Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A04
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: 82679320
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 4050000 characters in sequence are not A, C, G, or T
File 93 of 255
Found at i:28685925 original size:24 final size:22
Alignment explanation
Indices: 28685882--28685925 Score: 52
Period size: 24 Copynumber: 1.9 Consensus size: 22
28685872 CTGTCGGGAC
* *
28685882 TAAAAACATGAATCTTTGAAAG
1 TAAAAACATGAAACTCTGAAAG
28685904 TAAAAATCGATGAAACTCTGAA
1 TAAAAA-C-ATGAAACTCTGAA
28685926 GACTATATAG
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 6 0.33
23 1 0.06
24 11 0.61
ACGTcount: A:0.50, C:0.11, G:0.14, T:0.25
Consensus pattern (22 bp):
TAAAAACATGAAACTCTGAAAG
Found at i:28686903 original size:19 final size:19
Alignment explanation
Indices: 28686879--28686932 Score: 52
Period size: 19 Copynumber: 3.3 Consensus size: 19
28686869 ATAAGTTTAA
28686879 TATTTTATTAAACTATTCT
1 TATTTTATTAAACTATTCT
28686898 TATTTT-TT----TA--C-
1 TATTTTATTAAACTATTCT
28686909 TATTTTATTAAACTATTCT
1 TATTTTATTAAACTATTCT
28686928 TATTT
1 TATTT
28686933 CTAAATTGTA
Statistics
Matches: 27, Mismatches: 0, Indels: 16
0.63 0.00 0.37
Matches are distributed among these distances:
11 6 0.22
12 3 0.11
14 2 0.07
16 2 0.07
18 3 0.11
19 11 0.41
ACGTcount: A:0.28, C:0.09, G:0.00, T:0.63
Consensus pattern (19 bp):
TATTTTATTAAACTATTCT
Found at i:28686913 original size:30 final size:30
Alignment explanation
Indices: 28686874--28686932 Score: 109
Period size: 30 Copynumber: 2.0 Consensus size: 30
28686864 TTTGCATAAG
28686874 TTTAATATTTTATTAAACTATTCTTATTTT
1 TTTAATATTTTATTAAACTATTCTTATTTT
*
28686904 TTTACTATTTTATTAAACTATTCTTATTT
1 TTTAATATTTTATTAAACTATTCTTATTT
28686933 CTAAATTGTA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.29, C:0.08, G:0.00, T:0.63
Consensus pattern (30 bp):
TTTAATATTTTATTAAACTATTCTTATTTT
Found at i:28687403 original size:26 final size:25
Alignment explanation
Indices: 28687374--28687423 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
28687364 GCATAGCTAT
*
28687374 TCTCATAATTGCCATTGCATTTTTAC
1 TCTCAT-ATTGCCATAGCATTTTTAC
*
28687400 TCTCATTTTGCCATAGCATTTTTA
1 TCTCATATTGCCATAGCATTTTTA
28687424 GTTATTCATT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 16 0.73
26 6 0.27
ACGTcount: A:0.22, C:0.22, G:0.08, T:0.48
Consensus pattern (25 bp):
TCTCATATTGCCATAGCATTTTTAC
Found at i:28689873 original size:24 final size:24
Alignment explanation
Indices: 28689831--28689888 Score: 80
Period size: 24 Copynumber: 2.4 Consensus size: 24
28689821 TTTTCCTATC
*
28689831 TCTTTTCATTTTTCATTTTTGTTCT
1 TCTTTTC-TTTTTCATTTTTATTCT
*
28689856 TCTTTTCTTTTTCCTTTTTATTCT
1 TCTTTTCTTTTTCATTTTTATTCT
*
28689880 TCTTCTCTT
1 TCTTTTCTT
28689889 CCTTTCTTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
24 23 0.77
25 7 0.23
ACGTcount: A:0.05, C:0.21, G:0.02, T:0.72
Consensus pattern (24 bp):
TCTTTTCTTTTTCATTTTTATTCT
Found at i:28692541 original size:19 final size:19
Alignment explanation
Indices: 28692517--28692554 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
28692507 ATGGCCCATT
28692517 AGGCCCAATCACATTTATG
1 AGGCCCAATCACATTTATG
28692536 AGGCCCAATCACATTTATG
1 AGGCCCAATCACATTTATG
28692555 TGGCACATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.32, C:0.26, G:0.16, T:0.26
Consensus pattern (19 bp):
AGGCCCAATCACATTTATG
Found at i:28692569 original size:47 final size:48
Alignment explanation
Indices: 28692489--28692579 Score: 123
Period size: 47 Copynumber: 1.9 Consensus size: 48
28692479 ATGGCCCACT
* *
28692489 AGGCCCAATCTCTTTCATATGGCCCATTAGGCCC-AATCACATTTATG
1 AGGCCCAATCACTTTCATATGGCACATTAGGCCCAAATCACATTTATG
* *
28692536 AGGCCCAATCACATTT-ATGTGGCACATTTGGCCCAAATCACATT
1 AGGCCCAATCAC-TTTCATATGGCACATTAGGCCCAAATCACATT
28692580 CATTGTAACG
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
47 26 0.68
48 12 0.32
ACGTcount: A:0.27, C:0.29, G:0.15, T:0.29
Consensus pattern (48 bp):
AGGCCCAATCACTTTCATATGGCACATTAGGCCCAAATCACATTTATG
Found at i:28693952 original size:46 final size:45
Alignment explanation
Indices: 28693885--28694059 Score: 181
Period size: 46 Copynumber: 3.8 Consensus size: 45
28693875 TGTAACCCGC
28693885 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGC-TTCGCAT
* * *
28693931 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCTAG-TT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG--GCTTCGCAT
* *** * * * * *
28693977 ACATCTCTCGAACTTGGACTCAACTCAACGAGTTTGGACATTCACAT
1 CCATAAGT-GAACTCGGACTCAACTCAACGAGCTCGGGC-TTCGCAT
*
28694024 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGG
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG
28694060 ATGCCCAAAT
Statistics
Matches: 103, Mismatches: 21, Indels: 10
0.77 0.16 0.07
Matches are distributed among these distances:
45 1 0.01
46 68 0.66
47 32 0.31
48 2 0.02
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.22
Consensus pattern (45 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCTTCGCAT
Found at i:28694006 original size:93 final size:93
Alignment explanation
Indices: 28693893--28694064 Score: 281
Period size: 93 Copynumber: 1.8 Consensus size: 93
28693883 GCCCATAAGT
* * *
28693893 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCACATCCATAAGTGAACTCGGACTCAACTCAA
28693958 CGAGCTCGGATGCCTAGTTACATCTCTC
66 CGAGCTCGGATGCCTAGTTACATCTCTC
* * *
28693986 GAACTTGGACTCAACTCAACGAGTTTGGACATTCACATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCACATCCATAAGTGAACTCGGACTCAACTCAA
*
28694051 CGAGTTCGGATGCC
66 CGAGCTCGGATGCC
28694065 CAAATATCCT
Statistics
Matches: 72, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
93 72 1.00
ACGTcount: A:0.28, C:0.29, G:0.21, T:0.22
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCACATCCATAAGTGAACTCGGACTCAACTCAA
CGAGCTCGGATGCCTAGTTACATCTCTC
Found at i:28694079 original size:46 final size:46
Alignment explanation
Indices: 28693890--28694079 Score: 140
Period size: 46 Copynumber: 4.1 Consensus size: 46
28693880 CCCGCCCATA
* * ***
28693890 AGTGAACTCGGACTCAACTCAACGAGCTCGG--GCGTTCGCATCCAT
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAAACATCC-T
* *
28693935 AAGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTTACATCTCT
1 -AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTA--AACATC-CT
* * * * **
28693985 --CGAACTTGGACTCAACTCAACGAGTTTGGA--CATTCACATCCAT
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAAACATCC-T
* *
28694028 AAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCCAAATATCCT
1 -AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAAACATCCT
28694075 AGTGA
1 AGTGA
28694080 CATGTCACTT
Statistics
Matches: 114, Mismatches: 19, Indels: 22
0.74 0.12 0.14
Matches are distributed among these distances:
42 1 0.01
43 6 0.05
45 2 0.02
46 63 0.55
47 27 0.24
48 9 0.08
50 5 0.04
51 1 0.01
ACGTcount: A:0.29, C:0.28, G:0.21, T:0.23
Consensus pattern (46 bp):
AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAAACATCCT
Found at i:28706388 original size:28 final size:28
Alignment explanation
Indices: 28706356--28706465 Score: 102
Period size: 28 Copynumber: 3.9 Consensus size: 28
28706346 TACCTGTATA
*
28706356 TGGCCCATTAGGCCCAATCTC-TTTCAAT-
1 TGGCCCATTAGGCCCAATCACATTT--ATG
*
28706384 TGGCCCATT-GGTCCAATCACATTTATG
1 TGGCCCATTAGGCCCAATCACATTTATG
* * *
28706411 TGGCCCATTAGGCCCAAATCATATTCATA
1 TGGCCCATTAGGCCC-AATCACATTTATG
*
28706440 TGG-CTATTAGGCCCAAATCACATTTA
1 TGGCCCATTAGGCCC-AATCACATTTA
28706466 CAATCATGCT
Statistics
Matches: 69, Mismatches: 9, Indels: 8
0.80 0.10 0.09
Matches are distributed among these distances:
26 2 0.03
27 18 0.26
28 36 0.52
29 13 0.19
ACGTcount: A:0.26, C:0.27, G:0.15, T:0.31
Consensus pattern (28 bp):
TGGCCCATTAGGCCCAATCACATTTATG
Found at i:28706730 original size:16 final size:16
Alignment explanation
Indices: 28706686--28706730 Score: 72
Period size: 16 Copynumber: 2.8 Consensus size: 16
28706676 AATTTTTGAC
*
28706686 ATTTTGGCTTTTCGGT
1 ATTTTGGCTTTTTGGT
*
28706702 ATTTTGACTTTTTGGT
1 ATTTTGGCTTTTTGGT
28706718 ATTTTGGCTTTTT
1 ATTTTGGCTTTTT
28706731 CTGATCTACT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.09, C:0.09, G:0.20, T:0.62
Consensus pattern (16 bp):
ATTTTGGCTTTTTGGT
Found at i:28722985 original size:8 final size:8
Alignment explanation
Indices: 28722974--28723022 Score: 77
Period size: 8 Copynumber: 6.5 Consensus size: 8
28722964 AATATTAAAA
28722974 TTTTAAGT
1 TTTTAAGT
28722982 TTTTAAGT
1 TTTTAAGT
28722990 TTTTAAGT
1 TTTTAAGT
28722998 TTTTAAG-
1 TTTTAAGT
28723005 TTTTAA-T
1 TTTTAAGT
28723012 TTTTAA-T
1 TTTTAAGT
28723019 TTTT
1 TTTT
28723023 CAATTTTCAA
Statistics
Matches: 40, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
7 17 0.43
8 23 0.57
ACGTcount: A:0.24, C:0.00, G:0.08, T:0.67
Consensus pattern (8 bp):
TTTTAAGT
Found at i:28723027 original size:8 final size:7
Alignment explanation
Indices: 28722974--28723037 Score: 74
Period size: 8 Copynumber: 8.6 Consensus size: 7
28722964 AATATTAAAA
28722974 TTTTAAGT
1 TTTTAA-T
28722982 TTTTAAGT
1 TTTTAA-T
28722990 TTTTAAGT
1 TTTTAA-T
*
28722998 TTTTAAG
1 TTTTAAT
28723005 TTTTAAT
1 TTTTAAT
28723012 TTTTAAT
1 TTTTAAT
28723019 TTTTCAAT
1 TTTT-AAT
*
28723027 TTTCAAT
1 TTTTAAT
28723034 TTTT
1 TTTT
28723038 TTGAAGATTT
Statistics
Matches: 51, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
7 23 0.45
8 28 0.55
ACGTcount: A:0.25, C:0.03, G:0.06, T:0.66
Consensus pattern (7 bp):
TTTTAAT
Found at i:28723027 original size:15 final size:14
Alignment explanation
Indices: 28722974--28723037 Score: 74
Period size: 15 Copynumber: 4.3 Consensus size: 14
28722964 AATATTAAAA
28722974 TTTTAAGTTTTTAAGT
1 TTTTAA-TTTTTAA-T
*
28722990 TTTTAAGTTTTTAAG
1 TTTTAA-TTTTTAAT
28723005 TTTTAATTTTTAAT
1 TTTTAATTTTTAAT
*
28723019 TTTTCAATTTTCAAT
1 TTTT-AATTTTTAAT
28723034 TTTT
1 TTTT
28723038 TTGAAGATTT
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
14 11 0.25
15 19 0.43
16 14 0.32
ACGTcount: A:0.25, C:0.03, G:0.06, T:0.66
Consensus pattern (14 bp):
TTTTAATTTTTAAT
Found at i:28723436 original size:21 final size:21
Alignment explanation
Indices: 28723412--28723451 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
28723402 TAAAAATTAA
28723412 ATCCCAAATCCTAAACCATAT
1 ATCCCAAATCCTAAACCATAT
* *
28723433 ATCCTAAATCCTAGACCAT
1 ATCCCAAATCCTAAACCAT
28723452 GAACATATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.40, C:0.33, G:0.03, T:0.25
Consensus pattern (21 bp):
ATCCCAAATCCTAAACCATAT
Found at i:28723752 original size:66 final size:66
Alignment explanation
Indices: 28723620--28723753 Score: 153
