Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A07
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: 92880876
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2857347 characters in sequence are not A, C, G, or T
File 123 of 290
Found at i:38551183 original size:30 final size:30
Alignment explanation
Indices: 38551149--38551213 Score: 123
Period size: 30 Copynumber: 2.2 Consensus size: 30
38551139 GCTTGGATGT
38551149 AAGAAAAAAACACAATTCATACCATAGTAG
1 AAGAAAAAAACACAATTCATACCATAGTAG
38551179 AAGAAAAAAACACAATTCATACCATAGTAG
1 AAGAAAAAAACACAATTCATACCATAGTAG
38551209 -AGAAA
1 AAGAAA
38551214 GTTACATAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
29 5 0.14
30 30 0.86
ACGTcount: A:0.58, C:0.15, G:0.11, T:0.15
Consensus pattern (30 bp):
AAGAAAAAAACACAATTCATACCATAGTAG
Found at i:38584553 original size:44 final size:43
Alignment explanation
Indices: 38584417--38584565 Score: 142
Period size: 44 Copynumber: 3.5 Consensus size: 43
38584407 CAACGCCAAC
* * * * *
38584417 GTCCTAGACGTGGTCTTACATGTTATCACATATCGATGTCACT
1 GTCCCAGACATGGTCTTACAAGTAATTACATATCGATGTCACT
* * * * *
38584460 GTCCCAGACAGGGTCTTACACG-AACT-CATATACAATGCCGA-T
1 GTCCCAGACATGGTCTTACAAGTAATTACATAT-CGATGTC-ACT
*
38584502 GTCCCAGACATGGTCTTACAAGTAAATTACAAATCGATGTCACT
1 GTCCCAGACATGGTCTTACAAGT-AATTACATATCGATGTCACT
*
38584546 GTCCCAGACGTGGTCTTACA
1 GTCCCAGACATGGTCTTACA
38584566 CGAAATCACA
Statistics
Matches: 84, Mismatches: 16, Indels: 11
0.76 0.14 0.10
Matches are distributed among these distances:
41 5 0.06
42 27 0.32
43 20 0.24
44 28 0.33
45 4 0.05
ACGTcount: A:0.28, C:0.26, G:0.19, T:0.28
Consensus pattern (43 bp):
GTCCCAGACATGGTCTTACAAGTAATTACATATCGATGTCACT
Found at i:38592586 original size:24 final size:26
Alignment explanation
Indices: 38592553--38592605 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
38592543 AAATTATTTT
*
38592553 AAAATAAAATTA-AT-TAAAATTTAA
1 AAAATAAAATAACATATAAAATTTAA
* *
38592577 AAAATCAAATAACATATAAACTTTAA
1 AAAATAAAATAACATATAAAATTTAA
38592603 AAA
1 AAA
38592606 TTATATAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 10 0.42
25 2 0.08
26 12 0.50
ACGTcount: A:0.66, C:0.06, G:0.00, T:0.28
Consensus pattern (26 bp):
AAAATAAAATAACATATAAAATTTAA
Found at i:38597022 original size:22 final size:22
Alignment explanation
Indices: 38596997--38597041 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
38596987 AAAAAAATTG
38596997 TAGGAATATTCTGTAAATATTT
1 TAGGAATATTCTGTAAATATTT
* *
38597019 TAGGAATATTTTGTAGATATTT
1 TAGGAATATTCTGTAAATATTT
38597041 T
1 T
38597042 TTTTTATTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.33, C:0.02, G:0.16, T:0.49
Consensus pattern (22 bp):
TAGGAATATTCTGTAAATATTT
Found at i:38601622 original size:22 final size:22
Alignment explanation
Indices: 38601594--38601635 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
38601584 GGGAGTGTAA
38601594 GAATATTCTGTAAATATTTTAG
1 GAATATTCTGTAAATATTTTAG
* *
38601616 GAATATTTTGTAGATATTTT
1 GAATATTCTGTAAATATTTT
38601636 TTTTATTAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.33, C:0.02, G:0.14, T:0.50
Consensus pattern (22 bp):
GAATATTCTGTAAATATTTTAG
Found at i:38603841 original size:3 final size:3
Alignment explanation
Indices: 38603835--38603874 Score: 62
Period size: 3 Copynumber: 13.3 Consensus size: 3
38603825 GATAATAATG
* *
38603835 ACA ACA ACA ACA ACA ACA ACA ATA ACA ATA ACA ACA ACA A
1 ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA A
38603875 AACTAAGCAC
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.68, C:0.28, G:0.00, T:0.05
Consensus pattern (3 bp):
ACA
Found at i:38605752 original size:31 final size:31
Alignment explanation
Indices: 38605710--38605781 Score: 101
Period size: 31 Copynumber: 2.4 Consensus size: 31
38605700 CGAAATTCAA
* *
38605710 AAAAAAATTTTAACAGCTCAATGACTTAAAT
1 AAAAAATTTTTAACAGCTCAAAGACTTAAAT
* *
38605741 AAAAAATTTTTAATAGTTCAAAGACTTAAAT
1 AAAAAATTTTTAACAGCTCAAAGACTTAAAT
38605772 -AAAAATTTTT
1 AAAAAATTTTT
38605782 GAATAATTCA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
30 10 0.27
31 27 0.73
ACGTcount: A:0.51, C:0.08, G:0.06, T:0.35
Consensus pattern (31 bp):
AAAAAATTTTTAACAGCTCAAAGACTTAAAT
Found at i:38606412 original size:46 final size:45
Alignment explanation
Indices: 38606362--38606448 Score: 129
Period size: 46 Copynumber: 1.9 Consensus size: 45
38606352 AGATATTTTG
* *
38606362 TTAAGAGTTTAATTAATATTTGATTTATTCTATATTTAGTTAGTTA
1 TTAAGAGTTTAACTAATATTTGATGTA-TCTATATTTAGTTAGTTA
* *
38606408 TTAAGAGTTTAACTAATATTTTATGTATCTTTATTTAGTTA
1 TTAAGAGTTTAACTAATATTTGATGTATCTATATTTAGTTA
38606449 AATAAATGGT
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
45 13 0.35
46 24 0.65
ACGTcount: A:0.32, C:0.03, G:0.10, T:0.54
Consensus pattern (45 bp):
TTAAGAGTTTAACTAATATTTGATGTATCTATATTTAGTTAGTTA
Found at i:38612187 original size:28 final size:28
Alignment explanation
Indices: 38612152--38612215 Score: 78
Period size: 26 Copynumber: 2.4 Consensus size: 28
38612142 TTTATATTAA
* * *
38612152 ATAATTTTCTTATCCCAATTTTA-CCCC
1 ATAATTTTTTTTTCACAATTTTACCCCC
*
38612179 -TAATTTTTTTTTGACAATTTTACCCCC
1 ATAATTTTTTTTTCACAATTTTACCCCC
38612206 ATAATTTTTT
1 ATAATTTTTT
38612216 GATGATTTTA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
26 18 0.58
27 4 0.13
28 9 0.29
ACGTcount: A:0.25, C:0.22, G:0.02, T:0.52
Consensus pattern (28 bp):
ATAATTTTTTTTTCACAATTTTACCCCC
Found at i:38612214 original size:26 final size:25
Alignment explanation
Indices: 38612167--38612228 Score: 65
Period size: 25 Copynumber: 2.4 Consensus size: 25
38612157 TTTCTTATCC
38612167 CAATTTTA-CCCCTAATTTTTTTTTGA
1 CAATTTTACCCCCTAA--TTTTTTTGA
38612193 CAATTTTACCCCCATAA-TTTTTTGA
1 CAATTTTACCCCC-TAATTTTTTTGA
**
38612218 TGATTTTACCC
1 CAATTTTACCC
38612229 TTGGTAAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
25 17 0.53
26 8 0.25
27 4 0.12
28 3 0.09
ACGTcount: A:0.24, C:0.23, G:0.05, T:0.48
Consensus pattern (25 bp):
CAATTTTACCCCCTAATTTTTTTGA
Found at i:38612417 original size:12 final size:12
Alignment explanation
Indices: 38612387--38612424 Score: 51
Period size: 12 Copynumber: 3.1 Consensus size: 12
38612377 TGCAAATGTA
38612387 TCATTTCTC-TTT
1 TCATTTC-CATTT
38612399 CTCATTTCCATTT
1 -TCATTTCCATTT
38612412 TCATTTCCATTT
1 TCATTTCCATTT
38612424 T
1 T
38612425 GAGAAAATCA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
12 14 0.58
13 10 0.42
ACGTcount: A:0.13, C:0.26, G:0.00, T:0.61
Consensus pattern (12 bp):
TCATTTCCATTT
Found at i:38613151 original size:40 final size:40
Alignment explanation
Indices: 38613105--38613184 Score: 151
Period size: 40 Copynumber: 2.0 Consensus size: 40
38613095 GTCATGCATA
*
38613105 CATAGTTTGTCATCCACTCATGATTCAGGTATGACACACT
1 CATAGTTTGTCATCCACTCATGATTCAAGTATGACACACT
38613145 CATAGTTTGTCATCCACTCATGATTCAAGTATGACACACT
1 CATAGTTTGTCATCCACTCATGATTCAAGTATGACACACT
38613185 ATGAACATTA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.29, C:0.25, G:0.14, T:0.33
Consensus pattern (40 bp):
CATAGTTTGTCATCCACTCATGATTCAAGTATGACACACT
Found at i:38618354 original size:48 final size:48
Alignment explanation
Indices: 38618203--38618393 Score: 161
Period size: 48 Copynumber: 4.0 Consensus size: 48
38618193 TCATTAGGGG
* * * *
38618203 ATACATTGATTTGGCTTCGGGCCATAATATTAGCTCTTCGGGTGC-AA
1 ATACATTGATTTGGCTTCGAGCCATGATATTAGCACTTCAGGTGCGAA
* * * * * * * *
38618250 GTTGCATAGATTTGGCTTCGAGACATGATATCAGCACTTCGGGTGTGAG
1 -ATACATTGATTTGGCTTCGAGCCATGATATTAGCACTTCAGGTGCGAA
* * * * *
38618299 CTTCATTGATTTGGCTTTGGGCCATGATATTAGGACTTCAGGTGCGAA
1 ATACATTGATTTGGCTTCGAGCCATGATATTAGCACTTCAGGTGCGAA
* * * *
38618347 ATACATTGAGTTGACTTTGAGCCATGATATGAGCACTT-AGTGTGCGA
1 ATACATTGATTTGGCTTCGAGCCATGATATTAGCACTTCAG-GTGCGA
38618394 TATTCTTGAG
Statistics
Matches: 113, Mismatches: 28, Indels: 4
0.78 0.19 0.03
Matches are distributed among these distances:
47 2 0.02
48 110 0.97
49 1 0.01
ACGTcount: A:0.24, C:0.17, G:0.27, T:0.33
Consensus pattern (48 bp):
ATACATTGATTTGGCTTCGAGCCATGATATTAGCACTTCAGGTGCGAA
Found at i:38618373 original size:96 final size:96
Alignment explanation
Indices: 38618206--38618384 Score: 225
Period size: 96 Copynumber: 1.9 Consensus size: 96
38618196 TTAGGGGATA
* * * * * *
38618206 CATTGATTTGGCTTCGGGCCATAATATTAGCTCTTCGGGTGCAAGTTGCATAGATTTGGCTTCGA
1 CATTGATTTGGCTTCGGGCCATAATATTAGCACTTCAGGTGCAAGATACATAGAGTTGACTTCGA
38618271 GACATGATATCAGCACTTCGGGTGTGAGCTT
66 GACATGATATCAGCACTTCGGGTGTGAGCTT
* * * * *
38618302 CATTGATTTGGCTTTGGGCCATGATATTAGGACTTCAGGTGCGAA-ATACATTGAGTTGACTTTG
1 CATTGATTTGGCTTCGGGCCATAATATTAGCACTTCAGGTGC-AAGATACATAGAGTTGACTTCG
* *
38618366 AGCCATGATATGAGCACTT
65 AGACATGATATCAGCACTT
38618385 AGTGTGCGAT
Statistics
Matches: 69, Mismatches: 13, Indels: 2
0.82 0.15 0.02
Matches are distributed among these distances:
96 67 0.97
97 2 0.03
ACGTcount: A:0.23, C:0.17, G:0.26, T:0.34
Consensus pattern (96 bp):
CATTGATTTGGCTTCGGGCCATAATATTAGCACTTCAGGTGCAAGATACATAGAGTTGACTTCGA
GACATGATATCAGCACTTCGGGTGTGAGCTT
Found at i:38625625 original size:96 final size:96
Alignment explanation
Indices: 38625457--38625635 Score: 216
Period size: 96 Copynumber: 1.9 Consensus size: 96
38625447 GATTAGGATA
* * * ** * *
38625457 CATTGATTTGGCTTCGGGCCATGATATTAGCTCCTCGGGTGCGAGTTGCATAGATTTGGCTTCAG
1 CATTGATTTGGCTTCGGGCCATGATATTAGCACCTCAGGTGCGAGATAAATACAGTTGGCTTCAG
*
38625522 GATATGATATCG-GCACTTCGGGTTTGAGCTT
66 GACATGATAT-GAGCACTTCGGGTTTGAGCTT
* * * * *
38625553 CATTGATTTGGTTTTGGGCCATGATATTAGCACTTCAGGTGCGAGATAAATTCAGTTGGCTTCGG
1 CATTGATTTGGCTTCGGGCCATGATATTAGCACCTCAGGTGCGAGATAAATACAGTTGGCTTCAG
*
38625618 GCCATGATATGAGCACTT
66 GACATGATATGAGCACTT
38625636 AGTGTGCAAG
Statistics
Matches: 68, Mismatches: 14, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
95 1 0.01
96 67 0.99
ACGTcount: A:0.20, C:0.18, G:0.28, T:0.34
Consensus pattern (96 bp):
CATTGATTTGGCTTCGGGCCATGATATTAGCACCTCAGGTGCGAGATAAATACAGTTGGCTTCAG
GACATGATATGAGCACTTCGGGTTTGAGCTT
Found at i:38630688 original size:5 final size:5
Alignment explanation
Indices: 38630636--38630685 Score: 82
Period size: 5 Copynumber: 10.0 Consensus size: 5
38630626 AATAAAAATA
* *
38630636 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG GAAAG GAAAG
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG
38630686 GAAGGGAAAA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
5 44 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:38633822 original size:17 final size:18
Alignment explanation
Indices: 38633802--38633845 Score: 56
Period size: 17 Copynumber: 2.5 Consensus size: 18
38633792 CCAAAAATAA
38633802 TAATATTATAA-TAAATT
1 TAATATTATAATTAAATT
*
38633819 TAATATT-TAATTTAATT
1 TAATATTATAATTAAATT
38633836 TAATACTTAT
1 TAATA-TTAT
38633846 CCTGATAGTA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
16 3 0.13
17 17 0.74
18 2 0.09
19 1 0.04
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (18 bp):
TAATATTATAATTAAATT
Found at i:38633890 original size:68 final size:69
Alignment explanation
