Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr03 ID=Chr03-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 45765648
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 655849 characters in sequence are not A, C, G, or T
File 139 of 150
Found at i:41874033 original size:18 final size:18
Alignment explanation
Indices: 41874010--41874044 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
41874000 TTTTTTACTC
41874010 AATTAATATAT-AAAAATT
1 AATTAAT-TATGAAAAATT
41874028 AATTAATTATGAAAAAT
1 AATTAATTATGAAAAAT
41874045 GTATGGAAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 3 0.19
18 13 0.81
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (18 bp):
AATTAATTATGAAAAATT
Found at i:41875743 original size:21 final size:22
Alignment explanation
Indices: 41875719--41875760 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
41875709 TTTTTATCAT
41875719 AACTTAT-TTATATAAAAAAAA
1 AACTTATCTTATATAAAAAAAA
* *
41875740 AACTTATCTTATTTATAAAAA
1 AACTTATCTTATATAAAAAAA
41875761 GTGTTATGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.38
Consensus pattern (22 bp):
AACTTATCTTATATAAAAAAAA
Found at i:41878589 original size:26 final size:26
Alignment explanation
Indices: 41878569--41878637 Score: 79
Period size: 25 Copynumber: 2.7 Consensus size: 26
41878559 CCCGATATAT
41878569 GGCTCTTCGTGAGCTTCCCGATTAAA
1 GGCTCTTCGTGAGCTTCCCGATTAAA
* * *
41878595 GGCTCTTTGTGAGCTT-CCTATTAAC
1 GGCTCTTCGTGAGCTTCCCGATTAAA
* *
41878620 GACTCTCCG-GAGCTTCCC
1 GGCTCTTCGTGAGCTTCCC
41878638 AATATGGCTC
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
24 6 0.17
25 15 0.42
26 15 0.42
ACGTcount: A:0.16, C:0.30, G:0.22, T:0.32
Consensus pattern (26 bp):
GGCTCTTCGTGAGCTTCCCGATTAAA
Found at i:41881530 original size:20 final size:20
Alignment explanation
Indices: 41881501--41881539 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
41881491 TAACAGTAAA
41881501 CTGATAATGA-TCTGTATTAT
1 CTGATAATGACT-TGTATTAT
*
41881521 CTGATTATGACTTGTATTA
1 CTGATAATGACTTGTATTA
41881540 GGATAACAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 16 0.94
21 1 0.06
ACGTcount: A:0.28, C:0.10, G:0.15, T:0.46
Consensus pattern (20 bp):
CTGATAATGACTTGTATTAT
Found at i:41883850 original size:18 final size:18
Alignment explanation
Indices: 41883827--41883865 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
41883817 TTGAATATGT
41883827 TTTTAT-ATGTTTTATTAA
1 TTTTATAATGTTTTA-TAA
*
41883845 TTTTATAATTTTTTATAA
1 TTTTATAATGTTTTATAA
41883863 TTT
1 TTT
41883866 ATTAGAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 12 0.63
19 7 0.37
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (18 bp):
TTTTATAATGTTTTATAA
Found at i:41883963 original size:20 final size:18
Alignment explanation
Indices: 41883721--41884003 Score: 105
Period size: 19 Copynumber: 14.6 Consensus size: 18
41883711 TTATTTTAGG
*
41883721 TTATAATTTCTA-AATTT
1 TTATAATTTTTATAATTT
* *
41883738 TTATAGTTTCTTTACAATTT
1 TTATA-ATT-TTTATAATTT
* *
41883758 ATTAGAGTTTATTAT-ATTAT
1 -TTATAATTT-TTATAATT-T
41883778 TTATAATTTTTTATGAA-TT
1 TTATAA-TTTTTAT-AATTT
41883797 TTATAATCTTTTATAAAATTT
1 TTATAAT-TTTTAT--AATTT
* *
41883818 TGAATATGTTTTTAT-ATGTT
1 T-TATA-ATTTTTATAAT-TT
41883838 TTATTAA-TTTTATAATTTT
1 TTA-TAATTTTTATAA-TTT
*
41883857 TTATAATTTATTAGAATTT
1 TTATAATTT-TTATAATTT
* * * * *
41883876 CTATAAAATATTACAATAT
1 TTAT-AATTTTTATAATTT
41883895 TTATAAGCTTTTT-TGAATTT
1 TTATAA--TTTTTAT-AATTT
*
41883915 TTAT-ATTTTTATAAGTACTA
1 TTATAATTTTTATAA-T--TT
*
41883935 TTCTAATTTGTCTATAATTT
1 TTATAATTT-T-TATAATTT
* *
41883955 TTATAATTTTATATAAATA
1 TTATAATTTT-TATAATTT
41883974 TT-TAATTTTTATGATATTT
1 TTATAATTTTTAT-A-ATTT
41883993 TTATAATTTTT
1 TTATAATTTTT
41884004 TATGATAAAA
Statistics
Matches: 200, Mismatches: 32, Indels: 65
0.67 0.11 0.22
Matches are distributed among these distances:
17 15 0.08
18 24 0.12
19 69 0.34
20 63 0.31
21 12 0.06
22 11 0.05
23 6 0.03
ACGTcount: A:0.33, C:0.04, G:0.05, T:0.59
Consensus pattern (18 bp):
TTATAATTTTTATAATTT
Found at i:41883966 original size:8 final size:9
Alignment explanation
Indices: 41883721--41884003 Score: 105
Period size: 10 Copynumber: 29.2 Consensus size: 9
41883711 TTATTTTAGG
41883721 TTATAATTT
1 TTATAATTT
*
41883730 CTA-AATTT
1 TTATAATTT
*
41883738 TTATAGTTTCT