Period size: 66 Copynumber: 2.0 Consensus size: 66
28723610 GGGTTGGGGT
** * * *
28723620 TTAGTGGTTAGAGTTTTAAGAGTTTATGATTTGAGATTTAGGGTTTGGTGTTTAAAAAGTTATTG
1 TTAGTGGTTAGAGTTTTAAGAGTTTATGATTAAAGATTTAGGGTCTGGTGGTTAAAAAGGTATTG
28723685 A
66 A
* * * * * *
28723686 TTAGTGTTTATAGTTTTAGGGGTTTATGATTAAAGATTTAGGGTCTGAG-GGTTAAAAGGGTGTT
1 TTAGTGGTTAGAGTTTTAAGAGTTTATGATTAAAGATTTAGGGTCTG-GTGGTTAAAAAGGTATT
28723750 GA
65 GA
28723752 TT
1 TT
28723754 TAAGGGGTTA
Statistics
Matches: 56, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
66 55 0.98
67 1 0.02
ACGTcount: A:0.26, C:0.01, G:0.29, T:0.44
Consensus pattern (66 bp):
TTAGTGGTTAGAGTTTTAAGAGTTTATGATTAAAGATTTAGGGTCTGGTGGTTAAAAAGGTATTG
A
Found at i:28724254 original size:41 final size:41
Alignment explanation
Indices: 28724209--28724440 Score: 236
Period size: 41 Copynumber: 5.7 Consensus size: 41
28724199 ACCTCAATCT
28724209 ATAGCGGCGTTTTTCCAAAAGCGCCGCTAAAAAATTGAGCA
1 ATAGCGGCGTTTTTCCAAAAGCGCCGCTAAAAAATTGAGCA
*
28724250 ATAGCGGCGTTTTTCCAGAAA-CGCC-CT-AAAAACTGAGCA
1 ATAGCGGCGTTTTTCCA-AAAGCGCCGCTAAAAAATTGAGCA
* * * * ** * * *
28724289 ATAGTGGCATTTTCCCAAAATCGCCGCTAAAACCTCGATCT
1 ATAGCGGCGTTTTTCCAAAAGCGCCGCTAAAAAATTGAGCA
* * ** * * *
28724330 ATAGTGGTGTTTTTCCAAAAGCGCCGCTAAAACCTCGATCT
1 ATAGCGGCGTTTTTCCAAAAGCGCCGCTAAAAAATTGAGCA
* *
28724371 ATAGCGGCGTTTTTCCAAAAGCGGCGCTAAAAAACTGAGCA
1 ATAGCGGCGTTTTTCCAAAAGCGCCGCTAAAAAATTGAGCA
* * *
28724412 ATAACAGCGTTTTTCCAAAAGCGTCGCTA
1 ATAGCGGCGTTTTTCCAAAAGCGCCGCTA
28724441 TTGCTCCATT
Statistics
Matches: 161, Mismatches: 26, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
38 3 0.02
39 29 0.18
40 4 0.02
41 122 0.76
42 3 0.02
ACGTcount: A:0.31, C:0.25, G:0.20, T:0.24
Consensus pattern (41 bp):
ATAGCGGCGTTTTTCCAAAAGCGCCGCTAAAAAATTGAGCA
Found at i:28724543 original size:41 final size:41
Alignment explanation
Indices: 28724436--28724545 Score: 125
Period size: 41 Copynumber: 2.7 Consensus size: 41
28724426 CCAAAAGCGT
* *
28724436 CGCTATTGCTCCA-TTTTTAGCGGCATTTGGACCAAAGACCC
1 CGCTATTGCT-CAGTTTTTAGCGGCGTTTGGACCAAAAACCC
* * * **
28724477 CACTATTGCTTAGTTTTTAGTGGCGTTTGGACCAAAAATGC
1 CGCTATTGCTCAGTTTTTAGCGGCGTTTGGACCAAAAACCC
28724518 CGCTATTGCTCAGTTTTTTA-CGGCGTTT
1 CGCTATTGCTCAG-TTTTTAGCGGCGTTT
28724546 TTAATAAAAC
Statistics
Matches: 57, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
40 1 0.02
41 50 0.88
42 6 0.11
ACGTcount: A:0.20, C:0.23, G:0.21, T:0.36
Consensus pattern (41 bp):
CGCTATTGCTCAGTTTTTAGCGGCGTTTGGACCAAAAACCC
Found at i:28729328 original size:40 final size:40
Alignment explanation
Indices: 28729284--28729435 Score: 250
Period size: 40 Copynumber: 3.8 Consensus size: 40
28729274 GGATATAGCT
* **
28729284 ACTCGCTCAAATGCCTTCGGGACTTAGCCCGGTTATAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGAAATAGTA
* * *
28729324 ACTCGCACAATTGCTTTCGGGACTTAGCCCGGAAATAGCA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGAAATAGTA
28729364 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGAAATAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGAAATAGTA
28729404 ACTCGCACAAATGCCTTCGGGACTTAGCCCGG
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGG
28729436 TTATCATCCG
Statistics
Matches: 103, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 103 1.00
ACGTcount: A:0.26, C:0.29, G:0.23, T:0.22
Consensus pattern (40 bp):
ACTCGCACAAATGCCTTCGGGACTTAGCCCGGAAATAGTA
Found at i:28731712 original size:24 final size:24
Alignment explanation
Indices: 28731664--28731721 Score: 73
Period size: 24 Copynumber: 2.4 Consensus size: 24
28731654 ATTTCCTGTC
*
28731664 TCTTTTCCTTTTTCGTTCTTTTTCT
1 TCTTTT-CTTTTTCATTCTTTTTCT
28731689 TCTTTTCTTTTTCATT-TTTATTCT
1 TCTTTTCTTTTTCATTCTTT-TTCT
*
28731713 TCTTCTCTT
1 TCTTTTCTT
28731722 CCTTTCTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
23 3 0.10
24 21 0.70
25 6 0.20
ACGTcount: A:0.03, C:0.22, G:0.02, T:0.72
Consensus pattern (24 bp):
TCTTTTCTTTTTCATTCTTTTTCT
Found at i:28731728 original size:32 final size:31
Alignment explanation
Indices: 28731656--28731731 Score: 82
Period size: 32 Copynumber: 2.4 Consensus size: 31
28731646 AACGTCTTAT
* * *
28731656 TTCCTGTCTCTTTTCCTTTTTCGTTCTTTTTC
1 TTCCTTTCT-TTTTCATTTTTCATTCTTTTTC
*
28731688 TTCTTTTCTTTTTCATTTTT-ATTCTTCTTCTC
1 TTCCTTTCTTTTTCATTTTTCATTCTT-TT-TC
28731720 TTCCTTTCTTTT
1 TTCCTTTCTTTT
28731732 CTTTTCCTTG
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
30 5 0.14
31 12 0.32
32 20 0.54
ACGTcount: A:0.03, C:0.25, G:0.03, T:0.70
Consensus pattern (31 bp):
TTCCTTTCTTTTTCATTTTTCATTCTTTTTC
Found at i:28732389 original size:64 final size:64
Alignment explanation
Indices: 28732320--28732481 Score: 225
Period size: 64 Copynumber: 2.5 Consensus size: 64
28732310 AATGCGGGGT
* * * *
28732320 TCACATAGGCCAAGGATACGGGCATGTGTCCAGGCCGAGTAACTCACTGATTATAAGATAAGGA
1 TCACATGGGCCAAGGATACGGGCATGTGTCCAGGCCGAGTAACTCACTAATTACAAGATAACGA
* * * *
28732384 TCACATGGGCCAAGGATAAGGGCGTGTGTCCAGGCCGTGTAACTTACTAATTACAAGATAACGA
1 TCACATGGGCCAAGGATACGGGCATGTGTCCAGGCCGAGTAACTCACTAATTACAAGATAACGA
* * *
28732448 TCATATGGGCCAAGGACACCGGCATGTGTCCAGG
1 TCACATGGGCCAAGGATACGGGCATGTGTCCAGG
28732482 ACATAGCTAT
Statistics
Matches: 85, Mismatches: 13, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
64 85 1.00
ACGTcount: A:0.30, C:0.22, G:0.28, T:0.20
Consensus pattern (64 bp):
TCACATGGGCCAAGGATACGGGCATGTGTCCAGGCCGAGTAACTCACTAATTACAAGATAACGA
Found at i:28735198 original size:12 final size:12
Alignment explanation
Indices: 28735181--28735210 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
28735171 TTTTTAGTTT
28735181 TTTATTTGTTCA
1 TTTATTTGTTCA
28735193 TTTATTTGTTCA
1 TTTATTTGTTCA
28735205 TTTATT
1 TTTATT
28735211 CGTTATTCAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.17, C:0.07, G:0.07, T:0.70
Consensus pattern (12 bp):
TTTATTTGTTCA
Found at i:28735730 original size:29 final size:29
Alignment explanation
Indices: 28735697--28735915 Score: 162
Period size: 29 Copynumber: 7.6 Consensus size: 29
28735687 CTTTATGATG
*
28735697 ATCTCTATTATAAGGAAGCCTTTGTGGCT
1 ATCTCTATTAAAAGGAAGCCTTTGTGGCT
* * * * *
28735726 GTCTCAATT-AAATGAACGCCTATGTGGCA
1 ATCTCTATTAAAAGGAA-GCCTTTGTGGCT
* * *
28735755 ATCTCTGTTAAAATGATGCCTTTGTGGCT
1 ATCTCTATTAAAAGGAAGCCTTTGTGGCT
* *
28735784 ATCAT-TGTT-AAATGAATGCCTTTGTGGCT
1 ATC-TCTATTAAAAGGAA-GCCTTTGTGGCT
* * * * * *
28735813 ATCTCAAATAAAAGGATGTCTTTATGGTT
1 ATCTCTATTAAAAGGAAGCCTTTGTGGCT
* *
28735842 ATCTCTATTAAAAGGATGTCTTTGTGGCT
1 ATCTCTATTAAAAGGAAGCCTTTGTGGCT
* *
28735871 ATCTCTGTTAAAAGGATGTCC-TTGTGG-T
1 ATCTCTATTAAAAGGAAG-CCTTTGTGGCT
28735899 CATCTCTATT-AAAGGAA
1 -ATCTCTATTAAAAGGAA
28735916 TGTCTTGTGG
Statistics
Matches: 153, Mismatches: 29, Indels: 17
0.77 0.15 0.09
Matches are distributed among these distances:
28 19 0.12
29 121 0.79
30 13 0.08
ACGTcount: A:0.27, C:0.16, G:0.20, T:0.37
Consensus pattern (29 bp):
ATCTCTATTAAAAGGAAGCCTTTGTGGCT
Found at i:28735904 original size:87 final size:87
Alignment explanation
Indices: 28735714--28735921 Score: 208
Period size: 87 Copynumber: 2.4 Consensus size: 87
28735704 TTATAAGGAA
* * * * * * * ** * *
28735714 GCCTTTGTGGCTGTCTCAATTAAATGAACGCCTATGTGGCAATCTCTGTTAAAATGATGCCTTTG
1 GCCTTTGTGGCTATCTCAATAAAAGGAATGTCTTTATGGTTATCTCTATTAAAAGGATGCCTTTG
*
28735779 TGGCTATCATTGTTAAATGAAT
66 TGGCTATCATTGTTAAAAGAAT
*
28735801 GCCTTTGTGGCTATCTCAAATAAAAGG-ATGTCTTTATGGTTATCTCTATTAAAAGGATGTCTTT
1 GCCTTTGTGGCTATCTC-AATAAAAGGAATGTCTTTATGGTTATCTCTATTAAAAGGATGCCTTT
*
28735865 GTGGCTATC-TCTGTTAAAAGGAT
65 GTGGCTATCAT-TGTTAAAAGAAT
* *
28735888 GTCC-TTGTGG-TCATCTCTATTAAAGGAATGTCTT
1 G-CCTTTGTGGCT-ATCTCAATAAAAGGAATGTCTT
28735922 GTGGAAAACT
Statistics
Matches: 100, Mismatches: 16, Indels: 10
0.79 0.13 0.08
Matches are distributed among these distances:
86 9 0.09
87 82 0.82
88 9 0.09
ACGTcount: A:0.25, C:0.16, G:0.21, T:0.38
Consensus pattern (87 bp):
GCCTTTGTGGCTATCTCAATAAAAGGAATGTCTTTATGGTTATCTCTATTAAAAGGATGCCTTTG
TGGCTATCATTGTTAAAAGAAT
Found at i:28735940 original size:57 final size:58
Alignment explanation
Indices: 28735821--28735943 Score: 160
Period size: 58 Copynumber: 2.1 Consensus size: 58
28735811 CTATCTCAAA
* * ** *
28735821 TAAAAGGATGTCTTTATGGTTATCTCTATTAAAAGGATGTCTTTGTGGCTATCTCTGT
1 TAAAAGGATGTCCTTATGGTCATCTCTATTAAAAGGATGTCTTTGTGGAAAACTCTGT
* *
28735879 TAAAAGGATGTCCTTGTGGTCATCTCTATT-AAAGGAATGTC-TTGTGGAAAACTTTGT
1 TAAAAGGATGTCCTTATGGTCATCTCTATTAAAAGG-ATGTCTTTGTGGAAAACTCTGT
28735936 TAAAAGGA
1 TAAAAGGA
28735944 CGCCTTTGTG
Statistics
Matches: 57, Mismatches: 7, Indels: 3
0.85 0.10 0.04
Matches are distributed among these distances:
57 25 0.44
58 32 0.56
ACGTcount: A:0.28, C:0.11, G:0.22, T:0.38
Consensus pattern (58 bp):
TAAAAGGATGTCCTTATGGTCATCTCTATTAAAAGGATGTCTTTGTGGAAAACTCTGT
Found at i:28735941 original size:29 final size:28
Alignment explanation
Indices: 28735821--28735943 Score: 104
Period size: 29 Copynumber: 4.3 Consensus size: 28
28735811 CTATCTCAAA
* ** *
28735821 TAAAAGGATGTCTTTATGGTTATCTCTAT
1 TAAAAGGATGTC-TTGTGGAAATCTCTGT
**
28735850 TAAAAGGATGTCTTTGTGGCTATCTCTGT
1 TAAAAGGATGTC-TTGTGGAAATCTCTGT
** *
28735879 TAAAAGGATGTCCTTGTGGTCATCTCTAT
1 TAAAAGGATGT-CTTGTGGAAATCTCTGT
* *
28735908 T-AAAGGAATGTCTTGTGGAAAACTTTGT
1 TAAAAGG-ATGTCTTGTGGAAATCTCTGT
28735936 TAAAAGGA
1 TAAAAGGA
28735944 CGCCTTTGTG
Statistics
Matches: 80, Mismatches: 11, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
28 19 0.24
29 60 0.75
30 1 0.01
ACGTcount: A:0.28, C:0.11, G:0.22, T:0.38
Consensus pattern (28 bp):
TAAAAGGATGTCTTGTGGAAATCTCTGT
Found at i:28735953 original size:57 final size:58
Alignment explanation
Indices: 28735821--28735955 Score: 159
Period size: 57 Copynumber: 2.3 Consensus size: 58
28735811 CTATCTCAAA
* * * ** *
28735821 TAAAAGGATGTCTTTATGGTTATCTCTATTAAAAGGATGTCTTTGTGGCTATCTCTGT
1 TAAAAGGATGCCTTTGTGGTCATCTCTATTAAAAGGATGTCTTTGTGGAAAACTCTGT
*
28735879 TAAAAGGATGTCC-TTGTGGTCATCTCTATT-AAAGGAATGTC-TTGTGGAAAACTTTGT
1 TAAAAGGATG-CCTTTGTGGTCATCTCTATTAAAAGG-ATGTCTTTGTGGAAAACTCTGT
*
28735936 TAAAAGGACGCCTTTGTGGT
1 TAAAAGGATGCCTTTGTGGT
28735956 GTAATCTGAA
Statistics
Matches: 66, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
56 2 0.03
57 33 0.50
58 30 0.45
59 1 0.02
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (58 bp):
TAAAAGGATGCCTTTGTGGTCATCTCTATTAAAAGGATGTCTTTGTGGAAAACTCTGT
Found at i:28738426 original size:27 final size:27
Alignment explanation
Indices: 28738396--28738481 Score: 77
Period size: 27 Copynumber: 3.2 Consensus size: 27
28738386 TTGACATGGT
28738396 CTTACATAATTTCCTTGCCTTGTAGAA
1 CTTACATAATTTCCTTGCCTTGTAGAA
* * * * * **
28738423 CTTAC-CAGTGT-CATGCCTTGGCATGGT