Indices: 38633818--38633945 Score: 204
Period size: 68 Copynumber: 1.9 Consensus size: 69
38633808 TATAATAAAT
* * *
38633818 TTAATATTTAATTTAATTTAATACTTATCCTGAT-AGTATTTTATTAATTTAATATTAAATTGAT
1 TTAATATTAAATTTAATATAATACTTATCCTGATAAGTATTATATTAATTTAATATTAAATTGAT
38633882 TATC
66 TATC
* *
38633886 TTAATATTAAATTTAATATAATATTTATCTTGATAAGTATTATATTAATTTAATATTAAA
1 TTAATATTAAATTTAATATAATACTTATCCTGATAAGTATTATATTAATTTAATATTAAA
38633946 GTGAACTCTT
Statistics
Matches: 54, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
68 30 0.56
69 24 0.44
ACGTcount: A:0.41, C:0.04, G:0.04, T:0.52
Consensus pattern (69 bp):
TTAATATTAAATTTAATATAATACTTATCCTGATAAGTATTATATTAATTTAATATTAAATTGAT
TATC
Found at i:38642799 original size:27 final size:26
Alignment explanation
Indices: 38642759--38642863 Score: 113
Period size: 27 Copynumber: 3.9 Consensus size: 26
38642749 AGGAAGCGTC
*
38642759 CTGGTGGCTATGCCACAATTATCTGAT
1 CTGGTGGCTCTGCCAC-ATTATCTGAT
*
38642786 CTGGTGGCTCTGCCACATATATCTGTT
1 CTGGTGGCTCTGCCACAT-TATCTGAT
38642813 CTGGTGGCTCTGCCACGATTAT-TGTAT
1 CTGGTGGCTCTGCCAC-ATTATCTG-AT
** * *
38642840 CAAGTGACTCTGTCACATTATCTG
1 CTGGTGGCTCTGCCACATTATCTG
38642864 TTCTAACATC
Statistics
Matches: 67, Mismatches: 7, Indels: 8
0.82 0.09 0.10
Matches are distributed among these distances:
26 9 0.13
27 56 0.84
28 2 0.03
ACGTcount: A:0.19, C:0.24, G:0.22, T:0.35
Consensus pattern (26 bp):
CTGGTGGCTCTGCCACATTATCTGAT
Found at i:38642851 original size:54 final size:53
Alignment explanation
Indices: 38642759--38642867 Score: 139
Period size: 54 Copynumber: 2.0 Consensus size: 53
38642749 AGGAAGCGTC
** *
38642759 CTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATATCTGTT
1 CTGGTGGCTATGCCACAATTATCTGATCAAGTGACTCTGCCACAT-TATCTGTT
* * *
38642813 CTGGTGGCTCTGCCACGATTAT-TGTATCAAGTGACTCTGTCACATTATCTGTT
1 CTGGTGGCTATGCCACAATTATCTG-ATCAAGTGACTCTGCCACATTATCTGTT
38642866 CT
1 CT
38642868 AACATCCATG
Statistics
Matches: 48, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
53 12 0.25
54 36 0.75
ACGTcount: A:0.18, C:0.24, G:0.21, T:0.37
Consensus pattern (53 bp):
CTGGTGGCTATGCCACAATTATCTGATCAAGTGACTCTGCCACATTATCTGTT
Found at i:38646239 original size:5 final size:5
Alignment explanation
Indices: 38646229--38646299 Score: 63
Period size: 6 Copynumber: 13.2 Consensus size: 5
38646219 TATGTCTTTC
* *
38646229 AAAAT AAAAT AATAAT AAAAT GAAAAT GAAAAT AAAAAT CAAAAGA AAAAG
1 AAAAT AAAAT AA-AAT AAAAT -AAAAT -AAAAT -AAAAT -AAAA-T AAAAT
38646280 AAAAT -AAAT AAAAT AAAAT A
1 AAAAT AAAAT AAAAT AAAAT A
38646300 GGAGGATTCA
Statistics
Matches: 57, Mismatches: 5, Indels: 8
0.81 0.07 0.11
Matches are distributed among these distances:
4 4 0.07
5 24 0.42
6 29 0.51
ACGTcount: A:0.76, C:0.01, G:0.06, T:0.17
Consensus pattern (5 bp):
AAAAT
Found at i:38646261 original size:23 final size:22
Alignment explanation
Indices: 38646229--38646298 Score: 76
Period size: 23 Copynumber: 3.2 Consensus size: 22
38646219 TATGTCTTTC
38646229 AAAAT-AAAATAATAATAAAATG
1 AAAATGAAAATAA-AATAAAATG
38646251 AAAATGAAAATAAAAATCAAAA-G
1 AAAATGAAAAT-AAAAT-AAAATG
*
38646274 AAAAAGAAAAT-AAATAAAAT-
1 AAAATGAAAATAAAATAAAATG
38646294 AAAAT
1 AAAAT
38646299 AGGAGGATTC
Statistics
Matches: 42, Mismatches: 2, Indels: 10
0.78 0.04 0.19
Matches are distributed among these distances:
20 8 0.19
21 4 0.10
22 5 0.12
23 19 0.45
24 6 0.14
ACGTcount: A:0.76, C:0.01, G:0.06, T:0.17
Consensus pattern (22 bp):
AAAATGAAAATAAAATAAAATG
Found at i:38652480 original size:13 final size:13
Alignment explanation
Indices: 38652462--38652492 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
38652452 CTTTGAAAAA
*
38652462 GTGACACGCCCGT
1 GTGACACGACCGT
38652475 GTGACACGACCGT
1 GTGACACGACCGT
38652488 GTGAC
1 GTGAC
38652493 GTGATTACCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.19, C:0.32, G:0.32, T:0.16
Consensus pattern (13 bp):
GTGACACGACCGT
Found at i:38658385 original size:28 final size:28
Alignment explanation
Indices: 38658345--38658426 Score: 110
Period size: 28 Copynumber: 2.9 Consensus size: 28
38658335 GCAATCAAAT
* * *
38658345 ATGGTACTCAGTGTACGAAATATTGAGA
1 ATGGCACTTAGTGTGCGAAATATTGAGA
*
38658373 ATGGCACTTAGTGTGCGAGATATTGAGA
1 ATGGCACTTAGTGTGCGAAATATTGAGA
* *
38658401 ATGACACTTAGTGTGCAAAATATTGA
1 ATGGCACTTAGTGTGCGAAATATTGA
38658427 ATGATTCAAA
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 47 1.00
ACGTcount: A:0.34, C:0.11, G:0.26, T:0.29
Consensus pattern (28 bp):
ATGGCACTTAGTGTGCGAAATATTGAGA
Found at i:38663112 original size:6 final size:6
Alignment explanation
Indices: 38663091--38663136 Score: 56
Period size: 6 Copynumber: 7.3 Consensus size: 6
38663081 TATTTGTTTA
* *
38663091 TTATTA TTATTAT TTATTT TTACTT TTATTT TTAATTT TTATTT TT
1 TTATTT TTATT-T TTATTT TTATTT TTATTT TT-ATTT TTATTT TT
38663137 CTTCTTCTTC
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
6 24 0.69
7 11 0.31
ACGTcount: A:0.22, C:0.02, G:0.00, T:0.76
Consensus pattern (6 bp):
TTATTT
Found at i:38663123 original size:13 final size:13
Alignment explanation
Indices: 38663103--38663136 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
38663093 ATTATTATTA
38663103 TTTATTTTT-ACT
1 TTTATTTTTAACT
*
38663115 TTTATTTTTAATT
1 TTTATTTTTAACT
38663128 TTTATTTTT
1 TTTATTTTT
38663137 CTTCTTCTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 9 0.45
13 11 0.55
ACGTcount: A:0.18, C:0.03, G:0.00, T:0.79
Consensus pattern (13 bp):
TTTATTTTTAACT
Found at i:38674628 original size:13 final size:13
Alignment explanation
Indices: 38674610--38674635 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
38674600 CTCGACAGGA
38674610 ACACGCCCGTGTG
1 ACACGCCCGTGTG
38674623 ACACGCCCGTGTG
1 ACACGCCCGTGTG
38674636 CAATTGCTTA
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:0.15, C:0.38, G:0.31, T:0.15
Consensus pattern (13 bp):
ACACGCCCGTGTG
Found at i:38676129 original size:19 final size:20
Alignment explanation
Indices: 38676105--38676146 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
38676095 TAGGAGAGCG
38676105 AAAAAACGA-AAAACGGGCC
1 AAAAAACGAGAAAACGGGCC
* *
38676124 AAAAAAGGAGAAAATGGGCC
1 AAAAAACGAGAAAACGGGCC
38676144 AAA
1 AAA
38676147 GTACGAAATC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 8 0.40
20 12 0.60
ACGTcount: A:0.60, C:0.14, G:0.24, T:0.02
Consensus pattern (20 bp):
AAAAAACGAGAAAACGGGCC
Found at i:38681067 original size:40 final size:40
Alignment explanation
Indices: 38681019--38681285 Score: 480
Period size: 40 Copynumber: 6.7 Consensus size: 40
38681009 GCAAACACAT
* *
38681019 TTGCCTTCGGGTCTTAACCCGGACATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
* *
38681059 TTGCCTTCGGGTCTTAGCCCGGATATATCATCCCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
*
38681099 TTGCCTTCGGGTCATAGCCCGGATATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
*
38681139 TTGCCTTCGGGTCTTAGCCCGGATATGTCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
38681179 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
38681219 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
38681259 TTGCCTTCGGGTCTTAGCCCGGATATA
1 TTGCCTTCGGGTCTTAGCCCGGATATA
38681286 ATCCAATGTT
Statistics
Matches: 217, Mismatches: 10, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 217 1.00
ACGTcount: A:0.22, C:0.28, G:0.21, T:0.30
Consensus pattern (40 bp):
TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
Found at i:38685875 original size:12 final size:11
Alignment explanation
Indices: 38685842--38685902 Score: 59
Period size: 12 Copynumber: 5.0 Consensus size: 11
38685832 ACTTATTTAG
38685842 TTTATTTTATT
1 TTTATTTTATT
*
38685853 ATTATTATTATT
1 TTTATT-TTATT
38685865 TTTACTTTTATT
1 TTTA-TTTTATT
38685877 TTTAATTTTTAATT
1 TTT-A-TTTT-ATT
38685891 TTTAATTTTATT
1 TTT-ATTTTATT
38685903 CTTCTTCCTT
Statistics
Matches: 43, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
11 5 0.12
12 19 0.44
13 11 0.26
14 8 0.19
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.74
Consensus pattern (11 bp):
TTTATTTTATT
Found at i:38685884 original size:7 final size:7
Alignment explanation
Indices: 38685870--38685899 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
38685860 TTATTTTTAC
38685870 TTTT-AT
1 TTTTAAT
38685876 TTTTAAT
1 TTTTAAT
38685883 TTTTAAT
1 TTTTAAT
38685890 TTTTAAT
1 TTTTAAT
38685897 TTT
1 TTT
38685900 ATTCTTCTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 4 0.17
7 19 0.83
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (7 bp):
TTTTAAT
Found at i:38687354 original size:89 final size:89
Alignment explanation
Indices: 38687255--38687496 Score: 290
Period size: 89 Copynumber: 2.7 Consensus size: 89
38687245 TACGTACCAC
* * *
38687255 TATCTGATCTGGCAGTTTTTACTGCACGTCTATACCGCGGTTTACCGCATTGCACAGTACAGCTT
1 TATCTGATCTGGCAGTTTATACTGCATGTCTATACCGTGGTTTACCGCATTGCACAGTACAGCTT
* *
38687320 ATACGCTAGCCTTGCTGCGTAATA
66 ATACGCTAGCCTTGCTACATAATA
* * * **
38687344 TATCTGATCTGGGAGTTTATACTGCATGTCTATATCGTGGTCTT-CCGTATTATACAGTACAGCT
1 TATCTGATCTGGCAGTTTATACTGCATGTCTATACCGTGGT-TTACCGCATTGCACAGTACAGCT
*
38687408 TATATGCTAGCCTTGCTACATAATA
65 TATACGCTAGCCTTGCTACATAATA
* * * * * * *
38687433 TATTTGATCTGGTAGTTCATACTGCATGTCTGTACCGTAGTCTACTGCATTGCACCA-TACAGCT
1 TATCTGATCTGGCAGTTTATACTGCATGTCTATACCGTGGTTTACCGCATTGCA-CAGTACAGCT
38687497 CAGTAATAGC
Statistics
Matches: 128, Mismatches: 22, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
88 1 0.01
89 123 0.96
90 4 0.03
ACGTcount: A:0.23, C:0.23, G:0.19, T:0.36
Consensus pattern (89 bp):
TATCTGATCTGGCAGTTTATACTGCATGTCTATACCGTGGTTTACCGCATTGCACAGTACAGCTT
ATACGCTAGCCTTGCTACATAATA
Found at i:38688795 original size:24 final size:26
Alignment explanation
Indices: 38688753--38688801 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 26
38688743 TTTTTTCCAA
* *
38688753 CAATTGACATCCATAAATTGAACCAT
1 CAATTGACAACCATAAATTAAACCAT
38688779 CAATT-ACAACCA-AAATTAAACCA
1 CAATTGACAACCATAAATTAAACCA
38688802 GTCATCAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 10 0.48
25 6 0.29
26 5 0.24
ACGTcount: A:0.49, C:0.24, G:0.04, T:0.22
Consensus pattern (26 bp):
CAATTGACAACCATAAATTAAACCAT
Found at i:38690916 original size:43 final size:43
Alignment explanation
Indices: 38690836--38691276 Score: 632
Period size: 43 Copynumber: 10.2 Consensus size: 43
38690826 AGGATTTCTT
* * * * *
38690836 ATATCTGATTACGTGTAAGACCACATCTAGGATGTTGGCATTG
1 ATATGTGATTACGTGTAAGACCACGTCTGGGACGTTGGCATCG
*
38690879 ATATGTGATTACGTGTAAGATCACGTCTGGGACGTTGGCATCG
1 ATATGTGATTACGTGTAAGACCACGTCTGGGACGTTGGCATCG
* * *
38690922 ATATGTGATTAAGTGTAAGACCACGTCTCGTACGTTGGCATCG
1 ATATGTGATTACGTGTAAGACCACGTCTGGGACGTTGGCATCG
*
38690965 ATATGTGATT-CTGTGTAAGACCATGTCTGGGACGTTGGCATCG
1 ATATGTGATTAC-GTGTAAGACCACGTCTGGGACGTTGGCATCG
*
38691008 ATATGTGATTACGTGTAAGACCACGTCAGGGACGTTGGCATCG
1 ATATGTGATTACGTGTAAGACCACGTCTGGGACGTTGGCATCG
**
38691051 ATATGTGATTACGTGTAAGACCATTTCTGGGACGTTGGCATCG
1 ATATGTGATTACGTGTAAGACCACGTCTGGGACGTTGGCATCG
* * *
