Matches are distributed among these distances:
223 4 0.02
224 182 0.97
225 2 0.01
ACGTcount: A:0.30, C:0.26, G:0.17, T:0.27
Consensus pattern (224 bp):
CTGCCAATACAGGAAGACAAAATCTACTATATTCAGTCTACTTCGCTGCCAATACAGGAAGACAA
GACTTGCTATCTTCGATCTACTCCACTGCTGCTCAAGGAGACAAGATCTGCTATCTCCGATCTAC
TTCGCTGCCAATACAGGAAGACAAGATCTGCAATCTTCAATCCACTTTGCTCCCAATACAGGAAG
AAAAGACTTATTATCTTCAGTCTACTTCG
Found at i:49592595 original size:988 final size:988
Alignment explanation
Indices: 49590679--49592654 Score: 3952
Period size: 988 Copynumber: 2.0 Consensus size: 988
49590669 GGTGGTGACA
49590679 GTGGGCATGCGAGCGGCGGCTGGTCAGAGGCGCACATGCGTGAGGGGAGGTGAAGCAGCGACAGC
1 GTGGGCATGCGAGCGGCGGCTGGTCAGAGGCGCACATGCGTGAGGGGAGGTGAAGCAGCGACAGC
49590744 TGCAAAGCATGAGACTAGGGTTTTCTGAAAATTTTGAGTTTGTTGGGCTAGGGTTTCTATCCTTG
66 TGCAAAGCATGAGACTAGGGTTTTCTGAAAATTTTGAGTTTGTTGGGCTAGGGTTTCTATCCTTG
49590809 GGCCATTTGGGTTTGATTGGACTTAATTTGGGTAGTGGGTTTTTTTTTTGTTGAAATGGATTGTG
131 GGCCATTTGGGTTTGATTGGACTTAATTTGGGTAGTGGGTTTTTTTTTTGTTGAAATGGATTGTG
49590874 GACGTTCTATTATTTTTGCTTGTTTTGGGTTTTATTGGGCTCCGGGCAAAATGGGCTATTACAAT
196 GACGTTCTATTATTTTTGCTTGTTTTGGGTTTTATTGGGCTCCGGGCAAAATGGGCTATTACAAT
49590939 TTTAATAAGATTAAATGCAAGATGATTGGTTATATCTGTATTTGAATATTTTATTTTTAGATAAG
261 TTTAATAAGATTAAATGCAAGATGATTGGTTATATCTGTATTTGAATATTTTATTTTTAGATAAG
49591004 TATACACGTCTTTGAAAAAAAATTGTATAATAAATTAAAATTTAAGATTTTCATGTACACAATAA
326 TATACACGTCTTTGAAAAAAAATTGTATAATAAATTAAAATTTAAGATTTTCATGTACACAATAA
49591069 TTTTAATTTATATATTTTTTCAAAAATATTTTTTAATTATTTTGATTCATATTGGGTCATTGGTT
391 TTTTAATTTATATATTTTTTCAAAAATATTTTTTAATTATTTTGATTCATATTGGGTCATTGGTT
49591134 TCTTTTGGGTTCATATTTTGGCTAAAAATAATTTATTGAGCCAAAATTTTATCAATTACCTCAAA
456 TCTTTTGGGTTCATATTTTGGCTAAAAATAATTTATTGAGCCAAAATTTTATCAATTACCTCAAA
49591199 TATTCAATATATATGGTTTAATTAGTTTTTTAATCAGTTCAATCGATTTTGTTCCTAGCTGTACA
521 TATTCAATATATATGGTTTAATTAGTTTTTTAATCAGTTCAATCGATTTTGTTCCTAGCTGTACA
49591264 CTCAAAATCTAATTTAATATCTCGTGTTTGGATTAGTACACTTGCTGGTTCTTGATCCAATTGGT
586 CTCAAAATCTAATTTAATATCTCGTGTTTGGATTAGTACACTTGCTGGTTCTTGATCCAATTGGT
49591329 TGTATCAGTTGGTCCAATCTAATTTCAACAATATTATTTTAAGGAGCTTTTTTCTCTTTATGTTT
651 TGTATCAGTTGGTCCAATCTAATTTCAACAATATTATTTTAAGGAGCTTTTTTCTCTTTATGTTT
49591394 TATATGAAGCCTATGAAAATAAAATTAAATTAACACATTAGGGGTGAGGGTTCGATTGAATCGAG
716 TATATGAAGCCTATGAAAATAAAATTAAATTAACACATTAGGGGTGAGGGTTCGATTGAATCGAG
49591459 TCGAATCGAAGTGAAAATATATTGAGTTGATGAGTCATATTTTATCATCCTAGCTCGATTTTAAA
781 TCGAATCGAAGTGAAAATATATTGAGTTGATGAGTCATATTTTATCATCCTAGCTCGATTTTAAA
49591524 TTTTGTCGAATTGAGTCAAGTGAAATAAAATTCGAGTCGAATCGAATCAAGTGAAATTATTCGAG