1 CTTACATAATTTCCTTGCCTT-GTA-GAA
28738450 CTTACATAATTTCCTTGCCTTGTAGAA
1 CTTACATAATTTCCTTGCCTTGTAGAA
28738477 CTTAC
1 CTTAC
28738482 CAATGTCATG
Statistics
Matches: 41, Mismatches: 14, Indels: 8
0.65 0.22 0.13
Matches are distributed among these distances:
25 7 0.17
26 5 0.12
27 17 0.41
28 5 0.12
29 7 0.17
ACGTcount: A:0.22, C:0.24, G:0.15, T:0.38
Consensus pattern (27 bp):
CTTACATAATTTCCTTGCCTTGTAGAA
Found at i:28738440 original size:25 final size:25
Alignment explanation
Indices: 28738411--28738496 Score: 73
Period size: 25 Copynumber: 3.3 Consensus size: 25
28738401 ATAATTTCCT
*
28738411 TGCCTTGTAGAACTTACCAGTGTCA
1 TGCCTTGTAGAACTTACCAATGTCA
* ** * * *
28738436 TGCCTTGGCATGGTCTTACATAATTTCCT
1 TGCCTT-GTA-GAACTTAC-CAATGT-CA
28738465 TGCCTTGTAGAACTTACCAATGTCA
1 TGCCTTGTAGAACTTACCAATGTCA
28738490 TGCCTTG
1 TGCCTTG
28738497 GCATGGTCTT
Statistics
Matches: 44, Mismatches: 13, Indels: 8
0.68 0.20 0.12
Matches are distributed among these distances:
25 14 0.32
26 6 0.14
27 12 0.27
28 5 0.11
29 7 0.16
ACGTcount: A:0.21, C:0.24, G:0.19, T:0.36
Consensus pattern (25 bp):
TGCCTTGTAGAACTTACCAATGTCA
Found at i:28738507 original size:27 final size:27
Alignment explanation
Indices: 28738423--28738508 Score: 77
Period size: 27 Copynumber: 3.2 Consensus size: 27
28738413 CCTTGTAGAA
*
28738423 CTTACCAGTGTCATGCCTTGGCATGGT
1 CTTACCAATGTCATGCCTTGGCATGGT
* * * * **
28738450 CTTACATAATTTCCTTGCCTT-GTA-GAA
1 CTTAC-CAATGT-CATGCCTTGGCATGGT
28738477 CTTACCAATGTCATGCCTTGGCATGGT
1 CTTACCAATGTCATGCCTTGGCATGGT
28738504 CTTAC
1 CTTAC
28738509 TTGGTATCCT
Statistics
Matches: 42, Mismatches: 13, Indels: 8
0.67 0.21 0.13
Matches are distributed among these distances:
25 7 0.17
26 6 0.14
27 17 0.40
28 5 0.12
29 7 0.17
ACGTcount: A:0.20, C:0.26, G:0.19, T:0.36
Consensus pattern (27 bp):
CTTACCAATGTCATGCCTTGGCATGGT
Found at i:28738519 original size:54 final size:54
Alignment explanation
Indices: 28738374--28738508 Score: 234
Period size: 54 Copynumber: 2.5 Consensus size: 54
28738364 AGTAGTTTAT
* * *
28738374 CAATGCCATGTCTTGACATGGTCTTACATAATTTCCTTGCCTTGTAGAACTTAC
1 CAATGTCATGCCTTGGCATGGTCTTACATAATTTCCTTGCCTTGTAGAACTTAC
*
28738428 CAGTGTCATGCCTTGGCATGGTCTTACATAATTTCCTTGCCTTGTAGAACTTAC
1 CAATGTCATGCCTTGGCATGGTCTTACATAATTTCCTTGCCTTGTAGAACTTAC
28738482 CAATGTCATGCCTTGGCATGGTCTTAC
1 CAATGTCATGCCTTGGCATGGTCTTAC
28738509 TTGGTATCCT
Statistics
Matches: 76, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
54 76 1.00
ACGTcount: A:0.21, C:0.24, G:0.18, T:0.36
Consensus pattern (54 bp):
CAATGTCATGCCTTGGCATGGTCTTACATAATTTCCTTGCCTTGTAGAACTTAC
Found at i:28740259 original size:27 final size:28
Alignment explanation
Indices: 28740228--28740290 Score: 76
Period size: 27 Copynumber: 2.3 Consensus size: 28
28740218 TTAGTTTACC
*
28740228 AAATTACTGAAA-TACCCTCGACTTGTA
1 AAATTACTGAAAGTACCCTCGACTTATA
* * *
28740255 AAATTAC-CAAAGTACTCTCGATTTATA
1 AAATTACTGAAAGTACCCTCGACTTATA
28740282 AAATTACTG
1 AAATTACTG
28740291 TTTTACCCTC
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
26 3 0.10
27 26 0.90
ACGTcount: A:0.40, C:0.19, G:0.10, T:0.32
Consensus pattern (28 bp):
AAATTACTGAAAGTACCCTCGACTTATA
Found at i:28740301 original size:27 final size:27
Alignment explanation
Indices: 28740271--28740352 Score: 137
Period size: 27 Copynumber: 3.0 Consensus size: 27
28740261 CCAAAGTACT
*
28740271 CTCGATTTATAAAATTACTGTTTTACC
1 CTCGATTTACAAAATTACTGTTTTACC
* *
28740298 CTCGATTTACAGAATTACCGTTTTACC
1 CTCGATTTACAAAATTACTGTTTTACC
28740325 CTCGATTTACAAAATTACTGTTTTACC
1 CTCGATTTACAAAATTACTGTTTTACC
28740352 C
1 C
28740353 CTAGGGTGTT
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 50 1.00
ACGTcount: A:0.28, C:0.23, G:0.09, T:0.40
Consensus pattern (27 bp):
CTCGATTTACAAAATTACTGTTTTACC
Found at i:28740314 original size:54 final size:54
Alignment explanation
Indices: 28740222--28740352 Score: 140
Period size: 54 Copynumber: 2.4 Consensus size: 54
28740212 AATACTTTAG
* *** *
28740222 TTTACCAAATTACTGAAATACCCTCGACTTGTAAAATTACCAAAGTACTCTCGA
1 TTTACAAAATTACTGTTTTACCCTCGACTTGTAAAATTACCAAAGTACCCTCGA
* ****
28740276 TTTATAAAATTACTGTTTTACCCTCGA-TT-TACAGAATTACCGTTTTACCCTCGA
1 TTTACAAAATTACTGTTTTACCCTCGACTTGTA-A-AATTACCAAAGTACCCTCGA
28740330 TTTACAAAATTACTGTTTTACCC
1 TTTACAAAATTACTGTTTTACCC
28740353 CTAGGGTGTT
Statistics
Matches: 64, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
52 2 0.03
53 3 0.05
54 59 0.92
ACGTcount: A:0.32, C:0.23, G:0.08, T:0.37
Consensus pattern (54 bp):
TTTACAAAATTACTGTTTTACCCTCGACTTGTAAAATTACCAAAGTACCCTCGA
Found at i:28740724 original size:27 final size:26
Alignment explanation
Indices: 28740684--28740740 Score: 69
Period size: 27 Copynumber: 2.2 Consensus size: 26
28740674 ATATATATAT
* *
28740684 ATATCTGTTCTGGTGGCCTAGCCACA
1 ATATCTATTCTGGTGACCTAGCCACA
* *
28740710 ATATCTATATCTGGTGACTTAGTCACA
1 ATATCTAT-TCTGGTGACCTAGCCACA
28740737 ATAT
1 ATAT
28740741 TTGGTAGCCT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
26 7 0.27
27 19 0.73
ACGTcount: A:0.26, C:0.21, G:0.18, T:0.35
Consensus pattern (26 bp):
ATATCTATTCTGGTGACCTAGCCACA
Found at i:28740908 original size:31 final size:30
Alignment explanation
Indices: 28740873--28740995 Score: 89
Period size: 31 Copynumber: 4.2 Consensus size: 30
28740863 TCTAATTTTG
*
28740873 ATTCTGTTACCTGATACTGATTCTGATTCTA
1 ATTCTGTCACCTG-TACTGATTCTGATTCTA
28740904 ATTCTGTCACC--TA---ATTCTGATTCTA
1 ATTCTGTCACCTGTACTGATTCTGATTCTA
* * * *
28740929 ATTTTGTCACCTAATTCTGATTCTGATTCTG
1 ATTCTGTCACCT-GTACTGATTCTGATTCTA
* *
28740960 ATTCTG--ATTCTGTCACCTGATTCTGATTCTG
1 ATTCTGTCA-CCTGT-A-CTGATTCTGATTCTA
28740991 ATTCT
1 ATTCT
28740996 CATTTTGATT
Statistics
Matches: 75, Mismatches: 8, Indels: 18
0.74 0.08 0.18
Matches are distributed among these distances:
25 22 0.29
28 3 0.04
29 2 0.03
30 2 0.03
31 46 0.61
ACGTcount: A:0.20, C:0.21, G:0.12, T:0.46
Consensus pattern (30 bp):
ATTCTGTCACCTGTACTGATTCTGATTCTA
Found at i:28740919 original size:13 final size:13
Alignment explanation
Indices: 28740901--28740947 Score: 53
Period size: 13 Copynumber: 3.7 Consensus size: 13
28740891 GATTCTGATT
28740901 CTAATTCTGTCAC
1 CTAATTCTGTCAC
*
28740914 CTAATTCTG--ATT
1 CTAATTCTGTCA-C
*
28740926 CTAATTTTGTCAC
1 CTAATTCTGTCAC
28740939 CTAATTCTG
1 CTAATTCTG
28740948 ATTCTGATTC
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
11 1 0.04
12 8 0.30
13 17 0.63
14 1 0.04
ACGTcount: A:0.23, C:0.23, G:0.09, T:0.45
Consensus pattern (13 bp):
CTAATTCTGTCAC
Found at i:28740920 original size:25 final size:25
Alignment explanation
Indices: 28740892--28740959 Score: 118
Period size: 25 Copynumber: 2.7 Consensus size: 25
28740882 CCTGATACTG
28740892 ATTCTGATTCTAATTCTGTCACCTA
1 ATTCTGATTCTAATTCTGTCACCTA
*
28740917 ATTCTGATTCTAATTTTGTCACCTA
1 ATTCTGATTCTAATTCTGTCACCTA
*
28740942 ATTCTGATTCTGATTCTG
1 ATTCTGATTCTAATTCTG
28740960 ATTCTGATTC
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 40 1.00
ACGTcount: A:0.22, C:0.21, G:0.10, T:0.47
Consensus pattern (25 bp):
ATTCTGATTCTAATTCTGTCACCTA
Found at i:28740953 original size:6 final size:6
Alignment explanation
Indices: 28740942--28741016 Score: 82
Period size: 6 Copynumber: 12.3 Consensus size: 6
28740932 TTGTCACCTA
*
28740942 ATTCTG ATTCTG ATTCTG ATTCTG ATTCTG -TCACCTG ATTCTG ATTCTG
1 ATTCTG ATTCTG ATTCTG ATTCTG ATTCTG AT--TCTG ATTCTG ATTCTG
* *
28740991 ATTCTC ATTTTG ATTCT- AGTTCTG AT
1 ATTCTG ATTCTG ATTCTG A-TTCTG AT
28741017 AATGTTTCTT
Statistics
Matches: 58, Mismatches: 6, Indels: 10
0.78 0.08 0.14
Matches are distributed among these distances:
5 2 0.03
6 51 0.88
7 4 0.07
8 1 0.02
ACGTcount: A:0.17, C:0.19, G:0.15, T:0.49
Consensus pattern (6 bp):
ATTCTG
Found at i:28740958 original size:37 final size:37
Alignment explanation
Indices: 28740917--28740995 Score: 131
Period size: 37 Copynumber: 2.1 Consensus size: 37
28740907 CTGTCACCTA
*
28740917 ATTCTGATTCTAATTTTGTCACCTAATTCTGATTCTG
1 ATTCTGATTCTAATTCTGTCACCTAATTCTGATTCTG
* *
28740954 ATTCTGATTCTGATTCTGTCACCTGATTCTGATTCTG
1 ATTCTGATTCTAATTCTGTCACCTAATTCTGATTCTG
28740991 ATTCT
1 ATTCT
28740996 CATTTTGATT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.19, C:0.20, G:0.13, T:0.48
Consensus pattern (37 bp):
ATTCTGATTCTAATTCTGTCACCTAATTCTGATTCTG
Found at i:28741005 original size:37 final size:37
Alignment explanation
Indices: 28740917--28741007 Score: 128
Period size: 37 Copynumber: 2.5 Consensus size: 37
28740907 CTGTCACCTA
* * *
28740917 ATTCTGATTCTAATTTTGTCACCTAATTCTGATTCTG
1 ATTCTCATTCTGATTCTGTCACCTAATTCTGATTCTG
* *
28740954 ATTCTGATTCTGATTCTGTCACCTGATTCTGATTCTG
1 ATTCTCATTCTGATTCTGTCACCTAATTCTGATTCTG
*
28740991 ATTCTCATTTTGATTCT
1 ATTCTCATTCTGATTCT
28741008 AGTTCTGATA
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 49 1.00
ACGTcount: A:0.19, C:0.20, G:0.12, T:0.49
Consensus pattern (37 bp):
ATTCTCATTCTGATTCTGTCACCTAATTCTGATTCTG
Found at i:28745385 original size:11 final size:11
Alignment explanation
Indices: 28745369--28745452 Score: 64
Period size: 11 Copynumber: 7.6 Consensus size: 11
28745359 ACAACCAAAA
* *
28745369 CACCACTATAT
1 CACCACCATAG
*
28745380 CACCACAATA-
1 CACCACCATAG
28745390 CAACCACCATAG
1 C-ACCACCATAG
* *
28745402 CACCACCACAC
1 CACCACCATAG
*
28745413 CATCACCATAG
1 CACCACCATAG
*
28745424 CACCACCATAT
1 CACCACCATAG
*
28745435 CACCATCC-TTG
1 CACCA-CCATAG
28745446 CACCACC
1 CACCACC
28745453 TCCAAAACCA
Statistics
Matches: 59, Mismatches: 11, Indels: 7
0.77 0.14 0.09
Matches are distributed among these distances:
10 3 0.05
11 53 0.90
12 3 0.05
ACGTcount: A:0.36, C:0.46, G:0.04, T:0.14
Consensus pattern (11 bp):
CACCACCATAG
Found at i:28762408 original size:4 final size:4
Alignment explanation
Indices: 28762401--28762437 Score: 74
Period size: 4 Copynumber: 9.2 Consensus size: 4
28762391 AAAAAAGAAA
28762401 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT A
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT A
28762438 TTGGTAGTAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 33 1.00
ACGTcount: A:0.51, C:0.24, G:0.00, T:0.24
Consensus pattern (4 bp):
ACAT
Found at i:28771433 original size:40 final size:40
Alignment explanation
Indices: 28771388--28771659 Score: 368
Period size: 40 Copynumber: 6.8 Consensus size: 40
28771378 ATAACCACAA
* * * *
28771388 GCACAATTGCCTTCGGGTCTTAACCCGGGTATAGCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
28771428 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
* *
28771468 GCACAAATGCCTTCGGGTCTTAGCCCGGATAAAATC-ACTA
1 GCACAAATGCCTTCGGGTCTTAGCCCGGAT-ATATCAACTC
* * * * *
28771508 GCACAATTGCCATCGGGTCTTAACCCGGGTATAGCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