38691094 ATATGTGATTACGTGTAAGACCACATCTAGAACGTTGGCATCG
1 ATATGTGATTACGTGTAAGACCACGTCTGGGACGTTGGCATCG
* * *
38691137 ATATGTGATTATGTGTAAGACCACATCTGGGACGTTGGTATCG
1 ATATGTGATTACGTGTAAGACCACGTCTGGGACGTTGGCATCG
38691180 ATATGTGATTACGTGTAAGACCACGTCTGGGACGTTGGCATCG
1 ATATGTGATTACGTGTAAGACCACGTCTGGGACGTTGGCATCG
* * * ***
38691223 AATATGTGATTATGAGTAAGACCACGTTTAATACGTTGGCATCG
1 -ATATGTGATTACGTGTAAGACCACGTCTGGGACGTTGGCATCG
38691267 ATATGTGATT
1 ATATGTGATT
38691277 CCAATATGTG
Statistics
Matches: 359, Mismatches: 36, Indels: 6
0.90 0.09 0.01
Matches are distributed among these distances:
43 321 0.89
44 38 0.11
ACGTcount: A:0.26, C:0.16, G:0.27, T:0.31
Consensus pattern (43 bp):
ATATGTGATTACGTGTAAGACCACGTCTGGGACGTTGGCATCG
Found at i:38691309 original size:56 final size:56
Alignment explanation
Indices: 38691236--38691469 Score: 308
Period size: 56 Copynumber: 4.2 Consensus size: 56
38691226 ATGTGATTAT
*
38691236 GAGTAAGACCACGTTTAATACGTTGGCATCGATATGTGATTCCAATATGTGTGTTC
1 GAGTAAGACCACGTTTAATACGTTGGCATCGATATGTGATTCCGATATGTGTGTTC
* * *
38691292 GAGTAAGACCATGTTTAATACGTTGGCATCGATATGTGATTCTGATATGTGTGTGC
1 GAGTAAGACCACGTTTAATACGTTGGCATCGATATGTGATTCCGATATGTGTGTTC
* * ** *
38691348 GAGTAAGGCCACATTTAATACGTTCCCATCGATATGTGATTCCGATATGTATGTTC
1 GAGTAAGACCACGTTTAATACGTTGGCATCGATATGTGATTCCGATATGTGTGTTC
* * * * * *
38691404 GAGTAAGAACATGTTTAATATGTTGGCATTGATAGGTGATTTCGATATGTGT-TTAC
1 GAGTAAGACCACGTTTAATACGTTGGCATCGATATGTGATTCCGATATGTGTGTT-C
*
38691460 GAGAAAGACC
1 GAGTAAGACC
38691470 CTATTTGGGA
Statistics
Matches: 152, Mismatches: 25, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
55 2 0.01
56 150 0.99
ACGTcount: A:0.28, C:0.14, G:0.24, T:0.34
Consensus pattern (56 bp):
GAGTAAGACCACGTTTAATACGTTGGCATCGATATGTGATTCCGATATGTGTGTTC
Found at i:38700514 original size:32 final size:32
Alignment explanation
Indices: 38700462--38700533 Score: 85
Period size: 32 Copynumber: 2.2 Consensus size: 32
38700452 ACAAACAAGT
38700462 ATACAT-ACATAATATGCATAACAACACATAAC
1 ATACATAACATAATA-GCATAACAACACATAAC
** *
38700494 ATACATAACATACATA-CATAACAGTACATAAT
1 ATACATAACATA-ATAGCATAACAACACATAAC
38700526 ATACATAA
1 ATACATAA
38700534 AAATTTAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
32 27 0.77
33 5 0.14
34 3 0.09
ACGTcount: A:0.54, C:0.19, G:0.03, T:0.24
Consensus pattern (32 bp):
ATACATAACATAATAGCATAACAACACATAAC
Found at i:38700524 original size:10 final size:9
Alignment explanation
Indices: 38700464--38700513 Score: 57
Period size: 9 Copynumber: 5.6 Consensus size: 9
38700454 AAACAAGTAT
38700464 ACATACATA
1 ACATACATA
* *
38700473 ATATGCATA
1 ACATACATA
*
38700482 ACAACACATA
1 AC-ATACATA
38700492 ACATACATA
1 ACATACATA
38700501 ACATACAT-
1 ACATACATA
38700509 ACATA
1 ACATA
38700514 ACAGTACATA
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
8 5 0.15
9 22 0.65
10 7 0.21
ACGTcount: A:0.54, C:0.22, G:0.02, T:0.22
Consensus pattern (9 bp):
ACATACATA
Found at i:38700531 original size:19 final size:18
Alignment explanation
Indices: 38700464--38700533 Score: 60
Period size: 18 Copynumber: 4.1 Consensus size: 18
38700454 AAACAAGTAT
*
38700464 ACATACATAATATGCATA
1 ACATACATAATATACATA
*
38700482 ACA-ACA-CATA-ACAT-
1 ACATACATAATATACATA
*
38700496 ACATAACAT-ACATACATA
1 ACAT-ACATAATATACATA
38700514 ACAGTACATAATATACATA
1 ACA-TACATAATATACATA
38700533 A
1 A
38700534 AAATTTAAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 13
0.71 0.07 0.22
Matches are distributed among these distances:
14 3 0.07
15 3 0.07
16 8 0.20
17 7 0.17
18 10 0.24
19 10 0.24
ACGTcount: A:0.54, C:0.20, G:0.03, T:0.23
Consensus pattern (18 bp):
ACATACATAATATACATA
Found at i:38710138 original size:45 final size:45
Alignment explanation
Indices: 38710074--38710230 Score: 251
Period size: 45 Copynumber: 3.5 Consensus size: 45
38710064 AGGACTTTGC
38710074 TATGTGTTTTCGTGTAAGACCACGTCTGGGACATTGGCATCGATA
1 TATGTGTTTTCGTGTAAGACCACGTCTGGGACATTGGCATCGATA
*
38710119 TATGTTTTTTCGTGTAAGACCACGTCTGGGACATTGGCATCGATA
1 TATGTGTTTTCGTGTAAGACCACGTCTGGGACATTGGCATCGATA
* * *
38710164 TATGTGTTTTCGTGTAAGACCACGTCTGAGACGTTGGCTTCGATA
1 TATGTGTTTTCGTGTAAGACCACGTCTGGGACATTGGCATCGATA
* * *
38710209 TATGTGGTTACGAGTAAGACCA
1 TATGTGTTTTCGTGTAAGACCA
38710231 TGTTTAGACA
Statistics
Matches: 104, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 104 1.00
ACGTcount: A:0.23, C:0.17, G:0.26, T:0.34
Consensus pattern (45 bp):
TATGTGTTTTCGTGTAAGACCACGTCTGGGACATTGGCATCGATA
Found at i:38710227 original size:90 final size:88
Alignment explanation
Indices: 38710074--38710294 Score: 252
Period size: 90 Copynumber: 2.5 Consensus size: 88
38710064 AGGACTTTGC
* ** * *
38710074 TATGTGTTTTCGTGTAAGACCACGTCTGGGACATTGGCATCGATATATGTTTTTTCGTGTAAGAC
1 TATGTGTTTTCGTGTAAGACCACGTCTGAGACATTGGCATCGATATATGTGGTTACGAGTAAGAC
* *
38710139 CACGTCTGGGACATTGGCATCGATA
66 CACGT-TGAGACATCGGCATC-ATA
* *
38710164 TATGTGTTTTCGTGTAAGACCACGTCTGAGACGTTGGCTTCGATATATGTGGTTACGAGTAAGAC
1 TATGTGTTTTCGTGTAAGACCACGTCTGAGACATTGGCATCGATATATGTGGTTACGAGTAAGAC
* *
38710229 CATGTTTAGACATCGGCATCATA
66 CACGTTGAGACATCGGCATCATA
* * * *
38710252 T-T-TG-ATTCGTGTAAGACC-CTGTCTGAGATAGTGGCATCAATAT
1 TATGTGTTTTCGTGTAAGACCAC-GTCTGAGACATTGGCATCGATAT
38710295 GAGATAGCAT
Statistics
Matches: 113, Mismatches: 17, Indels: 7
0.82 0.12 0.05
Matches are distributed among these distances:
84 1 0.01
85 31 0.27
86 2 0.02
87 1 0.01
88 4 0.04
89 12 0.11
90 62 0.55
ACGTcount: A:0.24, C:0.17, G:0.25, T:0.34
Consensus pattern (88 bp):
TATGTGTTTTCGTGTAAGACCACGTCTGAGACATTGGCATCGATATATGTGGTTACGAGTAAGAC
CACGTTGAGACATCGGCATCATA
Found at i:38731377 original size:119 final size:119
Alignment explanation
Indices: 38731231--38731468 Score: 476
Period size: 119 Copynumber: 2.0 Consensus size: 119
38731221 GCATAGCTTC
38731231 CATCCTAAGCTTCTCAAGAGTCGTGTTAATCTTGTTGATATTTTTTCCATGTTTTTCCTTAATTA
1 CATCCTAAGCTTCTCAAGAGTCGTGTTAATCTTGTTGATATTTTTTCCATGTTTTTCCTTAATTA
38731296 GTTTAATGTATTCCATAACATTCATCAATGTTCTTATAAAGAGGAATGACCATA
66 GTTTAATGTATTCCATAACATTCATCAATGTTCTTATAAAGAGGAATGACCATA
38731350 CATCCTAAGCTTCTCAAGAGTCGTGTTAATCTTGTTGATATTTTTTCCATGTTTTTCCTTAATTA
1 CATCCTAAGCTTCTCAAGAGTCGTGTTAATCTTGTTGATATTTTTTCCATGTTTTTCCTTAATTA
38731415 GTTTAATGTATTCCATAACATTCATCAATGTTCTTATAAAGAGGAATGACCATA
66 GTTTAATGTATTCCATAACATTCATCAATGTTCTTATAAAGAGGAATGACCATA
38731469 AGTAAAATCT
Statistics
Matches: 119, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
119 119 1.00
ACGTcount: A:0.29, C:0.17, G:0.13, T:0.42
Consensus pattern (119 bp):
CATCCTAAGCTTCTCAAGAGTCGTGTTAATCTTGTTGATATTTTTTCCATGTTTTTCCTTAATTA
GTTTAATGTATTCCATAACATTCATCAATGTTCTTATAAAGAGGAATGACCATA
Found at i:38735445 original size:25 final size:25
Alignment explanation
Indices: 38735416--38735465 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
38735406 TCTGATCTGG
38735416 CAGTTTAACTACACTCTGGTGGCAT
1 CAGTTTAACTACACTCTGGTGGCAT
*
38735441 CAGTTTAACTACACTTTGGTGGCAT
1 CAGTTTAACTACACTCTGGTGGCAT
38735466 TGTCCACAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.24, C:0.22, G:0.20, T:0.34
Consensus pattern (25 bp):
CAGTTTAACTACACTCTGGTGGCAT
Found at i:38739518 original size:21 final size:21
Alignment explanation
Indices: 38739494--38739555 Score: 60
Period size: 21 Copynumber: 3.0 Consensus size: 21
38739484 AATTTTAAAA
38739494 TTAAATATTATTTACAATTTT
1 TTAAATATTATTTACAATTTT
38739515 TTAAATAATT-TTCT-CAA-TTT
1 TTAAAT-ATTATT-TACAATTTT
*
38739535 TT-AATAATATTTACATATTTT
1 TTAAATATTATTTACA-ATTTT
38739556 AATGTTTTAT
Statistics
Matches: 34, Mismatches: 1, Indels: 12
0.72 0.02 0.26
Matches are distributed among these distances:
18 3 0.09
19 7 0.21
20 6 0.18
21 14 0.41
22 4 0.12
ACGTcount: A:0.37, C:0.06, G:0.00, T:0.56
Consensus pattern (21 bp):
TTAAATATTATTTACAATTTT
Found at i:38739584 original size:21 final size:21
Alignment explanation
Indices: 38739560--38739613 Score: 67
Period size: 20 Copynumber: 2.6 Consensus size: 21
38739550 TATTTTAATG
*
38739560 TTTTATAATTTTTAATAA-CTT
1 TTTTATAATTTTTAA-AATATT
*
38739581 TTTTACAA-TTTTAAAATATT
1 TTTTATAATTTTTAAAATATT
38739601 TTTTATAATTTTT
1 TTTTATAATTTTT
38739614 TAGTCTAATC
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
19 2 0.07
20 15 0.54
21 11 0.39
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (21 bp):
TTTTATAATTTTTAAAATATT
Found at i:38739614 original size:10 final size:10
Alignment explanation
Indices: 38739555--38739615 Score: 52
Period size: 10 Copynumber: 6.0 Consensus size: 10
38739545 TTACATATTT
*
38739555 TAATGTTTTA
1 TAATTTTTTA
*
38739565 TAATTTTTAA
1 TAATTTTTTA
38739575 TAACTTTTTTA
1 TAA-TTTTTTA
* *
38739586 CAA-TTTTAA
1 TAATTTTTTA
*
38739595 AATATTTTTTA
1 TA-ATTTTTTA
38739606 TAATTTTTTA
1 TAATTTTTTA
38739616 GTCTAATCAG
Statistics
Matches: 40, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
9 6 0.15
10 20 0.50
11 14 0.35
ACGTcount: A:0.34, C:0.03, G:0.02, T:0.61
Consensus pattern (10 bp):
TAATTTTTTA
Found at i:38740594 original size:30 final size:30
Alignment explanation
Indices: 38740560--38740619 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
38740550 AAGCTCTTTG
38740560 GGGGTATTGGGTATTGTTAAAGAAAATTGT
1 GGGGTATTGGGTATTGTTAAAGAAAATTGT
38740590 GGGGTATTGGGTATTGTTAAAGAAAATTGT
1 GGGGTATTGGGTATTGTTAAAGAAAATTGT
38740620 TCTCTTTTGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.30, C:0.00, G:0.33, T:0.37
Consensus pattern (30 bp):
GGGGTATTGGGTATTGTTAAAGAAAATTGT
Found at i:38748502 original size:42 final size:42
Alignment explanation
Indices: 38748456--38748542 Score: 111
Period size: 42 Copynumber: 2.1 Consensus size: 42
38748446 TATTAATTTA
* * * * *
38748456 ATATTAATACGATATATTATATTTAATTTAATATTTGTCTAG
1 ATATTAATACGAGATATTAAATTAAATTAAATATTTATCTAG
* *
38748498 ATATTAATATGAGATATTAAATTAAATTAAATATTTATTTAG
1 ATATTAATACGAGATATTAAATTAAATTAAATATTTATCTAG
38748540 ATA
1 ATA
38748543 ATATTTTATT
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:0.44, C:0.02, G:0.07, T:0.47
Consensus pattern (42 bp):
ATATTAATACGAGATATTAAATTAAATTAAATATTTATCTAG
Found at i:38749902 original size:15 final size:15
Alignment explanation
Indices: 38749882--38749919 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
38749872 AAGTGAGTGG
38749882 TTAATTAAAGTTTAA-
1 TTAATTAAA-TTTAAC
*
38749897 TTAATTGAATTTAAC
1 TTAATTAAATTTAAC
38749912 TTAATTAA
1 TTAATTAA
38749920 GGATAATTGG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
14 5 0.25
15 15 0.75
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.47
Consensus pattern (15 bp):
TTAATTAAATTTAAC
Found at i:38751458 original size:20 final size:20
Alignment explanation
Indices: 38751433--38751480 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
38751423 ATTCCGACTG
38751433 TGTGTCGATGAGACACTATA
1 TGTGTCGATGAGACACTATA
*
38751453 TGTGTCAATGAGACACTATA
1 TGTGTCGATGAGACACTATA
38751473 TGTGTCGA
1 TGTGTCGA
38751481 CTACTGTGAC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.29, C:0.15, G:0.25, T:0.31
Consensus pattern (20 bp):
TGTGTCGATGAGACACTATA
