Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr09 ID=Chr09-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 70713020
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1142373 characters in sequence are not A, C, G, or T
File 173 of 226
Found at i:55300289 original size:25 final size:25
Alignment explanation
Indices: 55300212--55300289 Score: 79
Period size: 25 Copynumber: 3.1 Consensus size: 25
55300202 TCATTAGGGT
* *
55300212 TACCGATTC-TCAGCTCGTATGAGCT
1 TACCGATTCAT-AGCTCGTATAAGCA
* * *
55300237 TACCGATTTACAGCTCGTGA-AAGTA
1 TACCGATTCATAGCTCGT-ATAAGCA
55300262 TACCGATTCATAGCTCGTATAAGCA
1 TACCGATTCATAGCTCGTATAAGCA
55300287 TAC
1 TAC
55300290 ATGTATAGGA
Statistics
Matches: 42, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
24 1 0.02
25 40 0.95
26 1 0.02
ACGTcount: A:0.28, C:0.24, G:0.18, T:0.29
Consensus pattern (25 bp):
TACCGATTCATAGCTCGTATAAGCA
Found at i:55300477 original size:30 final size:29
Alignment explanation
Indices: 55300425--55300499 Score: 71
Period size: 31 Copynumber: 2.4 Consensus size: 29
55300415 TATTATTGGT
* * *
55300425 ATGTATATGAAATATATGGAAAT-GATGTTAT
1 ATGTATATG-AA-ACAT-GAAATGGATGATAC
55300456 ATGATATATTGAAACATGAAATGGATGATAC
1 ATG-TATA-TGAAACATGAAATGGATGATAC
55300487 ATGTATATGAAAC
1 ATGTATATGAAAC
55300500 TTGCTTAATT
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
29 6 0.16
30 9 0.24
31 15 0.39
32 6 0.16
33 2 0.05
ACGTcount: A:0.44, C:0.04, G:0.19, T:0.33
Consensus pattern (29 bp):
ATGTATATGAAACATGAAATGGATGATAC
Found at i:55305020 original size:30 final size:31
Alignment explanation
Indices: 55304981--55305038 Score: 91
Period size: 30 Copynumber: 1.9 Consensus size: 31
55304971 AAATTGGTAA
55304981 TTTTCCTTACCTCTCTTTAATTATGGATAAG
1 TTTTCCTTACCTCTCTTTAATTATGGATAAG
* *
55305012 TTTT-CTTACCTCTTTTTACTTATGGAT
1 TTTTCCTTACCTCTCTTTAATTATGGAT
55305039 GAAAGAAAGG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.19, C:0.19, G:0.09, T:0.53
Consensus pattern (31 bp):
TTTTCCTTACCTCTCTTTAATTATGGATAAG
Found at i:55307923 original size:50 final size:50
Alignment explanation
Indices: 55307819--55308013 Score: 211
Period size: 49 Copynumber: 3.9 Consensus size: 50
55307809 TCATTGATGT
* * * *
55307819 TATGAGAGGTCCCATGTATGACCATGT-TGGGACATGGCGTTGGCACCGA
1 TATGAGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGA
* * *
55307868 GATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCATCGA
1 TATGAGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGA
* * *
55307918 TATGAGA-ATTCCCATGTAAGACCATATCTGGGATATGACATTGGCAGTAC-A
1 TATGAGAGA-TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-T-CGA
* * *
55307969 -A-GAAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCAT
1 TATGAGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCAT
55308014 GTTATTATCA
Statistics
Matches: 125, Mismatches: 16, Indels: 11
0.82 0.11 0.07
Matches are distributed among these distances:
48 1 0.01
49 61 0.49
50 60 0.48
51 2 0.02
52 1 0.01
ACGTcount: A:0.28, C:0.20, G:0.28, T:0.24
Consensus pattern (50 bp):
TATGAGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGA
Found at i:55317309 original size:26 final size:26
Alignment explanation
Indices: 55317280--55317331 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
55317270 GGGAGTAAGT
55317280 CAATAATTCTATCAATATTCATAAAC
1 CAATAATTCTATCAATATTCATAAAC
55317306 CAATAATTCTATCAATATTCATAAAC
1 CAATAATTCTATCAATATTCATAAAC
55317332 AACTGAAGCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.46, C:0.19, G:0.00, T:0.35
Consensus pattern (26 bp):
CAATAATTCTATCAATATTCATAAAC
Found at i:55334710 original size:25 final size:26
Alignment explanation
Indices: 55334681--55334736 Score: 73
Period size: 25 Copynumber: 2.2 Consensus size: 26
55334671 TTTATTAGTA
*
55334681 TAAAATATT-AATAATTCAAT-AAAT
1 TAAAATATTAAATAATTAAATAAAAT
55334705 TGAAAA-ATTAAATAATTAAATAAAAT
1 T-AAAATATTAAATAATTAAATAAAAT
55334731 TAAAAT
1 TAAAAT
55334737 TTAGTAGAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
24 4 0.15
25 18 0.67
26 5 0.19
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (26 bp):
TAAAATATTAAATAATTAAATAAAAT
Found at i:55335377 original size:16 final size:15
Alignment explanation
Indices: 55335352--55335386 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
55335342 AAAGTTGATA
*
55335352 ATAATTAATATATATT
1 ATAATAAATATA-ATT
55335368 ATAATAAATATAATT
1 ATAATAAATATAATT
55335383 ATAA
1 ATAA
55335387 ACTAGTTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 7 0.39
16 11 0.61
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
ATAATAAATATAATT
Found at i:55343112 original size:61 final size:61
Alignment explanation
Indices: 55343038--55343194 Score: 172
Period size: 61 Copynumber: 2.6 Consensus size: 61
55343028 TAACAATAAC
* * * * *
55343038 CTTTGTGGCAAAACTCTGAATATGAAAGCCTTTGTGTTGAGTACTGAGTGTAATGGACAAA
1 CTTTGTGGAAAAACTCTGAACATGAAAGCCTTTGTGGTGAGTACTGAATGTAAAGGACAAA
* * * * * *
55343099 CTTTGTGGAAAAACTTTGGACATGAAAGCTTTTGTGGTGAGTATTGAATTTAAAGGACAAC
1 CTTTGTGGAAAAACTCTGAACATGAAAGCCTTTGTGGTGAGTACTGAATGTAAAGGACAAA
* * *
55343160 CTTTGTGGTAAAACTCTTG-ACAGGAGAGCCTTTGT
1 CTTTGTGGAAAAACTC-TGAACATGAAAGCCTTTGT
55343195 TGTAAAACTC
Statistics
Matches: 79, Mismatches: 16, Indels: 2
0.81 0.16 0.02
Matches are distributed among these distances:
61 77 0.97
62 2 0.03
ACGTcount: A:0.30, C:0.13, G:0.25, T:0.32
Consensus pattern (61 bp):
CTTTGTGGAAAAACTCTGAACATGAAAGCCTTTGTGGTGAGTACTGAATGTAAAGGACAAA
Found at i:55343191 original size:29 final size:29
Alignment explanation
Indices: 55343159--55343225 Score: 98
Period size: 29 Copynumber: 2.3 Consensus size: 29
55343149 TAAAGGACAA
* *
55343159 CCTTTGTGGTAAAACTCTTGACAGGAGAG
1 CCTTTGTGGTAAAACTCTAGACAGGAAAG
* *
55343188 CCTTTGTTGTAAAACTCTAGATAGGAAAG
1 CCTTTGTGGTAAAACTCTAGACAGGAAAG
55343217 CCTTTGTGG
1 CCTTTGTGG
55343226 CAATTATTGA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.27, C:0.16, G:0.25, T:0.31
Consensus pattern (29 bp):
CCTTTGTGGTAAAACTCTAGACAGGAAAG
Found at i:55345801 original size:3 final size:3
Alignment explanation
Indices: 55345793--55345818 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
55345783 TCGTCGATAG
55345793 CAA CAA CAA CAA CAA CAA CAA CAA CA
1 CAA CAA CAA CAA CAA CAA CAA CAA CA
55345819 GTAGATGTAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.35, G:0.00, T:0.00
Consensus pattern (3 bp):
CAA
Found at i:55350947 original size:20 final size:20
Alignment explanation
Indices: 55350922--55350970 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
55350912 TAAGTTATGC
55350922 TAAGTAAATGAAATGGAAAG
1 TAAGTAAATGAAATGGAAAG
* *
55350942 TAAGTAAATGGAATGGTAAG
1 TAAGTAAATGAAATGGAAAG
*
55350962 AAAGTAAAT
1 TAAGTAAAT
55350971 TGAGTGCTTC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.53, C:0.00, G:0.24, T:0.22
Consensus pattern (20 bp):
TAAGTAAATGAAATGGAAAG
Found at i:55367678 original size:46 final size:46
Alignment explanation
Indices: 55367611--55367701 Score: 182
Period size: 46 Copynumber: 2.0 Consensus size: 46
55367601 GAAATTGATG
55367611 TCAAACGGTGTATAAGCATAGGTTATCATTCATTCGAGTAACAATA
1 TCAAACGGTGTATAAGCATAGGTTATCATTCATTCGAGTAACAATA
55367657 TCAAACGGTGTATAAGCATAGGTTATCATTCATTCGAGTAACAAT
1 TCAAACGGTGTATAAGCATAGGTTATCATTCATTCGAGTAACAAT
55367702 CATTAATTTC
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 45 1.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (46 bp):
TCAAACGGTGTATAAGCATAGGTTATCATTCATTCGAGTAACAATA
Found at i:55375430 original size:13 final size:13
Alignment explanation
Indices: 55375412--55375446 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
55375402 CCGTGTGAGG
55375412 CACACGGCCTAAC
1 CACACGGCCTAAC
*
55375425 CACACGGCCTGAC
1 CACACGGCCTAAC
*
55375438 CGCACGGCC
1 CACACGGCC
55375447 GTGTGACCCT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.23, C:0.49, G:0.23, T:0.06
Consensus pattern (13 bp):
CACACGGCCTAAC
Found at i:55378012 original size:28 final size:28
Alignment explanation
Indices: 55377981--55378065 Score: 82
Period size: 28 Copynumber: 3.1 Consensus size: 28
55377971 AGTTCGTCAG
55377981 GATTGTCTTAAATGGGGATGTCCATCAA
1 GATTGTCTTAAATGGGGATGTCCATCAA
* * * * * *
55378009 GATTATCTT-AATGTGAAAGCCCGTCAA
1 GATTGTCTTAAATGGGGATGTCCATCAA
* * *
55378036 GACTGTATTAAATAGGGATGTCCATCAA
1 GATTGTCTTAAATGGGGATGTCCATCAA
55378064 GA
1 GA
55378066 CTATCATATG
Statistics
Matches: 41, Mismatches: 15, Indels: 2
0.71 0.26 0.03
Matches are distributed among these distances:
27 19 0.46
28 22 0.54
ACGTcount: A:0.33, C:0.15, G:0.22, T:0.29
Consensus pattern (28 bp):
GATTGTCTTAAATGGGGATGTCCATCAA
Found at i:55401571 original size:17 final size:17
Alignment explanation
Indices: 55401549--55401586 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
55401539 CTGAAGAGAT
55401549 ATGGAGTTAATCATAGA
1 ATGGAGTTAATCATAGA
55401566 ATGGAGTTAATCATAGA
1 ATGGAGTTAATCATAGA
55401583 ATGG
1 ATGG
55401587 CTACTACTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.39, C:0.05, G:0.26, T:0.29
Consensus pattern (17 bp):
ATGGAGTTAATCATAGA
Found at i:55404051 original size:21 final size:20
Alignment explanation
Indices: 55404000--55404053 Score: 58
Period size: 21 Copynumber: 2.7 Consensus size: 20
55403990 AAGAAAACAC
55404000 TGTTGTTGAG-A-AGGAAGT
1 TGTTGTTGAGAAGAGGAAGT
* *
55404018 TGCTGCTGCAGAAGAGGAAGT
1 TGTTGTTG-AGAAGAGGAAGT
55404039 TGTTGTTGAAGAAGA
1 TGTTGTTG-AGAAGA
55404054 AGTTGTTAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
18 6 0.21
19 2 0.07
20 1 0.04
21 19 0.68
ACGTcount: A:0.30, C:0.06, G:0.37, T:0.28
Consensus pattern (20 bp):
TGTTGTTGAGAAGAGGAAGT