1 TTATA-ATT-T
*
41883749 TTACAATTT
1 TTATAATTT
* *
41883758 ATTAGAGTTT
1 -TTATAATTT
41883768 ATTAT-ATTAT
1 -TTATAATT-T
41883778 TTATAATTTT
1 TTATAA-TTT
41883788 TTATGAA-TT
1 TTAT-AATTT
41883797 TTATAATCTT
1 TTATAAT-TT
41883807 TTATAAAATTT
1 TTAT--AATTT
* *
41883818 TGAATATGTTT
1 T-TATA-ATTT
41883829 TTAT-ATGTT
1 TTATAAT-TT
41883838 TTATTAA-TT
1 TTA-TAATTT
41883847 TTATAATTTT
1 TTATAA-TTT
41883857 TTATAATTT
1 TTATAATTT
*
41883866 ATTAGAATTT
1 -TTATAATTT
* * *
41883876 CTATAAAATA
1 TTAT-AATTT
* *
41883886 TTACAATAT
1 TTATAATTT
41883895 TTATAAGCTTT
1 TTATAA--TTT
41883906 TT-TGAATTT
1 TTAT-AATTT
41883915 TTAT-ATTT
1 TTATAATTT
*
41883923 TTATAAGTACTA
1 TTATAA-T--TT
*
41883935 TTCTAATTT
1 TTATAATTT
41883944 GTCTATAATTT
1 -T-TATAATTT
41883955 TTATAATTT
1 TTATAATTT
* *
41883964 TATATAAATA
1 T-TATAATTT
41883974 TT-TAATTT
1 TTATAATTT
41883982 TTATGATATTT
1 TTAT-A-ATTT
41883993 TTATAATTT
1 TTATAATTT
41884002 TT
1 TT
41884004 TATGATAAAA
Statistics
Matches: 206, Mismatches: 33, Indels: 70
0.67 0.11 0.23
Matches are distributed among these distances:
8 27 0.13
9 62 0.30
10 67 0.33
11 39 0.19
12 11 0.05
ACGTcount: A:0.33, C:0.04, G:0.05, T:0.59
Consensus pattern (9 bp):
TTATAATTT
Found at i:41887231 original size:2 final size:2
Alignment explanation
Indices: 41887226--41887264 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
41887216 TCGTATGTGT
41887226 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
41887265 GATTATTTCT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:41892542 original size:20 final size:17
Alignment explanation
Indices: 41892507--41892545 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 17
41892497 TTCTTTTCTC
41892507 TTTTTTTTTTTTTTCCT
1 TTTTTTTTTTTTTTCCT
41892524 TTTTTTTCTTTCTTCTTCCT
1 TTTTTTT-TTT-TT-TTCCT
41892544 TT
1 TT
41892546 ATAATGTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 7 0.37
18 3 0.16
19 2 0.11
20 7 0.37
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (17 bp):
TTTTTTTTTTTTTTCCT
Found at i:41897800 original size:22 final size:22
Alignment explanation
Indices: 41897775--41897836 Score: 56
Period size: 22 Copynumber: 2.8 Consensus size: 22
41897765 AAGATAGCAC
*
41897775 AAATTTAAAT-TTAATGATAAAA
1 AAATATAAATATTAAT-ATAAAA
*
41897797 AAATATGAATATTAATATAAAA
1 AAATATAAATATTAATATAAAA
* *
41897819 TTAATAT-AATATTCATAT
1 -AAATATAAATATTAATAT
41897837 TTTTTGGACC
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
22 24 0.71
23 10 0.29
ACGTcount: A:0.56, C:0.02, G:0.03, T:0.39
Consensus pattern (22 bp):
AAATATAAATATTAATATAAAA
Found at i:41897811 original size:23 final size:22
Alignment explanation
Indices: 41897785--41897836 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 22
41897775 AAATTTAAAT
41897785 TTAATGATAAAA-AAATATGAATA
1 TTAAT-ATAAAATAAATAT-AATA
*
41897808 TTAATATAAAATTAATATAATA
1 TTAATATAAAATAAATATAATA
*
41897830 TTCATAT
1 TTAATAT
41897837 TTTTTGGACC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
22 16 0.62
23 10 0.38
ACGTcount: A:0.56, C:0.02, G:0.04, T:0.38
Consensus pattern (22 bp):
TTAATATAAAATAAATATAATA
Found at i:41897836 original size:11 final size:11
Alignment explanation
Indices: 41897798--41897836 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
41897788 ATGATAAAAA
41897798 AATATGAATATT
1 AATAT-AATATT
*
41897810 AATATAAAATT
1 AATATAATATT
41897821 AATATAATATT
1 AATATAATATT
*
41897832 CATAT
1 AATAT
41897837 TTTTTGGACC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
11 19 0.79
12 5 0.21
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.41
Consensus pattern (11 bp):
AATATAATATT
Found at i:41901538 original size:43 final size:43
Alignment explanation
Indices: 41901477--41901564 Score: 176
Period size: 43 Copynumber: 2.0 Consensus size: 43
41901467 TTTTTTTTTA
41901477 CTTAGCTTATAGTCCCTATTTAAAGGGAAAATTCACAAGAATT
1 CTTAGCTTATAGTCCCTATTTAAAGGGAAAATTCACAAGAATT
41901520 CTTAGCTTATAGTCCCTATTTAAAGGGAAAATTCACAAGAATT
1 CTTAGCTTATAGTCCCTATTTAAAGGGAAAATTCACAAGAATT
41901563 CT
1 CT
41901565 ACTTAAACAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 45 1.00
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.33
Consensus pattern (43 bp):
CTTAGCTTATAGTCCCTATTTAAAGGGAAAATTCACAAGAATT
Found at i:41901670 original size:16 final size:16