Found at i:38766775 original size:11 final size:11
Alignment explanation
Indices: 38766759--38766787 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
38766749 TCGAATGACC
38766759 TAATAAAATAA
1 TAATAAAATAA
38766770 TAATAAAATAA
1 TAATAAAATAA
38766781 TAATAAA
1 TAATAAA
38766788 TTGATCATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (11 bp):
TAATAAAATAA
Found at i:38779785 original size:32 final size:32
Alignment explanation
Indices: 38779748--38779811 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
38779738 TGGGTTTATT
38779748 TAGTAAATATAGTATAAAGACATCATAATGTG
1 TAGTAAATATAGTATAAAGACATCATAATGTG
*
38779780 TAGTAAATATAGTATAGAGACATCATAATGTG
1 TAGTAAATATAGTATAAAGACATCATAATGTG
38779812 GAAAAGGCGA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.45, C:0.06, G:0.17, T:0.31
Consensus pattern (32 bp):
TAGTAAATATAGTATAAAGACATCATAATGTG
Found at i:38783971 original size:26 final size:26
Alignment explanation
Indices: 38783942--38784002 Score: 77
Period size: 27 Copynumber: 2.3 Consensus size: 26
38783932 CGGCGAACAT
* *
38783942 TGAAAGAATTCCTTTGTGGCGCAATA
1 TGAAAGAATGCATTTGTGGCGCAATA
*
38783968 TGAAAGGAATGCATTTGTGGTGCAATA
1 TGAAA-GAATGCATTTGTGGCGCAATA
*
38783995 TAAAAGAA
1 TGAAAGAA
38784003 AAACATTTGT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
26 8 0.27
27 22 0.73
ACGTcount: A:0.38, C:0.10, G:0.25, T:0.28
Consensus pattern (26 bp):
TGAAAGAATGCATTTGTGGCGCAATA
Found at i:38783985 original size:27 final size:27
Alignment explanation
Indices: 38783954--38784015 Score: 79
Period size: 27 Copynumber: 2.3 Consensus size: 27
38783944 AAAGAATTCC
* * **
38783954 TTTGTGGCGCAATATGAAAGGAATGCA
1 TTTGTGGCGCAATATAAAAGAAAAACA
*
38783981 TTTGTGGTGCAATATAAAAGAAAAACA
1 TTTGTGGCGCAATATAAAAGAAAAACA
38784008 TTTGTGGC
1 TTTGTGGC
38784016 AAATAATGAA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.35, C:0.10, G:0.26, T:0.29
Consensus pattern (27 bp):
TTTGTGGCGCAATATAAAAGAAAAACA
Found at i:38785308 original size:3 final size:3
Alignment explanation
Indices: 38785283--38785391 Score: 96
Period size: 3 Copynumber: 36.0 Consensus size: 3
38785273 GGTACAACTT
38785283 ATA ATA A-A ATA CATAA ATGA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA -AT-A AT-A ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * * * * * *
38785330 ATA ATA ATA GTG GTA ATA GTA CTA ATA GTA GTA ATA ATA ATA ATA TTA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
*
38785378 TTA A-A ATA ATA ATA
1 ATA ATA ATA ATA ATA
38785392 TTATTATCAA
Statistics
Matches: 90, Mismatches: 12, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
2 4 0.04
3 78 0.87
4 7 0.08
5 1 0.01
ACGTcount: A:0.59, C:0.02, G:0.06, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:38785387 original size:17 final size:17
Alignment explanation
Indices: 38785365--38785397 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
38785355 TAGTAGTAAT
38785365 AATAATAATATTATTAA
1 AATAATAATATTATTAA
38785382 AATAATAATATTATTA
1 AATAATAATATTATTA
38785398 TCAAAATTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
AATAATAATATTATTAA
Found at i:38785387 original size:20 final size:20
Alignment explanation
Indices: 38785362--38785404 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
38785352 TAATAGTAGT
*
38785362 AATAATAATAATATTATTAA
1 AATAATAATAATATTATCAA
*
38785382 AATAATAATATTATTATCAA
1 AATAATAATAATATTATCAA
38785402 AAT
1 AAT
38785405 TAATTAATCT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (20 bp):
AATAATAATAATATTATCAA
Found at i:38787978 original size:20 final size:20
Alignment explanation
Indices: 38787949--38787986 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
38787939 ATAATATATG
*
38787949 ATAATTTATAATATATATCT
1 ATAATCTATAATATATATCT
38787969 ATAATCTATAATATATAT
1 ATAATCTATAATATATAT
38787987 AAAAGCACGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (20 bp):
ATAATCTATAATATATATCT
Found at i:38788302 original size:27 final size:25
Alignment explanation
Indices: 38788272--38788322 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 25
38788262 TTGGGTAAAT
38788272 TAAATACAATAAAATTTAAATTTTAAG
1 TAAATA-AATAAAATTT-AATTTTAAG
* *
38788299 TAAATAAATATAATTTTATTTTAA
1 TAAATAAATAAAATTTAATTTTAA
38788323 ACATGATAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 7 0.32
26 9 0.41
27 6 0.27
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (25 bp):
TAAATAAATAAAATTTAATTTTAAG
Found at i:38789283 original size:21 final size:19
Alignment explanation
Indices: 38789229--38789283 Score: 56
Period size: 19 Copynumber: 2.8 Consensus size: 19
38789219 TTTAAATTAC
*
38789229 AATTTTATAAATAATAATC
1 AATTTTATAAATAATAATA
* **
38789248 AACTTTATATTTAATATATGA
1 AATTTTATAAATAATA-AT-A
38789269 AATTTTATAAATAAT
1 AATTTTATAAATAAT
38789284 GCATTTATAT
Statistics
Matches: 27, Mismatches: 7, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
19 13 0.48
20 2 0.07
21 12 0.44
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.45
Consensus pattern (19 bp):
AATTTTATAAATAATAATA
Found at i:38791479 original size:51 final size:51
Alignment explanation
Indices: 38791395--38791512 Score: 166
Period size: 51 Copynumber: 2.3 Consensus size: 51
38791385 TTCTGATCAG
38791395 TGACAAGTGATAAGTGGTAGCCTCAGCTACACTTATCTGATCAGTGACAAA
1 TGACAAGTGATAAGTGGTAGCCTCAGCTACACTTATCTGATCAGTGACAAA
* * * * *
38791446 TGACAAGTGATAAGTGGTAGCTTTAGCTGCACTTATCTGATTAGTGACAAG
1 TGACAAGTGATAAGTGGTAGCCTCAGCTACACTTATCTGATCAGTGACAAA
*
38791497 TGATC-AGTGACAAGTG
1 TGA-CAAGTGATAAGTG
38791513 ATAAATGTGA
Statistics
Matches: 60, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
51 59 0.98
52 1 0.02
ACGTcount: A:0.31, C:0.16, G:0.25, T:0.28
Consensus pattern (51 bp):
TGACAAGTGATAAGTGGTAGCCTCAGCTACACTTATCTGATCAGTGACAAA
Found at i:38791505 original size:14 final size:14
Alignment explanation
Indices: 38791483--38791514 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
38791473 TGCACTTATC
*
38791483 TGATTAGTGACAAG
1 TGATCAGTGACAAG
38791497 TGATCAGTGACAAG
1 TGATCAGTGACAAG
38791511 TGAT
1 TGAT
38791515 AAATGTGATC
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:0.34, C:0.09, G:0.28, T:0.28
Consensus pattern (14 bp):
TGATCAGTGACAAG
Found at i:38792962 original size:23 final size:23
Alignment explanation
Indices: 38792931--38792975 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
38792921 ATAATAGTAT
38792931 TAAAATAAA-GTTTTAATTGATGG
1 TAAAATAAATGTTTT-ATTGATGG
*
38792954 TAAATTAAATGTTTTATTGATG
1 TAAAATAAATGTTTTATTGATG
38792976 CAATCGACGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 15 0.75
24 5 0.25
ACGTcount: A:0.40, C:0.00, G:0.16, T:0.44
Consensus pattern (23 bp):
TAAAATAAATGTTTTATTGATGG
Found at i:38795236 original size:28 final size:28
Alignment explanation
Indices: 38795196--38795253 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
38795186 CTATGACAAG
38795196 TTAGAAACTTTTCTGCATTTAGATTAAT
1 TTAGAAACTTTTCTGCATTTAGATTAAT
38795224 TTAGAAACTTTTCTGCATTTAGATTAAT
1 TTAGAAACTTTTCTGCATTTAGATTAAT
38795252 TT
1 TT
38795254 TCGTTTCTGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.31, C:0.10, G:0.10, T:0.48
Consensus pattern (28 bp):
TTAGAAACTTTTCTGCATTTAGATTAAT
Found at i:38805725 original size:21 final size:21
Alignment explanation
Indices: 38805701--38805776 Score: 59
Period size: 22 Copynumber: 3.5 Consensus size: 21
38805691 TAACATTTAC
38805701 GGGCCTTAAAATGAGCTTATG
1 GGGCCTTAAAATGAGCTTATG
*
38805722 GGGCCCTAAAAAT-AG-TT-TG
1 GGG-CCTTAAAATGAGCTTATG
*
38805741 GGAACAACCTTAAAATGAGCTTATG
1 GG----GCCTTAAAATGAGCTTATG
*
38805766 GGGCCCTAAAA
1 GGGCCTTAAAA
38805777 ATAGTTTGGG
Statistics
Matches: 42, Mismatches: 5, Indels: 16
0.67 0.08 0.25
Matches are distributed among these distances:
19 4 0.10
20 2 0.05
21 12 0.29
22 16 0.38
23 2 0.05
24 2 0.05
25 4 0.10
ACGTcount: A:0.34, C:0.17, G:0.25, T:0.24
Consensus pattern (21 bp):
GGGCCTTAAAATGAGCTTATG
Found at i:38805754 original size:44 final size:44
Alignment explanation
Indices: 38805704--38805791 Score: 176
Period size: 44 Copynumber: 2.0 Consensus size: 44
38805694 CATTTACGGG
38805704 CCTTAAAATGAGCTTATGGGGCCCTAAAAATAGTTTGGGAACAA
1 CCTTAAAATGAGCTTATGGGGCCCTAAAAATAGTTTGGGAACAA
38805748 CCTTAAAATGAGCTTATGGGGCCCTAAAAATAGTTTGGGAACAA
1 CCTTAAAATGAGCTTATGGGGCCCTAAAAATAGTTTGGGAACAA
38805792 TCAAAGACTA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.36, C:0.16, G:0.23, T:0.25
Consensus pattern (44 bp):
CCTTAAAATGAGCTTATGGGGCCCTAAAAATAGTTTGGGAACAA
Found at i:38805755 original size:22 final size:22
Alignment explanation
Indices: 38805726--38805791 Score: 66
Period size: 22 Copynumber: 3.0 Consensus size: 22
38805716 CTTATGGGGC
38805726 CCTAAAAATAGTTTGGGAACAA
1 CCTAAAAATAGTTTGGGAACAA
* *
38805748 CCTTAAAATGAGCTTATGGG-GC--
1 CCTAAAAAT-AG-TT-TGGGAACAA
38805770 CCTAAAAATAGTTTGGGAACAA
1 CCTAAAAATAGTTTGGGAACAA
38805792 TCAAAGACTA
Statistics
Matches: 34, Mismatches: 4, Indels: 12
0.68 0.08 0.24
Matches are distributed among these distances:
19 4 0.12
20 3 0.09
21 2 0.06
22 16 0.47
23 2 0.06
24 3 0.09
25 4 0.12
ACGTcount: A:0.39, C:0.15, G:0.21, T:0.24
Consensus pattern (22 bp):
CCTAAAAATAGTTTGGGAACAA
Found at i:38808384 original size:44 final size:44
Alignment explanation
Indices: 38808336--38808426 Score: 146
Period size: 44 Copynumber: 2.1 Consensus size: 44
38808326 TGAAGTCAAA
* *
38808336 TAATATTAAAAAAACCTACATTAATTAAAGTTTAAGTGGGAAAC
1 TAATATTAAAAAAACCTACACTAATTAAAGTTTAAGTGAGAAAC
* *
38808380 TAATATTAAAATAAGCTACACTAATTAAAGTTTAAGTGAGAAAC
1 TAATATTAAAAAAACCTACACTAATTAAAGTTTAAGTGAGAAAC
38808424 TAA
1 TAA
38808427 AATCAGAGTT
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.51, C:0.09, G:0.11, T:0.30
Consensus pattern (44 bp):
TAATATTAAAAAAACCTACACTAATTAAAGTTTAAGTGAGAAAC
Found at i:38809562 original size:19 final size:18
Alignment explanation
Indices: 38809538--38809625 Score: 65
Period size: 19 Copynumber: 4.7 Consensus size: 18
38809528 ATTTTTATTT
38809538 ATTAAATAAAATTTAAATA
1 ATTAAATAAAA-TTAAATA
*
38809557 ATTAAATTAAATTAAATA
1 ATTAAATAAAATTAAATA
* *
38809575 ATATATCAATTACA-TAAGATA
1 AT-TA--AATAAAATTAA-ATA
*
38809596 ATTTAAGTAAAATT-AA-A
1 A-TTAAATAAAATTAAATA
38809613 ATTAAATAAAATT
1 ATTAAATAAAATT
38809626 TTAAATTATT
Statistics
Matches: 57, Mismatches: 6, Indels: 15
0.73 0.08 0.19
Matches are distributed among these distances:
16 11 0.19
17 2 0.04
18 10 0.18
19 17 0.30
20 4 0.07
21 12 0.21
22 1 0.02
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.36
Consensus pattern (18 bp):
ATTAAATAAAATTAAATA
Found at i:38809633 original size:17 final size:16
Alignment explanation
Indices: 38809538--38809625 Score: 53
Period size: 16 Copynumber: 5.8 Consensus size: 16
38809528 ATTTTTATTT
*
38809538 ATTAAATAAAATTTAA
1 ATTAAATAAAATTAAA
*
38809554 A-T-AATTAAATT-AA
1 ATTAAATAAAATTAAA
* *
38809567 ATTAAATAATA-TATCA
1 ATTAAATAAAATTA-AA
* *
38809583 ATTACATAAGA-T-AA
1 ATTAAATAAAATTAAA
* *
38809597 TTTAAGTAAAATTAAA
1 ATTAAATAAAATTAAA
38809613 ATTAAATAAAATT
1 ATTAAATAAAATT