*
28771548 GCACAAATGCCTCCGGGTCTTAGCCCGGATATATCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
* *
28771588 GCACAAATGCCTTCGGGTCTTAGCCCGGATAAAATC-ACTA
1 GCACAAATGCCTTCGGGTCTTAGCCCGGAT-ATATCAACTC
* *
28771628 GCATAAATGCCTTCGGGACTTAGCCCGGATAT
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATAT
28771660 CATTCAAATG
Statistics
Matches: 204, Mismatches: 25, Indels: 7
0.86 0.11 0.03
Matches are distributed among these distances:
39 4 0.02
40 192 0.94
41 8 0.04
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (40 bp):
GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
Found at i:28771585 original size:120 final size:120
Alignment explanation
Indices: 28771368--28771655 Score: 488
Period size: 120 Copynumber: 2.4 Consensus size: 120
28771358 TCTTCGGAAT
* * *
28771368 TTAG-CCGGATATAACCACAAGCACAATTGCCTTCGGGTCTTAACCCGGGTATAGCAACTCGCAC
1 TTAGCCCGGATAAAATCACTAGCACAATTGCCTTCGGGTCTTAACCCGGGTATAGCAACTCGCAC
*
28771432 AAATGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCACAAATGCCTTCGGGTC
66 AAATGCCTCCGGGTCTTAGCCCGGATATATCAACTCGCACAAATGCCTTCGGGTC
*
28771487 TTAGCCCGGATAAAATCACTAGCACAATTGCCATCGGGTCTTAACCCGGGTATAGCAACTCGCAC
1 TTAGCCCGGATAAAATCACTAGCACAATTGCCTTCGGGTCTTAACCCGGGTATAGCAACTCGCAC
28771552 AAATGCCTCCGGGTCTTAGCCCGGATATATCAACTCGCACAAATGCCTTCGGGTC
66 AAATGCCTCCGGGTCTTAGCCCGGATATATCAACTCGCACAAATGCCTTCGGGTC
* * * *
28771607 TTAGCCCGGATAAAATCACTAGCATAAATGCCTTCGGGACTTAGCCCGG
1 TTAGCCCGGATAAAATCACTAGCACAATTGCCTTCGGGTCTTAACCCGG
28771656 ATATCATTCA
Statistics
Matches: 158, Mismatches: 10, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
119 4 0.03
120 154 0.97
ACGTcount: A:0.27, C:0.29, G:0.21, T:0.23
Consensus pattern (120 bp):
TTAGCCCGGATAAAATCACTAGCACAATTGCCTTCGGGTCTTAACCCGGGTATAGCAACTCGCAC
AAATGCCTCCGGGTCTTAGCCCGGATATATCAACTCGCACAAATGCCTTCGGGTC
Found at i:28787132 original size:13 final size:13
Alignment explanation
Indices: 28787114--28787139 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
28787104 GAATTTGAAT
28787114 GGGTTGTTGGAGG
1 GGGTTGTTGGAGG
28787127 GGGTTGTTGGAGG
1 GGGTTGTTGGAGG
28787140 AGTAAACTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.08, C:0.00, G:0.62, T:0.31
Consensus pattern (13 bp):
GGGTTGTTGGAGG
Found at i:28788955 original size:27 final size:27
Alignment explanation
Indices: 28788924--28789029 Score: 122
Period size: 27 Copynumber: 3.9 Consensus size: 27
28788914 AGACCCCGAT
*
28788924 TTGTAAAACTACCGAAATACCCCTGGA
1 TTGTAAAATTACCGAAATACCCCTGGA
** *
28788951 TTGTAAAATTACCGAAATACCCCCAGT
1 TTGTAAAATTACCGAAATACCCCTGGA
* * *
28788978 TTGTAAAATTACTGAAATACCCTTGTA
1 TTGTAAAATTACCGAAATACCCCTGGA
* * *
28789005 GTGTAAAATTATCAAAATACCCCTG
1 TTGTAAAATTACCGAAATACCCCTG
28789030 TAGGATAAAA
Statistics
Matches: 64, Mismatches: 15, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 64 1.00
ACGTcount: A:0.38, C:0.22, G:0.12, T:0.28
Consensus pattern (27 bp):
TTGTAAAATTACCGAAATACCCCTGGA
Found at i:28788982 original size:54 final size:54
Alignment explanation
Indices: 28788923--28789027 Score: 147
Period size: 54 Copynumber: 1.9 Consensus size: 54
28788913 AAGACCCCGA
* *
28788923 TTTGTAAAACTACCGAAATACCCCTGGATTGTAAAATTACCGAAATACCCCCAG
1 TTTGTAAAACTACCGAAATACCCCTGGAGTGTAAAATTACCAAAATACCCCCAG
* * * * *
28788977 TTTGTAAAATTACTGAAATACCCTTGTAGTGTAAAATTATCAAAATACCCC
1 TTTGTAAAACTACCGAAATACCCCTGGAGTGTAAAATTACCAAAATACCCC
28789028 TGTAGGATAA
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
54 44 1.00
ACGTcount: A:0.38, C:0.22, G:0.11, T:0.29
Consensus pattern (54 bp):
TTTGTAAAACTACCGAAATACCCCTGGAGTGTAAAATTACCAAAATACCCCCAG
Found at i:28789562 original size:32 final size:32
Alignment explanation
Indices: 28789479--28789562 Score: 87
Period size: 32 Copynumber: 2.6 Consensus size: 32
28789469 ATTTACCCAA
* * * * * *
28789479 GGCTGTGTGCCGATTATATTACCGTTGCTGAT
1 GGCTATGTGCCAATTATAATACAGTTACCGAT
**
28789511 GGCTATGTGCCAAACATAATACAGTTACCGAT
1 GGCTATGTGCCAATTATAATACAGTTACCGAT
*
28789543 GGCTTTGTGCCAATTATAAT
1 GGCTATGTGCCAATTATAAT
28789563 GCCGCTACTG
Statistics
Matches: 41, Mismatches: 11, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
32 41 1.00
ACGTcount: A:0.25, C:0.19, G:0.23, T:0.33
Consensus pattern (32 bp):
GGCTATGTGCCAATTATAATACAGTTACCGAT
Found at i:28792706 original size:53 final size:54
Alignment explanation
Indices: 28792638--28792843 Score: 207
Period size: 53 Copynumber: 3.8 Consensus size: 54
28792628 TCCTTTATAT
* * * * *
28792638 ACTTACCATTTCCATGTCTTGACATGGTATTACGTGGTATCCTTGCCTTAT-GA
1 ACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATAGA
* * * *
28792691 ACTTACCATTGCCATGCCTTGGCATGGTCTTACATGGGATCTTTGCCTTATAGTA
1 ACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATAG-A
** * * * * * * *
28792746 GTTTATCAATGCCATGTCTTAACATGGTCTTACATGATTTTCTTGCCTTGTAGA
1 ACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATAGA
* * *
28792800 ACTTACCAATGTCATGCCTTGGCATGGTCTTACTTGGTATCCTT
1 ACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTT
28792844 AAACCCTAAT
Statistics
Matches: 120, Mismatches: 31, Indels: 3
0.78 0.20 0.02
Matches are distributed among these distances:
53 44 0.37
54 35 0.29
55 41 0.34
ACGTcount: A:0.20, C:0.22, G:0.18, T:0.39
Consensus pattern (54 bp):
ACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATAGA
Found at i:28802217 original size:40 final size:40
Alignment explanation
Indices: 28802173--28802252 Score: 108
Period size: 40 Copynumber: 2.0 Consensus size: 40
28802163 TACAGTCACG
*
28802173 TTCGACGACAA-ATCAGCTATATGTGGCACTTAGTGTGCGA
1 TTCGAC-ACAACATCAGCTATATATGGCACTTAGTGTGCGA
* * *
28802213 TTCGACATAACTTCGGCTATATATGGCACTTAGTGTGCGA
1 TTCGACACAACATCAGCTATATATGGCACTTAGTGTGCGA
28802253 GATCAAGATA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
39 3 0.09
40 32 0.91
ACGTcount: A:0.26, C:0.20, G:0.24, T:0.30
Consensus pattern (40 bp):
TTCGACACAACATCAGCTATATATGGCACTTAGTGTGCGA
Found at i:28802280 original size:41 final size:41
Alignment explanation
Indices: 28802188--28802337 Score: 203
Period size: 41 Copynumber: 3.7 Consensus size: 41
28802178 CGACAAATCA
* * * *
28802188 GCTATATGTGGCACTTAGTGTGCGA-TTCGACATAACTTCG
1 GCTATATATGGCACTTAGTGTGCGAGATCGAGATAGCTTCG
*
28802228 GCTATATATGGCACTTAGTGTGCGAGATCAAGATAGCTTCG
1 GCTATATATGGCACTTAGTGTGCGAGATCGAGATAGCTTCG
* * *
28802269 GCTACATATGGCACTTAGTGTGTGAGATTGAGATAGCTTCG
1 GCTATATATGGCACTTAGTGTGCGAGATCGAGATAGCTTCG
* *
28802310 GCTATATATGGCACATAGTGTGCAAGAT
1 GCTATATATGGCACTTAGTGTGCGAGAT
28802338 ATCGAGTATT
Statistics
Matches: 96, Mismatches: 13, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
40 24 0.25
41 72 0.75
ACGTcount: A:0.26, C:0.17, G:0.27, T:0.31
Consensus pattern (41 bp):
GCTATATATGGCACTTAGTGTGCGAGATCGAGATAGCTTCG
Found at i:28803368 original size:12 final size:12
Alignment explanation
Indices: 28803351--28803377 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
28803341 TAGGTTTGGT
28803351 ACGGCCTAGCAC
1 ACGGCCTAGCAC
28803363 ACGGCCTAGCAC
1 ACGGCCTAGCAC
28803375 ACG
1 ACG
28803378 AGCATGTGTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.26, C:0.41, G:0.26, T:0.07
Consensus pattern (12 bp):
ACGGCCTAGCAC
Found at i:28807262 original size:44 final size:43
Alignment explanation
Indices: 28807158--28807271 Score: 124
Period size: 44 Copynumber: 2.6 Consensus size: 43
28807148 CGGTATTTTT
* * *
28807158 CCTGCTAGGCTTGAAGCCCGATATCATTTCACCGGCATTATAG
1 CCTGCTAGGCTCGAAGCCCGATATCATTTCACCAGCATTAAAG
*
28807201 CCTGCTAGGCCCGAAGCCCGATAAT-ATTATTCACCAGC-TTAAAG
1 CCTGCTAGGCTCGAAGCCCGAT-ATCA-T-TTCACCAGCATTAAAG
* *
28807245 CTTGCTAGGCTCAAAGCCCGAATATCA
1 CCTGCTAGGCTCGAAGCCCG-ATATCA
28807272 CCATTATAAA
Statistics
Matches: 59, Mismatches: 7, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
43 21 0.36
44 27 0.46
45 11 0.19
ACGTcount: A:0.27, C:0.29, G:0.19, T:0.25
Consensus pattern (43 bp):
CCTGCTAGGCTCGAAGCCCGATATCATTTCACCAGCATTAAAG
Found at i:28807475 original size:28 final size:28
Alignment explanation
Indices: 28807382--28807473 Score: 130
Period size: 28 Copynumber: 3.3 Consensus size: 28
28807372 GAATCATTCG
* * *
28807382 ATATTTTGCACACGAAGTGTCATTCTCA
1 ATATTTCGCACACTAAGTGCCATTCTCA
* *
28807410 ATATCTCACACACTAAGTGCCATTCTCA
1 ATATTTCGCACACTAAGTGCCATTCTCA
*
28807438 ATATTTCGTACACTAAGTGCCATTCTCA
1 ATATTTCGCACACTAAGTGCCATTCTCA
28807466 ATATTTCG
1 ATATTTCG
28807474 TATACTGAGT
Statistics
Matches: 56, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 56 1.00
ACGTcount: A:0.29, C:0.25, G:0.11, T:0.35
Consensus pattern (28 bp):
ATATTTCGCACACTAAGTGCCATTCTCA
Found at i:28811417 original size:41 final size:41
Alignment explanation
Indices: 28811358--28811542 Score: 234
Period size: 41 Copynumber: 4.6 Consensus size: 41
28811348 CGAGCTTGGG
*
28811358 TTCGAAGGGCTTTTGAGCCAGTGCTAATAACCGAACTTAAT
1 TTCGAAGGGCTTTTGAGCCAGTGCTAATAACCGAACTTAGT
*
28811399 TACGAAGGGCTTTTGAGCCAGTGCTAATAACCGAACTTAGT
1 TTCGAAGGGCTTTTGAGCCAGTGCTAATAACCGAACTTAGT
* *
28811440 TTCGAAGGGCTTTTGAGCCAGTG-TCATAACCGGACTTAGT
1 TTCGAAGGGCTTTTGAGCCAGTGCTAATAACCGAACTTAGT
* * * *
28811480 TTCGAAGGGCCTTCGAGCCAGTGGCCTAAT--CCGAGCTTGGT
1 TTCGAAGGGCTTTTGAGCCAGT-G-CTAATAACCGAACTTAGT
* *
28811521 CTCGAAGGGC-TTTGAACCAGTG
1 TTCGAAGGGCTTTTGAGCCAGTG
28811543 TTAAGAATCG
Statistics
Matches: 127, Mismatches: 14, Indels: 8
0.85 0.09 0.05
Matches are distributed among these distances:
39 1 0.01
40 44 0.35
41 79 0.62
43 3 0.02
ACGTcount: A:0.24, C:0.22, G:0.27, T:0.27
Consensus pattern (41 bp):
TTCGAAGGGCTTTTGAGCCAGTGCTAATAACCGAACTTAGT
Found at i:28811498 original size:81 final size:81
Alignment explanation
Indices: 28811344--28811543 Score: 235
Period size: 81 Copynumber: 2.5 Consensus size: 81
28811334 TCTGGGTGTA
* * *
28811344 AATCCGAGCTTGGGTTCGAAGGGCTTTTGAGCCAGTGCTAATAACCGAACTTAATTACGAAGGGC
1 AATCCGAACTTAGTTTCGAAGGGCTTTTGAGCCAGTG-TAATAACCGAACTTAATTACGAAGGGC
* *
28811409 TTTTGAGCCAGT-G-CT
65 CTTCGAGCCAGTGGCCT
* * * *
28811424 AATAACCGAACTTAGTTTCGAAGGGCTTTTGAGCCAGTGTCATAACCGGACTTAGTTTCGAAGGG
1 AAT--CCGAACTTAGTTTCGAAGGGCTTTTGAGCCAGTGTAATAACCGAACTTAATTACGAAGGG
28811489 CCTTCGAGCCAGTGGCCT
64 CCTTCGAGCCAGTGGCCT
* * * *
28811507 AATCCGAGCTTGGTCTCGAAGGGC-TTTGAACCAGTGT
1 AATCCGAACTTAGTTTCGAAGGGCTTTTGAGCCAGTGT
28811544 TAAGAATCGT
Statistics
Matches: 103, Mismatches: 13, Indels: 8
0.83 0.10 0.06
Matches are distributed among these distances:
80 15 0.15
81 51 0.50
82 32 0.31
83 5 0.05
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.27
Consensus pattern (81 bp):
AATCCGAACTTAGTTTCGAAGGGCTTTTGAGCCAGTGTAATAACCGAACTTAATTACGAAGGGCC
TTCGAGCCAGTGGCCT
Found at i:28823078 original size:15 final size:16