Alignment explanation
Indices: 41901648--41901702 Score: 67
Period size: 16 Copynumber: 3.4 Consensus size: 16
41901638 GTTTGGTTCA
41901648 CTGTAATGGAATATG-G
1 CTGTAATGGAATA-GAG
* *
41901664 TTGTAATTGAATAGAG
1 CTGTAATGGAATAGAG
*
41901680 CTGTAATGGAATAGAA
1 CTGTAATGGAATAGAG
41901696 CTGTAAT
1 CTGTAAT
41901703 AAGTAATTCA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
15 1 0.03
16 32 0.97
ACGTcount: A:0.36, C:0.05, G:0.25, T:0.33
Consensus pattern (16 bp):
CTGTAATGGAATAGAG
Found at i:41901972 original size:17 final size:17
Alignment explanation
Indices: 41901946--41901978 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
41901936 AATTATTATT
41901946 AAATAAAATTTAATAAA
1 AAATAAAATTTAATAAA
*
41901963 AAATATAATTTAATAA
1 AAATAAAATTTAATAA
41901979 CATTCGTAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
AAATAAAATTTAATAAA
Found at i:41902796 original size:17 final size:18
Alignment explanation
Indices: 41902759--41902802 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
41902749 AATTTAATTT
* *
41902759 AATTTAATTATTTCTCTC
1 AATTAAATTATTTCTCCC
41902777 AATTAAATTATTT-TCCC
1 AATTAAATTATTTCTCCC
*
41902794 AATTCAATT
1 AATTAAATT
41902803 CTAATTCCGT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
17 11 0.48
18 12 0.52
ACGTcount: A:0.34, C:0.16, G:0.00, T:0.50
Consensus pattern (18 bp):
AATTAAATTATTTCTCCC
Found at i:41905778 original size:52 final size:52
Alignment explanation
Indices: 41905716--41905820 Score: 210
Period size: 52 Copynumber: 2.0 Consensus size: 52
41905706 TATCCAACAA
41905716 ATAATTATGAACAATAATAGCAAAATAAGGCTATCATAAAATCAGTCAAAGT
1 ATAATTATGAACAATAATAGCAAAATAAGGCTATCATAAAATCAGTCAAAGT
41905768 ATAATTATGAACAATAATAGCAAAATAAGGCTATCATAAAATCAGTCAAAGT
1 ATAATTATGAACAATAATAGCAAAATAAGGCTATCATAAAATCAGTCAAAGT
41905820 A
1 A
41905821 AGTTAATTGG
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 53 1.00
ACGTcount: A:0.52, C:0.11, G:0.11, T:0.25
Consensus pattern (52 bp):
ATAATTATGAACAATAATAGCAAAATAAGGCTATCATAAAATCAGTCAAAGT
Found at i:41905791 original size:26 final size:24
Alignment explanation
Indices: 41905714--41905795 Score: 69
Period size: 26 Copynumber: 3.2 Consensus size: 24
41905704 ATTATCCAAC
41905714 AAATAATTATGAACAATAATAGCA
1 AAATAATTATGAACAATAATAGCA
* * *
41905738 AAATAAGGCTAT-CATAA-AATCAGTCA
1 AAATAA--TTATGAACAATAAT-AG-CA
41905764 AAGTATAATTATGAACAATAATAGCA
1 AA--ATAATTATGAACAATAATAGCA
41905790 AAATAA
1 AAATAA
41905796 GGCTATCATA
Statistics
Matches: 44, Mismatches: 6, Indels: 16
0.67 0.09 0.24
Matches are distributed among these distances:
24 13 0.30
25 5 0.11
26 14 0.32
27 5 0.11
28 7 0.16
ACGTcount: A:0.56, C:0.10, G:0.10, T:0.24
Consensus pattern (24 bp):
AAATAATTATGAACAATAATAGCA
Found at i:41907358 original size:45 final size:46
Alignment explanation
Indices: 41907271--41907358 Score: 115
Period size: 45 Copynumber: 1.9 Consensus size: 46
41907261 AATGAATAGA
* *
41907271 AATAGAGAAATGGAAAACATTCAGAAATGATTATGGTTTTCTCTGG
1 AATAGAGAAATGGAAAACATTCAGAAATAAATATGGTTTTCTCTGG
* ** *
41907317 AATAGAGAAATGG-AATCATTTGGAAATAAATGTGGTTTTCTC
1 AATAGAGAAATGGAAAACATTCAGAAATAAATATGGTTTTCTC
41907359 AAAATGGAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
45 23 0.64
46 13 0.36
ACGTcount: A:0.39, C:0.08, G:0.22, T:0.32
Consensus pattern (46 bp):
AATAGAGAAATGGAAAACATTCAGAAATAAATATGGTTTTCTCTGG
Found at i:41909881 original size:43 final size:43
Alignment explanation
Indices: 41909820--41909906 Score: 158
Period size: 43 Copynumber: 2.0 Consensus size: 43
41909810 GGTGAGTCAC
41909820 ATAGTCAATGGGTAAAAGAAACATGTAATCAAAATTAACTTTA
1 ATAGTCAATGGGTAAAAGAAACATGTAATCAAAATTAACTTTA
41909863 ATAGTCAGA-GGGTAAAAGAAACATGTAATCAAAATTAACTTTA
1 ATAGTCA-ATGGGTAAAAGAAACATGTAATCAAAATTAACTTTA
41909906 A
1 A
41909907 AGGCTAAATC
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
43 42 0.98
44 1 0.02
ACGTcount: A:0.49, C:0.09, G:0.15, T:0.26
Consensus pattern (43 bp):
ATAGTCAATGGGTAAAAGAAACATGTAATCAAAATTAACTTTA
Found at i:41920361 original size:31 final size:33
Alignment explanation
Indices: 41920300--41920364 Score: 89
Period size: 31 Copynumber: 2.0 Consensus size: 33
41920290 AATATCCTTT
* * *
41920300 CATAATATTATGTTGTTTAATAAGATAATTTTA
1 CATAAAATTATATTGTTTAATAAGACAATTTTA
41920333 CATAAAATTATATT-TTT-ATAAGACAATTTTA