846 TTTTGTCGAATTGAGTCAAGTGAAATAAAATTCGAGTCGAATCGAATCAAGTGAAATTATTCGAG
49591589 TTAAATTAAAATCTTGTTACAGTATAACTAATTTCATGTTAGAGCACATAAATTTGAAACCATAT
911 TTAAATTAAAATCTTGTTACAGTATAACTAATTTCATGTTAGAGCACATAAATTTGAAACCATAT
49591654 ATATTCGAAATTT
976 ATATTCGAAATTT
49591667 GTGGGCATGCGAGCGGCGGCTGGTCAGAGGCGCACATGCGTGAGGGGAGGTGAAGCAGCGACAGC
1 GTGGGCATGCGAGCGGCGGCTGGTCAGAGGCGCACATGCGTGAGGGGAGGTGAAGCAGCGACAGC
49591732 TGCAAAGCATGAGACTAGGGTTTTCTGAAAATTTTGAGTTTGTTGGGCTAGGGTTTCTATCCTTG
66 TGCAAAGCATGAGACTAGGGTTTTCTGAAAATTTTGAGTTTGTTGGGCTAGGGTTTCTATCCTTG
49591797 GGCCATTTGGGTTTGATTGGACTTAATTTGGGTAGTGGGTTTTTTTTTTGTTGAAATGGATTGTG
131 GGCCATTTGGGTTTGATTGGACTTAATTTGGGTAGTGGGTTTTTTTTTTGTTGAAATGGATTGTG
49591862 GACGTTCTATTATTTTTGCTTGTTTTGGGTTTTATTGGGCTCCGGGCAAAATGGGCTATTACAAT
196 GACGTTCTATTATTTTTGCTTGTTTTGGGTTTTATTGGGCTCCGGGCAAAATGGGCTATTACAAT
49591927 TTTAATAAGATTAAATGCAAGATGATTGGTTATATCTGTATTTGAATATTTTATTTTTAGATAAG
261 TTTAATAAGATTAAATGCAAGATGATTGGTTATATCTGTATTTGAATATTTTATTTTTAGATAAG
49591992 TATACACGTCTTTGAAAAAAAATTGTATAATAAATTAAAATTTAAGATTTTCATGTACACAATAA
326 TATACACGTCTTTGAAAAAAAATTGTATAATAAATTAAAATTTAAGATTTTCATGTACACAATAA
49592057 TTTTAATTTATATATTTTTTCAAAAATATTTTTTAATTATTTTGATTCATATTGGGTCATTGGTT
391 TTTTAATTTATATATTTTTTCAAAAATATTTTTTAATTATTTTGATTCATATTGGGTCATTGGTT
49592122 TCTTTTGGGTTCATATTTTGGCTAAAAATAATTTATTGAGCCAAAATTTTATCAATTACCTCAAA
456 TCTTTTGGGTTCATATTTTGGCTAAAAATAATTTATTGAGCCAAAATTTTATCAATTACCTCAAA
49592187 TATTCAATATATATGGTTTAATTAGTTTTTTAATCAGTTCAATCGATTTTGTTCCTAGCTGTACA
521 TATTCAATATATATGGTTTAATTAGTTTTTTAATCAGTTCAATCGATTTTGTTCCTAGCTGTACA
49592252 CTCAAAATCTAATTTAATATCTCGTGTTTGGATTAGTACACTTGCTGGTTCTTGATCCAATTGGT
586 CTCAAAATCTAATTTAATATCTCGTGTTTGGATTAGTACACTTGCTGGTTCTTGATCCAATTGGT
49592317 TGTATCAGTTGGTCCAATCTAATTTCAACAATATTATTTTAAGGAGCTTTTTTCTCTTTATGTTT
651 TGTATCAGTTGGTCCAATCTAATTTCAACAATATTATTTTAAGGAGCTTTTTTCTCTTTATGTTT
49592382 TATATGAAGCCTATGAAAATAAAATTAAATTAACACATTAGGGGTGAGGGTTCGATTGAATCGAG
716 TATATGAAGCCTATGAAAATAAAATTAAATTAACACATTAGGGGTGAGGGTTCGATTGAATCGAG
49592447 TCGAATCGAAGTGAAAATATATTGAGTTGATGAGTCATATTTTATCATCCTAGCTCGATTTTAAA
781 TCGAATCGAAGTGAAAATATATTGAGTTGATGAGTCATATTTTATCATCCTAGCTCGATTTTAAA
49592512 TTTTGTCGAATTGAGTCAAGTGAAATAAAATTCGAGTCGAATCGAATCAAGTGAAATTATTCGAG
846 TTTTGTCGAATTGAGTCAAGTGAAATAAAATTCGAGTCGAATCGAATCAAGTGAAATTATTCGAG
49592577 TTAAATTAAAATCTTGTTACAGTATAACTAATTTCATGTTAGAGCACATAAATTTGAAACCATAT
911 TTAAATTAAAATCTTGTTACAGTATAACTAATTTCATGTTAGAGCACATAAATTTGAAACCATAT
49592642 ATATTCGAAATTT