Alignment explanation
Indices: 28823060--28823089 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
28823050 AACTATTTTA
28823060 TTACA-AATTTCACTC
1 TTACATAATTTCACTC
28823075 TTACATAATTTCACT
1 TTACATAATTTCACT
28823090 TACTACATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.33, C:0.23, G:0.00, T:0.43
Consensus pattern (16 bp):
TTACATAATTTCACTC
Found at i:28823473 original size:101 final size:99
Alignment explanation
Indices: 28823292--28823479 Score: 268
Period size: 101 Copynumber: 1.9 Consensus size: 99
28823282 AAAGCTATCT
* *
28823292 GGTACACATAGTAGCCTGCACTTGTACTACACATGCGACCAACAATCCAATACACGTAGTAGCCT
1 GGTACACATAATAGCCTGCACTTGTACTACACATACGACCAACAATCCAATACACGTAGTAGCCT
28823357 GCACTTAGTACTACACACGTGATTGAAATTGTCA
66 GCACTTAGTACTACACACGTGATTGAAATTGTCA
* * * ***
28823391 GGTACGCATAATAGCCTGCACTTTGTGCTACACATACGACCTAACTATCTGGTACACGTAGTAGC
1 GGTACACATAATAGCCTGCAC-TTGTACTACACATACGACC-AACAATCCAATACACGTAGTAGC
* *
28823456 CTGCACTTTGTATTACACACGTGA
64 CTGCACTTAGTACTACACACGTGA
28823480 CCTAAAACCA
Statistics
Matches: 77, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
99 19 0.25
100 17 0.22
101 41 0.53
ACGTcount: A:0.30, C:0.26, G:0.18, T:0.26
Consensus pattern (99 bp):
GGTACACATAATAGCCTGCACTTGTACTACACATACGACCAACAATCCAATACACGTAGTAGCCT
GCACTTAGTACTACACACGTGATTGAAATTGTCA
Found at i:28823482 original size:50 final size:50
Alignment explanation
Indices: 28823286--28823484 Score: 179
Period size: 50 Copynumber: 4.0 Consensus size: 50
28823276 GTAACCAAAG
*
28823286 CTATCTGGTACACATAGTAGCCTGCAC-TTGTACTACACATGCGACC-AA
1 CTATCTGGTACACATAGTAGCCTGCACTTTGTACTACACACGCGACCTAA
* *** * * * *
28823334 CAATCCAATACACGTAGTAGCCTGCACTTAGTACTACACACGTGA-TTGAAA
1 CTATCTGGTACACATAGTAGCCTGCACTTTGTACTACACACGCGACCT--AA
* * * * * * **
28823385 TTGTCAGGTACGCATAATAGCCTGCACTTTGTGCTACACATACGACCTAA
1 CTATCTGGTACACATAGTAGCCTGCACTTTGTACTACACACGCGACCTAA
* * *
28823435 CTATCTGGTACACGTAGTAGCCTGCACTTTGTATTACACACGTGACCTAA
1 CTATCTGGTACACATAGTAGCCTGCACTTTGTACTACACACGCGACCTAA
28823485 AACCATCTTA
Statistics
Matches: 111, Mismatches: 35, Indels: 8
0.72 0.23 0.05
Matches are distributed among these distances:
48 22 0.20
49 14 0.13
50 41 0.37
51 33 0.30
52 1 0.01
ACGTcount: A:0.30, C:0.27, G:0.17, T:0.27
Consensus pattern (50 bp):
CTATCTGGTACACATAGTAGCCTGCACTTTGTACTACACACGCGACCTAA
Found at i:28826300 original size:55 final size:55
Alignment explanation
Indices: 28826216--28826324 Score: 191
Period size: 55 Copynumber: 2.0 Consensus size: 55
28826206 TTAAATAAAA
* * *
28826216 AAATATAATTTTTATGCTATCATCTTCATCACTAGCTGAAAATACAAAGAAGAAC
1 AAATACAATTTTTATACTATCATCTTCATCACTAGCCGAAAATACAAAGAAGAAC
28826271 AAATACAATTTTTATACTATCATCTTCATCACTAGCCGAAAATACAAAGAAGAA
1 AAATACAATTTTTATACTATCATCTTCATCACTAGCCGAAAATACAAAGAAGAA
28826325 GAAGCCATAG
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
55 51 1.00
ACGTcount: A:0.45, C:0.17, G:0.08, T:0.29
Consensus pattern (55 bp):
AAATACAATTTTTATACTATCATCTTCATCACTAGCCGAAAATACAAAGAAGAAC
Found at i:28830829 original size:51 final size:49
Alignment explanation
Indices: 28830763--28830950 Score: 236
Period size: 49 Copynumber: 3.8 Consensus size: 49
28830753 TGAGGTCGCA
* * *
28830763 TGTGTAGTACTAAGTGCAGGCTACTATGCGTACCCGAAAACTGTGATCACG
1 TGTGTAGTACTAAGTGCAGGCTACTATGCGTACCGGATAA-T-TGGTCACG
*
28830814 TGTGTAGTACTAAGTGCAGGCTAC--TGCATGTACCGGATCATTGGTCACG
1 TGTGTAGTACTAAGTGCAGGCTACTATGC--GTACCGGATAATTGGTCACG
* * * *
28830863 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGGTTACA
1 TGTGTAGTACTAAGTGCAGGCTACTATGCGTACCGGATAATTGGTCACG
* *
28830912 TGTGTAGTACTATGTGCAGGCTACTATGCGTACCAGATA
1 TGTGTAGTACTAAGTGCAGGCTACTATGCGTACCGGATA
28830951 GCTTTGGCTA
Statistics
Matches: 120, Mismatches: 13, Indels: 10
0.84 0.09 0.07
Matches are distributed among these distances:
49 86 0.72
50 1 0.01
51 33 0.28
ACGTcount: A:0.26, C:0.19, G:0.27, T:0.29
Consensus pattern (49 bp):
TGTGTAGTACTAAGTGCAGGCTACTATGCGTACCGGATAATTGGTCACG
Found at i:28832919 original size:41 final size:41
Alignment explanation
Indices: 28832829--28833015 Score: 240
Period size: 41 Copynumber: 4.7 Consensus size: 41
28832819 CAACAAATCA
* * * *
28832829 GCTATATGTGGCACTTAATGTGCGA-TTCGACATAGCTTCG
1 GCTATATATGGCACTTAGTGTGCGAGATCGAGATAGCTTCG
*
28832869 GCTATATATGGCACTTAGTGTGCGAGATCAAGATAGCTTCG
1 GCTATATATGGCACTTAGTGTGCGAGATCGAGATAGCTTCG
* * *
28832910 GCTACATATGGCACTTAGTGTGTGAGATTGAGATAGCTTCG
1 GCTATATATGGCACTTAGTGTGCGAGATCGAGATAGCTTCG
* *
28832951 GCTATATATGGCACTTAGTGTGCGA-TTTGAGATAGCTTCG
1 GCTATATATGGCACTTAGTGTGCGAGATCGAGATAGCTTCG
*
28832991 GCTATGTA---CACTTAGTGTGCGAGAT
1 GCTATATATGGCACTTAGTGTGCGAGAT
28833016 ATCGAGTATT
Statistics
Matches: 131, Mismatches: 14, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
37 14 0.11
38 1 0.01
40 44 0.34
41 72 0.55
ACGTcount: A:0.24, C:0.17, G:0.27, T:0.32
Consensus pattern (41 bp):
GCTATATATGGCACTTAGTGTGCGAGATCGAGATAGCTTCG
Found at i:28836326 original size:15 final size:15
Alignment explanation
Indices: 28836306--28836371 Score: 55
Period size: 15 Copynumber: 4.3 Consensus size: 15
28836296 ACTACAAAAC
28836306 ATTTATTATTAATAT
1 ATTTATTATTAATAT
*
28836321 ATTTATAATTGGAATAAAT
1 ATTTATTATT--AAT--AT
*
28836340 ATTTATTATTAAAAT
1 ATTTATTATTAATAT
*
28836355 A-TTAATATTAA-AT
1 ATTTATTATTAATAT
28836368 ATTT
1 ATTT
28836372 TCAATAATAT
Statistics
Matches: 42, Mismatches: 4, Indels: 11
0.74 0.07 0.19
Matches are distributed among these distances:
13 3 0.07
14 11 0.26
15 12 0.29
17 5 0.12
19 11 0.26
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (15 bp):
ATTTATTATTAATAT
Found at i:28836361 original size:21 final size:21
Alignment explanation
Indices: 28836337--28836424 Score: 63
Period size: 21 Copynumber: 3.9 Consensus size: 21
28836327 AATTGGAATA
28836337 AATATTTATTATTAAAATATT
1 AATATTTATTATTAAAATATT
28836358 AATATTAAATATT-TTCAATAATATGT
1 AATATT---TATTATT-AA-AATAT-T
* *
28836384 GAATA-ATATTATTTAAAATTTT
1 -AATATTTATTA-TTAAAATATT
*
28836406 AAAATTTATTATTAAAATA
1 AATATTTATTATTAAAATA
28836425 AAATTGAAAT
Statistics
Matches: 52, Mismatches: 5, Indels: 20
0.68 0.06 0.26
Matches are distributed among these distances:
21 16 0.31
22 6 0.12
23 10 0.19
24 8 0.15
25 7 0.13
26 1 0.02
27 4 0.08
ACGTcount: A:0.49, C:0.01, G:0.02, T:0.48
Consensus pattern (21 bp):
AATATTTATTATTAAAATATT
Found at i:28836471 original size:22 final size:22
Alignment explanation
Indices: 28836431--28836486 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 22
28836421 AATAAAATTG
*
28836431 AAATATTAAA-TA-ATTTATTA
1 AAATAATAAATTATATTTATTA
28836451 AAATAATAAATTATATTTATTA
1 AAATAATAAATTATATTTATTA
* * *
28836473 TATTAATAATTTAT
1 AAATAATAAATTAT
28836487 TATATGGCTA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 9 0.30
21 2 0.07
22 19 0.63
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
AAATAATAAATTATATTTATTA
Found at i:28837175 original size:7 final size:7
Alignment explanation
Indices: 28837165--28837190 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
28837155 AAAATATTAC
28837165 TTAAATA
1 TTAAATA
28837172 TTAAATA
1 TTAAATA
28837179 TTAAATA
1 TTAAATA
28837186 TTAAA
1 TTAAA
28837191 CATAATTAAA
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):
TTAAATA
Found at i:28837849 original size:20 final size:20
Alignment explanation
Indices: 28837785--28837862 Score: 63
Period size: 19 Copynumber: 4.0 Consensus size: 20
28837775 AAAATTATTA
*
28837785 TTTTAGAATTTTTTTAAAAA
1 TTTTAGAATTTTTTTAAAAT
** * *
28837805 AATT--AACTTTTTTATATAT
1 TTTTAGAATTTTTTTA-AAAT
28837824 TCTTTAGAATTTTTTTAAAAT
1 T-TTTAGAATTTTTTTAAAAT
*
28837845 TTTTATAA-TTTTTTAAAA
1 TTTTAGAATTTTTTTAAAA
28837863 AAATATAATT
Statistics
Matches: 44, Mismatches: 10, Indels: 9
0.70 0.16 0.14
Matches are distributed among these distances:
18 9 0.20
19 12 0.27
20 10 0.23
21 4 0.09
22 9 0.20
ACGTcount: A:0.37, C:0.03, G:0.03, T:0.58
Consensus pattern (20 bp):
TTTTAGAATTTTTTTAAAAT
Found at i:28837863 original size:20 final size:21
Alignment explanation
Indices: 28837812--28837863 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 21
28837802 AAAAATTAAC
* *
28837812 TTTTTTATATATTCTTTAGAA
1 TTTTTTAAAAATTCTTTAGAA
* *
28837833 TTTTTTTAAAATT-TTTATAA
1 TTTTTTAAAAATTCTTTAGAA
28837853 TTTTTTAAAAA
1 TTTTTTAAAAA
28837864 AATATAATTT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 16 0.62
21 10 0.38
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.62
Consensus pattern (21 bp):
TTTTTTAAAAATTCTTTAGAA
Found at i:28837887 original size:18 final size:18
Alignment explanation
Indices: 28837866--28837921 Score: 51
Period size: 19 Copynumber: 3.1 Consensus size: 18
28837856 TTTAAAAAAA
28837866 TATAATTTTTTTTATTTT
1 TATAATTTTTTTTATTTT
* *
28837884 TATAAATATTTTGTA-TTT
1 TAT-AATTTTTTTTATTTT
* *
28837902 TAGATTTTTTTTTAATTTT
1 TATAATTTTTTTT-ATTTT
28837921 T
1 T
28837922 GTTGAGAAAG
Statistics
Matches: 29, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
17 7 0.24
18 9 0.31
19 13 0.45
ACGTcount: A:0.25, C:0.00, G:0.04, T:0.71
Consensus pattern (18 bp):
TATAATTTTTTTTATTTT
Found at i:28852008 original size:20 final size:20
Alignment explanation
Indices: 28851960--28852000 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
28851950 AGGAAAATAA
28851960 CAAAGTAAGCTTCAACTAAG
1 CAAAGTAAGCTTCAACTAAG
28851980 CAAAGTAAGCTTCAACTAAG
1 CAAAGTAAGCTTCAACTAAG
28852000 C
1 C
28852001 TTAGTAAGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.44, C:0.22, G:0.15, T:0.20
Consensus pattern (20 bp):
CAAAGTAAGCTTCAACTAAG
Found at i:28854328 original size:15 final size:15
Alignment explanation
Indices: 28854308--28854336 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
28854298 TCAATAAGAT
28854308 TTCAAAATTTCCTAA
1 TTCAAAATTTCCTAA
28854323 TTCAAAATTTCCTA
1 TTCAAAATTTCCTA
28854337 TTTTATCTCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.38, C:0.21, G:0.00, T:0.41
Consensus pattern (15 bp):
TTCAAAATTTCCTAA
Found at i:28855133 original size:29 final size:29
Alignment explanation
Indices: 28855081--28855270 Score: 84
Period size: 29 Copynumber: 6.7 Consensus size: 29
28855071 CACGAATGTG
* * *
28855081 TCCTTTTAA-AAA-ATAGCCATAAAGTAT
1 TCCTTTTAACAAAGATAGCAAAAAAGGAT
*
28855108 TCCTTTTAACAAAGATAGCAAAAAAGGCT
1 TCCTTTTAACAAAGATAGCAAAAAAGGAT
* * * * *
28855137 TCATTTTAACAGAGATAACCATAAAGGCA-
1 TCCTTTTAACAAAGATAGCAAAAAAGG-AT
* * * * * **
28855166 TCCTTTTAACAGAGATCGCCACAATGGCC
1 TCCTTTTAACAAAGATAGCAAAAAAGGAT
* * * * * *
28855195 TCCTTATAATAGAGATAGCCACAAAGAAT
1 TCCTTTTAACAAAGATAGCAAAAAAGGAT
* * * *
28855224 T-CATTTAACAGAGATAGCTATAAA-GAT
1 TCCTTTTAACAAAGATAGCAAAAAAGGAT