38809626 TTAAATTATT
Statistics
Matches: 53, Mismatches: 13, Indels: 12
0.68 0.17 0.15
Matches are distributed among these distances:
13 3 0.06
14 18 0.34
15 7 0.13
16 25 0.47
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.36
Consensus pattern (16 bp):
ATTAAATAAAATTAAA
Found at i:38811773 original size:22 final size:23
Alignment explanation
Indices: 38811729--38811774 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
38811719 AGTTTAAAAA
* **
38811729 TTAATTTTTAAAATATTTTATAT
1 TTAATTTTCAAAATATTAAATAT
38811752 TTAATTTTCAAAATA-TAAATAT
1 TTAATTTTCAAAATATTAAATAT
38811774 T
1 T
38811775 ATTTTTAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 6 0.30
23 14 0.70
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.54
Consensus pattern (23 bp):
TTAATTTTCAAAATATTAAATAT
Found at i:38812616 original size:22 final size:23
Alignment explanation
Indices: 38812586--38812633 Score: 71
Period size: 22 Copynumber: 2.1 Consensus size: 23
38812576 TTGTGAAATG
38812586 TTATAAAATAAAAATAA-TATTT
1 TTATAAAATAAAAATAAGTATTT
*
38812608 TTATTAAATAAAAATAAGGTATTT
1 TTATAAAATAAAAATAA-GTATTT
38812632 TT
1 TT
38812634 CTGCATCTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 16 0.70
24 7 0.30
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.44
Consensus pattern (23 bp):
TTATAAAATAAAAATAAGTATTT
Found at i:38815238 original size:48 final size:48
Alignment explanation
Indices: 38815182--38815503 Score: 281
Period size: 48 Copynumber: 6.7 Consensus size: 48
38815172 GGTGAATTGT
* * *
38815182 CGATGCCATGTTCCAAACATGGTCTTACACTGGCTCACATGTCGAGGC
1 CGATGCCATGTTCCAGACATGGTCTTACACTGGCTCTCATATCGAGGC
* * * * *
38815230 CGATGCCATG-TCCTAGACATGGTCTTACACTAGCTCTCGTCTCAATGC
1 CGATGCCATGTTCC-AGACATGGTCTTACACTGGCTCTCATATCGAGGC
* * *** * * *
38815278 CGGTGCCAT-TTCCTAGACATGGTCTTGCACTGGCTCTCGCGTTGTGGT
1 CGATGCCATGTTCC-AGACATGGTCTTACACTGGCTCTCATATCGAGGC
* * * * * *
38815326 CGATGCCATGTCCCAGACATGGTCTTACACTAGCACACATATCAATGC
1 CGATGCCATGTTCCAGACATGGTCTTACACTGGCTCTCATATCGAGGC
* * * * * *
38815374 CGATGCCATGTCCCAGACATGGTCTTACATTAGCTCTCACAAC-ATCGC
1 CGATGCCATGTTCCAGACATGGTCTTACACTGGCTCTCATATCGA-GGC
* * * *
38815422 TGATGCCTTGTTCCAAACATGGTCTTACACTGGCTCTCATATCGTGGC
1 CGATGCCATGTTCCAGACATGGTCTTACACTGGCTCTCATATCGAGGC
* * *
38815470 CAACGCCATGTCCCAGACATGGTCTTACACTGGC
1 CGATGCCATGTTCCAGACATGGTCTTACACTGGC
38815504 ATACATATCA
Statistics
Matches: 216, Mismatches: 53, Indels: 10
0.77 0.19 0.04
Matches are distributed among these distances:
47 4 0.02
48 209 0.97
49 3 0.01
ACGTcount: A:0.21, C:0.30, G:0.21, T:0.27
Consensus pattern (48 bp):
CGATGCCATGTTCCAGACATGGTCTTACACTGGCTCTCATATCGAGGC
Found at i:38815442 original size:144 final size:144
Alignment explanation
Indices: 38815180--38815513 Score: 404
Period size: 144 Copynumber: 2.3 Consensus size: 144
38815170 AGGGTGAATT
* * * * * *
38815180 GTCGATGCCATGTTCCAAACATGGTCTTACACTGGCTCACATGTCGAGGCCGATGCCATGTCCTA
1 GTCGATGCCATGTCCCAGACATGGTCTTACACTGGCACACATATCAAGGCCGATGCCATGTCCCA
* * * * *
38815245 GACATGGTCTTACACTAGCTCTCGTCTCAATGCCGGTGCCATTTCCTAGACATGGTCTTGCACTG
66 GACATGGTCTTACACTAGCTCTCGACACAATGCCGATGCCATTTCCTAAACATGGTCTTACACTG
* * *
38815310 GCTCTCGCGTTGTG
131 GCTCTCACATCGTG
* *
38815324 GTCGATGCCATGTCCCAGACATGGTCTTACACTAGCACACATATCAATGCCGATGCCATGTCCCA
1 GTCGATGCCATGTCCCAGACATGGTCTTACACTGGCACACATATCAAGGCCGATGCCATGTCCCA
* * *
38815389 GACATGGTCTTACATTAGCTCTC-ACA-ACATCGCTGATGCCTTGTTCC-AAACATGGTCTTACA
66 GACATGGTCTTACACTAGCTCTCGACACA-AT-GCCGATGCCAT-TTCCTAAACATGGTCTTACA
*
38815451 CTGGCTCTCATATCGTG
128 CTGGCTCTCACATCGTG
* * * *
38815468 GCCAACGCCATGTCCCAGACATGGTCTTACACTGGCATACATATCA
1 GTCGATGCCATGTCCCAGACATGGTCTTACACTGGCACACATATCA
38815514 CCCAAATGTC
Statistics
Matches: 162, Mismatches: 25, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
142 1 0.01
143 3 0.02
144 154 0.95
145 4 0.02
ACGTcount: A:0.22, C:0.30, G:0.20, T:0.28
Consensus pattern (144 bp):
GTCGATGCCATGTCCCAGACATGGTCTTACACTGGCACACATATCAAGGCCGATGCCATGTCCCA
GACATGGTCTTACACTAGCTCTCGACACAATGCCGATGCCATTTCCTAAACATGGTCTTACACTG
GCTCTCACATCGTG
Found at i:38822884 original size:47 final size:47
Alignment explanation
Indices: 38822823--38823355 Score: 842
Period size: 47 Copynumber: 11.4 Consensus size: 47
38822813 CAGCCAAGAC
38822823 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
* *
38822870 AGTGTATATGTGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
*
38822917 AGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
38822964 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
38823011 AGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 AGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
* * *
38823060 AGCGTATATGTGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
* *
38823107 AGTGTATATATGTGATAATGCCTAATAGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
*
38823154 AGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
*
38823201 AGTGTATATATGTAATAAGG-C----GGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
38823243 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
* * * * * * *
38823290 AGTGTATATATGTGACAGGGCCGAGTGGCCAACGTGATGGATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
* *
38823337 AGTGCATAAATGTGATAAG
1 AGTGTATATATGTGATAAG
38823356 TCCCGAAGGG
Statistics
Matches: 454, Mismatches: 25, Indels: 14
0.92 0.05 0.03
Matches are distributed among these distances:
42 39 0.09
43 1 0.00
46 1 0.00
47 367 0.81
49 46 0.10
ACGTcount: A:0.33, C:0.09, G:0.29, T:0.29
Consensus pattern (47 bp):
AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
Found at i:38823150 original size:190 final size:188
Alignment explanation
Indices: 38822823--38823355 Score: 869
Period size: 190 Copynumber: 2.9 Consensus size: 188
38822813 CAGCCAAGAC
38822823 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATGTGTGATAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATGTGTGATAA
38822888 GGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTG
66 GGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTG
*
38822953 ATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
131 ATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
*
38823011 AGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGCGTATATGTGTGAT
1 AGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATGTGTGAT
*
38823076 AAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAATGCCTAATAGCCGATG
64 AAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATG
38823141 TGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
129 TGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
* *
38823201 AGTGTATATATGTAATAAGG-C----GGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATGTGTGATAA
* * * * * * * *
38823261 GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGACAGGGCCGAGTGGCCAACGTG
66 GGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTG
* * *
38823326 ATGGATGTGAAAGTGCATAAATGTGATAAG
131 ATGAATGTGAAAGTGTATATATGTGATAAG
38823356 TCCCGAAGGG
Statistics
Matches: 325, Mismatches: 18, Indels: 9
0.92 0.05 0.03
Matches are distributed among these distances:
183 120 0.37
187 1 0.00
188 19 0.06
190 185 0.57
ACGTcount: A:0.33, C:0.09, G:0.29, T:0.29
Consensus pattern (188 bp):
AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATGTGTGATAA
GGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTG
ATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
Found at i:38823530 original size:37 final size:37
Alignment explanation
Indices: 38823474--38823552 Score: 106
Period size: 37 Copynumber: 2.1 Consensus size: 37
38823464 CCGAGCTCTA
* * *
38823474 AAGACCCGATGACTACGTGTGG-GAATTTTGTCCGGGT
1 AAGACCCAATAACTACGTGTGGAG-ATTATGTCCGGGT
*
38823511 AAGACCCAATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCAATAACTACGTGTGGAGATTATGTCCGGGT
38823548 AAGAC
1 AAGAC
38823553 TTCGTAATAA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
37 36 0.97
38 1 0.03
ACGTcount: A:0.27, C:0.19, G:0.29, T:0.25
Consensus pattern (37 bp):
AAGACCCAATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:38830447 original size:8 final size:7
Alignment explanation
Indices: 38830369--38830502 Score: 169
Period size: 7 Copynumber: 18.3 Consensus size: 7
38830359 TAAAGCTTCC
38830369 ACCCTAA
1 ACCCTAA
38830376 ACCCTAA
1 ACCCTAA
38830383 ACCCTAA
1 ACCCTAA
38830390 ACCCTAA
1 ACCCTAA
38830397 ACCCTAA
1 ACCCTAA
38830404 ACCCTAA
1 ACCCTAA
38830411 ACCCTAA
1 ACCCTAA
38830418 ACCCTAA
1 ACCCTAA
38830425 ACCCTAA
1 ACCCTAA
*
38830432 ACCATAAA
1 ACCCT-AA
38830440 ACCCTAAA
1 ACCCT-AA
*
38830448 ACCTTAAA
1 ACCCT-AA
*
38830456 ACCATAAA
1 ACCCT-AA
*
38830464 ACCATAA
1 ACCCTAA
38830471 ACCCTAAA
1 ACCCT-AA
38830479 ACCCTAAA
1 ACCCT-AA
*
38830487 ACCATAA
1 ACCCTAA
38830494 ACCCTAA
1 ACCCTAA
38830501 AC
1 AC
38830503 TTACTACTAT
Statistics
Matches: 118, Mismatches: 7, Indels: 4
0.91 0.05 0.03
Matches are distributed among these distances:
7 76 0.64
8 42 0.36
ACGTcount: A:0.49, C:0.37, G:0.00, T:0.14
Consensus pattern (7 bp):
ACCCTAA
Found at i:38832519 original size:137 final size:137
Alignment explanation
Indices: 38832273--38832559 Score: 511
Period size: 137 Copynumber: 2.1 Consensus size: 137
38832263 CATTGGGCCT
** *
38832273 AAGCCCATTCAGGTAACAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTT
1 AAGCCCATTTGGGTAACAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACCGGGCCTT
* * * *
38832338 AGGCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAATATTAGTAAA
66 AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACAAGCAACATCAGTAAA
38832403 CATATGC
131 CATATGC
38832410 AAGCCCATTTGGGTAACAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACCGGGCCTT
1 AAGCCCATTTGGGTAACAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACCGGGCCTT
38832475 AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACAAGCAACATCAGTAAA
66 AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACAAGCAACATCAGTAAA
38832540 CATATGC
131 CATATGC
38832547 AAGCCCATTTGGG
1 AAGCCCATTTGGG
38832560 GAGACTACTC
Statistics
Matches: 143, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
137 143 1.00
ACGTcount: A:0.32, C:0.24, G:0.20, T:0.24
Consensus pattern (137 bp):
AAGCCCATTTGGGTAACAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACCGGGCCTT
AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACAAGCAACATCAGTAAA
CATATGC
Found at i:38834386 original size:26 final size:26
Alignment explanation
Indices: 38834348--38834431 Score: 150
Period size: 26 Copynumber: 3.2 Consensus size: 26
38834338 CATGAAATTC
*
38834348 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGGAACATTTACCTAACCCA
38834374 TTATCATGGAACATTTACCTAACCCA
1 TTATCATGGAACATTTACCTAACCCA
*
38834400 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGGAACATTTACCTAACCCA
38834426 TTATCA
1 TTATCA
38834432 ATTTGCATCA
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 56 1.00
ACGTcount: A:0.36, C:0.25, G:0.06, T:0.33
Consensus pattern (26 bp):