976 ATATTCGAAATTT
49592655 TTTTCAAAGA
Statistics
Matches: 988, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
988 988 1.00
ACGTcount: A:0.30, C:0.11, G:0.19, T:0.40
Consensus pattern (988 bp):
GTGGGCATGCGAGCGGCGGCTGGTCAGAGGCGCACATGCGTGAGGGGAGGTGAAGCAGCGACAGC
TGCAAAGCATGAGACTAGGGTTTTCTGAAAATTTTGAGTTTGTTGGGCTAGGGTTTCTATCCTTG
GGCCATTTGGGTTTGATTGGACTTAATTTGGGTAGTGGGTTTTTTTTTTGTTGAAATGGATTGTG
GACGTTCTATTATTTTTGCTTGTTTTGGGTTTTATTGGGCTCCGGGCAAAATGGGCTATTACAAT
TTTAATAAGATTAAATGCAAGATGATTGGTTATATCTGTATTTGAATATTTTATTTTTAGATAAG
TATACACGTCTTTGAAAAAAAATTGTATAATAAATTAAAATTTAAGATTTTCATGTACACAATAA
TTTTAATTTATATATTTTTTCAAAAATATTTTTTAATTATTTTGATTCATATTGGGTCATTGGTT
TCTTTTGGGTTCATATTTTGGCTAAAAATAATTTATTGAGCCAAAATTTTATCAATTACCTCAAA
TATTCAATATATATGGTTTAATTAGTTTTTTAATCAGTTCAATCGATTTTGTTCCTAGCTGTACA
CTCAAAATCTAATTTAATATCTCGTGTTTGGATTAGTACACTTGCTGGTTCTTGATCCAATTGGT
TGTATCAGTTGGTCCAATCTAATTTCAACAATATTATTTTAAGGAGCTTTTTTCTCTTTATGTTT
TATATGAAGCCTATGAAAATAAAATTAAATTAACACATTAGGGGTGAGGGTTCGATTGAATCGAG
TCGAATCGAAGTGAAAATATATTGAGTTGATGAGTCATATTTTATCATCCTAGCTCGATTTTAAA
TTTTGTCGAATTGAGTCAAGTGAAATAAAATTCGAGTCGAATCGAATCAAGTGAAATTATTCGAG
TTAAATTAAAATCTTGTTACAGTATAACTAATTTCATGTTAGAGCACATAAATTTGAAACCATAT
ATATTCGAAATTT
Found at i:49592851 original size:18 final size:19
Alignment explanation
Indices: 49592808--49592852 Score: 58
Period size: 18 Copynumber: 2.5 Consensus size: 19
49592798 AGAATTTTTC
49592808 TTATAAA-TATTTTGAATT
1 TTATAAATTATTTTGAATT
*
49592826 TTAAAAATTATTTT-AATT
1 TTATAAATTATTTTGAATT
*
49592844 TTTTAAATT
1 TTATAAATT
49592853 TTGGTTGAGA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
18 17 0.74
19 6 0.26
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (19 bp):
TTATAAATTATTTTGAATT
Found at i:49603360 original size:20 final size:20
Alignment explanation
Indices: 49603335--49603374 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
49603325 ATTCATTAAA
49603335 ATAATTTTGGACAGCAACAG
1 ATAATTTTGGACAGCAACAG
49603355 ATAATTTTGGACAGCAACAG
1 ATAATTTTGGACAGCAACAG
49603375 TAGTTTAACT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.40, C:0.15, G:0.20, T:0.25
Consensus pattern (20 bp):
ATAATTTTGGACAGCAACAG
Found at i:49626905 original size:29 final size:30
Alignment explanation
Indices: 49626873--49626929 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
49626863 TAAGCCCTTT
49626873 TAAAATT-TAAA-AAAATTATTTAAAAATCA
1 TAAAATTATAAACAAAATT-TTTAAAAATCA
*
49626902 TAAAATTATAAACAAGATTTTTAAAAAT
1 TAAAATTATAAACAAAATTTTTAAAAAT
49626930 AAAGTTATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