Found at i:55406714 original size:9 final size:9
Alignment explanation
Indices: 55406700--55406730 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
55406690 GTTAAACGAA
55406700 TCGAGTTAT
1 TCGAGTTAT
*
55406709 TCGAGTTAA
1 TCGAGTTAT
55406718 TCGAGTTAT
1 TCGAGTTAT
55406727 TCGA
1 TCGA
55406731 ATCAACTCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:55406803 original size:9 final size:9
Alignment explanation
Indices: 55406784--55406820 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
55406774 TGAATTTTTA
*
55406784 AATTTGAAT
1 AATTCGAAT
*
55406793 AACTCGAAT
1 AATTCGAAT
55406802 AATTCGAAT
1 AATTCGAAT
55406811 AATTCGAAT
1 AATTCGAAT
55406820 A
1 A
55406821 TCAAACTATA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.46, C:0.11, G:0.11, T:0.32
Consensus pattern (9 bp):
AATTCGAAT
Found at i:55407033 original size:30 final size:31
Alignment explanation
Indices: 55406999--55407058 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 31
55406989 AAACCTTTTA
*
55406999 TTTTCTCCC-AAAATTTTTACTCCC-TCCCAC
1 TTTTC-CCCTAAAACTTTTACTCCCTTCCCAC
*
55407029 TTTTCCCCTAAAACTTTTATTCCCTTCCCA
1 TTTTCCCCTAAAACTTTTACTCCCTTCCCA
55407059 TCTCACCTCC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 3 0.12
30 18 0.69
31 5 0.19
ACGTcount: A:0.20, C:0.38, G:0.00, T:0.42
Consensus pattern (31 bp):
TTTTCCCCTAAAACTTTTACTCCCTTCCCAC
Found at i:55407327 original size:9 final size:9
Alignment explanation
Indices: 55407313--55407341 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
55407303 AATTTCACAT
55407313 TTTATATTA
1 TTTATATTA
55407322 TTTATATTA
1 TTTATATTA
55407331 TTTATATTA
1 TTTATATTA
55407340 TT
1 TT
55407342 GAATTGTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (9 bp):
TTTATATTA
Found at i:55410402 original size:20 final size:20
Alignment explanation
Indices: 55410379--55410418 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
55410369 TGTATTAAGC
*
55410379 ATTTTA-AATATTATTTAAAT
1 ATTTTATAATAAT-TTTAAAT
55410399 ATTTTATAATAATTTTAAAT
1 ATTTTATAATAATTTTAAAT
55410419 TAAATATAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
ATTTTATAATAATTTTAAAT
Found at i:55412566 original size:51 final size:51
Alignment explanation
Indices: 55412494--55412639 Score: 168
Period size: 51 Copynumber: 2.9 Consensus size: 51
55412484 TAATGATGTT
* * * *
55412494 CGATTCACATAGTATCCTGCACATAGTACTATACATGTGACCATTACCATC
1 CGATACACATAGTAGCCTGCACATAGTACTACACATGTGACCATAACCATC
* * * * *
55412545 CGATACACGTAGTAGCTTGCACATAGTACTACACACGTGATCGA-AACTATC
1 CGATACACATAGTAGCCTGCACATAGTACTACACATGTGA-CCATAACCATC
* * *
55412596 CGGTACGCATAGTAGCCTGCACATAGTACTACACCTGTGACCAT
1 CGATACACATAGTAGCCTGCACATAGTACTACACATGTGACCAT
55412640 CACTTTCACT
Statistics
Matches: 77, Mismatches: 16, Indels: 4
0.79 0.16 0.04
Matches are distributed among these distances:
50 2 0.03
51 73 0.95
52 2 0.03
ACGTcount: A:0.31, C:0.27, G:0.16, T:0.25
Consensus pattern (51 bp):
CGATACACATAGTAGCCTGCACATAGTACTACACATGTGACCATAACCATC
Found at i:55417006 original size:2 final size:2
Alignment explanation
Indices: 55416999--55417024 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
55416989 TAAGCATTTG
55416999 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
55417025 ACAAAAACGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:55418822 original size:6 final size:6
Alignment explanation
Indices: 55418811--55418835 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
55418801 TCTATTTAGA
55418811 TTAATT TTAATT TTAATT TTAATT T
1 TTAATT TTAATT TTAATT TTAATT T
55418836 GTTTGTGTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (6 bp):
TTAATT
Found at i:55422966 original size:43 final size:43
Alignment explanation
Indices: 55422904--55422991 Score: 131
Period size: 43 Copynumber: 2.0 Consensus size: 43
55422894 CTGAGTTGCC
** **
55422904 GAACGATAAAGATTGAATTTTCCTAAACCATACACGATTAAAG
1 GAACGATAAAGATCAAATTTTCCTAAACCATACAAAATTAAAG
*
55422947 GAACGATAAAGATCAAATTTTTCTAAACCATACAAAATTAAAG
1 GAACGATAAAGATCAAATTTTCCTAAACCATACAAAATTAAAG
55422990 GA
1 GA
55422992 TGATTAGAGA
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
43 40 1.00
ACGTcount: A:0.48, C:0.15, G:0.12, T:0.25
Consensus pattern (43 bp):
GAACGATAAAGATCAAATTTTCCTAAACCATACAAAATTAAAG
Found at i:55424933 original size:29 final size:29
Alignment explanation
Indices: 55424834--55425071 Score: 183
Period size: 29 Copynumber: 8.2 Consensus size: 29
55424824 CTGTATAAGT
** *
55424834 AAGCCTTTGTGGATATCTCTATTATAAGG
1 AAGCCTTTGTGGCGATCTCTATTAAAAGG
* * * *
55424863 AAGTCTTTTTGGTGATCAT-TGTTAAAAGG
1 AAGCCTTTGTGGCGATC-TCTATTAAAAGG
*
55424892 AAGCCTTTGTGGCGATCTCTATTAAATGG
1 AAGCCTTTGTGGCGATCTCTATTAAAAGG
* * * *
55424921 AAGCCTTTGTGGCGTTCTTTGTTAAATGG
1 AAGCCTTTGTGGCGATCTCTATTAAAAGG
* * * *
55424950 ATGCCTTGGTGACGATCTCTGTTAAAAGG
1 AAGCCTTTGTGGCGATCTCTATTAAAAGG
* * * *
55424979 AAGCTTTTGTGGCCATCTCTGTAAAAAAGG
1 AAGCCTTTGTGGCGATCTCTAT-TAAAAGG
* * * * *
55425009 ATGCTTTTATGGCTATCTC-AGTTAAATGG
1 AAGCCTTTGTGGCGATCTCTA-TTAAAAGG
* * *
55425038 ATGTCTTTGTGGCTATCTCTATTAAAAGG
1 AAGCCTTTGTGGCGATCTCTATTAAAAGG
55425067 AAGCC
1 AAGCC
55425072 CTCATAGCGA
Statistics
Matches: 166, Mismatches: 38, Indels: 10
0.78 0.18 0.05
Matches are distributed among these distances:
28 1 0.01
29 140 0.84
30 25 0.15
ACGTcount: A:0.25, C:0.15, G:0.24, T:0.37
Consensus pattern (29 bp):
AAGCCTTTGTGGCGATCTCTATTAAAAGG
Found at i:55424943 original size:58 final size:58
Alignment explanation
Indices: 55424834--55425071 Score: 203
Period size: 58 Copynumber: 4.1 Consensus size: 58
55424824 CTGTATAAGT
** * * *
55424834 AAGCCTTTGTGGATATCTCTATTATAA-GGAAGTCTTTTTGGTGATCAT-TGTTAAAAGG
1 AAGCCTTTGTGGCGATCTCTATTA-AATGGAAGCCTTTGTGGCGATC-TCTGTTAAAAGG
* * *
55424892 AAGCCTTTGTGGCGATCTCTATTAAATGGAAGCCTTTGTGGCGTTCTTTGTTAAATGG
1 AAGCCTTTGTGGCGATCTCTATTAAATGGAAGCCTTTGTGGCGATCTCTGTTAAAAGG
* * * * * * * *
55424950 ATGCCTTGGTGACGATCTCTGTTAAAAGGAAGCTTTTGTGGCCATCTCTGTAAAAAAGG
1 AAGCCTTTGTGGCGATCTCTATTAAATGGAAGCCTTTGTGGCGATCTCTGT-TAAAAGG
* * * * * * * *
55425009 ATGCTTTTATGGCTATCTC-AGTTAAATGGATGTCTTTGTGGCTATCTCTATTAAAAGG
1 AAGCCTTTGTGGCGATCTCTA-TTAAATGGAAGCCTTTGTGGCGATCTCTGTTAAAAGG
55425067 AAGCC
1 AAGCC
55425072 CTCATAGCGA
Statistics
Matches: 143, Mismatches: 33, Indels: 8
0.78 0.18 0.04
Matches are distributed among these distances:
57 3 0.02
58 97 0.68
59 43 0.30
ACGTcount: A:0.25, C:0.15, G:0.24, T:0.37
Consensus pattern (58 bp):
AAGCCTTTGTGGCGATCTCTATTAAATGGAAGCCTTTGTGGCGATCTCTGTTAAAAGG
Found at i:55425009 original size:30 final size:29
Alignment explanation
Indices: 55424964--55425027 Score: 83
Period size: 30 Copynumber: 2.2 Consensus size: 29
55424954 CTTGGTGACG
* *
55424964 ATCTCTGTTAAAAGGAAGCTTTTGTGGCC
1 ATCTCTGTAAAAAGGAAGCTTTTATGGCC
* *
55424993 ATCTCTGTAAAAAAGGATGCTTTTATGGCT
1 ATCTCTGT-AAAAAGGAAGCTTTTATGGCC
55425023 ATCTC
1 ATCTC
55425028 AGTTAAATGG
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
29 8 0.27
30 22 0.73
ACGTcount: A:0.27, C:0.17, G:0.20, T:0.36
Consensus pattern (29 bp):
ATCTCTGTAAAAAGGAAGCTTTTATGGCC
Found at i:55425068 original size:88 final size:87
Alignment explanation
Indices: 55424884--55425071 Score: 216
Period size: 88 Copynumber: 2.1 Consensus size: 87
55424874 GTGATCATTG
* * * * **
55424884 TTAAAAGGAAGCCTTTGTGGCGATCTCTATTAAATGGAAGCCTTTGTGGCGTTCTTTGTTAAATG
1 TTAAAAGGAAGCCTTTGTGGCCATCTCTATAAAAAGGAAGCCTTTATGGCGTTCTCAGTTAAATG
*
55424949 GATGCCTTGGTGACGATCTCTG
66 GATGCCTTGGTGACGATCTCTA
* * * *
55424971 TTAAAAGGAAGCTTTTGTGGCCATCTCTGTAAAAAAGGATGCTTTTATGGC-TATCTCAGTTAAA
1 TTAAAAGGAAGCCTTTGTGGCCATCTCTAT-AAAAAGGAAGCCTTTATGGCGT-TCTCAGTTAAA
* * * *
55425035 TGGATGTCTTTGTGGCTATCTCTA
64 TGGATGCCTTGGTGACGATCTCTA
55425059 TTAAAAGGAAGCC
1 TTAAAAGGAAGCC
55425072 CTCATAGCGA
Statistics
Matches: 83, Mismatches: 16, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
87 28 0.34
88 55 0.66
ACGTcount: A:0.26, C:0.15, G:0.24, T:0.35
Consensus pattern (87 bp):
TTAAAAGGAAGCCTTTGTGGCCATCTCTATAAAAAGGAAGCCTTTATGGCGTTCTCAGTTAAATG
GATGCCTTGGTGACGATCTCTA
Found at i:55426107 original size:41 final size:41
Alignment explanation
Indices: 55425951--55426099 Score: 280
Period size: 41 Copynumber: 3.6 Consensus size: 41
55425941 AAGTCTAATC
*
55425951 CAGTTCACTGGCACTTAGCCTGCTAGGCTTATAGCCTGATT
1 CAGTTCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATT
55425992 CAGTTCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATT
1 CAGTTCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATT
*
55426033 CAATTCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATT
1 CAGTTCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATT
55426074 CAGTTCACCGGCACTTAGCCTGCTAG
1 CAGTTCACCGGCACTTAGCCTGCTAG
55426100 ACATATAGTC
Statistics
Matches: 105, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 105 1.00
ACGTcount: A:0.20, C:0.30, G:0.21, T:0.29
Consensus pattern (41 bp):
CAGTTCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATT
Found at i:55426122 original size:41 final size:41
Alignment explanation
Indices: 55425952--55426127 Score: 255
Period size: 41 Copynumber: 4.3 Consensus size: 41
55425942 AGTCTAATCC
* *
55425952 AGTTCACTGGCACTTAGCCTGCTAGGCTTATAGCCTGATTC
1 AGTTCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTA
55425993 AGTTCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCA
1 AGTTCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATT-A
*
55426035 A-TTCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTC
1 AGTTCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTA
* * * *
55426075 AGTTCACCGGCACTTAGCCTGCTAGACATATAGTCTGAATA
1 AGTTCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTA
* *
55426116 ATTTCACTGGCA
1 AGTTCACCGGCA
55426128 ATAAATCCGA
Statistics
Matches: 123, Mismatches: 10, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
40 1 0.01
41 121 0.98
42 1 0.01
ACGTcount: A:0.23, C:0.27, G:0.20, T:0.30
Consensus pattern (41 bp):
AGTTCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTA
Found at i:55426122 original size:82 final size:82
Alignment explanation
Indices: 55425954--55426127 Score: 287
Period size: 82 Copynumber: 2.1 Consensus size: 82
55425944 TCTAATCCAG
*
55425954 TTCACTGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGTTCACCGGCACTTAGCCTGCTAGG
1 TTCACTGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGTTCACCGGCACTTAGCCTGCTAGA
* *
55426019 CTTATAGCCTGATTCAA
66 CATATAGCCTGAATCAA
*
55426036 TTCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGTTCACCGGCACTTAGCCTGCTAGA
1 TTCACTGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGTTCACCGGCACTTAGCCTGCTAGA
*
55426101 CATATAGTCTGAAT-AA
66 CATATAGCCTGAATCAA
55426117 TTTCACTGGCA
1 -TTCACTGGCA
55426128 ATAAATCCGA
Statistics
Matches: 85, Mismatches: 6, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
81 2 0.02
82 83 0.98
ACGTcount: A:0.22, C:0.28, G:0.20, T:0.30
Consensus pattern (82 bp):
TTCACTGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGTTCACCGGCACTTAGCCTGCTAGA
CATATAGCCTGAATCAA
Found at i:55427561 original size:13 final size:13
Alignment explanation
Indices: 55427543--55427567 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
55427533 ACCAACGATA
55427543 AAATTTTCACACG
1 AAATTTTCACACG
55427556 AAATTTTCACAC
1 AAATTTTCACAC
55427568 ATATAAATTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.24, G:0.04, T:0.32
Consensus pattern (13 bp):
AAATTTTCACACG
Found at i:55428733 original size:30 final size:30
Alignment explanation
Indices: 55428674--55428734 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
55428664 TTGTTTTCAG
* * *
55428674 GAGCCACACGGCCTGGGCACATGCTCATGT
1 GAGCCACACGGCCTGGACACACGCCCATGT
**
55428704 GAGCCACACGGGTTGGACACACGCCCATGT
1 GAGCCACACGGCCTGGACACACGCCCATGT
55428734 G
1 G
55428735 CCAGCCCATG
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.21, C:0.33, G:0.31, T:0.15
Consensus pattern (30 bp):
GAGCCACACGGCCTGGACACACGCCCATGT
Found at i:55429771 original size:18 final size:18
Alignment explanation
Indices: 55429750--55429792 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
55429740 TAATTTGGCC
55429750 ATTTTTATTTTTA-TTATA
1 ATTTTTATTTTTAGTT-TA
*
55429768 ATTTTTGTTTTTAGTTTA
1 ATTTTTATTTTTAGTTTA
55429786 ATTTTTA
1 ATTTTTA
55429793 CATTCCAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 20 0.91
19 2 0.09
ACGTcount: A:0.23, C:0.00, G:0.05, T:0.72
Consensus pattern (18 bp):
ATTTTTATTTTTAGTTTA
Found at i:55431448 original size:21 final size:21
Alignment explanation
Indices: 55431422--55431461 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
55431412 CACATGAACG
*
55431422 AACAATTTTGTAAAATTCTCA
1 AACAATTTGGTAAAATTCTCA
55431443 AACAATTTGGTAAAATTCT
1 AACAATTTGGTAAAATTCT
55431462 TAAGCTCTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.42, C:0.12, G:0.07, T:0.38
Consensus pattern (21 bp):
AACAATTTGGTAAAATTCTCA
Found at i:55433016 original size:20 final size:20
Alignment explanation
Indices: 55432993--55433067 Score: 96
Period size: 20 Copynumber: 3.8 Consensus size: 20
55432983 CCGCACGAGT
* *
55432993 GTGTAGGCTCTCACACGGGC
1 GTGTGGGCTCTCACACGGGA
** *
55433013 GTGTGGGCTCTCACTTGGGT
1 GTGTGGGCTCTCACACGGGA
*
55433033 GTGTGGGCTCTCACTCGGGA
1 GTGTGGGCTCTCACACGGGA
55433053 GTGTGGGCTCTCACA
1 GTGTGGGCTCTCACA
55433068 TAGGCGTGGG
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.11, C:0.25, G:0.37, T:0.27
Consensus pattern (20 bp):
GTGTGGGCTCTCACACGGGA
Found at i:55433046 original size:40 final size:40
Alignment explanation
Indices: 55432991--55433066 Score: 125
Period size: 40 Copynumber: 1.9 Consensus size: 40
55432981 AGCCGCACGA
*
55432991 GTGTGTAGGCTCTCACACGGGCGTGTGGGCTCTCACTTGG
1 GTGTGTAGGCTCTCACACGGGAGTGTGGGCTCTCACTTGG
* *
55433031 GTGTGTGGGCTCTCACTCGGGAGTGTGGGCTCTCAC
1 GTGTGTAGGCTCTCACACGGGAGTGTGGGCTCTCAC
55433067 ATAGGCGTGG
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 33 1.00
ACGTcount: A:0.09, C:0.25, G:0.38, T:0.28
Consensus pattern (40 bp):
GTGTGTAGGCTCTCACACGGGAGTGTGGGCTCTCACTTGG
Found at i:55433744 original size:22 final size:22
Alignment explanation
Indices: 55433713--55433795 Score: 73
Period size: 22 Copynumber: 3.8 Consensus size: 22
55433703 TGCCCATTCC
55433713 TTTATT-TTATTTTATTATTTA
1 TTTATTATTATTTTATTATTTA
*
55433734 TTTATTATTA-TTTGTTATATTA
1 TTTATTATTATTTTATTAT-TTA
* *
55433756 TTTTTTATCTATTTTCTTATTT-
1 TTTATTAT-TATTTTATTATTTA
* *
55433778 TTTCTTATTTGTTTTATT
1 TTTATTA-TTATTTTATT
55433796 TTTCTTATGC
Statistics
Matches: 51, Mismatches: 6, Indels: 9
0.77 0.09 0.14
Matches are distributed among these distances:
21 13 0.25
22 26 0.51
23 5 0.10
24 7 0.14
ACGTcount: A:0.19, C:0.04, G:0.02, T:0.75
Consensus pattern (22 bp):
TTTATTATTATTTTATTATTTA
Found at i:55433775 original size:19 final size:19
Alignment explanation
Indices: 55433753--55433798 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
55433743 ATTTGTTATA
55433753 TTATTTTTTATCTATTT-TC
1 TTATTTTTTAT-TATTTGTC
* *
55433772 TTATTTTTTCTTATTTGTT
1 TTATTTTTTATTATTTGTC
55433791 TTATTTTT
1 TTATTTTT
55433799 CTTATGCTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 5 0.21
19 19 0.79
ACGTcount: A:0.13, C:0.07, G:0.02, T:0.78
Consensus pattern (19 bp):
TTATTTTTTATTATTTGTC
Found at i:55433776 original size:34 final size:34
Alignment explanation
Indices: 55433714--55433795 Score: 87
Period size: 34 Copynumber: 2.4 Consensus size: 34
55433704 GCCCATTCCT
* * *
55433714 TTATTTTATTTTATTATTTATTTATTATTATTTG
1 TTATATTATTTTATTATCTATTTATTATTATTTC
* *
55433748 TTATATTATTTT-TTATCTATTTTCTTATTTTTTC
1 TTATATTATTTTATTATCTA-TTTATTATTATTTC
*
55433782 TTAT-TTGTTTTATT
1 TTATATTATTTTATT
55433796 TTTCTTATGC
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
33 12 0.30
34 28 0.70
ACGTcount: A:0.20, C:0.04, G:0.02, T:0.74
Consensus pattern (34 bp):
TTATATTATTTTATTATCTATTTATTATTATTTC
Found at i:55433786 original size:18 final size:19
Alignment explanation
Indices: 55433753--55433803 Score: 61
Period size: 18 Copynumber: 2.7 Consensus size: 19
55433743 ATTTGTTATA
*
55433753 TTATTTTTTATCTATTT-TC
1 TTATTTTTTCT-TATTTGTC
*
55433772 TTATTTTTTCTTATTTGTT
1 TTATTTTTTCTTATTTGTC
55433791 TTA-TTTTTCTTAT
1 TTATTTTTTCTTAT
55433804 GCTTAGATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
18 15 0.52
19 14 0.48
ACGTcount: A:0.14, C:0.08, G:0.02, T:0.76
Consensus pattern (19 bp):
TTATTTTTTCTTATTTGTC
Found at i:55433853 original size:22 final size:22
Alignment explanation
Indices: 55433828--55433874 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
55433818 TTTTGTTTTA
*
55433828 ATTTATTT-CTATTATTTTTAGT
1 ATTT-TTTACTATTATTTTTACT
*
55433850 ATTTTTTAGTATTATTTTTACT
1 ATTTTTTACTATTATTTTTACT
55433872 ATT
1 ATT
55433875 ACCTTTAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 3 0.14
22 19 0.86
ACGTcount: A:0.23, C:0.04, G:0.04, T:0.68
Consensus pattern (22 bp):
ATTTTTTACTATTATTTTTACT
Found at i:55433867 original size:12 final size:12
Alignment explanation
Indices: 55433837--55433875 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
55433827 AATTTATTTC
55433837 TATTATTTTTAG
1 TATTATTTTTAG
55433849 TA-T-TTTTTAG
1 TATTATTTTTAG
*
55433859 TATTATTTTTAC
1 TATTATTTTTAG
55433871 TATTA
1 TATTA
55433876 CCTTTAATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
10 9 0.38
11 2 0.08
12 13 0.54
ACGTcount: A:0.26, C:0.03, G:0.05, T:0.67
Consensus pattern (12 bp):
TATTATTTTTAG
Found at i:55436047 original size:29 final size:28
Alignment explanation
Indices: 55436002--55436098 Score: 97
Period size: 29 Copynumber: 3.4 Consensus size: 28
55435992 TGTATAAGTG
* * *
55436002 AGCCATTGTGGCT-ATCTCTATTATAAGAA
1 AGCCTTTGTGG-TGATCTCTGTTA-AAGGA
*
55436031 AGCCTTTGTGGTGATCTTTGTTAAATGGA
1 AGCCTTTGTGGTGATCTCTGTTAAA-GGA
* *
55436060 AGCCTTGGTGATGATCTCTGTTAAAAGGA
1 AGCCTTTGTGGTGATCTCTGTT-AAAGGA
55436089 AGCCTTTGTG
1 AGCCTTTGTG
55436099 ACCATCTCTG
Statistics
Matches: 57, Mismatches: 8, Indels: 6
0.80 0.11 0.08
Matches are distributed among these distances:
28 3 0.05
29 51 0.89
30 3 0.05
ACGTcount: A:0.25, C:0.14, G:0.25, T:0.36
Consensus pattern (28 bp):
AGCCTTTGTGGTGATCTCTGTTAAAGGA
Found at i:55436099 original size:29 final size:29
Alignment explanation
Indices: 55436015--55436114 Score: 110
Period size: 29 Copynumber: 3.4 Consensus size: 29
55436005 CATTGTGGCT
* * * *
55436015 ATCTCTATTATAAGAAAGCCTTTGTGGTG
1 ATCTCTGTTAAAAGGAAGCCTTTGTGATG
* * *
55436044 ATCTTTGTTAAATGGAAGCCTTGGTGATG
1 ATCTCTGTTAAAAGGAAGCCTTTGTGATG
**
55436073 ATCTCTGTTAAAAGGAAGCCTTTGTGACC
1 ATCTCTGTTAAAAGGAAGCCTTTGTGATG
*
55436102 ATCTCTGTAAAAA
1 ATCTCTGTTAAAA
55436115 AAAGATGCTT
Statistics
Matches: 58, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 58 1.00
ACGTcount: A:0.29, C:0.15, G:0.21, T:0.35
Consensus pattern (29 bp):
ATCTCTGTTAAAAGGAAGCCTTTGTGATG
Found at i:55439241 original size:26 final size:26
Alignment explanation
Indices: 55439200--55439269 Score: 97
Period size: 26 Copynumber: 2.7 Consensus size: 26
55439190 ATATAAGTGA
* * *
55439200 GCCTTTTTGGCAATCTTTGAATGGAT
1 GCCTTTGTGGCTATCTCTGAATGGAT
55439226 G-CTTTGGTGGCTATCTCTGAATGGAT
1 GCCTTT-GTGGCTATCTCTGAATGGAT
55439252 GCCTTTGTGGCTATCTCT
1 GCCTTTGTGGCTATCTCT
55439270 ATTGTAAGGA
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
25 4 0.10
26 31 0.79
27 4 0.10