1 CATAAAATTATATTGTTTAATAAGACAATTTTA
41920364 C
1 C
41920365 GTACAAAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
31 14 0.48
32 3 0.10
33 12 0.41
ACGTcount: A:0.42, C:0.06, G:0.06, T:0.46
Consensus pattern (33 bp):
CATAAAATTATATTGTTTAATAAGACAATTTTA
Found at i:41929233 original size:28 final size:28
Alignment explanation
Indices: 41929168--41929226 Score: 88
Period size: 25 Copynumber: 2.2 Consensus size: 28
41929158 AATAAACACC
41929168 AAAAATTTATTTTAAATATAAAAAAATA
1 AAAAATTTATTTTAAATATAAAAAAATA
*
41929196 AAAAA-GTATTTTAAA-AT-AAAAAATA
1 AAAAATTTATTTTAAATATAAAAAAATA
41929221 AAAAAT
1 AAAAAT
41929227 ATTTATTATA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
25 13 0.45
26 2 0.07
27 9 0.31
28 5 0.17
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.31
Consensus pattern (28 bp):
AAAAATTTATTTTAAATATAAAAAAATA
Found at i:41932033 original size:2 final size:2
Alignment explanation
Indices: 41932021--41932057 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
41932011 AGGGTTGATG
*
41932021 TA TA TA GA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
41932058 GCGTGTGTGT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:41937019 original size:25 final size:25
Alignment explanation
Indices: 41936987--41937073 Score: 113
Period size: 25 Copynumber: 3.5 Consensus size: 25
41936977 GAGTTGTAAA
** *
41936987 CGGGAAGCTCATGCAAGCTAAGTAT
1 CGGGAAGCTCATGTGAGCTAAATAT
* *
41937012 CTGGAAGCTCACGTGAGCTAAATAT
1 CGGGAAGCTCATGTGAGCTAAATAT
41937037 -GGAGAAGCTCATGTGAGCTAAATAT
1 CGG-GAAGCTCATGTGAGCTAAATAT
41937062 CGGGAAGCTCAT
1 CGGGAAGCTCAT
41937074 AAGAGTTGTG
Statistics
Matches: 53, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
24 1 0.02
25 50 0.94
26 2 0.04
ACGTcount: A:0.32, C:0.18, G:0.28, T:0.22
Consensus pattern (25 bp):
CGGGAAGCTCATGTGAGCTAAATAT
Found at i:41939948 original size:99 final size:99
Alignment explanation
Indices: 41939673--41939949 Score: 317
Period size: 99 Copynumber: 2.8 Consensus size: 99
41939663 ATGCTCACTT
* * ** * *
41939673 CACCAATTATTGATGTTGGGTATCAACAAG-GGGGAGACACAGTGGAGGGAGTGGCGGTGTTGGT
1 CACCAATTATTGATGTTGGGTATCAAAAAGAGGGGAGATATGGAGGAGGGAGTGGTGGTGTTGGT
* *
41939737 GAAGG-TCGGTTCATCCAATTTGGGCAGAGAGTCG
66 GAAGGCT-AGTTCACCCAATTTGGGCAGAGAGTCG
* * * * * * * *
41939771 CACCGATTGTTGATGTAGGGTATCAAAAAGAGGGGAGATATGAATGAGGGAGTGATGGTGCTAGT
1 CACCAATTATTGATGTTGGGTATCAAAAAGAGGGGAGATATGGAGGAGGGAGTGGTGGTGTTGGT
* * *
41939836 GAAGGC-CGATTCACCCAGTTTGGGCGGAGAGTCG
66 GAAGGCTAG-TTCACCCAATTTGGGCAGAGAGTCG
* *
41939870 CACCAATTATTGATGTTGGGTATCAAAAAGAGGGGAGATATGGAGGAGAGAGTGGTGATGTTGGT
1 CACCAATTATTGATGTTGGGTATCAAAAAGAGGGGAGATATGGAGGAGGGAGTGGTGGTGTTGGT
*
41939935 GATGGCTAGTTCACC
66 GAAGGCTAGTTCACC
41939950 TTTTCTAGGT
Statistics
Matches: 145, Mismatches: 30, Indels: 7
0.80 0.16 0.04
Matches are distributed among these distances:
98 27 0.19
99 117 0.81
100 1 0.01
ACGTcount: A:0.27, C:0.13, G:0.37, T:0.24
Consensus pattern (99 bp):
CACCAATTATTGATGTTGGGTATCAAAAAGAGGGGAGATATGGAGGAGGGAGTGGTGGTGTTGGT
GAAGGCTAGTTCACCCAATTTGGGCAGAGAGTCG
Found at i:41941494 original size:18 final size:18
Alignment explanation
Indices: 41941471--41941510 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
41941461 ACCCAATCTA
**
41941471 AACCCAAGTATTCAACCC
1 AACCCAAGTACCCAACCC
*
41941489 AACCCAATTACCCAACCC
1 AACCCAAGTACCCAACCC
41941507 AACC
1 AACC
41941511 GAATCATAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.40, C:0.45, G:0.03, T:0.12
Consensus pattern (18 bp):
AACCCAAGTACCCAACCC
Found at i:41944313 original size:54 final size:54
Alignment explanation
Indices: 41944245--41944563 Score: 151
Period size: 54 Copynumber: 5.4 Consensus size: 54
41944235 TTATTAGTTA
*
41944245 TAATTATTTTAAATTTTATTAAATCATATATTTTAATTAAAATATATTTAATAT
1 TAATTATTTAAAATTTTATTAAATCATATATTTTAATTAAAATATATTTAATAT
* * * * **
41944299 TAATTATTTCAAATTATCTTTTATAGTATCATATATTATGATTTGAGAAAATTCATATAAGAATA
1 TAATTATTTAAAATT-T-TATTA-A--ATCATATATT-TTAATT---AAAA-T-ATAT-TTAATA
41944364 T
54 T
* * * *
41944365 TAATTA-TTAAGAATTTTATTAAATTATATATTTTTATTATAATATATTTAATAA
1 TAATTATTTAA-AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATAT
* * * *
41944419 TAATTATGTTAATTTATATTTTA-TAGGATCATATATTATGATTTGAGTAAAT-TCATGTAAGAA