29 7 0.28
30 13 0.52
31 5 0.20
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.35
Consensus pattern (30 bp):
TAAAATTATAAACAAAATTTTTAAAAATCA
Found at i:49639827 original size:9 final size:10
Alignment explanation
Indices: 49639802--49639827 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
49639792 AATGATTGAA
49639802 TTAAAAAATT
1 TTAAAAAATT
49639812 TTAAAAAATT
1 TTAAAAAATT
49639822 TTAAAA
1 TTAAAA
49639828 TATAATAACT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (10 bp):
TTAAAAAATT
Found at i:49640305 original size:22 final size:20
Alignment explanation
Indices: 49640288--49640325 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
49640278 TTAAATTTAT
49640288 ATTATAAA-AAATAAAAATA
1 ATTATAAATAAATAAAAATA
49640307 ATTATAAATTAAATAAAAA
1 ATTATAAA-TAAATAAAAA
49640326 CAAAATTTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 8 0.47
21 9 0.53
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (20 bp):
ATTATAAATAAATAAAAATA
Found at i:49648336 original size:17 final size:17
Alignment explanation
Indices: 49648324--49648359 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 17
49648314 AGAGAAGGAA
49648324 AGAAAGAAAAGAAAAAG
1 AGAAAGAAAAGAAAAAG
49648341 AGAAAGAAAGGAGAAAAAG
1 AGAAAGAAA--AGAAAAAG
49648360 TTAGGGTTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 9 0.53
19 8 0.47
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (17 bp):
AGAAAGAAAAGAAAAAG
Found at i:49649272 original size:41 final size:39
Alignment explanation
Indices: 49649227--49649329 Score: 129
Period size: 37 Copynumber: 2.6 Consensus size: 39
49649217 ACTTCAAGTT
**
49649227 GATGAGACACTGGGTGTCAATTTACTACTTCGGATTAATTC
1 GATGAGACACTGGGTGTCAATTTA-TACTTCGG-TTAAGCC
* * *
49649268 GATGAGGCACTGGGTGCCAA-TT-TACTTCGGTTTAGCC
1 GATGAGACACTGGGTGTCAATTTATACTTCGGTTAAGCC
49649305 GATGAGACACTGGGTGTCAATTTAT
1 GATGAGACACTGGGTGTCAATTTAT
49649330 TTCTTCAAAT
Statistics
Matches: 53, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
37 22 0.42
38 10 0.19
39 1 0.02
40 2 0.04
41 18 0.34
ACGTcount: A:0.24, C:0.17, G:0.26, T:0.32
Consensus pattern (39 bp):
GATGAGACACTGGGTGTCAATTTATACTTCGGTTAAGCC
Found at i:49649550 original size:21 final size:22
Alignment explanation
Indices: 49649519--49649567 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
49649509 GTGAAAAGCT
49649519 ATTTG-AATAGCAAAT-ATGAG
1 ATTTGAAATAGCAAATGATGAG
*
49649539 ATTTGAAATAGCAAGTGATGAG
1 ATTTGAAATAGCAAATGATGAG
*
49649561 AATTGAA
1 ATTTGAA
49649568 TATGTTATGA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 5 0.20