TTATCATGGAACATTTACCTAACCCA
Found at i:38835894 original size:43 final size:43
Alignment explanation
Indices: 38835828--38835999 Score: 170
Period size: 43 Copynumber: 4.0 Consensus size: 43
38835818 AGCTCGTACA
* * *
38835828 ATGCCAATGTCCTAGACGTGGTCTTACATGTAATCAAATATCG
1 ATGCCAATGTCCCAGACGTGGTCTTACACGAAATCAAATATCG
* * * *
38835871 ATGCCACTGTCCCAGACAG-GGTCTTTCACGAAATTAAATA-AG
1 ATGCCAATGTCCCAGAC-GTGGTCTTACACGAAATCAAATATCG
* * * *
38835913 ATGCCAATGTCCTAGACATGGTCTTACATGTAAATCTCAA-ATCG
1 ATGCCAATGTCCCAGACGTGGTCTTACACG-AAATC-AAATATCG
** *
38835957 ATGCCAACATCCCAGACGTGGTCTTACACGAAATCACATATCG
1 ATGCCAATGTCCCAGACGTGGTCTTACACGAAATCAAATATCG
38836000 GAAATCCTAT
Statistics
Matches: 101, Mismatches: 22, Indels: 12
0.75 0.16 0.09
Matches are distributed among these distances:
42 26 0.26
43 46 0.46
44 29 0.29
ACGTcount: A:0.32, C:0.24, G:0.17, T:0.26
Consensus pattern (43 bp):
ATGCCAATGTCCCAGACGTGGTCTTACACGAAATCAAATATCG
Found at i:38835990 original size:86 final size:85
Alignment explanation
Indices: 38835828--38835990 Score: 233
Period size: 86 Copynumber: 1.9 Consensus size: 85
38835818 AGCTCGTACA
* *
38835828 ATGCCAATGTCCTAGACGTGGTCTTACATGTAATCAAATATCGATGCCACTGTCCCAGACAGGGT
1 ATGCCAATGTCCTAGACATGGTCTTACATGTAATCAAATATCGATGCCACTATCCCAGACAGGGT
*
38835893 CTTTCACGAAATTAAATAAG
66 CTTACACGAAATTAAATAAG
*
38835913 ATGCCAATGTCCTAGACATGGTCTTACATGTAAATCTCAA-ATCGATGCCAAC-ATCCCAGAC-G
1 ATGCCAATGTCCTAGACATGGTCTTACATGT-AATC-AAATATCGATGCC-ACTATCCCAGACAG
38835975 TGGTCTTACACGAAAT
63 -GGTCTTACACGAAAT
38835991 CACATATCGG
Statistics
Matches: 70, Mismatches: 4, Indels: 7
0.86 0.05 0.09
Matches are distributed among these distances:
85 31 0.44
86 35 0.50
87 4 0.06
ACGTcount: A:0.32, C:0.24, G:0.18, T:0.26
Consensus pattern (85 bp):
ATGCCAATGTCCTAGACATGGTCTTACATGTAATCAAATATCGATGCCACTATCCCAGACAGGGT
CTTACACGAAATTAAATAAG
Found at i:38842437 original size:23 final size:22
Alignment explanation
Indices: 38842395--38842437 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
38842385 ATAATCCATA
**
38842395 CCAAATCATACCAATTCATAAG
1 CCAAATCATACCAAAACATAAG
38842417 CCAAAGTCATACCAAAACATA
1 CCAAA-TCATACCAAAACATA
38842438 TGTTTCATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 5 0.28
23 13 0.72
ACGTcount: A:0.49, C:0.28, G:0.05, T:0.19
Consensus pattern (22 bp):
CCAAATCATACCAAAACATAAG
Found at i:38844138 original size:43 final size:43
Alignment explanation
Indices: 38844062--38844231 Score: 200
Period size: 43 Copynumber: 4.0 Consensus size: 43
38844052 TCGTACAATA
* * * *
38844062 CCAAAGTCCCAGACGTGGTCTTACATGTAATCAAATATCGATG
1 CCAATGTCCCAGACATGGTCTTACACGAAATCAAATATCGATG
* **
38844105 CCACTGTCATAGACATGGTCTTACACGAAATCAAATA-CGATG
1 CCAATGTCCCAGACATGGTCTTACACGAAATCAAATATCGATG
* *
38844147 TCAATGTCCCAGACATTGTCTTACACGTAAATCTAAA-ATCGATG
1 CCAATGTCCCAGACATGGTCTTACACG-AAATC-AAATATCGATG
* * *
38844191 CCAATGTCCCAGACGTGGTCTTACATGAAATCACATATCGA
1 CCAATGTCCCAGACATGGTCTTACACGAAATCAAATATCGA
38844232 AAATCCTATG
Statistics
Matches: 106, Mismatches: 17, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
42 29 0.27
43 46 0.43
44 31 0.29
ACGTcount: A:0.34, C:0.24, G:0.16, T:0.26
Consensus pattern (43 bp):
CCAATGTCCCAGACATGGTCTTACACGAAATCAAATATCGATG
Found at i:38858101 original size:45 final size:45
Alignment explanation
Indices: 38858036--38858157 Score: 158
Period size: 46 Copynumber: 2.7 Consensus size: 45
38858026 GGGTATAATA
*
38858036 CCGATGCCATGTCCCAGACATGGTCTTACACTGAC-ACATCTTGTA-G
1 CCGATG-CATGTCCCAGACAT-GTCTTACACTGACTACATCTT-AAGG
* *
38858082 CCGATGCATGTCCCAGACATGTTTTACACTGGCTTACATCTTAAGG
1 CCGATGCATGTCCCAGACATGTCTTACACTGAC-TACATCTTAAGG
*
38858128 CCGATGCATGTCCCAAACATGTCTTACACT
1 CCGATGCATGTCCCAGACATGTCTTACACT
38858158 AGCACACAAT
Statistics
Matches: 68, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
44 11 0.16
45 15 0.22
46 42 0.62
ACGTcount: A:0.25, C:0.30, G:0.18, T:0.28
Consensus pattern (45 bp):
CCGATGCATGTCCCAGACATGTCTTACACTGACTACATCTTAAGG
Found at i:38861423 original size:40 final size:40
Alignment explanation
Indices: 38861368--38861591 Score: 261
Period size: 40 Copynumber: 5.5 Consensus size: 40
38861358 TATTCGGATG
*
38861368 ATATCCAGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
* * *
38861408 ATATCCGGGCTAAGTCTCGAAGGCATTTGTACGAGTAGTTGCT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGC-A--AGTTACT
* * *
38861451 ATACCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
* ** * * *
38861491 ATATCCGGGCTAAGTCTCGAAGGCATTCATGCTAGTGACC
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
* * *
38861531 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
*
38861571 ATATCC-GGCTAAATCCCGAAG
1 ATATCCGGGCTAAGTCCCGAAG
38861592 ATACTTAGGT
Statistics
Matches: 156, Mismatches: 25, Indels: 7
0.83 0.13 0.04
Matches are distributed among these distances:
39 13 0.08
40 107 0.69
41 1 0.01
43 35 0.22
ACGTcount: A:0.25, C:0.23, G:0.26, T:0.26
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
Found at i:38861514 original size:83 final size:80
Alignment explanation
Indices: 38861375--38861591 Score: 269
Period size: 83 Copynumber: 2.7 Consensus size: 80
38861365 ATGATATCCA
* *
38861375 GGCTAAGTCCCGAAGGCATTTGTGCAAGTTACTATATCCGGGCTAAGTCTCGAAGGCATTTGTAC
1 GGCTAAGTCCCGAAGGCATTTGTGCAAGTGACTATATCCGGGCTAAGTCTCGAAGGCA-TT-CAC
* *
38861440 GAGTAGTTG-CTATACCCG
64 G-CTAG-TGACCATACCCG
* *
38861458 GGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTCTCGAAGGCATTCATGC
1 GGCTAAGTCCCGAAGGCATTTGTGCAAGTGACTATATCCGGGCTAAGTCTCGAAGGCATTCACGC
*
38861523 TAGTGACCATATCCG
66 TAGTGACCATACCCG
* * * *
38861538 GGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CTATATCC-GGCTAAATCCCGAAG
1 GGCTAAGTCCCGAAGGCATTTGTGCAAG-TGACTATATCCGGGCTAAGTCTCGAAG
38861592 ATACTTAGGT
Statistics
Matches: 121, Mismatches: 11, Indels: 8
0.86 0.08 0.06
Matches are distributed among these distances:
79 15 0.12
80 44 0.36
81 4 0.03
82 2 0.02
83 56 0.46
ACGTcount: A:0.24, C:0.23, G:0.27, T:0.26
Consensus pattern (80 bp):
GGCTAAGTCCCGAAGGCATTTGTGCAAGTGACTATATCCGGGCTAAGTCTCGAAGGCATTCACGC
TAGTGACCATACCCG
Found at i:38865108 original size:45 final size:45
Alignment explanation
Indices: 38865039--38865383 Score: 423
Period size: 45 Copynumber: 7.8 Consensus size: 45
38865029 GACGGAATTT
* *
38865039 GGGCTTTTGAGCCTAGCAGGCTATAATGCCAGTGAAATGTTATTC
1 GGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAAATGTTATTC
* * * *
38865084 GGGCCTTTGAGCCTAGCAGTCTATAATGCTGATGAAATGTTATTT
1 GGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAAATGTTATTC
*
38865129 GGGCCTTTGAGCCTAGCAGGCTATAATGTCGGTGAAATGTTATTC
1 GGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAAATGTTATTC
* *
38865174 TGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAGA--TTATTC
1 GGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAAATGTTATTC
* * *
38865217 GGGCCTTTGAGCCTAGAAGGCTATAATGCCGGTGAGATATTATTC
1 GGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAAATGTTATTC
* * * * **
38865262 AGGCCTTTGAGCCTAGTAGGCTATAATGCCGATGAGATACTATTC
1 GGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAAATGTTATTC
* * *
38865307 GGG-CTTTCGAGCCTAACAGGCTATAATGCAGGTGAAATGATA-TC
1 GGGCCTTT-GAGCCTAGCAGGCTATAATGCCGGTGAAATGTTATTC
* * *
38865351 GGGCC-TCGAGCCTAGCAGGCGA-AATGCTGGTGA
1 GGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGA
38865384 TTTGAGAAAA
Statistics
Matches: 264, Mismatches: 32, Indels: 11
0.86 0.10 0.04
Matches are distributed among these distances:
42 10 0.04
43 54 0.20
44 10 0.04
45 190 0.72
ACGTcount: A:0.24, C:0.19, G:0.28, T:0.29
Consensus pattern (45 bp):
GGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAAATGTTATTC
Found at i:38865284 original size:133 final size:132
Alignment explanation
Indices: 38865044--38865383 Score: 423
Period size: 133 Copynumber: 2.6 Consensus size: 132
38865034 AATTTGGGCT
* *
38865044 TTTGAGCCTAGCAGGCTATAATGCCAGTGAAATGTTATTCGGGCCTTTGAGCCTAGCAGTCTATA
1 TTTGAGCCTAGCAGGCTATAATGCCGGTGAAA--TTATTCGGGCCTTTGAGCCTAGCAGGCTATA
* * ** * * **
38865109 ATGCTGATGAAATGTTATTTGGGCCTTTGAGCCTAGCAGGCTATAATGTCGGTGAAATGTTATTC
64 ATGCTGGTGAAATATTATTCAGGCCTTTGAGCCTAGCAGGCTATAATGCCGATGAAATACTATTC
38865174 TGGCC
129 -GGCC
* *
38865179 TTTGAGCCTAGCAGGCTATAATGCCGGTGAGATTATTCGGGCCTTTGAGCCTAGAAGGCTATAAT
1 TTTGAGCCTAGCAGGCTATAATGCCGGTGAAATTATTCGGGCCTTTGAGCCTAGCAGGCTATAAT
* * * *
38865244 GCCGGTGAGATATTATTCAGGCCTTTGAGCCTAGTAGGCTATAATGCCGATGAGATACTATTCGG
66 GCTGGTGAAATATTATTCAGGCCTTTGAGCCTAGCAGGCTATAATGCCGATGAAATACTATTCGG
*
38865309 GC
131 CC
* * * * *
38865311 TTTCGAGCCTAACAGGCTATAATGCAGGTGAAATGATATCGGGCC-TCGAGCCTAGCAGGCGA-A
1 TTT-GAGCCTAGCAGGCTATAATGCCGGTGAAATTAT-TCGGGCCTTTGAGCCTAGCAGGCTATA
38865374 ATGCTGGTGA
64 ATGCTGGTGA
38865384 TTTGAGAAAA
Statistics
Matches: 178, Mismatches: 25, Indels: 7
0.85 0.12 0.03
Matches are distributed among these distances:
132 16 0.09
133 125 0.70
134 7 0.04
135 30 0.17
ACGTcount: A:0.25, C:0.19, G:0.28, T:0.29
Consensus pattern (132 bp):
TTTGAGCCTAGCAGGCTATAATGCCGGTGAAATTATTCGGGCCTTTGAGCCTAGCAGGCTATAAT
GCTGGTGAAATATTATTCAGGCCTTTGAGCCTAGCAGGCTATAATGCCGATGAAATACTATTCGG
CC
Found at i:38868198 original size:25 final size:25
Alignment explanation
Indices: 38868170--38868256 Score: 95
Period size: 25 Copynumber: 3.5 Consensus size: 25
38868160 CATCTCGAGA
*
38868170 GAGCTTACCGATATTTAGCTCGTAT
1 GAGCTTACCGATATTCAGCTCGTAT
* **
38868195 GAGCTTA-CTATTATTCAATTCGTAT
1 GAGCTTACCGA-TATTCAGCTCGTAT
* * *
38868220 GAGCTTACTGTTACTCAGCTCGTAT
1 GAGCTTACCGATATTCAGCTCGTAT
38868245 GAGCTTACCGAT
1 GAGCTTACCGAT
38868257 TATAGCTCAA
Statistics
Matches: 48, Mismatches: 12, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
24 2 0.04
25 46 0.96
ACGTcount: A:0.24, C:0.21, G:0.18, T:0.37
Consensus pattern (25 bp):
GAGCTTACCGATATTCAGCTCGTAT
Found at i:38868297 original size:25 final size:24
Alignment explanation
Indices: 38868236--38868301 Score: 78
Period size: 24 Copynumber: 2.7 Consensus size: 24
38868226 ACTGTTACTC
* *
38868236 AGCTCGTATGAGCTTACCGATTAT
1 AGCTCGTATGAGCATACCGATTAG
** *
38868260 AGCTCAAAAGAGCATACCGATTCAG
1 AGCTCGTATGAGCATACCGATT-AG
38868285 AGCTCGTATGAGCATAC
1 AGCTCGTATGAGCATAC
38868302 ATGTACAAAA
Statistics
Matches: 33, Mismatches: 8, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
24 18 0.55
25 15 0.45
ACGTcount: A:0.32, C:0.23, G:0.21, T:0.24
Consensus pattern (24 bp):
AGCTCGTATGAGCATACCGATTAG
Found at i:38869152 original size:20 final size:20
Alignment explanation
Indices: 38869127--38869166 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
38869117 AAATGTAATA
*
38869127 AGAAAGTCCACGCAGTTGTG
1 AGAAAGTCCACGCAGATGTG
*
38869147 AGAAAGTCCATGCAGATGTG
1 AGAAAGTCCACGCAGATGTG
38869167 TGGCCACCTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.33, C:0.17, G:0.30, T:0.20
Consensus pattern (20 bp):
AGAAAGTCCACGCAGATGTG
Found at i:38869803 original size:17 final size:17
Alignment explanation
Indices: 38869781--38869814 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