1 TAATTAT-TTAA---A-ATTTTATTA-AATCATATATT-TTAATT-A--AAATAT-AT-T--TAA
41944482 TAT
52 TAT
* * * *
41944485 TGATTA-TTAAGAATTTTATTAAATTATATATTTTAATTATAATATATTTAATAA
1 TAATTATTTAA-AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATAT
* * *
41944539 TAATTATGTTTAAATATGATTAAAT
1 TAATTAT-TTAAAATTTTATTAAAT
41944564 TATTTATTAT
Statistics
Matches: 196, Mismatches: 38, Indels: 61
0.66 0.13 0.21
Matches are distributed among these distances:
54 33 0.17
55 16 0.08
56 13 0.07
57 9 0.05
58 4 0.02
59 26 0.13
60 14 0.07
61 25 0.13
62 4 0.02
63 10 0.05
64 10 0.05
65 8 0.04
66 24 0.12
ACGTcount: A:0.42, C:0.02, G:0.06, T:0.50
Consensus pattern (54 bp):
TAATTATTTAAAATTTTATTAAATCATATATTTTAATTAAAATATATTTAATAT
Found at i:41944393 original size:59 final size:59
Alignment explanation
Indices: 41944330--41944513 Score: 146
Period size: 59 Copynumber: 3.1 Consensus size: 59
41944320 TATAGTATCA
41944330 TATATTATGATTTGAGAAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAAT
1 TATATTATGATTTGAGAAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAAT
* * * * * * * * *
41944389 TATA-TAT--TTTTATTATAATAT-ATTTAATAATAATTATGTTAATTTA-TATTTTA-TAGGAT
1 TATATTATGATTTGA-GAAAAT-TCATATAAGAAT-ATTA-ATT-ATTAAGAATTTTATTA-AAT
* * *
41944448 CATATATTATGATTTGAGTAAATTCATGTAAGAATATTGATTATTAAGAATTTTATTAAAT
1 --TATATTATGATTTGAGAAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAAT
41944509 TATAT
1 TATAT
41944514 ATTTTAATTA
Statistics
Matches: 91, Mismatches: 20, Indels: 28
0.65 0.14 0.20
Matches are distributed among these distances:
56 4 0.04
57 12 0.13
58 10 0.11
59 19 0.21
60 8 0.09
61 14 0.15
62 9 0.10
63 11 0.12
64 4 0.04
ACGTcount: A:0.42, C:0.02, G:0.08, T:0.48
Consensus pattern (59 bp):
TATATTATGATTTGAGAAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAAT
Found at i:41944458 original size:120 final size:121
Alignment explanation
Indices: 41944256--41944553 Score: 483
Period size: 120 Copynumber: 2.5 Consensus size: 121
41944246 AATTATTTTA
* * * *
41944256 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATATTAATTAT-TTCAAATTATCTTT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTCAAATTATATTT
*
41944320 TATAGTATCATATATTATGATTTGAGAAAATTCATATAAGAATATTAATTATTAAG
66 TATAGGATCATATATTATGATTTGAGAAAATTCATATAAGAATATTAATTATTAAG
* *
41944376 AATTTTATTAAATTATATATTTTTATTATAATATATTTAATAATAATTATGTT-AATTTATATTT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTCAAATTATATTT
* * *
41944440 TATAGGATCATATATTATGATTTGAGTAAATTCATGTAAGAATATTGATTATTAAG
66 TATAGGATCATATATTATGATTTGAGAAAATTCATATAAGAATATTAATTATTAAG
*
41944496 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTTAAAT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTCAAAT
41944554 ATGATTAAAT
Statistics
Matches: 164, Mismatches: 12, Indels: 3
0.92 0.07 0.02
Matches are distributed among these distances:
120 159 0.97
121 5 0.03
ACGTcount: A:0.42, C:0.02, G:0.06, T:0.50
Consensus pattern (121 bp):
AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTCAAATTATATTT
TATAGGATCATATATTATGATTTGAGAAAATTCATATAAGAATATTAATTATTAAG
Found at i:41944531 original size:16 final size:16
Alignment explanation
Indices: 41944510--41944551 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
41944500 TTATTAAATT
*
41944510 ATATATTTTAATTATA
1 ATATATTTTAATAATA
41944526 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
41944541 AT-TATGTTTAA
1 ATATAT-TTTAA
41944552 ATATGATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 2 0.09
15 11 0.48
16 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATAATA
Found at i:41944536 original size:15 final size:15
Alignment explanation
Indices: 41944501--41944542 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
41944491 TTAAGAATTT
*
41944501 TATTAAATTAT-ATA
1 TATTTAATTATAATA
41944515 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
41944529 TATTTAATAATAAT
1 TATTTAATTATAAT
41944543 TATGTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:41944793 original size:16 final size:16
Alignment explanation
Indices: 41944768--41944805 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
41944758 TTGATTTGCT
41944768 ATTACACCTCTATTCC
1 ATTACACCTCTATTCC
*
41944784 ATTACGCCTCTATTCC
1 ATTACACCTCTATTCC
*
41944800 AATACA
1 ATTACA
41944806 GCGAACCAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.29, C:0.34, G:0.03, T:0.34