21 9 0.36
22 11 0.44
ACGTcount: A:0.45, C:0.04, G:0.22, T:0.29
Consensus pattern (22 bp):
ATTTGAAATAGCAAATGATGAG
Found at i:49649569 original size:21 final size:20
Alignment explanation
Indices: 49649521--49649569 Score: 62
Period size: 21 Copynumber: 2.4 Consensus size: 20
49649511 GAAAAGCTAT
*
49649521 TTGAATAGCAAATATGAGAT
1 TTGAATAGCAAATATGAGAA
*
49649541 TTGAAATAGCAAGTGATGAGAA
1 TTG-AATAGCAAAT-ATGAGAA
49649563 TTGAATA
1 TTGAATA
49649570 TGTTATGAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 3 0.12
21 13 0.52
22 9 0.36
ACGTcount: A:0.45, C:0.04, G:0.22, T:0.29
Consensus pattern (20 bp):
TTGAATAGCAAATATGAGAA
Found at i:49650999 original size:19 final size:20
Alignment explanation
Indices: 49650975--49651012 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
49650965 GTACGTCCCT
49650975 ATTTTTTT-GAAAAATTTTG
1 ATTTTTTTGGAAAAATTTTG
49650994 ATTTTTTTGGAAAAATTTT
1 ATTTTTTTGGAAAAATTTT
49651013 CTAAGTACCC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.58
Consensus pattern (20 bp):
ATTTTTTTGGAAAAATTTTG
Found at i:49653466 original size:30 final size:30
Alignment explanation
Indices: 49653432--49653492 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
49653422 CACATTAAGA
*
49653432 CCATATATAATCACATCAAAATATGTCTTT
1 CCATATATAATCACATCAAAATATATCTTT
49653462 CCATATATAATCACATCAAAATATATCTTT
1 CCATATATAATCACATCAAAATATATCTTT
49653492 C
1 C
49653493 ACAAGTCATT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.41, C:0.21, G:0.02, T:0.36
Consensus pattern (30 bp):
CCATATATAATCACATCAAAATATATCTTT
Found at i:49654110 original size:25 final size:25
Alignment explanation
Indices: 49654074--49654121 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
49654064 AAGCTCTTTC
49654074 GAGCCATATAACGGAAAACTTATGT
1 GAGCCATATAACGGAAAACTTATGT
* * *
49654099 GAGCCATGTAACGGGAAGCTTAT
1 GAGCCATATAACGGAAAACTTAT
49654122 CCAGGCTGTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.35, C:0.17, G:0.25, T:0.23
Consensus pattern (25 bp):
GAGCCATATAACGGAAAACTTATGT
Found at i:49654228 original size:25 final size:25
Alignment explanation
Indices: 49654188--49654239 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 25
49654178 AATATCAGGT
49654188 AGCTTCGAAGAACCATAAATCGGGA
1 AGCTTCGAAGAACCATAAATCGGGA
* * * *
49654213 AGCTTCGAATAGCCATATATTGGGA
1 AGCTTCGAAGAACCATAAATCGGGA
49654238 AG
1 AG
49654240 TTCAAGCGAG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.37, C:0.17, G:0.25, T:0.21
Consensus pattern (25 bp):
AGCTTCGAAGAACCATAAATCGGGA