*
28855251 ATCCTTTTAACAGAGATAGC
1 -TCCTTTTAACAAAGATAGC
28855271 CACAGAGGCA
Statistics
Matches: 127, Mismatches: 30, Indels: 10
0.76 0.18 0.06
Matches are distributed among these distances:
27 11 0.09
28 22 0.17
29 94 0.74
ACGTcount: A:0.41, C:0.18, G:0.14, T:0.27
Consensus pattern (29 bp):
TCCTTTTAACAAAGATAGCAAAAAAGGAT
Found at i:28855287 original size:29 final size:29
Alignment explanation
Indices: 28855111--28855362 Score: 149
Period size: 29 Copynumber: 8.9 Consensus size: 29
28855101 AAAGTATTCC
* * * *
28855111 TTTTAACAAAGATAGCAAAAAAGGCTTCA
1 TTTTAACAGAGATAGCCACAAAGGCATCA
* * *
28855140 TTTTAACAGAGATAACCATAAAGGCATCC
1 TTTTAACAGAGATAGCCACAAAGGCATCA
* * * *
28855169 TTTTAACAGAGATCGCCACAATGGCCTCC
1 TTTTAACAGAGATAGCCACAAAGGCATCA
* * *
28855198 TTATAATAGAGATAGCCACAAA-GAATTCA
1 TTTTAACAGAGATAGCCACAAAGGCA-TCA
* * ** *
28855227 -TTTAACAGAGATAGCTATAAAGATATCC
1 TTTTAACAGAGATAGCCACAAAGGCATCA
* *
28855255 TTTTAACAGAGATAGCCACAGAGGCATAA
1 TTTTAACAGAGATAGCCACAAAGGCATCA
** * * * *
28855284 TTTTAATTGATATAGCCATAAAGAC-TTA
1 TTTTAACAGAGATAGCCACAAAGGCATCA
* * *
28855312 -TTTATACATAGATCGCCACAAAGGCTTC-
1 TTTTA-ACAGAGATAGCCACAAAGGCATCA
* *
28855340 TTTT--CAAAGATACCCACAAAGGC
1 TTTTAACAGAGATAGCCACAAAGGC
28855363 CTACTTATAC
Statistics
Matches: 167, Mismatches: 50, Indels: 15
0.72 0.22 0.06
Matches are distributed among these distances:
26 16 0.10
27 4 0.02
28 35 0.21
29 112 0.67
ACGTcount: A:0.40, C:0.19, G:0.15, T:0.26
Consensus pattern (29 bp):
TTTTAACAGAGATAGCCACAAAGGCATCA
Found at i:28855299 original size:86 final size:86
Alignment explanation
Indices: 28855136--28855324 Score: 211
Period size: 86 Copynumber: 2.2 Consensus size: 86
28855126 CAAAAAAGGC
* * * **
28855136 TTCATTTTAACAGAGATAACCATAAAGGCATCCTTTTAACAGAGATCGCCACAATGGCCTCCTTA
1 TTCA-TTTAACAGAGATAACCATAAAGACATCCTTTTAACAGAGATAGCCACAATGGCATAATTA
28855201 TAATAGAGATAGCCACAAAGAA
65 TAATAGAGATAGCCACAAAGAA
* * * *
28855223 TTCATTTAACAGAGATAGCTATAAAGATATCCTTTTAACAGAGATAGCCACAGA-GGCATAATTT
1 TTCATTTAACAGAGATAACCATAAAGACATCCTTTTAACAGAGATAGCCACA-ATGGCATAATTA
* * * *
28855287 TAATTGATATAGCCATAAAGAC
65 TAATAGAGATAGCCACAAAGAA
*
28855309 TT-ATTTATACATAGAT
1 TTCATTTA-ACAGAGAT
28855325 CGCCACAAAG
Statistics
Matches: 86, Mismatches: 14, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
85 5 0.06
86 76 0.88
87 5 0.06
ACGTcount: A:0.40, C:0.17, G:0.14, T:0.29
Consensus pattern (86 bp):
TTCATTTAACAGAGATAACCATAAAGACATCCTTTTAACAGAGATAGCCACAATGGCATAATTAT
AATAGAGATAGCCACAAAGAA
Found at i:28870430 original size:19 final size:19
Alignment explanation
Indices: 28870406--28870443 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
28870396 TTTAAAGAAT
*
28870406 ATATAAAAAAACTTAAAAA
1 ATATAAAAAAAATTAAAAA
28870425 ATATAAAAAAAATTAAAAA
1 ATATAAAAAAAATTAAAAA
28870444 TTCTATATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.76, C:0.03, G:0.00, T:0.21
Consensus pattern (19 bp):
ATATAAAAAAAATTAAAAA
Found at i:28871156 original size:20 final size:20
Alignment explanation
Indices: 28871131--28871172 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
28871121 TCTTAGAGTA
* * *
28871131 AATTATACAAATATTCATTT
1 AATTATAAAAAAATTAATTT
28871151 AATTATAAAAAAATTAATTT
1 AATTATAAAAAAATTAATTT
28871171 AA
1 AA
28871173 ACACCCAAAA
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:0.55, C:0.05, G:0.00, T:0.40
Consensus pattern (20 bp):
AATTATAAAAAAATTAATTT
Found at i:28871298 original size:24 final size:25
Alignment explanation
Indices: 28871271--28871321 Score: 59
Period size: 25 Copynumber: 2.1 Consensus size: 25
28871261 CACTTATATC
* *
28871271 AATTAG-TCATAATTTTTAAAAATT
1 AATTAGATCATAATTCTAAAAAATT
* *
28871295 AATTTGATCCTAATTCTAAAAAATT
1 AATTAGATCATAATTCTAAAAAATT
28871320 AA
1 AA
28871322 AAGAAATATA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
24 5 0.23
25 17 0.77
ACGTcount: A:0.47, C:0.08, G:0.04, T:0.41
Consensus pattern (25 bp):
AATTAGATCATAATTCTAAAAAATT
Found at i:28871364 original size:19 final size:19
Alignment explanation
Indices: 28871325--28871364 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
28871315 AAATTAAAAG
*
28871325 AAATATATAAAAAATACAT
1 AAATATATAAAAAAAACAT
* *
28871344 AAATATCTAAAAAAAATAT
1 AAATATATAAAAAAAACAT
28871363 AA
1 AA
28871365 TAATAAATTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.70, C:0.05, G:0.00, T:0.25
Consensus pattern (19 bp):
AAATATATAAAAAAAACAT
Found at i:28871421 original size:25 final size:24
Alignment explanation
Indices: 28871387--28871440 Score: 81
Period size: 25 Copynumber: 2.2 Consensus size: 24
28871377 ATTTTATATC
* *
28871387 AATATTTATATTAATATTAAATAA
1 AATAATTATAATAATATTAAATAA
28871411 ATATAATTATAATAATATTAAATAA
1 A-ATAATTATAATAATATTAAATAA
28871436 AATAA
1 AATAA
28871441 AAATCCGCCC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
24 5 0.19
25 22 0.81
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (24 bp):
AATAATTATAATAATATTAAATAA
Found at i:28872291 original size:21 final size:21
Alignment explanation
Indices: 28872253--28872293 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
28872243 TATAACATGA
***
28872253 GTGCTTAAAATTTTATTTTTG
1 GTGCTTAAAATGAAATTTTTG
28872274 GTGCTTAAAATGAAATTTTT
1 GTGCTTAAAATGAAATTTTT
28872294 TGATAATTTG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.29, C:0.05, G:0.15, T:0.51
Consensus pattern (21 bp):
GTGCTTAAAATGAAATTTTTG
Found at i:28873406 original size:17 final size:17
Alignment explanation
Indices: 28873384--28873420 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
28873374 ATTTGTTTAG
28873384 TTTAGTG-CTTATTGTGA
1 TTTAGTGTC-TATTGTGA
28873401 TTTAGTGTCTATTGTGA
1 TTTAGTGTCTATTGTGA
28873418 TTT
1 TTT
28873421 GTTCAGTATG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 18 0.95
18 1 0.05
ACGTcount: A:0.16, C:0.05, G:0.22, T:0.57
Consensus pattern (17 bp):
TTTAGTGTCTATTGTGA
Found at i:28873813 original size:14 final size:14
Alignment explanation
Indices: 28873796--28873827 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
28873786 TGTAATGATA
28873796 TTATTTTACTATAT
1 TTATTTTACTATAT
*
28873810 TTATTTTATTATAT
1 TTATTTTACTATAT
28873824 TTAT
1 TTAT
28873828 GTGTTTTGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (14 bp):
TTATTTTACTATAT
Found at i:28876255 original size:44 final size:44
Alignment explanation
Indices: 28876127--28876255 Score: 161
Period size: 44 Copynumber: 2.9 Consensus size: 44
28876117 ATACATGCAA
* * * *
28876127 AAATTAAATGCATTGAAAGAAATTTGGAACAAACTTTATAATTT
1 AAATTAGATGCATTGAAACAAACTTGGAACAAACTTTGTAATTT
* *
28876171 AAATGAGATGCATT-ACACCAAACTTGGAACAAACTTTGTAATTT
1 AAATTAGATGCATTGA-AACAAACTTGGAACAAACTTTGTAATTT
* * *
28876215 AAATTAGATGCATTGGAACAAACTTGGAACAATCTCTGTAA
1 AAATTAGATGCATTGAAACAAACTTGGAACAAACTTTGTAA
28876256 AATATATATA
Statistics
Matches: 72, Mismatches: 11, Indels: 4
0.83 0.13 0.05
Matches are distributed among these distances:
43 1 0.01
44 71 0.99
ACGTcount: A:0.43, C:0.12, G:0.14, T:0.30
Consensus pattern (44 bp):
AAATTAGATGCATTGAAACAAACTTGGAACAAACTTTGTAATTT
Found at i:28882103 original size:43 final size:43
Alignment explanation
Indices: 28882048--28882248 Score: 235
Period size: 43 Copynumber: 4.7 Consensus size: 43
28882038 AGAAAGTGCC
** *
28882048 GCTAAAGAACATGACCTTTAATGGCGCTTACCATACAAACGCT
1 GCTAAAGAACATGACCTTTAGCGGCGCTTTCCATACAAACGCT
* * *
28882091 GCTAAAGAACATGACCTTTACCGGCGC-TTCCTGTACAAATGCT
1 GCTAAAGAACATGACCTTTAGCGGCGCTTTCC-ATACAAACGCT
* * * * * *
28882134 GCTAAAGAACGTGACATTTAGTGGCACTTTTCACACAAACGCT
1 GCTAAAGAACATGACCTTTAGCGGCGCTTTCCATACAAACGCT
* * *
28882177 GCTAAAGAACGTGACCTTTAGCGGCGCTTTTCATACAAACGCC
1 GCTAAAGAACATGACCTTTAGCGGCGCTTTCCATACAAACGCT
*
28882220 GCTAAAGAACATG-CCTTTAGCGACGCTTT
1 GCTAAAGAACATGACCTTTAGCGGCGCTTT
28882249 TCTCAAAAAA
Statistics
Matches: 135, Mismatches: 21, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
42 18 0.13
43 114 0.84
44 3 0.02
ACGTcount: A:0.30, C:0.26, G:0.19, T:0.25
Consensus pattern (43 bp):
GCTAAAGAACATGACCTTTAGCGGCGCTTTCCATACAAACGCT
Found at i:28883001 original size:13 final size:14
Alignment explanation
Indices: 28882971--28883003 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
28882961 GAATATACCT
28882971 TTATAATTAAACCA
1 TTATAATTAAACCA
*
28882985 TTATGATTAAA-CA
1 TTATAATTAAACCA
28882998 TTATAA
1 TTATAA
28883004 ATATTTAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
13 7 0.41
14 10 0.59
ACGTcount: A:0.48, C:0.09, G:0.03, T:0.39
Consensus pattern (14 bp):
TTATAATTAAACCA
Found at i:28890109 original size:33 final size:36
Alignment explanation
Indices: 28890054--28890167 Score: 123
Period size: 33 Copynumber: 3.2 Consensus size: 36
28890044 GATATAATCG
28890054 TAGCACAAATGCCTTCGGGACTTAGCCGATATAGTCAC
1 TAGCAC-AA-GCCTTCGGGACTTAGCCGATATAGTCAC
* *
28890092 TAGCACAAG-C-TC-GGACTTAGCCCG-GATAGT-AA
1 TAGCACAAGCCTTCGGGACTTAG-CCGATATAGTCAC
*
28890124 TAG-AAAAGCCTTCGGGACTTAGCCGGATATAGTCAC
1 TAGCACAAGCCTTCGGGACTTAGCC-GATATAGTCAC
28890160 TAGCACAA
1 TAGCACAA
28890168 ATGCTTCGGA
Statistics
Matches: 62, Mismatches: 6, Indels: 17
0.73 0.07 0.20
Matches are distributed among these distances:
31 4 0.06
32 5 0.08
33 17 0.27
34 14 0.23
35 6 0.10
36 5 0.08
37 5 0.08
38 6 0.10
ACGTcount: A:0.32, C:0.25, G:0.23, T:0.21
Consensus pattern (36 bp):
TAGCACAAGCCTTCGGGACTTAGCCGATATAGTCAC
Found at i:28902571 original size:28 final size:28
Alignment explanation
Indices: 28902524--28902591 Score: 109
Period size: 28 Copynumber: 2.4 Consensus size: 28
28902514 AAATTAACCC
* **
28902524 TAGGGGTATAAAGGTCATTTTGCATACA
1 TAGGGGTATAATGGAAATTTTGCATACA
28902552 TAGGGGTATAATGGAAATTTTGCATACA
1 TAGGGGTATAATGGAAATTTTGCATACA
28902580 TAGGGGTATAAT
1 TAGGGGTATAAT
28902592 AGTATATCTA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
28 37 1.00
ACGTcount: A:0.34, C:0.07, G:0.26, T:0.32
Consensus pattern (28 bp):
TAGGGGTATAATGGAAATTTTGCATACA
Found at i:28910587 original size:28 final size:28
Alignment explanation
Indices: 28910548--28910636 Score: 126
Period size: 28 Copynumber: 3.1 Consensus size: 28
28910538 AGCATGGCTG
*
28910548 CCAGATACAGATATTTTGTGGCAGTGCCA
1 CCAGA-ACAGATAATTTGTGGCAGTGCCA
*
28910577 CCAGAACAGATAATTTGTGGCAGGGCCA
1 CCAGAACAGATAATTTGTGGCAGTGCCA
*
28910605 CTAGAACAGATAATTTGTGGCA-TAGCCA
1 CCAGAACAGATAATTTGTGGCAGT-GCCA
28910633 CCAG
1 CCAG
28910637 GACGCTTCCT
Statistics
Matches: 54, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
28 49 0.91
29 5 0.09
ACGTcount: A:0.31, C:0.21, G:0.25, T:0.22
Consensus pattern (28 bp):
CCAGAACAGATAATTTGTGGCAGTGCCA
Found at i:28910789 original size:28 final size:28
Alignment explanation