Consensus pattern (16 bp):
ATTACACCTCTATTCC
Found at i:41944879 original size:9 final size:9
Alignment explanation
Indices: 41944867--41944916 Score: 73
Period size: 9 Copynumber: 5.6 Consensus size: 9
41944857 TCAATTTGGT
*
41944867 TAATTCGGA
1 TAATTCGGG
41944876 TAATTCGGG
1 TAATTCGGG
*
41944885 TAATTCGGT
1 TAATTCGGG
41944894 TAATTCGGG
1 TAATTCGGG
*
41944903 TAATTCGGT
1 TAATTCGGG
41944912 TAATT
1 TAATT
41944917 TTTAACCAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 37 1.00
ACGTcount: A:0.26, C:0.10, G:0.24, T:0.40
Consensus pattern (9 bp):
TAATTCGGG
Found at i:41944888 original size:18 final size:18
Alignment explanation
Indices: 41944867--41944916 Score: 91
Period size: 18 Copynumber: 2.8 Consensus size: 18
41944857 TCAATTTGGT
*
41944867 TAATTCGGATAATTCGGG
1 TAATTCGGTTAATTCGGG
41944885 TAATTCGGTTAATTCGGG
1 TAATTCGGTTAATTCGGG
41944903 TAATTCGGTTAATT
1 TAATTCGGTTAATT
41944917 TTTAACCAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.26, C:0.10, G:0.24, T:0.40
Consensus pattern (18 bp):
TAATTCGGTTAATTCGGG
Found at i:41944894 original size:27 final size:27
Alignment explanation
Indices: 41944859--41944916 Score: 89
Period size: 27 Copynumber: 2.1 Consensus size: 27
41944849 GTAGTGATTC
*
41944859 AATTTGGTTAATTCGGATAATTCGGGT
1 AATTCGGTTAATTCGGATAATTCGGGT
* *
41944886 AATTCGGTTAATTCGGGTAATTCGGTT
1 AATTCGGTTAATTCGGATAATTCGGGT
41944913 AATT
1 AATT
41944917 TTTAACCAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.26, C:0.09, G:0.24, T:0.41
Consensus pattern (27 bp):
AATTCGGTTAATTCGGATAATTCGGGT
Found at i:41945578 original size:3 final size:3
Alignment explanation
Indices: 41945570--41945600 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
41945560 GTCTGCTTTC
41945570 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
41945601 CTTTTCCGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:41949032 original size:19 final size:19
Alignment explanation
Indices: 41949000--41949044 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
41948990 ATTTTTTAAC
*
41949000 AATAATTCTAAAAAATAAA
1 AATAAATCTAAAAAATAAA
*
41949019 AATAAATCTTAAAAATAAA
1 AATAAATCTAAAAAATAAA
*
41949038 TATAAAT
1 AATAAAT
41949045 TATTGAAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.29
Consensus pattern (19 bp):
AATAAATCTAAAAAATAAA
Found at i:41952509 original size:23 final size:21
Alignment explanation
Indices: 41952470--41952513 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 21
41952460 ATAATTTTAA
*
41952470 AATGTAATAAAAGTATAATTT
1 AATGTAATAAAAATATAATTT
41952491 AATGTAAATACAAAATATAATTT
1 AATGT-AATA-AAAATATAATTT
41952514 CATCTTTAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 5 0.25
22 4 0.20
23 11 0.55
ACGTcount: A:0.55, C:0.02, G:0.07, T:0.36
Consensus pattern (21 bp):
AATGTAATAAAAATATAATTT
Found at i:41953089 original size:45 final size:45
Alignment explanation
Indices: 41953039--41953568 Score: 675
Period size: 45 Copynumber: 11.8 Consensus size: 45
41953029 CAAATATAGT
* * *
41953039 AGATCTTGTCTTCCTATATTGGTAGCGAAGTAGATCGAATATAAC
1 AGATCTTGTCTTCCTATATTGGCAGCGAAGTAGATCAAAGATAAC
* * **
41953084 TGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCAAAGATAGT
1 AGATCTTGTCTTCCTATATTGGCAGCGAAGTAGATCAAAGATAAC
* *
41953129 AGATCTTGTCTTCCTATGTTGGTAGCGAAGTAGATCAAAGATAAC
1 AGATCTTGTCTTCCTATATTGGCAGCGAAGTAGATCAAAGATAAC
* * * * *
41953174 AGATATTGTCTTCTTATATCGGTAGCGAAGTAGATCAAAGATAGC
1 AGATCTTGTCTTCCTATATTGGCAGCGAAGTAGATCAAAGATAAC
* * *
41953219 AGATCTTGTCTTCCTATATTGGTAGCGAAGTAGATCGAAGATAGC
1 AGATCTTGTCTTCCTATATTGGCAGCGAAGTAGATCAAAGATAAC
* * *
41953264 AGATCTTGTCTTCCTATATTGGTAGCGAAGTAGATCGAAGATAGC
1 AGATCTTGTCTTCCTATATTGGCAGCGAAGTAGATCAAAGATAAC
* * * *
41953309 AGATCTTGTCTTCGTGTATTGGCAGTGAAGTAGATAAAAGATAAC
1 AGATCTTGTCTTCCTATATTGGCAGCGAAGTAGATCAAAGATAAC
* * * *
41953354 AGATCTTGTCTTACTGTATTGGTAGCGAAGTAGATCAAAGATAGC
1 AGATCTTGTCTTCCTATATTGGCAGCGAAGTAGATCAAAGATAAC
* * ** *
41953399 AGACCTTGTCTTCCTATATTGGCAACGAAGTAGATTGAAGATAGC
1 AGATCTTGTCTTCCTATATTGGCAGCGAAGTAGATCAAAGATAAC
* * *
41953444 GGATTTTGTCTTCCTATATTGGCAGCGAAGTAAATCAAAGATAAC
1 AGATCTTGTCTTCCTATATTGGCAGCGAAGTAGATCAAAGATAAC
* *
41953489 AGATCTTGTCTTCCTGTATTGGCAGCAAAGTAGATCAAAGATAGA-
1 AGATCTTGTCTTCCTATATTGGCAGCGAAGTAGATCAAAGATA-AC