Found at i:49654371 original size:24 final size:25
Alignment explanation
Indices: 49654338--49654404 Score: 66
Period size: 25 Copynumber: 2.7 Consensus size: 25
49654328 CACAACCAAT
*
49654338 CGGGATGCTCTGAAGAGCTA-CTAA
1 CGGGAAGCTCTGAAGAGCTATCTAA
** * *
49654362 CGGGAAGCTCACAAGAACTATTTAA
1 CGGGAAGCTCTGAAGAGCTATCTAA
49654387 CGGGAAGCTCATG-AGAGC
1 CGGGAAGCTC-TGAAGAGC
49654405 CAATATCGGG
Statistics
Matches: 33, Mismatches: 8, Indels: 3
0.75 0.18 0.07
Matches are distributed among these distances:
24 16 0.48
25 17 0.52
ACGTcount: A:0.33, C:0.21, G:0.28, T:0.18
Consensus pattern (25 bp):
CGGGAAGCTCTGAAGAGCTATCTAA
Found at i:49665510 original size:43 final size:43
Alignment explanation
Indices: 49665426--49665545 Score: 145
Period size: 43 Copynumber: 2.8 Consensus size: 43
49665416 TCGTACAATT
* * * * *
49665426 CCAACGTCCTAGACGTGGTCTTACATGTAATCAC-AGATCGATG
1 CCAATGTCCCAGACGTGGTCTTACACGAAAACACAAG-TCGATG
*
49665469 CCACTGTCCCAGACAG-GGTCTTACACGAAAACACAAGTCGATG
1 CCAATGTCCCAGAC-GTGGTCTTACACGAAAACACAAGTCGATG
*
49665512 CCAATGTCCCAGACGTGGTCTTACATGAAAACAC
1 CCAATGTCCCAGACGTGGTCTTACACGAAAACAC
49665546 TTTTCGAAAA
Statistics
Matches: 66, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
42 1 0.02
43 62 0.94
44 3 0.05
ACGTcount: A:0.31, C:0.28, G:0.20, T:0.21
Consensus pattern (43 bp):
CCAATGTCCCAGACGTGGTCTTACACGAAAACACAAGTCGATG
Found at i:49667912 original size:25 final size:25
Alignment explanation
Indices: 49667884--49667973 Score: 69
Period size: 25 Copynumber: 3.6 Consensus size: 25
49667874 ATATAACGAA
49667884 AAGCTCATGTGAGCCATGTAATGGG
1 AAGCTCATGTGAGCCATGTAATGGG
* * ** *
49667909 AAGCTTAT-TCGGGCTGTATAATGGG
1 AAGCTCATGT-GAGCCATGTAATGGG
* * *
49667934 AAGCTCA-GAAGAGCCATGT-TTAGG
1 AAGCTCATG-TGAGCCATGTAATGGG
49667958 AAGCTCATGTGAGCCA
1 AAGCTCATGTGAGCCA
49667974 ATATCGGGTA
Statistics
Matches: 47, Mismatches: 14, Indels: 9
0.67 0.20 0.13
Matches are distributed among these distances:
24 17 0.36
25 30 0.64
ACGTcount: A:0.29, C:0.17, G:0.30, T:0.24
Consensus pattern (25 bp):
AAGCTCATGTGAGCCATGTAATGGG
Found at i:49676244 original size:43 final size:43
Alignment explanation
Indices: 49676175--49676452 Score: 198
Period size: 43 Copynumber: 6.4 Consensus size: 43
49676165 CTAGCATCAT
* * * * *
49676175 AATGCATCATCAGATAAAACCGAAACAATTATACTAGCACACAC
1 AATGCATCATCGGAT-AAATCAAAACAACTATACTGGCACACAC
* * ** * *
49676219 AATGCATCATCGGATATATCAAAACAATTATACTATCACAAAA
1 AATGCATCATCGGATAAATCAAAACAACTATACTGGCACACAC
* * * * *
49676262 AATGCATCTTCTGATAAATCAAAGCAACTATGCTGGCACATAC