ACGTcount: A:0.14, C:0.19, G:0.26, T:0.41
Consensus pattern (26 bp):
GCCTTTGTGGCTATCTCTGAATGGAT
Found at i:55439309 original size:29 final size:30
Alignment explanation
Indices: 55439245--55439311 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 30
55439235 GCTATCTCTG
* * *
55439245 AATGGATGCCTTTGTGGCTATCTCTATTGT
1 AATGGAAGCCTTTGTGGCGATCTCTATTGA
*
55439275 AA-GGAAGCCTTTGTGGCGATCTTTATT-A
1 AATGGAAGCCTTTGTGGCGATCTCTATTGA
55439303 AATGGAAGC
1 AATGGAAGC
55439312 TTTTTTCGTG
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
28 2 0.06
29 28 0.88
30 2 0.06
ACGTcount: A:0.24, C:0.15, G:0.25, T:0.36
Consensus pattern (30 bp):
AATGGAAGCCTTTGTGGCGATCTCTATTGA
Found at i:55439398 original size:29 final size:29
Alignment explanation
Indices: 55439219--55439414 Score: 82
Period size: 29 Copynumber: 6.8 Consensus size: 29
55439209 GCAATCTTTG
*
55439219 AATGGATGCTTTGGTGGCTATCTC--TG-
1 AATGGATGCTTTTGTGGCTATCTCAGTGA
* * *
55439245 AATGGATGCCTTTGTGGCTATCTCTATTGT
1 AATGGATGCTTTTGTGGCTATCTC-AGTGA
* * * * *
55439275 AA-GGAAGCCTTTGTGGCGATCTTTA-TTA
1 AATGGATGCTTTTGTGGCTATC-TCAGTGA
* * * * * *
55439303 AATGGAAGCTTTTTTCG-TGACCTCTGTTA
1 AATGGATGCTTTTGTGGCT-ATCTCAGTGA
* * * * * * *
55439332 AAAGTAAGCCTTTGCGGCCATCTCAGTAAA
1 AATGGATGCTTTTGTGGCTATCTCAGT-GA
**
55439362 AAAAGATGCTTTTGTGGCTATCTCAGTGA
1 AATGGATGCTTTTGTGGCTATCTCAGTGA
55439391 AATGGATG-TCTTTGTGGCTATCTC
1 AATGGATGCT-TTTGTGGCTATCTC
55439415 TATTAGAAGG
Statistics
Matches: 126, Mismatches: 33, Indels: 19
0.71 0.19 0.11
Matches are distributed among these distances:
26 22 0.17
28 5 0.04
29 74 0.59
30 25 0.20
ACGTcount: A:0.22, C:0.17, G:0.24, T:0.37
Consensus pattern (29 bp):
AATGGATGCTTTTGTGGCTATCTCAGTGA
Found at i:55441863 original size:22 final size:23
Alignment explanation
Indices: 55441821--55441863 Score: 54
Period size: 22 Copynumber: 1.9 Consensus size: 23
55441811 TTTATTCAAA
*
55441821 ATTATTATTAAATAATATAAAAT
1 ATTATTATTAAAAAATATAAAAT
55441844 ATTA-TATTAATAAAAT-TAAA
1 ATTATTATTAA-AAAATATAAA
55441864 CTTATGAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 10 0.56
23 8 0.44
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (23 bp):
ATTATTATTAAAAAATATAAAAT
Found at i:55442661 original size:18 final size:17
Alignment explanation
Indices: 55442635--55442674 Score: 53
Period size: 18 Copynumber: 2.3 Consensus size: 17
55442625 AATATTTTAA
*
55442635 TATTATAATTATTATATT
1 TATTATAATAATT-TATT
*
55442653 TATTTTAATAATTTATT
1 TATTATAATAATTTATT
55442670 TATTA
1 TATTA
55442675 GTATTATATT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
17 8 0.42
18 11 0.58
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
TATTATAATAATTTATT
Found at i:55442672 original size:26 final size:28
Alignment explanation
Indices: 55442626--55442702 Score: 81
Period size: 26 Copynumber: 2.8 Consensus size: 28
55442616 GCTAGACATA
55442626 ATATTTTAATATTATAATTATTA-TATT
1 ATATTTTAATATTATAATTATTAGTATT
*
55442653 -TATTTTAATAATT-TATTTATTAGTATT
1 ATATTTTAAT-ATTATAATTATTAGTATT
55442680 ATATTAATT-ATAGTTATAATTAT
1 ATATT--TTAATA-TTATAATTAT
55442703 AATTATAGTT
Statistics
Matches: 41, Mismatches: 2, Indels: 11
0.76 0.04 0.20
Matches are distributed among these distances:
26 17 0.41
27 7 0.17
28 5 0.12
29 4 0.10
30 8 0.20
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (28 bp):
ATATTTTAATATTATAATTATTAGTATT
Found at i:55457868 original size:31 final size:31
Alignment explanation
Indices: 55457809--55457877 Score: 88
Period size: 31 Copynumber: 2.2 Consensus size: 31
55457799 AAAAAAAATC
**
55457809 TAGTGACTTAAATAAAATCTTTTGAATAG-T
1 TAGTGACTTAAATAAAATCTTTCAAATAGCT
55457839 TCAGTGACTTAAATGAAAA-CTTTCAAATAGCT
1 T-AGTGACTTAAAT-AAAATCTTTCAAATAGCT
55457871 TAGTGAC
1 TAGTGAC
55457878 CGTTTTGTAA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
30 1 0.03
31 27 0.79
32 6 0.18
ACGTcount: A:0.39, C:0.12, G:0.14, T:0.35
Consensus pattern (31 bp):
TAGTGACTTAAATAAAATCTTTCAAATAGCT
Found at i:55459111 original size:2 final size:2
Alignment explanation
Indices: 55459104--55459132 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
55459094 TACCTGATTG
55459104 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
55459133 TAAAATTTTA
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:55461719 original size:19 final size:18
Alignment explanation
Indices: 55461697--55461735 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
55461687 TGAGGTAGGA
* *
55461697 TATTTTGGTTTATTTTGTT
1 TATTTTGCTTGATTTT-TT
55461716 TATTTTGCTTGATTTTTT
1 TATTTTGCTTGATTTTTT
55461734 TA
1 TA
55461736 GCTTGGTTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.13, C:0.03, G:0.13, T:0.72
Consensus pattern (18 bp):
TATTTTGCTTGATTTTTT
Found at i:55465857 original size:26 final size:26
Alignment explanation
Indices: 55465823--55465875 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
55465813 CAACAAGAAA
*
55465823 TTGAAGATTTTACCCTTGGTAAAATT
1 TTGAAGATTTTACCCCTGGTAAAATT
* * *
55465849 TTGACGATTTTGCCCCTGGTTAAATT
1 TTGAAGATTTTACCCCTGGTAAAATT
55465875 T
1 T
55465876 CGAGAAAATA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.25, C:0.15, G:0.17, T:0.43
Consensus pattern (26 bp):
TTGAAGATTTTACCCCTGGTAAAATT
Found at i:55472263 original size:42 final size:43
Alignment explanation
Indices: 55472120--55472270 Score: 141
Period size: 42 Copynumber: 3.6 Consensus size: 43
55472110 TAACTGTTAC
* * * **
55472120 TCGGTGGAATCAACACTTAGCAACCA-CATTATATTCTTTGAT
1 TCGGTGGAATCAACACTTAGCAACCACCTTTACAATCAATGAT
* * * *
55472162 ACGG-GGAATCAACACATAACAACC-CCTTTCACAATCAAGGAT
1 TCGGTGGAATCAACACTTAGCAACCACCTTT-ACAATCAATGAT
* * *
55472204 AT-GGTGGAATCAGCACTTAGCAACCACCTTTAGAATCAATAAT
1 -TCGGTGGAATCAACACTTAGCAACCACCTTTACAATCAATGAT
55472247 TCGG-GGAATCAACACTTAGCAACC
1 TCGGTGGAATCAACACTTAGCAACC
55472271 TCTCGGGGAA
Statistics
Matches: 86, Mismatches: 17, Indels: 12
0.75 0.15 0.10
Matches are distributed among these distances:
41 21 0.24
42 32 0.37
43 28 0.33
44 5 0.06
ACGTcount: A:0.36, C:0.25, G:0.16, T:0.24
Consensus pattern (43 bp):
TCGGTGGAATCAACACTTAGCAACCACCTTTACAATCAATGAT
Found at i:55472276 original size:26 final size:26
Alignment explanation
Indices: 55472247--55472296 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
55472237 AATCAATAAT
55472247 TCGGGGAATCAACACTTAGCAACCTC
1 TCGGGGAATCAACACTTAGCAACCTC
**
55472273 TCGGGGAATCTGCACTTAGCAACC
1 TCGGGGAATCAACACTTAGCAACC
55472297 CCTTTTTGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.28, C:0.30, G:0.22, T:0.20
Consensus pattern (26 bp):
TCGGGGAATCAACACTTAGCAACCTC
Found at i:55472318 original size:41 final size:41
Alignment explanation
Indices: 55472273--55472382 Score: 166
Period size: 41 Copynumber: 2.7 Consensus size: 41
55472263 TAGCAACCTC
* *
55472273 TCGGGGAATCTGCACTTAGCAACCCCTTTTTGATCGGAGTT
1 TCGGGGAATCTGCACTTAGCAACCCCTTTTTGATCAGAGAT
*
55472314 TCGGGGAATCTGCACTTAGCAACCCCTTTTTGATCAGTGAT
1 TCGGGGAATCTGCACTTAGCAACCCCTTTTTGATCAGAGAT
* * *
55472355 TCGAGGAATATACACTTAGCAACCCCTT
1 TCGGGGAATCTGCACTTAGCAACCCCTT
55472383 AAATTCAATG
Statistics
Matches: 63, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 63 1.00
ACGTcount: A:0.24, C:0.25, G:0.21, T:0.30
Consensus pattern (41 bp):
TCGGGGAATCTGCACTTAGCAACCCCTTTTTGATCAGAGAT
Found at i:55475160 original size:28 final size:28
Alignment explanation
Indices: 55475087--55475160 Score: 121
Period size: 28 Copynumber: 2.6 Consensus size: 28
55475077 TAGCTAAGTC
* * *
55475087 ATGGACTACCCTCTACAAATTTTGCGTT
1 ATGGACTACCCTCTACATATTTTGAGCT
55475115 ATGGACTACCCTCTACATATTTTGAGCT
1 ATGGACTACCCTCTACATATTTTGAGCT
55475143 ATGGACTACCCTCTACAT
1 ATGGACTACCCTCTACAT
55475161 GTGCTCTTTG
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 43 1.00
ACGTcount: A:0.26, C:0.27, G:0.14, T:0.34
Consensus pattern (28 bp):
ATGGACTACCCTCTACATATTTTGAGCT
Found at i:55475273 original size:93 final size:92
Alignment explanation
Indices: 55475114--55475288 Score: 296
Period size: 93 Copynumber: 1.9 Consensus size: 92
55475104 AATTTTGCGT
* * *
55475114 TATGGACTACCCTCTACATATTTTGAGCTATGGACTACCCTCTACATGTGCTCTTTGATGTGATT
1 TATGGACTACCATCTACATATTTTGAGCTATGGACTACCCTCTACATATGCTATTTGATGTGATT
*
55475179 AAAGATGTGTTGTTCTATCCGGGGACTC
66 -AAGAAGTGTTGTTCTATCCGGGGACTC
*
55475207 TATGGACTACCATCTACATATTTTGAGTTATGGACTACCCTCTACATATGCTATTTGATGTGATT
1 TATGGACTACCATCTACATATTTTGAGCTATGGACTACCCTCTACATATGCTATTTGATGTGATT
55475272 AAGAAGTGTTGTTCTAT
66 AAGAAGTGTTGTTCTAT
55475289 AGGGGGACCC
Statistics
Matches: 77, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
92 16 0.21
93 61 0.79
ACGTcount: A:0.24, C:0.19, G:0.19, T:0.38
Consensus pattern (92 bp):
TATGGACTACCATCTACATATTTTGAGCTATGGACTACCCTCTACATATGCTATTTGATGTGATT
AAGAAGTGTTGTTCTATCCGGGGACTC
Found at i:55478964 original size:27 final size:27
Alignment explanation
Indices: 55478933--55478991 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 27
55478923 TTTGGTTAAA
* *
55478933 AATTAGCCGAATTAACC-GAATTAACCG
1 AATTACCCGAATT-ACCTAAATTAACCG
* *
55478960 AATTACCCTAATTACCTAAATTATCCG
1 AATTACCCGAATTACCTAAATTAACCG
55478987 AATTA
1 AATTA
55478992 TCCAATTGAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
26 3 0.11
27 24 0.89
ACGTcount: A:0.41, C:0.22, G:0.08, T:0.29
Consensus pattern (27 bp):
AATTACCCGAATTACCTAAATTAACCG
Found at i:55478994 original size:9 final size:9
Alignment explanation
Indices: 55478933--55478991 Score: 57
Period size: 9 Copynumber: 6.6 Consensus size: 9
55478923 TTTGGTTAAA
*
55478933 AATTAGCCG
1 AATTAACCG
55478942 AATTAACCG
1 AATTAACCG
55478951 AATTAACCG
1 AATTAACCG
* *
55478960 AATTACCCT
1 AATTAACCG
*
55478969 AATT-ACCTA