* * *
41953534 AGACCTTGTCTCCCTATATCGGCAGCGAAGTAGAT
1 AGATCTTGTCTTCCTATATTGGCAGCGAAGTAGAT
41953569 TAAATATACA
Statistics
Matches: 424, Mismatches: 60, Indels: 2
0.87 0.12 0.00
Matches are distributed among these distances:
45 423 1.00
46 1 0.00
ACGTcount: A:0.31, C:0.16, G:0.23, T:0.31
Consensus pattern (45 bp):
AGATCTTGTCTTCCTATATTGGCAGCGAAGTAGATCAAAGATAAC
Found at i:41953268 original size:135 final size:135
Alignment explanation
Indices: 41953034--41953568 Score: 746
Period size: 135 Copynumber: 4.0 Consensus size: 135
41953024 TAGGTCAAAT
* * * * *
41953034 ATAGTAGATCTTGTCTTCCTATATTGGTAGCGAAGTAGATCGAATATAACTGATCTTGTCTTCCT
1 ATAGCAGATCTTGTCTTCCTATATTGGCAGCGAAGTAGATCAAAGATAACAGATCTTGTCTTCCT
* * * *
41953099 GTATTGGCAGCGAAGTAGATCAAAGATAGTAGATCTTGTCTTCCTATGTTGGTAGCGAAGTAGAT
66 GTATTGGCAGCGAAGTAGATCAAAGATAGCAGACCTTGTCTTCCTATATTGGCAGCGAAGTAGAT
*
41953164 CAAAG
131 CGAAG
* * * * * *
41953169 ATAACAGATATTGTCTTCTTATATCGGTAGCGAAGTAGATCAAAGATAGCAGATCTTGTCTTCCT
1 ATAGCAGATCTTGTCTTCCTATATTGGCAGCGAAGTAGATCAAAGATAACAGATCTTGTCTTCCT
* * * * *
41953234 ATATTGGTAGCGAAGTAGATCGAAGATAGCAGATCTTGTCTTCCTATATTGGTAGCGAAGTAGAT
66 GTATTGGCAGCGAAGTAGATCAAAGATAGCAGACCTTGTCTTCCTATATTGGCAGCGAAGTAGAT
41953299 CGAAG
131 CGAAG
* * * * *
41953304 ATAGCAGATCTTGTCTTCGTGTATTGGCAGTGAAGTAGATAAAAGATAACAGATCTTGTCTTACT
1 ATAGCAGATCTTGTCTTCCTATATTGGCAGCGAAGTAGATCAAAGATAACAGATCTTGTCTTCCT
* *
41953369 GTATTGGTAGCGAAGTAGATCAAAGATAGCAGACCTTGTCTTCCTATATTGGCAACGAAGTAGAT
66 GTATTGGCAGCGAAGTAGATCAAAGATAGCAGACCTTGTCTTCCTATATTGGCAGCGAAGTAGAT
*
41953434 TGAAG
131 CGAAG
* * *
41953439 ATAGCGGATTTTGTCTTCCTATATTGGCAGCGAAGTAAATCAAAGATAACAGATCTTGTCTTCCT
1 ATAGCAGATCTTGTCTTCCTATATTGGCAGCGAAGTAGATCAAAGATAACAGATCTTGTCTTCCT
* * * *
41953504 GTATTGGCAGCAAAGTAGATCAAAGATAGAAGACCTTGTCTCCCTATATCGGCAGCGAAGTAGAT
66 GTATTGGCAGCGAAGTAGATCAAAGATAGCAGACCTTGTCTTCCTATATTGGCAGCGAAGTAGAT
41953569 TAAATATACA
Statistics
Matches: 355, Mismatches: 45, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
135 355 1.00
ACGTcount: A:0.31, C:0.16, G:0.23, T:0.31
Consensus pattern (135 bp):
ATAGCAGATCTTGTCTTCCTATATTGGCAGCGAAGTAGATCAAAGATAACAGATCTTGTCTTCCT
GTATTGGCAGCGAAGTAGATCAAAGATAGCAGACCTTGTCTTCCTATATTGGCAGCGAAGTAGAT
CGAAG
Found at i:41954405 original size:20 final size:20
Alignment explanation
Indices: 41954363--41954405 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
41954353 GGGAGACAAA
* * *
41954363 AAAATACAGAGACAGATACT
1 AAAATACAGAGAAAAAGACT
*
41954383 AAAATACAGAGAAAAAGATT
1 AAAATACAGAGAAAAAGACT
41954403 AAA
1 AAA
41954406 GAGAGATACA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.63, C:0.09, G:0.14, T:0.14
Consensus pattern (20 bp):
AAAATACAGAGAAAAAGACT
Found at i:41956618 original size:16 final size:16
Alignment explanation
Indices: 41956597--41956628 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
41956587 ATAGGTATCT
41956597 AATAATATTAATTTCA
1 AATAATATTAATTTCA
41956613 AATAATATTAATTTCA
1 AATAATATTAATTTCA
41956629 CCACACGATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (16 bp):
AATAATATTAATTTCA
Found at i:41958834 original size:14 final size:14
Alignment explanation
Indices: 41958815--41958841 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
41958805 TCTAATTTTA
41958815 TATTTTTTTAAATT
1 TATTTTTTTAAATT
41958829 TATTTTTTTAAAT
1 TATTTTTTTAAAT
41958842 AAAAAAAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (14 bp):
TATTTTTTTAAATT
Found at i:41962103 original size:19 final size:19
Alignment explanation
Indices: 41962079--41962189 Score: 168
Period size: 19 Copynumber: 5.8 Consensus size: 19
41962069 AATTTTTGAG
*
41962079 GATATGCAATCTTATATAT
1 GATATGCAATCTTAGATAT
*
41962098 GATATGCAATCGTAGATAT
1 GATATGCAATCTTAGATAT
41962117 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
41962136 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
* ** *
41962155 GATGTATAATCTTTGATAT
1 GATATGCAATCTTAGATAT
41962174 GATATGCAATCTTAGA
1 GATATGCAATCTTAGA
41962190 AGATATGATT
Statistics
Matches: 81, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 81 1.00
ACGTcount: A:0.36, C:0.10, G:0.16, T:0.38
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:41963347 original size:3 final size:3
Alignment explanation
Indices: 41963341--41963389 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