1 AATGCATCATCGGATAAATCAAAACAACTATACTGGCACACAC
* * * * ** * * * *
49676305 AGTGCATCACCAGATATATCGGAATAATTATATTGGCATACAC
1 AATGCATCATCGGATAAATCAAAACAACTATACTGGCACACAC
* * *
49676348 AATGCATCATCGGATAAACCAAAGCAACTATA-TTGCACACAC
1 AATGCATCATCGGATAAATCAAAACAACTATACTGGCACACAC
* * ** * *
49676390 AGTGCGTCATCAAATAAATCAAAGCAACTATATTGGCATACACAC
1 AATGCATCATCGGATAAATCAAAACAACTATACTGGC--ACACAC
*
49676435 AATGTATCATCGGATAAA
1 AATGCATCATCGGATAAA
49676453 CCGAACCCCT
Statistics
Matches: 177, Mismatches: 54, Indels: 5
0.75 0.23 0.02
Matches are distributed among these distances:
42 35 0.20
43 109 0.62
44 14 0.08
45 19 0.11
ACGTcount: A:0.43, C:0.22, G:0.12, T:0.23
Consensus pattern (43 bp):
AATGCATCATCGGATAAATCAAAACAACTATACTGGCACACAC
Found at i:49676431 original size:85 final size:87
Alignment explanation
Indices: 49676262--49676454 Score: 221
Period size: 85 Copynumber: 2.2 Consensus size: 87
49676252 TATCACAAAA
* * * * * * * *
49676262 AATGCATCTTCTGATAAATCAAAGCAACTATGCTGGCACATACAGTGCATCACCAGATATATCGG
1 AATGCATCATCGGATAAACCAAAGCAACTATGATGGCACACACAGTGCATCACCAAATAAATCGA
* *
49676327 AATAATTATATTGGCAT-ACAC
66 AACAACTATATTGGCATAACAC
* * *
49676348 AATGCATCATCGGATAAACCAAAGCAACTAT-ATTGCACACACAGTGCGTCATCAAATAAATC-A
1 AATGCATCATCGGATAAACCAAAGCAACTATGATGGCACACACAGTGCATCACCAAATAAATCGA
49676411 AAGCAACTATATTGGCATACACAC
66 AA-CAACTATATTGGCATA-ACAC
*
49676435 AATGTATCATCGGATAAACC
1 AATGCATCATCGGATAAACC
49676455 GAACCCCTTA
Statistics
Matches: 90, Mismatches: 14, Indels: 5
0.83 0.13 0.05
Matches are distributed among these distances:
84 2 0.02
85 37 0.41
86 28 0.31
87 23 0.26
ACGTcount: A:0.40, C:0.22, G:0.14, T:0.24
Consensus pattern (87 bp):
AATGCATCATCGGATAAACCAAAGCAACTATGATGGCACACACAGTGCATCACCAAATAAATCGA
AACAACTATATTGGCATAACAC
Found at i:49676452 original size:45 final size:45
Alignment explanation
Indices: 49676333--49676454 Score: 155
Period size: 42 Copynumber: 2.8 Consensus size: 45
49676323 TCGGAATAAT
49676333 TATATTGGCAT--ACACAATGCATCATCGGATAAACCAAAGCAAC
1 TATATTGGCATACACACAATGCATCATCGGATAAACCAAAGCAAC
* * ** *
49676376 TATATT-GC--ACACACAGTGCGTCATCAAATAAATCAAAGCAAC
1 TATATTGGCATACACACAATGCATCATCGGATAAACCAAAGCAAC
*
49676418 TATATTGGCATACACACAATGTATCATCGGATAAACC
1 TATATTGGCATACACACAATGCATCATCGGATAAACC
49676455 GAACCCCTTA
Statistics
Matches: 63, Mismatches: 11, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
42 35 0.56
43 8 0.13
45 20 0.32
ACGTcount: A:0.41, C:0.23, G:0.13, T:0.23
Consensus pattern (45 bp):
TATATTGGCATACACACAATGCATCATCGGATAAACCAAAGCAAC
Found at i:49676510 original size:47 final size:47