1 AATTAACC-G
*
55478978 AATTATCCG
1 AATTAACCG
55478987 AATTA
1 AATTA
55478992 TCCAATTGAA
Statistics
Matches: 41, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
8 2 0.05
9 37 0.90
10 2 0.05
ACGTcount: A:0.41, C:0.22, G:0.08, T:0.29
Consensus pattern (9 bp):
AATTAACCG
Found at i:55479075 original size:37 final size:37
Alignment explanation
Indices: 55478997--55479072 Score: 109
Period size: 37 Copynumber: 2.0 Consensus size: 37
55478987 AATTATCCAA
* *
55478997 TTGAATCACTACATAATTAAAAATATTACTCAAGTCT
1 TTGAATCACTACATAATTAAAAAAATTACTCAAATCT
55479034 TTGAATCACTACATAATTAAAAAAAATTACAT-AAATCT
1 TTGAATCACTACATAATT-AAAAAAATTAC-TCAAATCT
55479072 T
1 T
55479073 GAAATTAACA
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
37 18 0.51
38 16 0.46
39 1 0.03
ACGTcount: A:0.47, C:0.14, G:0.04, T:0.34
Consensus pattern (37 bp):
TTGAATCACTACATAATTAAAAAAATTACTCAAATCT
Found at i:55479285 original size:39 final size:39
Alignment explanation
Indices: 55479203--55479319 Score: 209
Period size: 39 Copynumber: 3.0 Consensus size: 39
55479193 ACTTAAGAGT
* *
55479203 TAGACTTTAGTTTTATTTTTATTGGGTT-GGTAATCGGG
1 TAGACTTTAGTTTTAGTTTTATTGGGTTGGGTAATTGGG
55479241 TAGACTTTAGTTTTAGTTTTATTGGGTTGGGTAATTGGG
1 TAGACTTTAGTTTTAGTTTTATTGGGTTGGGTAATTGGG
55479280 TAGACTTTAGTTTTAGTTTTATTGGGTTGGGTAATTGGG
1 TAGACTTTAGTTTTAGTTTTATTGGGTTGGGTAATTGGG
55479319 T
1 T
55479320 TGGGTTGGAT
Statistics
Matches: 76, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
38 27 0.36
39 49 0.64
ACGTcount: A:0.18, C:0.03, G:0.29, T:0.50
Consensus pattern (39 bp):
TAGACTTTAGTTTTAGTTTTATTGGGTTGGGTAATTGGG
Found at i:55479318 original size:13 final size:13
Alignment explanation
Indices: 55479300--55479324 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
55479290 TTTTAGTTTT
55479300 ATTGGGTTGGGTA
1 ATTGGGTTGGGTA
55479313 ATTGGGTTGGGT
1 ATTGGGTTGGGT
55479325 TGGATAATTT
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:0.00, G:0.48, T:0.40
Consensus pattern (13 bp):
ATTGGGTTGGGTA
Found at i:55490827 original size:24 final size:25
Alignment explanation
Indices: 55490766--55490827 Score: 63
Period size: 24 Copynumber: 2.5 Consensus size: 25
55490756 TACTGATTTT
* * *
55490766 AGCTCTTATGAGCTTACTATTTTTC
1 AGCTCGTATGAGCTTACCATTTTAC
* * *
55490791 AGCTTGAAGGAGCTTACCA-TTTAC
1 AGCTCGTATGAGCTTACCATTTTAC
55490815 AGCTCGTATGAGC
1 AGCTCGTATGAGC
55490828 ATATATAGGA
Statistics
Matches: 28, Mismatches: 9, Indels: 1
0.74 0.24 0.03
Matches are distributed among these distances:
24 14 0.50
25 14 0.50
ACGTcount: A:0.24, C:0.21, G:0.19, T:0.35
Consensus pattern (25 bp):
AGCTCGTATGAGCTTACCATTTTAC
Found at i:55490994 original size:26 final size:26
Alignment explanation
Indices: 55490965--55491016 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 26
55490955 CATAGGTATT
*
55490965 TACATGAGATATATGA-AAATGATTTG
1 TACACGAGATATA-GATAAATGATTTG
* *
55490991 TACACGATATATAGATACATGATTTG
1 TACACGAGATATAGATAAATGATTTG
55491017 GAAATTATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
25 2 0.09
26 20 0.91
ACGTcount: A:0.40, C:0.08, G:0.17, T:0.35
Consensus pattern (26 bp):
TACACGAGATATAGATAAATGATTTG
Found at i:55496450 original size:107 final size:107
Alignment explanation
Indices: 55496264--55496481 Score: 436
Period size: 107 Copynumber: 2.0 Consensus size: 107
55496254 TGTGTTGCGA
55496264 CATAGCAATCAGTATACTCCTCTACAACTATCTTCAAGGGTATATGACAACACCCTCATTCTGTG
1 CATAGCAATCAGTATACTCCTCTACAACTATCTTCAAGGGTATATGACAACACCCTCATTCTGTG
55496329 TCATGACATCGAAAGCAGTCTTGATTTTTTTCAATTCTGTTT
66 TCATGACATCGAAAGCAGTCTTGATTTTTTTCAATTCTGTTT
55496371 CATAGCAATCAGTATACTCCTCTACAACTATCTTCAAGGGTATATGACAACACCCTCATTCTGTG
1 CATAGCAATCAGTATACTCCTCTACAACTATCTTCAAGGGTATATGACAACACCCTCATTCTGTG
55496436 TCATGACATCGAAAGCAGTCTTGATTTTTTTCAATTCTGTTT
66 TCATGACATCGAAAGCAGTCTTGATTTTTTTCAATTCTGTTT
55496478 CATA
1 CATA
55496482 TGTTGCTGCA
Statistics
Matches: 111, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
107 111 1.00
ACGTcount: A:0.28, C:0.23, G:0.13, T:0.35
Consensus pattern (107 bp):
CATAGCAATCAGTATACTCCTCTACAACTATCTTCAAGGGTATATGACAACACCCTCATTCTGTG
TCATGACATCGAAAGCAGTCTTGATTTTTTTCAATTCTGTTT
Found at i:55498045 original size:61 final size:61
Alignment explanation
Indices: 55497858--55498118 Score: 204
Period size: 61 Copynumber: 4.3 Consensus size: 61
55497848 CCAGGAGAAG
* * * ** * * * * *
55497858 GAAAGCCCTTATGGCAAGTACTGAATGTAAAATACAACCTTTGTGGTAAAAATTTTGACGA
1 GAAAGCCTTTGTGGCAAGTACTGAATATAAAGGATAACCTTTGTGGCAAAAATCTAGACAA
* * *** * * ** *
55497919 GAAAGCCTTTGTGGCGAGTACTGGATATAAAGGATGGTCTTTGTGGCACAACTCCGGACAT
1 GAAAGCCTTTGTGGCAAGTACTGAATATAAAGGATAACCTTTGTGGCAAAAATCTAGACAA
* * *
55497980 GAAAGCCTTTATGGCAAGTACT-AATTGTAAAGGATAGCCTTTGTGGCAAAAATCTAGACAA
1 GAAAGCCTTTGTGGCAAGTACTGAA-TATAAAGGATAACCTTTGTGGCAAAAATCTAGACAA
* * * * * * *
55498041 GAAAGCTTTTGTGACGAGCA-TCGAATATAAAGGATAACCTTTGTGGAAAAAATCTATA-GA
1 GAAAGCCTTTGTGGCAAGTACT-GAATATAAAGGATAACCTTTGTGGCAAAAATCTAGACAA
55498101 GAAAAGCCTTTGTGGCAA
1 G-AAAGCCTTTGTGGCAA
55498119 CCTCTGTTTA
Statistics
Matches: 153, Mismatches: 43, Indels: 8
0.75 0.21 0.04
Matches are distributed among these distances:
60 4 0.03
61 147 0.96
62 2 0.01
ACGTcount: A:0.35, C:0.15, G:0.23, T:0.26
Consensus pattern (61 bp):
GAAAGCCTTTGTGGCAAGTACTGAATATAAAGGATAACCTTTGTGGCAAAAATCTAGACAA
Found at i:55498083 original size:122 final size:122
Alignment explanation
Indices: 55497858--55498086 Score: 282
Period size: 122 Copynumber: 1.9 Consensus size: 122
55497848 CCAGGAGAAG
* * * * *
55497858 GAAAGCCCTTATGGCAAGTACTGAATGTAAAATACAACCTTTGTGGTAAAAATTTTGACGAGAAA
1 GAAAGCCCTTATGGCAAGTACTGAATGTAAAAGACAACCTTTGTGGCAAAAATCTAGACAAGAAA
* * * ***
55497923 GCCTTTGTGGCGAGTACTGGATATAAAGGATGGTCTTTGTGGCACAACTCCGGACAT
66 GCCTTTGTGACGAGCACTGAATATAAAGGATAACCTTTGTGGCACAACTCCGGACAT
* * * *
55497980 GAAAGCCTTTATGGCAAGTACT-AATTGTAAAGGATAGCCTTTGTGGCAAAAATCTAGACAAGAA
1 GAAAGCCCTTATGGCAAGTACTGAA-TGTAAAAGACAACCTTTGTGGCAAAAATCTAGACAAGAA
*
55498044 AGCTTTTGTGACGAGCA-TCGAATATAAAGGATAACCTTTGTGG
65 AGCCTTTGTGACGAGCACT-GAATATAAAGGATAACCTTTGTGG
55498087 AAAAAATCTA
Statistics
Matches: 89, Mismatches: 16, Indels: 4
0.82 0.15 0.04
Matches are distributed among these distances:
121 3 0.03
122 86 0.97
ACGTcount: A:0.34, C:0.15, G:0.24, T:0.27
Consensus pattern (122 bp):
GAAAGCCCTTATGGCAAGTACTGAATGTAAAAGACAACCTTTGTGGCAAAAATCTAGACAAGAAA
GCCTTTGTGACGAGCACTGAATATAAAGGATAACCTTTGTGGCACAACTCCGGACAT
Found at i:55498219 original size:29 final size:30
Alignment explanation
Indices: 55498154--55498219 Score: 73
Period size: 29 Copynumber: 2.3 Consensus size: 30
55498144 AAAATCTCTG
* * * *
55498154 AAAGGAAATGTCTTTGTGGCGATCTCTGTC
1 AAAGGAAAAGTCTCTGTGGCGACCTCAGTC
*
55498184 AAA-GAAAAGTCTCTGTGGCTACCTCAGT-
1 AAAGGAAAAGTCTCTGTGGCGACCTCAGTC
55498212 AAAGGAAA
1 AAAGGAAA
55498220 CATTCATGGC
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
28 3 0.10
29 24 0.80
30 3 0.10
ACGTcount: A:0.33, C:0.17, G:0.24, T:0.26
Consensus pattern (30 bp):
AAAGGAAAAGTCTCTGTGGCGACCTCAGTC
Found at i:55503498 original size:261 final size:261
Alignment explanation
Indices: 55503028--55503548 Score: 954
Period size: 261 Copynumber: 2.0 Consensus size: 261
55503018 CGCCTATGTG
* *
55503028 CAAGAAATGGGGCTGTTTTGTTTCTTGGTTCTTCCCTATATTTTTCCAGGATTAATTTTAGTTCT
1 CAAGAAATGGGGCTGTTTTGTTTCTTGGTTCTTCCCTATATTTTTCCAGCAATAATTTTAGTTCT
* **
55503093 TGAAGACTCCTAATCAGCTTTTAAACCCATTTCAACTAGGGAAAAATGTTCTTGATCAATGGCCA
66 TGAAGACTCATAATCAGCTTTTAAACCCATTTCAACTAGGGAAAAAAATTCTTGATCAATGGCCA
55503158 TTCGGATTCCACAAATCGTGAAGCGTAAGTGCAATTAAAGGTAACTAGTTTGTTATTTCGACATA
131 TTCGGATTCCACAAATCGTGAAGCGTAAGTGCAATTAAAGGTAACTAGTTTGTTATTTCGACATA
*
55503223 GTTGTTGGGTAAAGGTTATGAATTGATTAAATGAAGGAATTTAATCATTAATTACCTACTTATTT
196 GTTGTTGAGTAAAGGTTATGAATTGATTAAATGAAGGAATTTAATCATTAATTACCTACTTATTT
55503288 C
261 C
55503289 CAAGAAA-GGGGCTGTTTTGTTTCTTGGTTCTTCCCTATATTTTTCCAGCAATAATTTTAGTTCT
1 CAAGAAATGGGGCTGTTTTGTTTCTTGGTTCTTCCCTATATTTTTCCAGCAATAATTTTAGTTCT
55503353 TGAAGACTCATAATCAGCTTTTAAACCCATTTCAACTAGGGAAAAAAATTCTTGATCAATTGGCC
66 TGAAGACTCATAATCAGCTTTTAAACCCATTTCAACTAGGGAAAAAAATTCTTGATCAA-TGGCC
55503418 ATTCGGATTCCACAAATCGTGAAGCGTAAGTGCAATTAAAGGTAACTAGTTTGTTATTTCGACAT
130 ATTCGGATTCCACAAATCGTGAAGCGTAAGTGCAATTAAAGGTAACTAGTTTGTTATTTCGACAT
* *
55503483 GGTTGTTGAGTAAAGGTTATGAATTGATTAAATGAAGGAATTTAATCATTAATTAGCTACTTATT
195 AGTTGTTGAGTAAAGGTTATGAATTGATTAAATGAAGGAATTTAATCATTAATTACCTACTTATT
55503548 T
260 T
55503549 TCCAGTATAT
Statistics
Matches: 251, Mismatches: 8, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
260 111 0.44
261 140 0.56
ACGTcount: A:0.30, C:0.15, G:0.18, T:0.37
Consensus pattern (261 bp):
CAAGAAATGGGGCTGTTTTGTTTCTTGGTTCTTCCCTATATTTTTCCAGCAATAATTTTAGTTCT
TGAAGACTCATAATCAGCTTTTAAACCCATTTCAACTAGGGAAAAAAATTCTTGATCAATGGCCA
TTCGGATTCCACAAATCGTGAAGCGTAAGTGCAATTAAAGGTAACTAGTTTGTTATTTCGACATA
GTTGTTGAGTAAAGGTTATGAATTGATTAAATGAAGGAATTTAATCATTAATTACCTACTTATTT
C
Found at i:55525306 original size:21 final size:22
Alignment explanation
Indices: 55525282--55525324 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 22
55525272 AAATGAAAAA
*
55525282 AATGCTAATTT-TTGTTATTTT
1 AATGATAATTTCTTGTTATTTT
* *
55525303 AATGATATTTTCTTGTTGTTTT
1 AATGATAATTTCTTGTTATTTT
55525325 CTCCCTATTT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.21, C:0.05, G:0.12, T:0.63
Consensus pattern (22 bp):
AATGATAATTTCTTGTTATTTT
Found at i:55530160 original size:42 final size:41
Alignment explanation
Indices: 55530102--55530189 Score: 167
Period size: 42 Copynumber: 2.1 Consensus size: 41
55530092 CGAGATAAAC