38869771 CCCAAAAGTA
38869781 GGTCCACAGTCGTCTCG
1 GGTCCACAGTCGTCTCG
38869798 GGTCCACAGTCGTCTCG
1 GGTCCACAGTCGTCTCG
38869815 AGTGACCTGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.12, C:0.35, G:0.29, T:0.24
Consensus pattern (17 bp):
GGTCCACAGTCGTCTCG
Found at i:38875536 original size:40 final size:40
Alignment explanation
Indices: 38875478--38875669 Score: 269
Period size: 40 Copynumber: 4.8 Consensus size: 40
38875468 CGGATGATAA
38875478 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACCAAAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACCAAAT
* * * *
38875518 CCGGGCTAAGTCCTGAAGGCATTTGTGTGAGTTACTAATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACCAAAT
*
38875558 CCGGGCTAAGTCCCTAAGGCATTTGTGCGAGTTACCAAAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACCAAAT
* *
38875598 CCGGGCTAAGTCCCGAAGGCATTGGTGCGAGTTACTATAA-
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACCA-AAT
** * *
38875638 CTAGGCTATGTCCCGAAGGCATTTGAGCGAGT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGT
38875670 AGCTATATCC
Statistics
Matches: 134, Mismatches: 17, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
40 132 0.99
41 2 0.01
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACCAAAT
Found at i:38883269 original size:40 final size:40
Alignment explanation
Indices: 38883211--38883402 Score: 305
Period size: 40 Copynumber: 4.8 Consensus size: 40
38883201 CGGATGATAA
38883211 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACCAAAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACCAAAT
* * *
38883251 CCGGGCTAAGTCCTGAAGGCATTTGTGCGAGTTACTAATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACCAAAT
38883291 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACCAAAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACCAAAT
* *
38883331 CCGGGCTAAGTCCCGAAGGCATTGGTGCGAGTTACTATAA-
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACCA-AAT
* *
38883371 CCGGGCTATGTCCCGAAGGCATTTGAGCGAGT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGT
38883403 AGCTATATCC
Statistics
Matches: 140, Mismatches: 11, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
40 138 0.99
41 2 0.01
ACGTcount: A:0.23, C:0.23, G:0.29, T:0.24
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACCAAAT
Found at i:38886015 original size:40 final size:40
Alignment explanation
Indices: 38885955--38886218 Score: 332
Period size: 40 Copynumber: 6.5 Consensus size: 40
38885945 TATTCGGATG
*
38885955 ATATTCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
38885995 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
*
38886035 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTAGTTGCT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGC-A--AGTTACT
* * * *
38886078 ATACCCAGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
** * * *
38886118 ATATCCGGGCTAAGTCCCGAAGGCATTCATGCTAGTGACC
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
* * * **
38886158 ATATTCGGGCTAAGACCCGAAGGCATTTGTGCGAGTCGCT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
* *
38886198 ATATTC-GGCTAAATCCCGAAG
1 ATATCCGGGCTAAGTCCCGAAG
38886219 ATACTTGGGT
Statistics
Matches: 199, Mismatches: 22, Indels: 7
0.87 0.10 0.03
Matches are distributed among these distances:
39 13 0.07
40 149 0.75
41 1 0.01
43 36 0.18
ACGTcount: A:0.25, C:0.23, G:0.26, T:0.26
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
Found at i:38886181 original size:123 final size:123
Alignment explanation
Indices: 38885962--38886193 Score: 383
Period size: 123 Copynumber: 1.9 Consensus size: 123
38885952 ATGATATTCG
* **
38885962 GGCTAAGTCCCGAAGGCATTTGTGCAAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTTGTGC
1 GGCTAAGTCCCGAAGGCATTTGTGCAAGTGACTATATCCGGGCTAAGTCCCGAAGGCATTCATGC
* * *
38886027 AAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTAGTTGCTATACCCA
66 AAGTGACCATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTAGTTGCTATACCCA
*
38886085 GGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTCCCGAAGGCATTCATGC
1 GGCTAAGTCCCGAAGGCATTTGTGCAAGTGACTATATCCGGGCTAAGTCCCGAAGGCATTCATGC
* *
38886150 TAGTGACCATATTCGGGCTAAGACCCGAAGGCATTTGTGCGAGT
66 AAGTGACCATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGT
38886194 CGCTATATTC
Statistics
Matches: 100, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
123 100 1.00
ACGTcount: A:0.24, C:0.23, G:0.27, T:0.26
Consensus pattern (123 bp):
GGCTAAGTCCCGAAGGCATTTGTGCAAGTGACTATATCCGGGCTAAGTCCCGAAGGCATTCATGC
AAGTGACCATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTAGTTGCTATACCCA
Found at i:38901244 original size:12 final size:12
Alignment explanation
Indices: 38901227--38901253 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
38901217 GTCAGAATCA
38901227 GCTCCAAAATAG
1 GCTCCAAAATAG
38901239 GCTCCAAAATAG
1 GCTCCAAAATAG
38901251 GCT
1 GCT
38901254 GCATAATGTG
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:0.37, C:0.26, G:0.19, T:0.19
Consensus pattern (12 bp):
GCTCCAAAATAG
Found at i:38906703 original size:21 final size:21
Alignment explanation
Indices: 38906677--38906750 Score: 67
Period size: 21 Copynumber: 3.5 Consensus size: 21
38906667 TAACTCATGA
38906677 GTTTCAGTTTAACCCTTTTGG
1 GTTTCAGTTTAACCCTTTTGG
* * *
38906698 GTTTCAGTTTAGCTCTTTTGA
1 GTTTCAGTTTAACCCTTTTGG
* * * * *
38906719 GCTTCAGATTAATCCTTATAG
1 GTTTCAGTTTAACCCTTTTGG
*
38906740 GTTTCCGTTTA
1 GTTTCAGTTTA
38906751 GCTCCTACGA
Statistics
Matches: 39, Mismatches: 14, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.18, C:0.18, G:0.18, T:0.47
Consensus pattern (21 bp):
GTTTCAGTTTAACCCTTTTGG
Found at i:38906743 original size:42 final size:42
Alignment explanation
Indices: 38906674--38906794 Score: 109
Period size: 42 Copynumber: 2.9 Consensus size: 42
38906664 AGTTAACTCA
* * * *
38906674 TGAGTTTCAGTTTAACCCTTTTGGGTTTCAGTTTAGCTCTTT
1 TGAGCTTCAGATTAACCCTTATAGGTTTCAGTTTAGCTCTTT
* * * *
38906716 TGAGCTTCAGATTAATCCTTATAGGTTTCCGTTTAGCTCCTA
1 TGAGCTTCAGATTAACCCTTATAGGTTTCAGTTTAGCTCTTT
* * * * *
38906758 CGAGCTTCCA-TTTAACCCTTACAAGTTTCCGTTTAGC
1 TGAGCTT-CAGATTAACCCTTATAGGTTTCAGTTTAGC
38906795 ACTTATGTGC
Statistics
Matches: 65, Mismatches: 13, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
42 63 0.97
43 2 0.03
ACGTcount: A:0.19, C:0.22, G:0.17, T:0.42
Consensus pattern (42 bp):
TGAGCTTCAGATTAACCCTTATAGGTTTCAGTTTAGCTCTTT
Found at i:38906766 original size:21 final size:21
Alignment explanation
Indices: 38906742--38906799 Score: 55
Period size: 21 Copynumber: 2.8 Consensus size: 21
38906732 CCTTATAGGT
*
38906742 TTCCGTTTAGCTCC-TACGAGC
1 TTCCGTTTAGC-CCTTACAAGC
* * *
38906763 TTCCATTTAACCCTTACAAGT
1 TTCCGTTTAGCCCTTACAAGC
*
38906784 TTCCGTTTAGCACTTA
1 TTCCGTTTAGCCCTTA
38906800 TGTGCAGCCT
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
20 2 0.07
21 27 0.93
ACGTcount: A:0.21, C:0.29, G:0.12, T:0.38
Consensus pattern (21 bp):
TTCCGTTTAGCCCTTACAAGC
Found at i:38909301 original size:177 final size:177
Alignment explanation
Indices: 38908994--38909349 Score: 676
Period size: 177 Copynumber: 2.0 Consensus size: 177
38908984 TCTAACTGCC
38908994 AAACCTGACATTTGAAGAAAACCATGTCAGCAACACCGAGTTCAATTCAAAAATTAGAATTTTGA
1 AAACCTGACATTTGAAGAAAACCATGTCAGCAACACCGAGTTCAATTCAAAAATTAGAATTTTGA
*
38909059 ATACTTGGTAAAATAATACTAGGCCATAACCAATTCATATCAAAAGGATCTACCCTTAGAACCTG
66 ATACTTGGTAAAATAATACTAGGCCATAACCAATTCATATCAAAAGGATCTACCCTTAAAACCTG
*
38909124 CATCGTTGTGTTAGATGTTAGATAGGATATATTATAAGTCAAATATT
131 CATCATTGTGTTAGATGTTAGATAGGATATATTATAAGTCAAATATT
*
38909171 AAACCTGACATTTGAAGAAAACCATGTCAGCAACACTGAGTTCAATTCAAAAATTAGAATTTTGA
1 AAACCTGACATTTGAAGAAAACCATGTCAGCAACACCGAGTTCAATTCAAAAATTAGAATTTTGA
*
38909236 ATACTTGGTAAAATAATACTAGGCCATAACCAATTCATATCAAAAGGATCTACCTTTAAAACCTG
66 ATACTTGGTAAAATAATACTAGGCCATAACCAATTCATATCAAAAGGATCTACCCTTAAAACCTG
38909301 CATCATTGTGTTAGATGTTAGATAGGATATATTATAAGTCAAATATT
131 CATCATTGTGTTAGATGTTAGATAGGATATATTATAAGTCAAATATT
38909348 AA
1 AA
38909350 GATTTGTTTT
Statistics
Matches: 175, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
177 175 1.00
ACGTcount: A:0.40, C:0.16, G:0.14, T:0.30
Consensus pattern (177 bp):
AAACCTGACATTTGAAGAAAACCATGTCAGCAACACCGAGTTCAATTCAAAAATTAGAATTTTGA
ATACTTGGTAAAATAATACTAGGCCATAACCAATTCATATCAAAAGGATCTACCCTTAAAACCTG
CATCATTGTGTTAGATGTTAGATAGGATATATTATAAGTCAAATATT
Found at i:38911831 original size:48 final size:48
Alignment explanation
Indices: 38911765--38911939 Score: 185
Period size: 48 Copynumber: 3.6 Consensus size: 48
38911755 TGAATTTCCA
* *
38911765 ATGCCATGTTCCGA-ACATGGTCTTACACTGGCTCACATGTCGAGGCTG
1 ATGCCATG-TCCTAGACATGGTCTTACACTGGCTCACATATCGAGGCTG
* * *
38911813 AAGCCATGTCCTAGACATGGTCTTACACTGGCTCTCATAAT-GTGG-TCG
1 ATGCCATGTCCTAGACATGGTCTTACACTGGCTCACAT-ATCGAGGCT-G
* * * ** *
38911861 ATGCCATGTCCTAGACATGGTCTTACACTAGCGCACATATCAATACCG
1 ATGCCATGTCCTAGACATGGTCTTACACTGGCTCACATATCGAGGCTG
* *
38911909 ATGCCATGTACAAGACATGGTCTTACACTGG
1 ATGCCATGTCCTAGACATGGTCTTACACTGG
38911940 ATCTCATTAC
Statistics
Matches: 105, Mismatches: 17, Indels: 10
0.80 0.13 0.08
Matches are distributed among these distances:
47 7 0.07
48 97 0.92
49 1 0.01
ACGTcount: A:0.25, C:0.26, G:0.22, T:0.27
Consensus pattern (48 bp):
ATGCCATGTCCTAGACATGGTCTTACACTGGCTCACATATCGAGGCTG
Found at i:38911929 original size:96 final size:96
Alignment explanation
Indices: 38911765--38911998 Score: 276
Period size: 96 Copynumber: 2.4 Consensus size: 96
38911755 TGAATTTCCA
* * * * * * * * *
38911765 ATGCCATGTTCCGAACATGGTCTTACACTGGCTCACATGTCGAGGCTGAAGCCATGTCCTAGACA
1 ATGCCATGTTCCCAACATGGTCTTACACTAGCACACATATCAAGACCGAAGCCATGTACAAGACA
* *
38911830 TGGTCTTACACTGGCTCTCA-TA-ATGTGGTCG
66 TGGTCTTACACTGGATCTCATTACAT-T-ATCG
* * * *
38911861 ATGCCATG-TCCTAGACATGGTCTTACACTAGCGCACATATCAATACCGATGCCATGTACAAGAC
1 ATGCCATGTTCCCA-ACATGGTCTTACACTAGCACACATATCAAGACCGAAGCCATGTACAAGAC
38911925 ATGGTCTTACACTGGATCTCATTACATTATCG
65 ATGGTCTTACACTGGATCTCATTACATTATCG
*
38911957 ATGCCATGTTCCCAACATGGTCTTACACTAGCACACGTATCA
1 ATGCCATGTTCCCAACATGGTCTTACACTAGCACACATATCA
38911999 CCCAAATGTC
Statistics
Matches: 118, Mismatches: 16, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
95 4 0.03
96 105 0.89
97 7 0.06
98 2 0.02
ACGTcount: A:0.26, C:0.27, G:0.19, T:0.28
Consensus pattern (96 bp):
ATGCCATGTTCCCAACATGGTCTTACACTAGCACACATATCAAGACCGAAGCCATGTACAAGACA
TGGTCTTACACTGGATCTCATTACATTATCG
Found at i:38911959 original size:48 final size:47
Alignment explanation
Indices: 38911815--38911985 Score: 193
Period size: 48 Copynumber: 3.6 Consensus size: 47
38911805 CGAGGCTGAA
*
38911815 GCCATGTCCTAGACATGGTCTTACACTGGCTCTCATA-ATGTGGTCGAT
1 GCCATGTCCTAGACATGGTCTTACACTGGCTCTCATACAT-T-ATCGAT
* * * * *
38911863 GCCATGTCCTAGACATGGTCTTACACTAGCGCACATATCAATACCGAT
1 GCCATGTCCTAGACATGGTCTTACACTGGCTCTCATA-CATTATCGAT
* * *
38911911 GCCATGTACAAGACATGGTCTTACACTGGATCTCATTACATTATCGAT
1 GCCATGTCCTAGACATGGTCTTACACTGGCTCTCA-TACATTATCGAT
*
38911959 GCCATGTTCCCA-ACATGGTCTTACACT