Alignment explanation
Indices: 49676454--49676743 Score: 307
Period size: 47 Copynumber: 6.2 Consensus size: 47
49676444 TCGGATAAAC
* * *
49676454 CGAACCCCTTAGTGAATATTTTTGCAAACCCCCTTAGTGAATGTTATG
1 CGAACCCCTCAGTGAATATTTATGCGAA-CCCCTTAGTGAATGTTATG
* * *
49676502 C-AACCCCTTAATGAATATTTATGCGAACCCCTCAGTGAATGTTATG
1 CGAACCCCTCAGTGAATATTTATGCGAACCCCTTAGTGAATGTTATG
49676548 CGAACCCCTCAGTGAATATTTATGCGAACCCCTTAGTGAATGTTATG
1 CGAACCCCTCAGTGAATATTTATGCGAACCCCTTAGTGAATGTTATG
* * * * * *
49676595 CGAACCCCTCAGTGAATATTCATGTGAACCACTTAATGAATATTTGTG
1 CGAACCCCTCAGTGAATATTTATGCGAACCCCTTAGTGAAT-GTTATG
* * * * * * * *
49676643 CGAACCCCTTAGTAAATGTTGA-GTGAACCTCTTAATGAATGTTGTG
1 CGAACCCCTCAGTGAATATTTATGCGAACCCCTTAGTGAATGTTATG
* * * * * *
49676689 TGAACCTCTTAGTGAAT-GTTATGCGAACCCCTTAGTGAACGATATG
1 CGAACCCCTCAGTGAATATTTATGCGAACCCCTTAGTGAATGTTATG
49676735 CGAACCCCT
1 CGAACCCCT
49676744 TTTATAAACT
Statistics
Matches: 207, Mismatches: 32, Indels: 8
0.84 0.13 0.03
Matches are distributed among these distances:
45 2 0.01
46 63 0.30
47 119 0.57
48 23 0.11
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.31
Consensus pattern (47 bp):
CGAACCCCTCAGTGAATATTTATGCGAACCCCTTAGTGAATGTTATG
Found at i:49676523 original size:23 final size:24
Alignment explanation
Indices: 49676454--49676744 Score: 267
Period size: 23 Copynumber: 12.4 Consensus size: 24
49676444 TCGGATAAAC
*
49676454 CGAACCCCTTAGTGAATATTTTTG
1 CGAACCCCTTAGTGAATATTTATG
* *
49676478 CAAACCCCCTTAGTGAAT-GTTATG
1 CGAA-CCCCTTAGTGAATATTTATG
*
49676502 C-AACCCCTTAATGAATATTTATG
1 CGAACCCCTTAGTGAATATTTATG
* *
49676525 CGAACCCCTCAGTGAAT-GTTATG
1 CGAACCCCTTAGTGAATATTTATG
*
49676548 CGAACCCCTCAGTGAATATTTATG
1 CGAACCCCTTAGTGAATATTTATG
*
49676572 CGAACCCCTTAGTGAAT-GTTATG
1 CGAACCCCTTAGTGAATATTTATG
* *
49676595 CGAACCCCTCAGTGAATATTCATG
1 CGAACCCCTTAGTGAATATTTATG
* * * *
49676619 TGAACCACTTAATGAATATTTGTG
1 CGAACCCCTTAGTGAATATTTATG
* * *
49676643 CGAACCCCTTAGTAAATGTTGA-G
1 CGAACCCCTTAGTGAATATTTATG
* * * * *
49676666 TGAACCTCTTAATGAAT-GTTGTG
1 CGAACCCCTTAGTGAATATTTATG
* * *
49676689 TGAACCTCTTAGTGAAT-GTTATG
1 CGAACCCCTTAGTGAATATTTATG
*
49676712 CGAACCCCTTAGTGAACGA--TATG
1 CGAACCCCTTAGTGAA-TATTTATG
49676735 CGAACCCCTT
1 CGAACCCCTT
49676745 TTATAAACTG
Statistics
Matches: 220, Mismatches: 39, Indels: 17
0.80 0.14 0.06
Matches are distributed among these distances:
22 13 0.06
23 115 0.52
24 79 0.36
25 13 0.06
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.31
Consensus pattern (24 bp):
CGAACCCCTTAGTGAATATTTATG
Done.