55530102 CAAAATCATCCCTATCATCTCCATTGTATCAAGGGCAAGGT
1 CAAAATCATCCCTATCATCTCCATTGTATCAAGGGCAAGGT
55530143 CAAAACTCATCCCTATCATCTCCATTGTATCAAGGGCAAGGT
1 CAAAA-TCATCCCTATCATCTCCATTGTATCAAGGGCAAGGT
55530185 CAAAA
1 CAAAA
55530190 AGTTGCTTTT
Statistics
Matches: 46, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
41 5 0.11
42 41 0.89
ACGTcount: A:0.34, C:0.27, G:0.14, T:0.25
Consensus pattern (41 bp):
CAAAATCATCCCTATCATCTCCATTGTATCAAGGGCAAGGT
Found at i:55537252 original size:21 final size:24
Alignment explanation
Indices: 55537209--55537252 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
55537199 GGAATTTATT
*
55537209 TACAAATATGAATCTAGTCTTTAC
1 TACAAATATGAATCTAATCTTTAC
55537233 TACAAATAT-AA-CTAAT-TTTA
1 TACAAATATGAATCTAATCTTTA
55537253 ACCCCCAGGC
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 4 0.21
22 4 0.21
23 2 0.11
24 9 0.47
ACGTcount: A:0.43, C:0.14, G:0.05, T:0.39
Consensus pattern (24 bp):
TACAAATATGAATCTAATCTTTAC
Found at i:55543847 original size:24 final size:24
Alignment explanation
Indices: 55543790--55543841 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
55543780 TTTCTAGAAG
* *
55543790 ATTTAGTATTTATTAGTATAATAT
1 ATTTAGCATTTATTAGCATAATAT
*
55543814 ATTTAGCATTTATTAGCATAATTT
1 ATTTAGCATTTATTAGCATAATAT
55543838 ATTT
1 ATTT
55543842 GACATTGATT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.35, C:0.04, G:0.08, T:0.54
Consensus pattern (24 bp):
ATTTAGCATTTATTAGCATAATAT
Found at i:55543852 original size:24 final size:24
Alignment explanation
Indices: 55543790--55543853 Score: 67
Period size: 24 Copynumber: 2.7 Consensus size: 24
55543780 TTTCTAGAAG
* * *
55543790 ATTTAGTATTTATTAGTATAATAT
1 ATTTAGCATTGATTAGCATAATAT
* *
55543814 ATTTAGCATTTATTAGCATAATTT
1 ATTTAGCATTGATTAGCATAATAT
55543838 ATTT-GACATTGATTAG
1 ATTTAG-CATTGATTAG
55543854 TATTAGGTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
23 1 0.03
24 34 0.97
ACGTcount: A:0.34, C:0.05, G:0.11, T:0.50
Consensus pattern (24 bp):
ATTTAGCATTGATTAGCATAATAT
Found at i:55547181 original size:24 final size:24
Alignment explanation
Indices: 55547161--55547217 Score: 78
Period size: 24 Copynumber: 2.4 Consensus size: 24
55547151 AAGATTTAGT
*
55547161 ATTTATTAGTATAATATATTTAAC
1 ATTTATTAGCATAATATATTTAAC
* *
55547185 ATTTATTAGCATAATTTATTTGAC
1 ATTTATTAGCATAATATATTTAAC
*
55547209 ATTGATTAG
1 ATTTATTAG
55547218 AATTAGGTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.37, C:0.05, G:0.09, T:0.49
Consensus pattern (24 bp):
ATTTATTAGCATAATATATTTAAC
Found at i:55549699 original size:24 final size:23
Alignment explanation
Indices: 55549646--55549695 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 23
55549636 TTTATTTATT
*
55549646 ATTAAAATATTTTAAATAATGATA
1 ATTAATATATTTTAAATAA-GATA
55549670 ATTAATATATTTTAAATCAA-ATA
1 ATTAATATATTTTAAAT-AAGATA
55549693 ATT
1 ATT
55549696 TAATCTATCT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
23 6 0.25
24 16 0.67
25 2 0.08
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (23 bp):
ATTAATATATTTTAAATAAGATA
Found at i:55552865 original size:38 final size:41
Alignment explanation
Indices: 55552823--55552909 Score: 103
Period size: 38 Copynumber: 2.2 Consensus size: 41
55552813 AAAATAAGAA
* *
55552823 AAAAATTATAAA-ATAT-TATAAAGTCGT-AATAAAA-TTAT
1 AAAAATTATAAAGAAATATA-AAAGTCGTAAAAAAAATTTAT
*
55552861 AAAAA-TATAAAGAAATATAAAATTCGTAAAAAAAATTTAT
1 AAAAATTATAAAGAAATATAAAAGTCGTAAAAAAAATTTAT
55552901 AAAAATTAT
1 AAAAATTAT
55552910 CGTACCAGAA
Statistics
Matches: 41, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
37 6 0.15
38 15 0.37
39 8 0.20
40 9 0.22
41 3 0.07
ACGTcount: A:0.62, C:0.02, G:0.05, T:0.31
Consensus pattern (41 bp):
AAAAATTATAAAGAAATATAAAAGTCGTAAAAAAAATTTAT
Found at i:55553112 original size:19 final size:19
Alignment explanation
Indices: 55553079--55553158 Score: 76
Period size: 19 Copynumber: 4.2 Consensus size: 19
55553069 TTAAAGGTAT
55553079 TTTTTTATGCA-TTTTATAA
1 TTTTTTATG-ATTTTTATAA
55553098 TTTTTTATGATTTTTATGAA
1 TTTTTTATGATTTTTAT-AA
** *
55553118 -AATTTATAATTTTTATAA
1 TTTTTTATGATTTTTATAA
*
55553136 TTTTTTTATGATTTCTAT-A
1 -TTTTTTATGATTTTTATAA
55553155 TTTT
1 TTTT
55553159 ACAAAGTTAA
Statistics
Matches: 50, Mismatches: 7, Indels: 9
0.76 0.11 0.14
Matches are distributed among these distances:
18 7 0.14
19 29 0.58
20 14 0.28
ACGTcount: A:0.28, C:0.03, G:0.05, T:0.65
Consensus pattern (19 bp):
TTTTTTATGATTTTTATAA
Found at i:55553141 original size:10 final size:9
Alignment explanation
Indices: 55553090--55553140 Score: 57
Period size: 9 Copynumber: 5.4 Consensus size: 9
55553080 TTTTTATGCA
55553090 TTTTATAATT
1 TTTTATAA-T
*
55553100 TTTTATGAT
1 TTTTATAAT
*
55553109 TTTTATGAAA
1 TTTTAT-AAT
*
55553119 ATTTATAAT
1 TTTTATAAT
55553128 TTTTATAAT
1 TTTTATAAT
55553137 TTTT
1 TTTT
55553141 TTATGATTTC
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
9 21 0.62
10 13 0.38
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (9 bp):
TTTTATAAT
Found at i:55553144 original size:30 final size:28
Alignment explanation
Indices: 55553076--55553146 Score: 81
Period size: 29 Copynumber: 2.5 Consensus size: 28
55553066 TGGTTAAAGG
* *
55553076 TATTTTTTTATG-CATTTTATAATTTTT
1 TATTTTTTTATGAAAATTTATAATTTTT
*
55553103 TATGATTTTTATGAAAATTTATAATTTTT
1 TAT-TTTTTTATGAAAATTTATAATTTTT
55553132 ATAATTTTTTTATGA
1 -T-ATTTTTTTATGA
55553147 TTTCTATATT
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
27 3 0.08
28 8 0.22
29 13 0.36
30 10 0.28
31 2 0.06
ACGTcount: A:0.30, C:0.01, G:0.06, T:0.63
Consensus pattern (28 bp):
TATTTTTTTATGAAAATTTATAATTTTT
Found at i:55553154 original size:29 final size:27
Alignment explanation
Indices: 55553076--55553158 Score: 80
Period size: 28 Copynumber: 3.0 Consensus size: 27
55553066 TGGTTAAAGG
*
55553076 TATTTTTTTATGCATTTTATAATTTTT
1 TATTTTTTTATGAATTTTATAATTTTT
* *
55553103 TATGATTTTTATGAAAATTTATAATTTTT
1 TAT-TTTTTTATG-AATTTTATAATTTTT
55553132 ATAATTTTTTTATG-ATTTCTAT-ATTTT
1 -T-ATTTTTTTATGAATTT-TATAATTTT
55553159 ACAAAGTTAA
Statistics
Matches: 46, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
27 3 0.07
28 16 0.35
29 16 0.35
30 9 0.20
31 2 0.04
ACGTcount: A:0.28, C:0.02, G:0.05, T:0.65
Consensus pattern (27 bp):
TATTTTTTTATGAATTTTATAATTTTT
Found at i:55556144 original size:42 final size:42
Alignment explanation
Indices: 55556085--55556171 Score: 111
Period size: 42 Copynumber: 2.1 Consensus size: 42
55556075 GCCTGCGACG
* * * * *
55556085 CGGCCGTGTGACCCAAGTTAGTGAGTTACATGGGTAGAGACA
1 CGGCCGTGTGACCCAAGTCAATAAGTTACATGGGAAAAGACA
* *
55556127 CGGCCGTGTGTCTCAAGTCAATAAGTTACATGGGAAAAGACA
1 CGGCCGTGTGACCCAAGTCAATAAGTTACATGGGAAAAGACA
55556169 CGG
1 CGG
55556172 GTTGGGACAT
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.29, C:0.20, G:0.31, T:0.21
Consensus pattern (42 bp):
CGGCCGTGTGACCCAAGTCAATAAGTTACATGGGAAAAGACA
Found at i:55557102 original size:17 final size:17
Alignment explanation
Indices: 55557080--55557130 Score: 84
Period size: 17 Copynumber: 3.0 Consensus size: 17
55557070 GACTAATCCC
*
55557080 TATACATCACTTAGGTA
1 TATACATTACTTAGGTA
55557097 TATACATTACTTAGGTA
1 TATACATTACTTAGGTA
*
55557114 TGTACATTACTTAGGTA
1 TATACATTACTTAGGTA
55557131 CATGCCACAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 32 1.00
ACGTcount: A:0.33, C:0.14, G:0.14, T:0.39
Consensus pattern (17 bp):
TATACATTACTTAGGTA
Found at i:55557883 original size:23 final size:23
Alignment explanation
Indices: 55557813--55557897 Score: 108
Period size: 21 Copynumber: 3.9 Consensus size: 23
55557803 CCTGATCAGT
55557813 ATACGACACAT-AAGTGCCTGA-
1 ATACGACACATAAAGTGCCTGAG
** *
55557834 A-ACGACACACGAGGTGCCT--G
1 ATACGACACATAAAGTGCCTGAG
55557854 ATACGACACATAAAGTGCCTGAG
1 ATACGACACATAAAGTGCCTGAG
55557877 ATACGACACATAAAGTGCCTG
1 ATACGACACATAAAGTGCCTG
55557898 GTCGGCAAAG
Statistics
Matches: 54, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
20 9 0.17
21 23 0.43
23 22 0.41
ACGTcount: A:0.36, C:0.25, G:0.22, T:0.16
Consensus pattern (23 bp):
ATACGACACATAAAGTGCCTGAG
Found at i:55557895 original size:44 final size:41
Alignment explanation
Indices: 55557813--55557897 Score: 116
Period size: 44 Copynumber: 2.0 Consensus size: 41
55557803 CCTGATCAGT
* *
55557813 ATACGACACATAAGTGCCTGAAACGACACACGAGGTGCCTG
1 ATACGACACATAAGTGCCTGAAACGACACACAAAGTGCCTG
*
55557854 ATACGACACATAAAGTGCCTGAGATACGACACATAAAGTGCCTG
1 ATACGACACAT-AAGTGCCTGA-A-ACGACACACAAAGTGCCTG
55557898 GTCGGCAAAG
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
41 11 0.29
42 10 0.26
43 1 0.03
44 16 0.42
ACGTcount: A:0.36, C:0.25, G:0.22, T:0.16
Consensus pattern (41 bp):
ATACGACACATAAGTGCCTGAAACGACACACAAAGTGCCTG
Found at i:55559070 original size:13 final size:13
Alignment explanation
Indices: 55559041--55559078 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
55559031 CCCGTTTTGC
55559041 TCTCTGTTTCT-T
1 TCTCTGTTTCTAT
55559053 TCTCTGTTTCTAT
1 TCTCTGTTTCTAT
*
55559066 TCTCTTTTTCTAT
1 TCTCTGTTTCTAT
55559079 CCTTTCTTTG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 11 0.46
13 13 0.54
ACGTcount: A:0.05, C:0.24, G:0.05, T:0.66
Consensus pattern (13 bp):
TCTCTGTTTCTAT
Found at i:55559108 original size:8 final size:8
Alignment explanation
Indices: 55559097--55559124 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
55559087 TGTTATATAC
55559097 ATATAATA
1 ATATAATA
55559105 ATATAATA
1 ATATAATA
55559113 ATATAATA
1 ATATAATA
55559121 ATAT
1 ATAT
55559125 TTTTTTAACA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (8 bp):
ATATAATA
Found at i:55560920 original size:45 final size:45
Alignment explanation
Indices: 55560851--55560982 Score: 142