Indices: 28910742--28910809 Score: 118
Period size: 28 Copynumber: 2.4 Consensus size: 28
28910732 AAATTAACCC
* *
28910742 TAGGGGTATAAAGGTCATTTTGCATACA
1 TAGGGGTATAATGGTAATTTTGCATACA
28910770 TAGGGGTATAATGGTAATTTTGCATACA
1 TAGGGGTATAATGGTAATTTTGCATACA
28910798 TAGGGGTATAAT
1 TAGGGGTATAAT
28910810 AGTATATCTA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
28 38 1.00
ACGTcount: A:0.32, C:0.07, G:0.26, T:0.34
Consensus pattern (28 bp):
TAGGGGTATAATGGTAATTTTGCATACA
Found at i:28921508 original size:21 final size:21
Alignment explanation
Indices: 28921484--28921526 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
28921474 CAACTACATG
28921484 TTAGTCTTAATGCATTATTGT
1 TTAGTCTTAATGCATTATTGT
28921505 TTAGTCTTAATGCATTATTGT
1 TTAGTCTTAATGCATTATTGT
28921526 T
1 T
28921527 GTCCTAGTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.23, C:0.09, G:0.14, T:0.53
Consensus pattern (21 bp):
TTAGTCTTAATGCATTATTGT
Found at i:28925374 original size:20 final size:23
Alignment explanation
Indices: 28925351--28925405 Score: 71
Period size: 23 Copynumber: 2.5 Consensus size: 23
28925341 CAAGTTGGAG
*
28925351 TTAATTTGTCTTAG-T-T-GAAT
1 TTAATTTGTCCTAGCTGTCGAAT
*
28925371 TTAAGTTGTCCTAGCTGTCGAAT
1 TTAATTTGTCCTAGCTGTCGAAT
28925394 TTAATTTGTCCT
1 TTAATTTGTCCT
28925406 TAAGATTGAC
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
20 12 0.41
21 1 0.03
22 1 0.03
23 15 0.52
ACGTcount: A:0.22, C:0.13, G:0.16, T:0.49
Consensus pattern (23 bp):
TTAATTTGTCCTAGCTGTCGAAT
Found at i:28926327 original size:8 final size:8
Alignment explanation
Indices: 28926314--28926346 Score: 66
Period size: 8 Copynumber: 4.1 Consensus size: 8
28926304 AAATTATCCC
28926314 TCACATTT
1 TCACATTT
28926322 TCACATTT
1 TCACATTT
28926330 TCACATTT
1 TCACATTT
28926338 TCACATTT
1 TCACATTT
28926346 T
1 T
28926347 AGTCCCTAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 25 1.00
ACGTcount: A:0.24, C:0.24, G:0.00, T:0.52
Consensus pattern (8 bp):
TCACATTT
Found at i:28929346 original size:27 final size:27
Alignment explanation
Indices: 28929299--28929539 Score: 250
Period size: 27 Copynumber: 8.9 Consensus size: 27
28929289 GGGCAAAATG
* * * * *
28929299 GTAATTTTACCCCACAAGGGTATCTCG
1 GTAATTCTACCCTACAGGGGTATTTCA
* * *
28929326 GTAATTCTAACCTATAGGGGTATTTTA
1 GTAATTCTACCCTACAGGGGTATTTCA
* ** *
28929353 GTATTTCTACCCTACAACGGTATTTCG
1 GTAATTCTACCCTACAGGGGTATTTCA
** **
28929380 GTAATTCTACCCTTTAGCAGTATTTCA
1 GTAATTCTACCCTACAGGGGTATTTCA
*
28929407 GTAATTCTACCCTACAGGGGTGTTTC-
1 GTAATTCTACCCTACAGGGGTATTTCA
*
28929433 GATAATTCTACCCTATAGGGGTATTTCA
1 G-TAATTCTACCCTACAGGGGTATTTCA
*
28929461 GTAATTCTACCCTACAGGGCTATTTCA
1 GTAATTCTACCCTACAGGGGTATTTCA
* * *
28929488 ATAATTCTACCCTATAGGGATATTTCA
1 GTAATTCTACCCTACAGGGGTATTTCA
* *
28929515 GTATTTCTACCCTACAAGGGTATTT
1 GTAATTCTACCCTACAGGGGTATTT
28929540 TGGTAATTTT
Statistics
Matches: 174, Mismatches: 38, Indels: 4
0.81 0.18 0.02
Matches are distributed among these distances:
26 1 0.01
27 172 0.99
28 1 0.01
ACGTcount: A:0.26, C:0.21, G:0.16, T:0.37
Consensus pattern (27 bp):
GTAATTCTACCCTACAGGGGTATTTCA
Found at i:28929364 original size:54 final size:54
Alignment explanation
Indices: 28929302--28929547 Score: 316
Period size: 54 Copynumber: 4.6 Consensus size: 54
28929292 CAAAATGGTA
* * * *
28929302 ATTT-TACCCCACAAGGGTATCTCGGTAATTCTAACCTATAGGGGTATTTTAGT
1 ATTTCTACCCTACAAGGGTATTTCGGTAATTCTACCCTATAGGGGTATTTCAGT
* * **
28929355 ATTTCTACCCTACAACGGTATTTCGGTAATTCTACCCTTTAGCAGTATTTCAGT
1 ATTTCTACCCTACAAGGGTATTTCGGTAATTCTACCCTATAGGGGTATTTCAGT
* * * *
28929409 AATTCTACCCTACAGGGGTGTTTCGATAATTCTACCCTATAGGGGTATTTCAGT
1 ATTTCTACCCTACAAGGGTATTTCGGTAATTCTACCCTATAGGGGTATTTCAGT
* ** *
28929463 AATTCTACCCTAC-AGGGCTATTTCAATAATTCTACCCTATAGGGATATTTCAGT
1 ATTTCTACCCTACAAGGG-TATTTCGGTAATTCTACCCTATAGGGGTATTTCAGT
*
28929517 ATTTCTACCCTACAAGGGTATTTTGGTAATT
1 ATTTCTACCCTACAAGGGTATTTCGGTAATT
28929548 TTATAAATCG
Statistics
Matches: 166, Mismatches: 24, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
53 7 0.04
54 155 0.93
55 4 0.02
ACGTcount: A:0.26, C:0.21, G:0.16, T:0.37
Consensus pattern (54 bp):
ATTTCTACCCTACAAGGGTATTTCGGTAATTCTACCCTATAGGGGTATTTCAGT
Found at i:28929566 original size:81 final size:79
Alignment explanation
Indices: 28929315--28929734 Score: 237
Period size: 81 Copynumber: 5.2 Consensus size: 79
28929305 TTACCCCACA
* * * * *
28929315 AGGGTATCTCGGTAATTCTAACCTATAGGGGTATTTTAGTATTTCTACCCTACAACGGTATTTCG
1 AGGGTATTTCAGTAATTCTACCCTATA-GGGTATTTCAGTATTTCTACCCTACAAGGGTATTTCG
* *** **
28929380 GTAATTCTACCCTTT
65 GTAATTTTAAAATCG
* * * * * *
28929395 AGCAGTATTTCAGTAATTCTACCCTACAGGGGTGTTTC-GATAATTCTACCCTATAGGGGTATTT
1 AG-GGTATTTCAGTAATTCTACCCTATA-GGGTATTTCAG-TATTTCTACCCTACAAGGGTATTT
* * ***
28929459 CAGTAATTCTACCCTAC-
63 CGGTAATTTTAAAAT-CG
* *
28929476 AGGGCTATTTCAATAATTCTACCCTATAGGGATATTTCAGTATTTCTACCCTACAAGGGTATTTT
1 AGGG-TATTTCAGTAATTCTACCCTATAGGG-TATTTCAGTATTTCTACCCTACAAGGGTATTTC
28929541 GGTAATTTTATAAATCG
64 GGTAATTTTA-AAATCG
* ** * * ** **
28929558 AGGGTATTTCAGTAATTTTACAAT-TAACGGTATTTCAGTAATTTATAAAC--CGGGGGTACTTT
1 AGGGTATTTCAGTAATTCTACCCTAT-AGGGTATTTCAGT-ATTTCTACCCTACAAGGGTA-TTT
*
28929620 -GGTAATTTTACAAGTCG
63 CGGTAATTTTA-AAATCG
** ** * ** *
28929637 AGGGTATTTCAGTAATT-TTGCAAATCGAGGGTATTTCAGTAATTT-T-GCAAATTAAGGGTATT
1 AGGGTATTTCAGTAATTCTACCCTAT--AGGGTATTTCAGT-ATTTCTACCCTA-CAAGGGTATT
28929699 TCGGTAATTTTACAAATCG
62 TCGGTAATTTTA-AAATCG
*
28929718 AGGGTATTTCAATAATT
1 AGGGTATTTCAGTAATT
28929735 TTACAATCGA
Statistics
Matches: 271, Mismatches: 52, Indels: 33
0.76 0.15 0.09
Matches are distributed among these distances:
78 2 0.01
79 40 0.15
80 40 0.15
81 183 0.68
82 6 0.02
ACGTcount: A:0.28, C:0.15, G:0.18, T:0.38
Consensus pattern (79 bp):
AGGGTATTTCAGTAATTCTACCCTATAGGGTATTTCAGTATTTCTACCCTACAAGGGTATTTCGG
TAATTTTAAAATCG
Found at i:28929794 original size:26 final size:27
Alignment explanation
Indices: 28929531--28929793 Score: 259
Period size: 27 Copynumber: 9.9 Consensus size: 27
28929521 CTACCCTACA
* *
28929531 AGGGTATTTTGGTAATTTTATAAATCG
1 AGGGTATTTCGGTAATTTTACAAATCG
* **
28929558 AGGGTATTTCAGTAATTTTAC-AATTA
1 AGGGTATTTCGGTAATTTTACAAATCG
* * * *
28929584 ACGGTATTTCAGTAA-TTTATAAACCG
1 AGGGTATTTCGGTAATTTTACAAATCG
* *
28929610 GGGGTACTTT-GGTAATTTTACAAGTCG
1 AGGGTA-TTTCGGTAATTTTACAAATCG
* *
28929637 AGGGTATTTCAGTAATTTTGCAAATCG
1 AGGGTATTTCGGTAATTTTACAAATCG
* * **
28929664 AGGGTATTTCAGTAATTTTGCAAATTA
1 AGGGTATTTCGGTAATTTTACAAATCG
28929691 AGGGTATTTCGGTAATTTTACAAATCG
1 AGGGTATTTCGGTAATTTTACAAATCG
**
28929718 AGGGTATTTCAATAATTTTAC-AATCG
1 AGGGTATTTCGGTAATTTTACAAATCG
* * * *
28929744 ATGGTATTTCGATAATTTTATAAACCG
1 AGGGTATTTCGGTAATTTTACAAATCG
28929771 -GGGTACTTT-GGTAATTTTACAAA
1 AGGGTA-TTTCGGTAATTTTACAAA
28929794 CTAGGGGTAT
Statistics
Matches: 195, Mismatches: 35, Indels: 13
0.80 0.14 0.05
Matches are distributed among these distances:
25 4 0.02
26 69 0.35
27 122 0.63
ACGTcount: A:0.31, C:0.10, G:0.20, T:0.39
Consensus pattern (27 bp):
AGGGTATTTCGGTAATTTTACAAATCG
Found at i:28942372 original size:15 final size:14
Alignment explanation
Indices: 28942354--28942413 Score: 66
Period size: 15 Copynumber: 4.0 Consensus size: 14
28942344 GATAAGAAGA
*
28942354 CCAAAATAAAGAAAT
1 CCAAGATAAA-AAAT
28942369 CCAAGATAGAAAAAT
1 CCAAGATA-AAAAAT
*
28942384 CCAAGATGAATAAAT
1 CCAAGAT-AAAAAAT
28942399 CCAAGATACAAAAAT
1 CCAAGATA-AAAAAT
28942414 ACAATATACG
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
14 1 0.03
15 35 0.90
16 3 0.08
ACGTcount: A:0.60, C:0.15, G:0.10, T:0.15
Consensus pattern (14 bp):
CCAAGATAAAAAAT
Found at i:28950602 original size:20 final size:19
Alignment explanation
Indices: 28950591--28950671 Score: 92
Period size: 19 Copynumber: 4.2 Consensus size: 19
28950581 ATTTATATAT
28950591 ATAA-ATTTTAATATATTA
1 ATAATATTTTAATATATTA
*
28950609 ATAATATTTTAATATCTTA
1 ATAATATTTTAATATATTA
*
28950628 ATAATATTTAATAATATATAA
1 ATAATATTT--TAATATATTA
* *
28950649 ATAATATTAATAATATAATA
1 ATAATATT-TTAATATATTA
28950669 ATA
1 ATA
28950672 TAGAAAGAAA
Statistics
Matches: 53, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
18 4 0.08
19 22 0.42
20 11 0.21
21 16 0.30
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (19 bp):
ATAATATTTTAATATATTA
Found at i:28950615 original size:11 final size:11
Alignment explanation
Indices: 28950599--28950671 Score: 77
Period size: 11 Copynumber: 7.2 Consensus size: 11
28950589 ATATAAATTT
28950599 TAATATATTAA
1 TAATATATTAA
28950610 TAATAT-TT--
1 TAATATATTAA
*
28950618 TAATATCTTAA
1 TAATATATTAA
28950629 TAATAT-TTAA
1 TAATATATTAA
*
28950639 TAATATATAAA
1 TAATATATTAA
28950650 T-A-ATATTAA
1 TAATATATTAA
*
28950659 TAATATAATAA
1 TAATATATTAA
28950670 TA
1 TA
28950672 TAGAAAGAAA
Statistics
Matches: 53, Mismatches: 3, Indels: 12
0.78 0.04 0.18
Matches are distributed among these distances:
8 6 0.11
9 9 0.17
10 14 0.26
11 24 0.45
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.45
Consensus pattern (11 bp):
TAATATATTAA
Found at i:28950685 original size:30 final size:29
Alignment explanation
Indices: 28950625--28950685 Score: 70
Period size: 30 Copynumber: 2.0 Consensus size: 29
28950615 TTTTAATATC
* *
28950625 TTAATAATATTTAATAATATATAAATAATA
1 TTAATAATA-TTAATAATATAAAAAAAATA
28950655 TTAATAATA-TAATAATATAGAAAGAAAATA
1 TTAATAATATTAATAATATA-AAA-AAAATA
28950685 T
1 T
28950686 GTGTTATATA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
28 10 0.37
29 2 0.07
30 15 0.56
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (29 bp):
TTAATAATATTAATAATATAAAAAAAATA
Found at i:28951365 original size:64 final size:64
Alignment explanation
Indices: 28951260--28951467 Score: 188
Period size: 67 Copynumber: 3.2 Consensus size: 64
28951250 CATCATGTGT
*
28951260 ACAAGAGAGCTACAAGACATAATGATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATG
1 ACAAGAGAGCTAC--GAGATAA--ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATG
28951325 TAG
62 TAG
* * * * * * * *
28951328 ACAAGAGAGCTACGGGATATATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGACACCATGT
1 ACAAGAGAGCTACGAGATAAATGTAGCTAGGTCGCATGGGT-GATACTA-TG-TGTACACCATGT
28951393 AG
63 AG
* * * * *
28951395 ACAAGAGAGCTATGAGATAAACTG--GCTAGGTCACATGGGTGGTACTAAGTGTTCACCATGT-G
1 ACAAGAGAGCTACGAGATAAA-TGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAG
28951457 TACAAGAGAGC
1 -ACAAGAGAGC
28951468 CGAACTATAT
Statistics
Matches: 114, Mismatches: 21, Indels: 15
0.76 0.14 0.10
Matches are distributed among these distances:
62 1 0.01
63 19 0.17
64 21 0.18
65 8 0.07
66 20 0.18
67 30 0.26
68 15 0.13
ACGTcount: A:0.32, C:0.17, G:0.29, T:0.22
Consensus pattern (64 bp):
ACAAGAGAGCTACGAGATAAATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAG
Found at i:28957501 original size:46 final size:46
Alignment explanation
Indices: 28957434--28957562 Score: 204
Period size: 46 Copynumber: 2.8 Consensus size: 46
28957424 TATTTGGGCA
* * *
28957434 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
*
28957480 TCCGAACTCTTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* *
28957526 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
28957563 GCGGGTTACA
Statistics
Matches: 76, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
46 76 1.00
ACGTcount: A:0.21, C:0.22, G:0.27, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
Found at i:28960534 original size:15 final size:15
Alignment explanation
Indices: 28960514--28960582 Score: 84
Period size: 15 Copynumber: 4.6 Consensus size: 15
28960504 GTATCTTGGG
28960514 TTTCTTTATCCTGGA
1 TTTCTTTATCCTGGA
* *
28960529 TCTCTTTATTCTGGA
1 TTTCTTTATCCTGGA
* *
28960544 TTTCTTTATTCTGGG
1 TTTCTTTATCCTGGA
* *
28960559 TTTCTCTATCTTGGA
1 TTTCTTTATCCTGGA
28960574 TTTCTTTAT
1 TTTCTTTAT
28960583 TCAGTTTTCT
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 45 1.00
ACGTcount: A:0.12, C:0.17, G:0.13, T:0.58
Consensus pattern (15 bp):
TTTCTTTATCCTGGA
Found at i:28960583 original size:30 final size:30
Alignment explanation
Indices: 28960505--28960584 Score: 99
Period size: 30 Copynumber: 2.7 Consensus size: 30
28960495 CATAGTATTG
* * *
28960505 TATCTTGGGTTTCTTTATCCTGGATCTCTT
1 TATCTTGGATTTCTTTATTCTGGATCTCTC
* *
28960535 TAT-TCTGGATTTCTTTATTCTGGGTTTCTC
1 TATCT-TGGATTTCTTTATTCTGGATCTCTC
28960565 TATCTTGGATTTCTTTATTC
1 TATCTTGGATTTCTTTATTC
28960585 AGTTTTCTTG
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
29 1 0.02
30 41 0.95
31 1 0.02
ACGTcount: A:0.11, C:0.17, G:0.15, T:0.56
Consensus pattern (30 bp):
TATCTTGGATTTCTTTATTCTGGATCTCTC
Found at i:28963045 original size:46 final size:46
Alignment explanation
Indices: 28962978--28963106 Score: 213
Period size: 46 Copynumber: 2.8 Consensus size: 46
28962968 TATTTGGGCA
* *
28962978 TCCGAACTCGTTGAGTTGAGTCTGAGTTCACCTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCGAACG
*
28963024 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCGAACG
* *
28963070 CCCGAGCTCGTTGAGTTGAGTCTGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCTGAGTTCACTTATGG
28963107 GCGGGTTACA
Statistics
Matches: 77, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 77 1.00
ACGTcount: A:0.20, C:0.21, G:0.29, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCGAACG
Found at i:28970566 original size:22 final size:22
Alignment explanation
Indices: 28970539--28970582 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
28970529 AAAAATGATC
*
28970539 AAAATTATTCAAAATTTATTAT
1 AAAATTATTCAAAATTCATTAT
*
28970561 AAAATTATTTAAAATTCATTAT
1 AAAATTATTCAAAATTCATTAT
28970583 GTTAATAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (22 bp):
AAAATTATTCAAAATTCATTAT
Found at i:28970640 original size:21 final size:22
Alignment explanation
Indices: 28970603--28970643 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
28970593 TAAGTCCAAA
*
28970603 ATAATTATTTTATAATAATTAT
1 ATAATTATTTTACAATAATTAT
28970625 ATAATT-TTTTACAATAATT
1 ATAATTATTTTACAATAATT
28970644 TTATCGAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (22 bp):
ATAATTATTTTACAATAATTAT
Found at i:28972196 original size:43 final size:43
Alignment explanation
Indices: 28971921--28972189 Score: 321
Period size: 43 Copynumber: 6.3 Consensus size: 43
28971911 TATGTGTATG
* * * *
28971921 CGAGTAAGACCACGTTTAATACGTTGGCATTGATATATGATTA
1 CGAGTAAGACCACGTCTGAGACGTTGGCATCGATATATGATTA
*
28971964 C-ATGTAAGACCACGTCT-AGGACGTTGGCA-CTGATATATGATTG
1 CGA-GTAAGACCACGTCTGA-GACGTTGGCATC-GATATATGATTA
*
28972007 CGTGTAAGACCACGTCTGAGACGTTGGCATCGATATATGATTA
1 CGAGTAAGACCACGTCTGAGACGTTGGCATCGATATATGATTA
* * * *
28972050 CGTA-TAAGACCACGCCTGAGAGGTTGGCATCGATATGTAATTA
1 CG-AGTAAGACCACGTCTGAGACGTTGGCATCGATATATGATTA
* *
28972093 CGTGTAAGACCACGTCTGGGACGTTGGCATCGATATATGATTA
1 CGAGTAAGACCACGTCTGAGACGTTGGCATCGATATATGATTA
* * * *
28972136 CGTGTAAGACCATGTCTGAGACGTTGGCATCGATATGTGTTTA
1 CGAGTAAGACCACGTCTGAGACGTTGGCATCGATATATGATTA
*
28972179 TGAGTAAGACC
1 CGAGTAAGACC
28972190 CTGTCTGGGA
Statistics
Matches: 195, Mismatches: 23, Indels: 16
0.83 0.10 0.07
Matches are distributed among these distances:
42 2 0.01
43 191 0.98
44 2 0.01
ACGTcount: A:0.28, C:0.17, G:0.26, T:0.29
Consensus pattern (43 bp):
CGAGTAAGACCACGTCTGAGACGTTGGCATCGATATATGATTA
Found at i:28976268 original size:43 final size:43
Alignment explanation
Indices: 28976220--28976315 Score: 124
Period size: 43 Copynumber: 2.3 Consensus size: 43
28976210 TAGGGTTTCT
* * * *
28976220 GATATGTG-TTCTAGTGTAAGACCATGTCTGGGACGTTGGCATC
1 GATATGTGATTATA-TGTAAGACCATGTCTAGGACATCGGCATC
28976263 GATATGTGATTATATGTAAGACCATGTCTAGGACATCGGCATC
1 GATATGTGATTATATGTAAGACCATGTCTAGGACATCGGCATC
*
28976306 G-TATTTGATT
1 GATATGTGATT
28976316 CGTGTACACC
Statistics
Matches: 47, Mismatches: 5, Indels: 3
0.85 0.09 0.05
Matches are distributed among these distances:
42 8 0.17
43 35 0.74
44 4 0.09
ACGTcount: A:0.25, C:0.15, G:0.26, T:0.34
Consensus pattern (43 bp):
GATATGTGATTATATGTAAGACCATGTCTAGGACATCGGCATC
Found at i:28981794 original size:43 final size:42
Alignment explanation
Indices: 28981650--28981806 Score: 140
Period size: 43 Copynumber: 3.7 Consensus size: 42
28981640 TGTGTTTTCG
* * *
28981650 TGTAAGACCACATCTGGGACGTTGGCATCGACTTTTGTTTTACG
1 TGTAAGACCACGTCTGGGACGTTGGCATCGA-TTTTG-ATTACA
* * * * * *
28981694 TGTAAGACCATGTCTGGGACATCGACATC-ATATCTGATTTCA
1 TGTAAGACCACGTCTGGGACGTTGGCATCGAT-TTTGATTACA
*
28981736 TGTAAGACC-CTGTCTGGGACAG-TGGCATCGATGTTTGATTGCA
1 TGTAAGACCAC-GTCTGGGAC-GTTGGCATCGAT-TTTGATTACA
*
28981779 TGTAATACCACGTCTGGGACGTTGGCAT
1 TGTAAGACCACGTCTGGGACGTTGGCAT
28981807 TGTATATGCT
Statistics
Matches: 90, Mismatches: 17, Indels: 13
0.75 0.14 0.11
Matches are distributed among these distances:
42 28 0.31
43 37 0.41
44 25 0.28
ACGTcount: A:0.23, C:0.20, G:0.25, T:0.31
Consensus pattern (42 bp):
TGTAAGACCACGTCTGGGACGTTGGCATCGATTTTGATTACA
Found at i:28983757 original size:27 final size:26
Alignment explanation
Indices: 28983722--28983833 Score: 134
Period size: 27 Copynumber: 4.2 Consensus size: 26
28983712 AGCATGGCTG
* *
28983722 CCAGAACAGATAATGTGACAGAGTCA
1 CCAGAACAGATAATGTGGCAGAGCCA
28983748 CCAGATACAGATAATCGTGGCAGAGCCA
1 CCAGA-ACAGATAAT-GTGGCAGAGCCA
* *
28983776 CCATAACAGAAATATGTGGCAGAGCCA
1 CCAGAACAGATA-ATGTGGCAGAGCCA
* *
28983803 CCAGATCAGATAATTGTGGCATAGCCA
1 CCAGAACAGATAA-TGTGGCAGAGCCA
28983830 CCAG
1 CCAG
28983834 GACGCTTCCT
Statistics
Matches: 74, Mismatches: 8, Indels: 7
0.83 0.09 0.08
Matches are distributed among these distances:
26 6 0.08
27 52 0.70
28 16 0.22
ACGTcount: A:0.38, C:0.23, G:0.23, T:0.16
Consensus pattern (26 bp):
CCAGAACAGATAATGTGGCAGAGCCA
Found at i:28983822 original size:54 final size:54
Alignment explanation
Indices: 28983726--28983832 Score: 153
Period size: 54 Copynumber: 2.0 Consensus size: 54
28983716 TGGCTGCCAG
* *
28983726 AACAGATAATGTGACAGAGTCACCAGATACAGATAATCGTGGCAGAGCCACCAT
1 AACAGAAAATGTGACAGAGCCACCAGATACAGATAATCGTGGCAGAGCCACCAT
* * *
28983780 AACAGAAATATGTGGCAGAGCCACCAGAT-CAGATAATTGTGGCATAGCCACCA
1 AACAGAAA-ATGTGACAGAGCCACCAGATACAGATAATCGTGGCAGAGCCACCA
28983833 GGACGCTTCC
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
54 29 0.62
55 18 0.38
ACGTcount: A:0.38, C:0.22, G:0.22, T:0.17
Consensus pattern (54 bp):
AACAGAAAATGTGACAGAGCCACCAGATACAGATAATCGTGGCAGAGCCACCAT
Found at i:28985102 original size:22 final size:22
Alignment explanation
Indices: 28985075--28985117 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
28985065 ATAGAAGAAG
* *
28985075 AAAAGAATAACAAATGGAGAGA
1 AAAAGAAAAACAAAAGGAGAGA
*
28985097 AAAAGAAAAATAAAAGGAGAG
1 AAAAGAAAAACAAAAGGAGAG
28985118 GAAGAGTGAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.67, C:0.02, G:0.23, T:0.07
Consensus pattern (22 bp):
AAAAGAAAAACAAAAGGAGAGA
Found at i:28994588 original size:37 final size:37
Alignment explanation
Indices: 28994538--28994613 Score: 152
Period size: 37 Copynumber: 2.1 Consensus size: 37
28994528 GCCACCTGAG
28994538 TTAGAAAAGATCCATAATGTATTCCATGTTTCGATGC
1 TTAGAAAAGATCCATAATGTATTCCATGTTTCGATGC
28994575 TTAGAAAAGATCCATAATGTATTCCATGTTTCGATGC
1 TTAGAAAAGATCCATAATGTATTCCATGTTTCGATGC
28994612 TT
1 TT
28994614 CATAGATATC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.37
Consensus pattern (37 bp):
TTAGAAAAGATCCATAATGTATTCCATGTTTCGATGC
Found at i:28996275 original size:41 final size:43
Alignment explanation
Indices: 28996144--28996275 Score: 148
Period size: 43 Copynumber: 3.1 Consensus size: 43
28996134 GTGTTCTTGT
* *
28996144 GCATTGATATGTGATTACGTGTAAGACCAC-GCCTGGGAC-GTTA
1 GCATCGATATGTGATTACGTGTAAGACC-CTGTCTGGGACAG-TA
* *
28996187 GCATCGATATGTGATTACGTGTAAGACCATGTCTGGAACA-TCA
1 GCATCGATATGTGATTACGTGTAAGACCCTGTCTGGGACAGT-A
* *
28996230 GCATCG-TATTTGATT-CGTGTAAGACCCTGTCTGGGACAGTG
1 GCATCGATATGTGATTACGTGTAAGACCCTGTCTGGGACAGTA
28996271 GCATC
1 GCATC
28996276 AAGATAGCAT
Statistics
Matches: 77, Mismatches: 8, Indels: 10
0.81 0.08 0.11
Matches are distributed among these distances:
41 26 0.34
42 10 0.13
43 41 0.53
ACGTcount: A:0.25, C:0.20, G:0.27, T:0.29
Consensus pattern (43 bp):
GCATCGATATGTGATTACGTGTAAGACCCTGTCTGGGACAGTA
Found at i:29002426 original size:28 final size:28
Alignment explanation
Indices: 29002391--29002461 Score: 97
Period size: 28 Copynumber: 2.5 Consensus size: 28
29002381 TACTCAATTC
* * *
29002391 CTCGCACACTAAGTGGCATACGCGATAT
1 CTCGCACACTAAGTGCCACACGCAATAT
* *
29002419 CTTGCACACTAAGTGCCACACTCAATAT
1 CTCGCACACTAAGTGCCACACGCAATAT
29002447 CTCGCACACTAAGTG
1 CTCGCACACTAAGTG
29002462 TGCCATACAT
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 37 1.00
ACGTcount: A:0.30, C:0.31, G:0.17, T:0.23
Consensus pattern (28 bp):
CTCGCACACTAAGTGCCACACGCAATAT
Found at i:29002520 original size:40 final size:40
Alignment explanation
Indices: 29002448--29002546 Score: 135
Period size: 40 Copynumber: 2.4 Consensus size: 40
29002438 ACTCAATATC
* *
29002448 TCGCACACTAAGTGTGCCATACATAGCTGAAGCTATCTCAAA
1 TCGCACACTAA--GTGCCATACATAGCCGAAGCTAACTCAAA
* * *
29002490 TCGCACACTAAGTGCCATATATAGCCGAAGCTAAGTCGAA
1 TCGCACACTAAGTGCCATACATAGCCGAAGCTAACTCAAA
29002530 TCGCACACTAAGTGCCA
1 TCGCACACTAAGTGCCA
29002547 CAAATAGTCG
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
40 41 0.79
42 11 0.21
ACGTcount: A:0.33, C:0.27, G:0.18, T:0.21
Consensus pattern (40 bp):
TCGCACACTAAGTGCCATACATAGCCGAAGCTAACTCAAA
Done.