1 GCCATG-TCCTAGACATGGTCTTACACT
38911986 AGCACACGTA
Statistics
Matches: 103, Mismatches: 16, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
48 96 0.93
49 6 0.06
50 1 0.01
ACGTcount: A:0.26, C:0.27, G:0.18, T:0.29
Consensus pattern (47 bp):
GCCATGTCCTAGACATGGTCTTACACTGGCTCTCATACATTATCGAT
Found at i:38912390 original size:25 final size:25
Alignment explanation
Indices: 38912360--38912416 Score: 96
Period size: 25 Copynumber: 2.3 Consensus size: 25
38912350 ACAAAAATTA
38912360 CGATTTTACCACTAGGCTCGTAAAT
1 CGATTTTACCACTAGGCTCGTAAAT
* *
38912385 CGATTTTACCCCTAGGCTTGTAAAT
1 CGATTTTACCACTAGGCTCGTAAAT
38912410 CGATTTT
1 CGATTTT
38912417 TATCGAATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.25, C:0.23, G:0.16, T:0.37
Consensus pattern (25 bp):
CGATTTTACCACTAGGCTCGTAAAT
Found at i:38916218 original size:37 final size:37
Alignment explanation
Indices: 38916172--38916244 Score: 146
Period size: 37 Copynumber: 2.0 Consensus size: 37
38916162 GAGGTTTTGG
38916172 GTTTGAATCTTTTCCTTGAGTTTTTGTTATTTTTTTT
1 GTTTGAATCTTTTCCTTGAGTTTTTGTTATTTTTTTT
38916209 GTTTGAATCTTTTCCTTGAGTTTTTGTTATTTTTTT
1 GTTTGAATCTTTTCCTTGAGTTTTTGTTATTTTTTT
38916245 GGTAATCTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.11, C:0.08, G:0.14, T:0.67
Consensus pattern (37 bp):
GTTTGAATCTTTTCCTTGAGTTTTTGTTATTTTTTTT
Found at i:38918837 original size:43 final size:43
Alignment explanation
Indices: 38918782--38918997 Score: 283
Period size: 43 Copynumber: 5.0 Consensus size: 43
38918772 ATATCGCGCA
* * *
38918782 ATGCCAAC-GTCCCAGATATGGTTTTACACGTAATCACATATTG
1 ATGCC-ACTGTCCCAGACATGGTCTTACACGTAATCACATATCG
* *
38918825 ATGCCACTGTCCCAGATATGGTCTTACACGTAATCACATATTG
1 ATGCCACTGTCCCAGACATGGTCTTACACGTAATCACATATCG
* * *
38918868 ATGCCAAC-ATCCCAAACGTGGTCTTACACGTAATCACATATCG
1 ATGCC-ACTGTCCCAGACATGGTCTTACACGTAATCACATATCG
* *
38918911 ATGCCATTTTCCCAGACATGGTCTTACACGTAATCACATATCG
1 ATGCCACTGTCCCAGACATGGTCTTACACGTAATCACATATCG
* * *
38918954 ATGCCATTGTCCCGGACAGGGTCTTACACGTAATCACATATCG
1 ATGCCACTGTCCCAGACATGGTCTTACACGTAATCACATATCG
38918997 A
1 A
38918998 AAATCCTATG
Statistics
Matches: 157, Mismatches: 13, Indels: 6
0.89 0.07 0.03
Matches are distributed among these distances:
42 3 0.02
43 152 0.97
44 2 0.01
ACGTcount: A:0.29, C:0.27, G:0.16, T:0.28
Consensus pattern (43 bp):
ATGCCACTGTCCCAGACATGGTCTTACACGTAATCACATATCG
Found at i:38920639 original size:33 final size:34
Alignment explanation
Indices: 38920566--38920646 Score: 110
Period size: 34 Copynumber: 2.4 Consensus size: 34
38920556 TCTGATATAT
*
38920566 TATGACATTTTGATATGATATATGTTTCTAAAAA
1 TATGACATTCTGATATGATATATGTTTCTAAAAA
* * **
38920600 TATGACATTCTGATCTGGTATATGTTT-TGGAAA
1 TATGACATTCTGATATGATATATGTTTCTAAAAA
38920633 TATGACATTCTGAT
1 TATGACATTCTGAT
38920647 TTGACATTCG
Statistics
Matches: 42, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
33 18 0.43
34 24 0.57
ACGTcount: A:0.32, C:0.09, G:0.16, T:0.43
Consensus pattern (34 bp):
TATGACATTCTGATATGATATATGTTTCTAAAAA
Found at i:38923736 original size:37 final size:37
Alignment explanation
Indices: 38923691--38923761 Score: 142
Period size: 37 Copynumber: 1.9 Consensus size: 37
38923681 TATTTTCATG
38923691 ATTCTATAAAATGTTATATTATTCAATACATAGAAAT
1 ATTCTATAAAATGTTATATTATTCAATACATAGAAAT
38923728 ATTCTATAAAATGTTATATTATTCAATACATAGA
1 ATTCTATAAAATGTTATATTATTCAATACATAGA
38923762 TTAGTTCAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.45, C:0.08, G:0.06, T:0.41
Consensus pattern (37 bp):
ATTCTATAAAATGTTATATTATTCAATACATAGAAAT
Found at i:38934808 original size:12 final size:11
Alignment explanation
Indices: 38934791--38934821 Score: 53
Period size: 12 Copynumber: 2.7 Consensus size: 11
38934781 ACAAAATGCA
38934791 TTTTTTTTCACT
1 TTTTTTTTCA-T
38934803 TTTTTTTTCAT
1 TTTTTTTTCAT
38934814 TTTTTTTT
1 TTTTTTTT
38934822 GAGAACAATG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 9 0.47
12 10 0.53
ACGTcount: A:0.06, C:0.10, G:0.00, T:0.84
Consensus pattern (11 bp):
TTTTTTTTCAT
Found at i:38935843 original size:3 final size:3
Alignment explanation
Indices: 38935835--38935859 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
38935825 AAGGAAGATA
38935835 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
38935860 GACTCAATGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:38935951 original size:9 final size:8
Alignment explanation
Indices: 38935906--38935991 Score: 57
Period size: 8 Copynumber: 10.4 Consensus size: 8
38935896 ATGATAATAG
38935906 TAAAACAAA
1 TAAAA-AAA
38935915 TACAAAAAA
1 TA-AAAAAA
* *
38935924 -ATAGAAA
1 TAAAAAAA
*
38935931 TAGAAAAA
1 TAAAAAAA
38935939 TAAAAATAA
1 TAAAAA-AA
*
38935948 TAAAAACA
1 TAAAAAAA
38935956 TATAAAAAA
1 TA-AAAAAA
* *
38935965 TTAAAATA
1 TAAAAAAA
*
38935973 TAAAAAAT
1 TAAAAAAA
*
38935981 TAAAAATA
1 TAAAAAAA
38935989 TAA
1 TAA
38935992 GTATAAGAAT
Statistics
Matches: 59, Mismatches: 14, Indels: 9
0.72 0.17 0.11
Matches are distributed among these distances:
7 4 0.07
8 33 0.56
9 19 0.32
10 3 0.05
ACGTcount: A:0.74, C:0.03, G:0.02, T:0.20
Consensus pattern (8 bp):
TAAAAAAA
Found at i:38935952 original size:15 final size:14
Alignment explanation
Indices: 38935918--38935988 Score: 63
Period size: 14 Copynumber: 5.1 Consensus size: 14
38935908 AAACAAATAC
*
38935918 AAAAAAATAGAAAT
1 AAAAAAATAAAAAT
*
38935932 AGAAAAATAAAAAT
1 AAAAAAATAAAAAT
* * *
38935946 AATAAAA-ACATAT
1 AAAAAAATAAAAAT
*
38935959 AAAAAATTAAAATAT
1 AAAAAAATAAAA-AT
*
38935974 AAAAAATTAAAAAT
1 AAAAAAATAAAAAT
38935988 A
1 A
38935989 TAAGTATAAG
Statistics
Matches: 45, Mismatches: 10, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
13 9 0.20
14 22 0.49
15 14 0.31
ACGTcount: A:0.76, C:0.01, G:0.03, T:0.20
Consensus pattern (14 bp):
AAAAAAATAAAAAT
Found at i:38936045 original size:22 final size:23
Alignment explanation
Indices: 38936006--38936051 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 23
38935996 AAGAATAATT
* *
38936006 AATTAATTAATTAGTAAAATAAA
1 AATTAATTAATAAATAAAATAAA
38936029 AATTAA-TAATAAATAAAATAAA
1 AATTAATTAATAAATAAAATAAA
38936051 A
1 A
38936052 TAAAATTTGG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 15 0.71
23 6 0.29
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.30
Consensus pattern (23 bp):
AATTAATTAATAAATAAAATAAA
Found at i:38939308 original size:39 final size:39
Alignment explanation
Indices: 38939253--38939341 Score: 164
Period size: 39 Copynumber: 2.3 Consensus size: 39
38939243 TACCAGAAGC
38939253 AAATAAAA-G-AAAAGTTAGTAAATTAAAGTAAAAACAA
1 AAATAAAATGCAAAAGTTAGTAAATTAAAGTAAAAACAA
38939290 AAATAAAATGCAAAAGTTAGTAAATTAAAGTAAAAACAA
1 AAATAAAATGCAAAAGTTAGTAAATTAAAGTAAAAACAA
38939329 AAATAAAATGCAA
1 AAATAAAATGCAA
38939342 TAAAAATAAA
Statistics
Matches: 50, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
37 8 0.16
38 1 0.02
39 41 0.82
ACGTcount: A:0.66, C:0.04, G:0.10, T:0.19
Consensus pattern (39 bp):
AAATAAAATGCAAAAGTTAGTAAATTAAAGTAAAAACAA
Found at i:38941088 original size:24 final size:23
Alignment explanation
Indices: 38941044--38941088 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
38941034 AGGTAAGCAT
38941044 TTTCCAAATTTCTTCTCTCTTCC
1 TTTCCAAATTTCTTCTCTCTTCC
38941067 TTTCCAAGATTTGCTTCT-TCTT
1 TTTCCAA-ATTT-CTTCTCTCTT
38941089 AATTTGCAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
23 7 0.35
24 8 0.40
25 5 0.25
ACGTcount: A:0.13, C:0.29, G:0.04, T:0.53
Consensus pattern (23 bp):
TTTCCAAATTTCTTCTCTCTTCC
Found at i:38949486 original size:43 final size:41
Alignment explanation
Indices: 38949318--38949527 Score: 276
Period size: 41 Copynumber: 5.0 Consensus size: 41
38949308 TATTCGGGCT
* *
38949318 TTATTGCCTAGCAGGCTTTGTGCCGCTGTATTAAATCAGGC
1 TTATTGCCTAGCAGGCTTTGTGCCGGTGTATTATATCAGGC
* *
38949359 TTATTTCCTAGCAGGCTTTGTGCCGGTGTATTAAATCAGGC
1 TTATTGCCTAGCAGGCTTTGTGCCGGTGTATTATATCAGGC
* *
38949400 TTATTGCCTAGCAGGCTTTGTGCCAGTGTATTATATCAAGC
1 TTATTGCCTAGCAGGCTTTGTGCCGGTGTATTATATCAGGC
* **
38949441 TTATTGCCTAGCAGGCTTTATATTTCGGTGTATTATATCAGGC
1 TTATTGCCTAGCAGGC-TT-TGTGCCGGTGTATTATATCAGGC
* **
38949484 TTATTGCCTAGCAGGCTTTATATTTCGGTGTATTATATCAGGC
1 TTATTGCCTAGCAGGC-TT-TGTGCCGGTGTATTATATCAGGC
38949527 T
1 T
38949528 CTGTGTCGGT
Statistics
Matches: 156, Mismatches: 11, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
41 92 0.59
42 2 0.01
43 62 0.40
ACGTcount: A:0.20, C:0.19, G:0.22, T:0.39
Consensus pattern (41 bp):
TTATTGCCTAGCAGGCTTTGTGCCGGTGTATTATATCAGGC
Found at i:38963979 original size:28 final size:28
Alignment explanation
Indices: 38963916--38964094 Score: 270
Period size: 28 Copynumber: 6.4 Consensus size: 28
38963906 ATATTAAGTC
*
38963916 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
*
38963943 CGCACACTTACTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
*
38963971 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
*
38963999 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
38964027 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
38964055 CGCACACTTAGTGCTGTACAATTTAAACC
1 CGCACACTTAGTGCTATATAA-TCAAACT
38964084 CGCACACTTAG
1 CGCACACTTAG
38964095 CGCCAATCTC
Statistics
Matches: 141, Mismatches: 9, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
27 21 0.15
28 104 0.74
29 16 0.11
ACGTcount: A:0.34, C:0.28, G:0.11, T:0.26
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:38972138 original size:27 final size:27
Alignment explanation
Indices: 38972108--38972227 Score: 188
Period size: 27 Copynumber: 4.4 Consensus size: 27
38972098 ATTAAGTCCG
* *
38972108 CACTCAGTGCTATATAATCAACTCACA
1 CACTTAGTGCTATATAATCAACTCGCA
38972135 CACTTAGTGCTATATAATCAACTCGCA
1 CACTTAGTGCTATATAATCAACTCGCA
*
38972162 CACTTAGTGCTACATAATCAACTCGCA
1 CACTTAGTGCTATATAATCAACTCGCA
38972189 CACTTAGTGCT-TATTAATCAAACTCGCA
1 CACTTAGTGCTATA-TAATC-AACTCGCA
38972217 CACTTAGTGCT
1 CACTTAGTGCT
38972228 GTACAATTTA
Statistics
Matches: 87, Mismatches: 4, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
26 1 0.01
27 67 0.77
28 19 0.22
ACGTcount: A:0.33, C:0.28, G:0.11, T:0.29
Consensus pattern (27 bp):
CACTTAGTGCTATATAATCAACTCGCA
Found at i:38972250 original size:29 final size:28
Alignment explanation
Indices: 38972108--38972252 Score: 115
Period size: 27 Copynumber: 5.2 Consensus size: 28
38972098 ATTAAGTCCG
* * *
38972108 CACTCAGTGCTATAT-AATC-AACTCACA
1 CACTTAGTGCT-TATCAATCAAACCCGCA
*
38972135 CACTTAGTGCTATAT-AATC-AACTCGCA
1 CACTTAGTGCT-TATCAATCAAACCCGCA
* *
38972162 CACTTAGTGCTACAT-AATC-AACTCGCA
1 CACTTAGTGCT-TATCAATCAAACCCGCA
* *
38972189 CACTTAGTGCTTATTAATCAAACTCGCA
1 CACTTAGTGCTTATCAATCAAACCCGCA
*
38972217 CACTTAGTGCTGTA-CAATTTAAACCCGCA
1 CACTTAGTGCT-TATCAA-TCAAACCCGCA
38972246 CACTTAG
1 CACTTAG
38972253 CGCCAATCTC
Statistics
Matches: 107, Mismatches: 7, Indels: 6
0.89 0.06 0.05
Matches are distributed among these distances:
26 2 0.02
27 66 0.62
28 21 0.20
29 18 0.17
ACGTcount: A:0.33, C:0.28, G:0.11, T:0.28
Consensus pattern (28 bp):
CACTTAGTGCTTATCAATCAAACCCGCA
Done.