Period size: 45 Copynumber: 2.9 Consensus size: 45
55560841 GTGCTTTCGT
* * * * *
55560851 ATGATTCCATATCGTCTTTTAGCTATGGTCTTATTCAT-TTCTATC
1 ATGATGCCATAACATCTTTCAGCTATGGTCTTATTCATCTT-TACC
*
55560896 ATGATGCTATAACATCTTTCAGCTATGGTCTTACTT-ATCTTTACC
1 ATGATGCCATAACATCTTTCAGCTATGGTCTTA-TTCATCTTTACC
* * * *
55560941 ATGATGCCATAGCATCTTTCAACTACGGTCTTACTCATCTTT
1 ATGATGCCATAACATCTTTCAGCTATGGTCTTATTCATCTTT
55560983 GATGTATAGC
Statistics
Matches: 73, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
44 1 0.01
45 68 0.93
46 4 0.05
ACGTcount: A:0.23, C:0.23, G:0.11, T:0.43
Consensus pattern (45 bp):
ATGATGCCATAACATCTTTCAGCTATGGTCTTATTCATCTTTACC
Found at i:55566965 original size:51 final size:50
Alignment explanation
Indices: 55566840--55566976 Score: 159
Period size: 50 Copynumber: 2.7 Consensus size: 50
55566830 GTGAAAGTGA
* * *
55566840 TGATCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGAATGAT
1 TGATCACATGTGTAGTACTATGTGCAGGCTACTATGCGTACCAGAATGAT
* * * * * * *
55566890 AGGTCGCATGTCTAGTACTATGTGCAAGCTACTATGCGTACC-GGATAGCTT
1 TGATCACATGTGTAGTACTATGTGCAGGCTACTATGCGTACCAGAAT-G-AT
55566941 TGATCACATGTGTAGTACTATGTGCAGGCTACTATG
1 TGATCACATGTGTAGTACTATGTGCAGGCTACTATG
55566977 TGAACCGGTA
Statistics
Matches: 70, Mismatches: 15, Indels: 3
0.80 0.17 0.03
Matches are distributed among these distances:
49 3 0.04
50 35 0.50
51 32 0.46
ACGTcount: A:0.25, C:0.19, G:0.26, T:0.31
Consensus pattern (50 bp):
TGATCACATGTGTAGTACTATGTGCAGGCTACTATGCGTACCAGAATGAT
Found at i:55566984 original size:51 final size:50
Alignment explanation
Indices: 55566840--55566984 Score: 166
Period size: 51 Copynumber: 2.9 Consensus size: 50
55566830 GTGAAAGTGA
* * *
55566840 TGATCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGAATGAT
1 TGATCACATGTGTAGTACTATGTGCAGGCTACTATGTGTACCGGAATGAT
* * * * * * *
55566890 AGGTCGCATGTCTAGTACTATGTGCAAGCTACTATGCGTACCGG-ATAGCTT
1 TGATCACATGTGTAGTACTATGTGCAGGCTACTATGTGTACCGGAAT-G-AT
*
55566941 TGATCACATGTGTAGTACTATGTGCAGGCTACTATGTGAACCGG
1 TGATCACATGTGTAGTACTATGTGCAGGCTACTATGTGTACCGG
55566985 TATTATTAAT
Statistics
Matches: 76, Mismatches: 17, Indels: 3
0.79 0.18 0.03
Matches are distributed among these distances:
49 2 0.03
50 36 0.47
51 38 0.50
ACGTcount: A:0.25, C:0.19, G:0.26, T:0.30
Consensus pattern (50 bp):
TGATCACATGTGTAGTACTATGTGCAGGCTACTATGTGTACCGGAATGAT
Found at i:55568950 original size:25 final size:25
Alignment explanation
Indices: 55568922--55568970 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
55568912 GATTAACTAT
* *
55568922 TTTAAAAATAATATTATTTTAATAG
1 TTTAAAAATAAAATTAATTTAATAG
* *
55568947 TTTAATATTAAAATTAATTTAATA
1 TTTAAAAATAAAATTAATTTAATA
55568971 CTTATCTGAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (25 bp):
TTTAAAAATAAAATTAATTTAATAG
Found at i:55576936 original size:50 final size:50
Alignment explanation
Indices: 55576808--55577155 Score: 428
Period size: 50 Copynumber: 6.8 Consensus size: 50
55576798 ATTTGGGTAA
* * *
55576808 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCATTAAGATTATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-C----CGA-GATG
* *
55576864 AGAGGTCCCATATAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* *
55576914 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGACACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* *
55576964 AGATGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* *
55577014 AGAGGTCCCATGTAAGACCATGTTTGGGACATGGCATTGGCACCAAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** * * * *
55577064 AGAGGTCCCCCGTAAGACCATGTTTGGGACATGGCATGGGCACCTATATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** * * *
55577114 AGAACTCTCATGTAAGACCATATC-GGAGATATGGCATTGGCA
1 AGAGGTCCCATGTAAGACCATGTCTGG-GACATGGCATTGGCA
55577156 GTACAAGAAA
Statistics
Matches: 264, Mismatches: 27, Indels: 8
0.88 0.09 0.03
Matches are distributed among these distances:
49 2 0.01
50 220 0.83
51 2 0.01
55 1 0.00
56 39 0.15
ACGTcount: A:0.27, C:0.21, G:0.29, T:0.22
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
Found at i:55593027 original size:3 final size:3
Alignment explanation
Indices: 55593019--55593061 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
55593009 ATTTAAAAAT
55593019 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
55593062 ATGTAATTAC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:55593696 original size:16 final size:17
Alignment explanation
Indices: 55593664--55593704 Score: 59
Period size: 15 Copynumber: 2.5 Consensus size: 17
55593654 GTCATTTATG
55593664 TTTAAAAACTAATAATA
1 TTTAAAAACTAATAATA
55593681 TATTAAAAA-T-ATAATA
1 T-TTAAAAACTAATAATA
55593697 TTTAAAAA
1 TTTAAAAA
55593705 ATTAATAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
15 7 0.30
16 7 0.30
17 2 0.09
18 7 0.30
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (17 bp):
TTTAAAAACTAATAATA
Found at i:55593705 original size:16 final size:16
Alignment explanation
Indices: 55593664--55593711 Score: 55
Period size: 16 Copynumber: 3.0 Consensus size: 16
55593654 GTCATTTATG
*
55593664 TTTAAAAACTAATAATA
1 TTTAAAAAAT-ATAATA
55593681 TATT-AAAAATATAATA
1 T-TTAAAAAATATAATA
55593697 TTTAAAAAAT-TAATA
1 TTTAAAAAATATAATA
55593712 AAATATATAA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
15 7 0.25
16 13 0.46
17 6 0.21
18 2 0.07
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (16 bp):
TTTAAAAAATATAATA
Found at i:55594259 original size:17 final size:17
Alignment explanation
Indices: 55594233--55594279 Score: 69
Period size: 17 Copynumber: 2.8 Consensus size: 17
55594223 AAAAACTCAT
55594233 TAAAAT-TAAAAAAATA
1 TAAAATATAAAAAAATA
* *
55594249 TAAAATATAAAAGAATT
1 TAAAATATAAAAAAATA
55594266 TAAAATATAAAAAA
1 TAAAATATAAAAAA
55594280 TTCCAAAATT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
16 6 0.22
17 21 0.78
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (17 bp):
TAAAATATAAAAAAATA
Found at i:55594287 original size:17 final size:17
Alignment explanation
Indices: 55594250--55594288 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
55594240 AAAAAAATAT
*
55594250 AAAATATAAAAGAATTT
1 AAAATATAAAAGAATTC
55594267 AAAATATAAAA-AATTCC
1 AAAATATAAAAGAATT-C
55594284 AAAAT
1 AAAAT
55594289 TTAATATTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 4 0.20
17 16 0.80
ACGTcount: A:0.67, C:0.05, G:0.03, T:0.26
Consensus pattern (17 bp):
AAAATATAAAAGAATTC
Found at i:55603981 original size:22 final size:23
Alignment explanation
Indices: 55603943--55604026 Score: 68
Period size: 22 Copynumber: 3.7 Consensus size: 23
55603933 ATTAAATAAT
*
55603943 TTAAATTAA-TTAT-ATAATTTA
1 TTAAAATAATTTATAATAATTTA
**
55603964 TTAAAAT-ATTTATAATAAAATA
1 TTAAAATAATTTATAATAATTTA
*
55603986 TTAGAAGATACATTT-TAATATTTTA
1 TTA-AA-ATA-ATTTATAATAATTTA
*
55604011 TTAAATTAATTTATAA
1 TTAAAATAATTTATAA
55604027 ATTCACATAT
Statistics
Matches: 49, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
20 1 0.02
21 10 0.20
22 13 0.27
23 7 0.14
24 4 0.08
25 10 0.20
26 4 0.08
ACGTcount: A:0.49, C:0.01, G:0.02, T:0.48
Consensus pattern (23 bp):
TTAAAATAATTTATAATAATTTA
Found at i:55604201 original size:21 final size:21
Alignment explanation
Indices: 55604177--55604218 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
55604167 CCACCATTGT
*
55604177 TACAGTATCCAATCTCACCGC
1 TACAGTAACCAATCTCACCGC
*
55604198 TACAGTAACTAATCTCACCGC
1 TACAGTAACCAATCTCACCGC
55604219 CACCGTTATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.31, C:0.36, G:0.10, T:0.24
Consensus pattern (21 bp):
TACAGTAACCAATCTCACCGC
Found at i:55604425 original size:20 final size:20
Alignment explanation
Indices: 55604400--55604451 Score: 104
Period size: 20 Copynumber: 2.6 Consensus size: 20
55604390 GAATTTTGGA
55604400 ATTTTTATATTTAAAAATAT
1 ATTTTTATATTTAAAAATAT
55604420 ATTTTTATATTTAAAAATAT
1 ATTTTTATATTTAAAAATAT
55604440 ATTTTTATATTT
1 ATTTTTATATTT
55604452 TTAATTTTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (20 bp):
ATTTTTATATTTAAAAATAT
Found at i:55604504 original size:36 final size:35
Alignment explanation
Indices: 55604436--55604507 Score: 90
Period size: 37 Copynumber: 2.0 Consensus size: 35
55604426 ATATTTAAAA
*
55604436 ATATATTTTTATATTTTTAATTTTAAAGGTTTTTC
1 ATATATTTTTATATTTTTAATTATAAAGGTTTTTC
* * *
55604471 ATATATTTTTAATTTTTTTAAATTATAATGTTTTTTC
1 ATATATTTTT-ATATTTTT-AATTATAAAGGTTTTTC
55604508 TTTAAATTAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
35 10 0.32
36 7 0.23
37 14 0.45
ACGTcount: A:0.29, C:0.03, G:0.04, T:0.64
Consensus pattern (35 bp):
ATATATTTTTATATTTTTAATTATAAAGGTTTTTC
Found at i:55622891 original size:56 final size:50
Alignment explanation
Indices: 55622804--55623091 Score: 242
Period size: 50 Copynumber: 5.7 Consensus size: 50
55622794 AAAAGATCCA
* *
55622804 ATGTAAGACCATGTCTGGGACATGGCATTGGCATCATTGAGATTATGTGAGGTCCC
1 ATGTAAGACCATGTCTGGGACATGGCGTTGGCA-C--TGAG---ATGAGAGGTCCC
* *
55622860 ATGTAAGACCATGTCTGGGAGATGGCGTTGGCACCGAGATGAGAGGTCCC
1 ATGTAAGACCATGTCTGGGACATGGCGTTGGCACTGAGATGAGAGGTCCC
55622910 ATGTAAGACCCCAT-TC-GGGACATGGCGTTGGCACTGAGATGAGAGGTTCCC
1 ATGTAAGA--CCATGTCTGGGACATGGCGTTGGCACTGAGATGAGAGG-TCCC
* * * * * **
55622961 -CGTAAGACCATGTCTGGGACATGGCATGGGCACCGATATGAGAACTCCC
1 ATGTAAGACCATGTCTGGGACATGGCGTTGGCACTGAGATGAGAGGTCCC
* * * * * * * * ** *
55623010 ATGTAAGACCATATCTGGGATATGACATTGGCAGT-ACATAAAACATCCT
1 ATGTAAGACCATGTCTGGGACATGGCGTTGGCACTGAGATGAGAGGTCCC
* * *
55623059 ATGTAAGACTATGTCTGGGACATAGCTTTGGCA
1 ATGTAAGACCATGTCTGGGACATGGCGTTGGCA
55623092 TGTATTATCA
Statistics
Matches: 194, Mismatches: 32, Indels: 19
0.79 0.13 0.08
Matches are distributed among these distances:
48 4 0.02
49 41 0.21
50 104 0.54
51 6 0.03
52 4 0.02
53 3 0.02
55 1 0.01
56 31 0.16
ACGTcount: A:0.27, C:0.20, G:0.28, T:0.24
Consensus pattern (50 bp):
ATGTAAGACCATGTCTGGGACATGGCGTTGGCACTGAGATGAGAGGTCCC
Found at i:55623041 original size:100 final size:102
Alignment explanation
Indices: 55622804--55623042 Score: 272
Period size: 100 Copynumber: 2.3 Consensus size: 102
55622794 AAAAGATCCA
* *
55622804 ATGTAAGACCATGTCTGGGACATGGCATTGGCATCATTGAGATTATGTGAGGTCCCATGTAAGAC
1 ATGTAAGACCAT-TCTGGGACATGGCATTGGCATCA-TGAG--TATGAGAGGTCCCACGTAAGAC
* * * **
55622869 CATGTCTGGGAGATGGCGTTGGCACCGAGATGAGAGGTCCC
62 CATGTCTGGGACATGGCATGGGCACCGAGATGAGAACTCCC
*
55622910 ATGTAAGACCCCATTC-GGGACATGGCGTTGGCA-C-TGAG-ATGAGAGGTTCCC-CGTAAGACC
1 ATGTAAGA--CCATTCTGGGACATGGCATTGGCATCATGAGTATGAGAGG-TCCCACGTAAGACC
*
55622970 ATGTCTGGGACATGGCATGGGCACCGATATGAGAACTCCC
63 ATGTCTGGGACATGGCATGGGCACCGAGATGAGAACTCCC
* *
55623010 ATGTAAGACCATATCTGGGATATGACATTGGCA
1 ATGTAAGACCAT-TCTGGGACATGGCATTGGCA
55623043 GTACATAAAA
Statistics
Matches: 116, Mismatches: 12, Indels: 16
0.81 0.08 0.11
Matches are distributed among these distances:
98 4 0.03
99 2 0.02
100 71 0.61
101 4 0.03
103 4 0.03
105 1 0.01
106 24 0.21
107 2 0.02
108 4 0.03
ACGTcount: A:0.26, C:0.21, G:0.30, T:0.23
Consensus pattern (102 bp):
ATGTAAGACCATTCTGGGACATGGCATTGGCATCATGAGTATGAGAGGTCCCACGTAAGACCATG
TCTGGGACATGGCATGGGCACCGAGATGAGAACTCCC
Found at i:55630547 original size:50 final size:50
Alignment explanation
Indices: 55630422--55630669 Score: 244
Period size: 50 Copynumber: 4.8 Consensus size: 50
55630412 ATTTGGATAA
* * * * *
55630422 AGAGATCCCACGTAAGACCATGTTTGGGACATGGCATTGGCATCATTGAGATTATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA-C--CGAG---ATG
* * * *
55630478 TGAGGTCCTATGTAAGACCATGTCTGGGAGATGGTGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
* *
55630528 AGAGGTCCCATGTAAGACCATGTTTGGGACATGGCGTTGGCAGCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
** * * *
55630578 AGAGGTCCCCCGTAAGACCATGTCTGGGACATGGCATGGGCACCGATATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
** * * * *
55630628 AGAACTCCGATGTAAGACCATATCTGGGATATGGCATTGGCA
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA
55630670 GTACAGAAAA
Statistics
Matches: 162, Mismatches: 30, Indels: 6
0.82 0.15 0.03
Matches are distributed among these distances:
50 124 0.77
53 3 0.02
55 1 0.01
56 34 0.21
ACGTcount: A:0.26, C:0.19, G:0.31, T:0.23
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
Found at i:55630629 original size:100 final size:102
Alignment explanation
Indices: 55630422--55630670 Score: 279
Period size: 100 Copynumber: 2.4 Consensus size: 102
55630412 ATTTGGATAA
* * * *
55630422 AGAGATCCCACGTAAGACCATGTTTGGGACATGGCATTGGCATCATTGAGATTATGTGAGGTCCT
1 AGAGATCCCATGTAAGACCATGTTTGGGACATGGCATTGGCAGC--TGAG--TATGAGAGGTCCC
* * ** *
55630487 ATGTAAGACCATGTCTGGGAGATGGTGTTGGCACCGAGATG
62 ACGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGATG
* * *
55630528 AGAGGTCCCATGTAAGACCATGTTTGGGACATGGCGTTGGCAGC-GAG-ATGAGAGGTCCCCCGT
1 AGAGATCCCATGTAAGACCATGTTTGGGACATGGCATTGGCAGCTGAGTATGAGAGGTCCCACGT
*
55630591 AAGACCATGTCTGGGACATGGCATGGGCACCGATATG
66 AAGACCATGTCTGGGACATGGCATGGGCACCGAGATG
* * * *
55630628 AGA-ACTCCGATGTAAGACCATATCTGGGATATGGCATTGGCAG
1 AGAGA-TCCCATGTAAGACCATGTTTGGGACATGGCATTGGCAG
55630671 TACAGAAAAC
Statistics
Matches: 123, Mismatches: 19, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
100 80 0.65
103 3 0.02
106 40 0.33
ACGTcount: A:0.26, C:0.19, G:0.32, T:0.23
Consensus pattern (102 bp):
AGAGATCCCATGTAAGACCATGTTTGGGACATGGCATTGGCAGCTGAGTATGAGAGGTCCCACGT
AAGACCATGTCTGGGACATGGCATGGGCACCGAGATG
Found at i:55630703 original size:49 final size:49
Alignment explanation
Indices: 55630589--55630708 Score: 136
Period size: 50 Copynumber: 2.4 Consensus size: 49
55630579 GAGGTCCCCC
* *
55630589 GTAAGACCATGTCTGGGACATGGCATGGGCACCGATATGAGAACTCCGAT
1 GTAAGACCATGTCTGGGACATGGCATGGGCA-CGATAAGAAAACTCCGAT
* * * *
55630639 GTAAGACCATATCTGGGATATGGCATTGGCA-G-TACAGAAAACATCCTAT
1 GTAAGACCATGTCTGGGACATGGCATGGGCACGATA-AGAAAAC-TCCGAT
*
55630688 GTAAGACTATGTCTGGGACAT
1 GTAAGACCATGTCTGGGACAT
55630709 AGCTTTGGCA
Statistics
Matches: 59, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
47 2 0.03
48 6 0.10
49 23 0.39
50 28 0.47
ACGTcount: A:0.31, C:0.19, G:0.27, T:0.23
Consensus pattern (49 bp):
GTAAGACCATGTCTGGGACATGGCATGGGCACGATAAGAAAACTCCGAT
Found at i:55630935 original size:12 final size:12
Alignment explanation
Indices: 55630918--55630949 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
55630908 ATGAGTTATT
*
55630918 TAAGTAAGCAAG
1 TAAGTAAACAAG
55630930 TAAGTAAACAAG
1 TAAGTAAACAAG
55630942 TAAGTAAA
1 TAAGTAAA
55630950 AAAGCGAGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.56, C:0.06, G:0.19, T:0.19
Consensus pattern (12 bp):
TAAGTAAACAAG
Found at i:55631574 original size:20 final size:19
Alignment explanation
Indices: 55631532--55631572 Score: 55
Period size: 21 Copynumber: 2.1 Consensus size: 19
55631522 CCCTATTTTG
*
55631532 AATTTATAAAATCATTAAA
1 AATTTATAAAATAATTAAA
55631551 AATTGTATAGAAATAATTAAA
1 AATT-TATA-AAATAATTAAA
55631572 A
1 A
55631573 TTCATAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 4 0.21
20 4 0.21
21 11 0.58
ACGTcount: A:0.59, C:0.02, G:0.05, T:0.34
Consensus pattern (19 bp):
AATTTATAAAATAATTAAA
Found at i:55634439 original size:14 final size:14
Alignment explanation
Indices: 55634420--55634453 Score: 68
Period size: 14 Copynumber: 2.4 Consensus size: 14
55634410 TGGCTTCCAA
55634420 GGTTTCTTTTTGTT
1 GGTTTCTTTTTGTT
55634434 GGTTTCTTTTTGTT
1 GGTTTCTTTTTGTT
55634448 GGTTTC
1 GGTTTC
55634454 AGTGGAGAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.00, C:0.09, G:0.24, T:0.68
Consensus pattern (14 bp):
GGTTTCTTTTTGTT
Found at i:55649478 original size:25 final size:26
Alignment explanation
Indices: 55649447--55649502 Score: 71
Period size: 25 Copynumber: 2.2 Consensus size: 26
55649437 AAATTAAAAG
55649447 AAAAGAAAAAG-AACGAAGAAGA-AGA
1 AAAAG-AAAAGTAACGAAGAAGAGAGA
*
55649472 AAAAGAAGAGTAACGAAGAAGATGAGA
1 AAAAGAAAAGTAACGAAGAAGA-GAGA
55649499 AAAA
1 AAAA
55649503 CTAAAGAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
24 4 0.15
25 16 0.59
27 7 0.26
ACGTcount: A:0.68, C:0.04, G:0.25, T:0.04
Consensus pattern (26 bp):
AAAAGAAAAGTAACGAAGAAGAGAGA
Found at i:55662219 original size:13 final size:13
Alignment explanation
Indices: 55662203--55662227 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
55662193 ATATGTGGAT
55662203 TGTATAATTACTA
1 TGTATAATTACTA
55662216 TGTATAATTACT
1 TGTATAATTACT
55662228 TATCGCATAT
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:0.36, C:0.08, G:0.08, T:0.48
Consensus pattern (13 bp):
TGTATAATTACTA
Found at i:55662352 original size:25 final size:25
Alignment explanation
Indices: 55662324--55662435 Score: 86
Period size: 25 Copynumber: 4.5 Consensus size: 25
55662314 TATTGATTTT
*
55662324 AGCTCTTATGAGCTTACTGATACTC
1 AGCTCGTATGAGCTTACTGATACTC
* * *
55662349 AGCTCGTATGAGCTTATTGTTATTC
1 AGCTCGTATGAGCTTACTGATACTC
* * * * *
55662374 AGCTCGGAGGAGCTTACCGTTATTC
1 AGCTCGTATGAGCTTACTGATACTC
* *
55662399 AGCTCCGGA-GAGCTTACTGTTTA-T-
1 AGCT-CGTATGAGCTTACTG-ATACTC
55662423 AGCTCGTATGAGC
1 AGCTCGTATGAGC
55662436 ATACATGTAC
Statistics
Matches: 74, Mismatches: 10, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
23 3 0.04
24 8 0.11
25 56 0.76
26 7 0.09
ACGTcount: A:0.21, C:0.21, G:0.23, T:0.34
Consensus pattern (25 bp):
AGCTCGTATGAGCTTACTGATACTC
Found at i:55678666 original size:14 final size:14
Alignment explanation
Indices: 55678645--55678678 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
55678635 TGGTATGGGT
55678645 TTAT-GGGTTTTGG
1 TTATAGGGTTTTGG
55678658 TTATAGGGTTTTGG
1 TTATAGGGTTTTGG
55678672 TTATAGG
1 TTATAGG
55678679 CAAATGATGA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 4 0.20
14 16 0.80
ACGTcount: A:0.15, C:0.00, G:0.35, T:0.50
Consensus pattern (14 bp):
TTATAGGGTTTTGG
Found at i:55681949 original size:16 final size:17
Alignment explanation
Indices: 55681916--55681967 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
55681906 TTTAAAATTT
* *
55681916 ATATATGAATTCTAAAA
1 ATATATAAATTATAAAA
55681933 ATATATAAATT-TAAAA
1 ATATATAAATTATAAAA
*
55681949 A-ATCTAAAATTATAAAA
1 ATATAT-AAATTATAAAA
55681966 AT
1 AT
55681968 TAAAATAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
15 3 0.10
16 11 0.37
17 16 0.53
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.35
Consensus pattern (17 bp):
ATATATAAATTATAAAA
Found at i:55681962 original size:25 final size:24
Alignment explanation
Indices: 55681926--55681972 Score: 67
Period size: 25 Copynumber: 1.9 Consensus size: 24
55681916 ATATATGAAT
*
55681926 TCTAAAAATATATAAATTTAAAAAA
1 TCTAAAAATATA-AAAATTAAAAAA
*
55681951 TCTAAAATTATAAAAATTAAAA
1 TCTAAAAATATAAAAATTAAAA
55681973 TAAAAAACAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 9 0.45
25 11 0.55
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (24 bp):
TCTAAAAATATAAAAATTAAAAAA
Found at i:55681972 original size:15 final size:15
Alignment explanation
Indices: 55681923--55681973 Score: 50
Period size: 17 Copynumber: 3.2 Consensus size: 15
55681913 TTTATATATG
55681923 AATTCTAAAAATATATA
1 AATT-TAAAAATATA-A
*
55681940 AATTTAAAAAATCTAA
1 AATTT-AAAAATATAA
55681956 AATTATAAAAAT-TAA
1 AATT-TAAAAATATAA
55681971 AAT
1 AAT
55681974 AAAAAACAGA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
15 6 0.19
16 12 0.39
17 13 0.42
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (15 bp):
AATTTAAAAATATAA
Done.