41963331 GATGATGTAT
41963341 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
41963389 T
1 T
41963390 GTATAAAATC
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:41963772 original size:98 final size:98
Alignment explanation
Indices: 41963656--41963852 Score: 349
Period size: 98 Copynumber: 2.0 Consensus size: 98
41963646 TTAAAAATCA
* *
41963656 TAAAGGAAATATTCCGAGTTTGAGATTCTAAAGGAATTGTGCCCTAACGTACTGGGTGTGATTTC
1 TAAAGGAAATATTCCGAGTTTGAGATTCTAAAGGAATCGTGCCCTAACGTACTGGGCGTGATTTC
41963721 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
66 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
* *
41963754 TAAAGGAAATATTCCGAGTTTGAGATTCTAAAGGGATCGTGCCCTAACGTATTGGGCGTGATTTC
1 TAAAGGAAATATTCCGAGTTTGAGATTCTAAAGGAATCGTGCCCTAACGTACTGGGCGTGATTTC
*
41963819 TTAAATCTTGGATGAGTGGATGTTCTTTTAAAG
66 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
41963852 T
1 T
41963853 TTTATTGTAT
Statistics
Matches: 94, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
98 94 1.00
ACGTcount: A:0.28, C:0.12, G:0.24, T:0.36
Consensus pattern (98 bp):
TAAAGGAAATATTCCGAGTTTGAGATTCTAAAGGAATCGTGCCCTAACGTACTGGGCGTGATTTC
TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
Found at i:41965225 original size:22 final size:22
Alignment explanation
Indices: 41965195--41965237 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
41965185 AATTTTTTAT
* *
41965195 ACAATAAAAATCCCCTTATATA
1 ACAAAAAAAATCCCATTATATA
*
41965217 ACAAAAAAAATCTCATTATAT
1 ACAAAAAAAATCCCATTATAT
41965238 TCTCAATTTT
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:0.53, C:0.19, G:0.00, T:0.28
Consensus pattern (22 bp):
ACAAAAAAAATCCCATTATATA
Found at i:41965839 original size:26 final size:26
Alignment explanation
Indices: 41965809--41965859 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
41965799 AAACTCTTAA
*
41965809 TTAATTAAAAATTAATATAATATATT
1 TTAATTAAAAATTAAAATAATATATT
** *
41965835 TTAATTATTAATTAAAATAGTATAT
1 TTAATTAAAAATTAAAATAATATAT
41965860 ATCTAAAATA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (26 bp):
TTAATTAAAAATTAAAATAATATATT
Found at i:41967282 original size:23 final size:21
Alignment explanation
Indices: 41967243--41967286 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 21
41967233 ATAATTTTAA
*
41967243 AATGTAATAAAAGTATAATTT
1 AATGTAATAAAAATATAATTT
41967264 AATGTAAATACAAAATATAATTT
1 AATGT-AATA-AAAATATAATTT
41967287 CATCTTTAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 5 0.25
22 4 0.20
23 11 0.55
ACGTcount: A:0.55, C:0.02, G:0.07, T:0.36
Consensus pattern (21 bp):
AATGTAATAAAAATATAATTT
Found at i:41967862 original size:45 final size:45
Alignment explanation
Indices: 41967788--41968328 Score: 651
Period size: 45 Copynumber: 12.3 Consensus size: 45
41967778 GCAATAGTGG
* * * * * *
41967788 AGTAGGTCAAAGATAGCAGATCTTTTCTTCCTATGTTGGTAGCAA
1 AGTAGATCGAAGATAGCAGATCTTGTCTTCCTATATTGGCAGCGA
* * * *
41967833 AGCAGATCGAAGATAACAAATCTTGTCTTCCTGTATTGGCAGCGA
1 AGTAGATCGAAGATAGCAGATCTTGTCTTCCTATATTGGCAGCGA
* * *
41967878 AGTAGATCAAAGATAGTAGATCTTGTCTTCCTATATTGGTAGCGA
1 AGTAGATCGAAGATAGCAGATCTTGTCTTCCTATATTGGCAGCGA
*
41967923 AGTAGATCG-A-AT-----ATCTTGTCTTCCTATATTGGTAGCGA
1 AGTAGATCGAAGATAGCAGATCTTGTCTTCCTATATTGGCAGCGA
* *
41967961 AGTAGATCGAAGATAACAGATCTTGTCTTCCTGTATTGGCAGCGA
1 AGTAGATCGAAGATAGCAGATCTTGTCTTCCTATATTGGCAGCGA
* * * *
41968006 AGTAGATCAAAGGTAGCAGATATTGTCTTCCTATATTGGTAGCGA
1 AGTAGATCGAAGATAGCAGATCTTGTCTTCCTATATTGGCAGCGA
* *
41968051 AGTAGATCGAAGATAGCAGAACTTGTCTTCCTGTATTGGCAGCGA
1 AGTAGATCGAAGATAGCAGATCTTGTCTTCCTATATTGGCAGCGA
* * *
41968096 AGTAGATCAAAGATAGCAGATCTTGTCTTCCTATATTGGTAGCAA
1 AGTAGATCGAAGATAGCAGATCTTGTCTTCCTATATTGGCAGCGA
* *
41968141 AGTAGATCGAAGATAACAGATCTTGTCTTCCTGTATTGGCAGC--
1 AGTAGATCGAAGATAGCAGATCTTGTCTTCCTATATTGGCAGCGA
*
41968184 -GTAG-T---AGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGA
1 AGTAGATCGAAGATAGCAGATCTTGTCTTCCTATATTGGCAGCGA
* * *
41968224 AGTAGATCAAAGATAACAGATCTTGTCTTCCTGTATTGGCAGCGA
1 AGTAGATCGAAGATAGCAGATCTTGTCTTCCTATATTGGCAGCGA
* * * *
41968269 AGTAGATCAAAGATAGCAGACCTTGTCTTCCTATATCGGCAGTGA
1 AGTAGATCGAAGATAGCAGATCTTGTCTTCCTATATTGGCAGCGA
* *
41968314 AATAGATTGAAGATA
1 AGTAGATCGAAGATA
41968329 CAAGTCTTAT
Statistics
Matches: 431, Mismatches: 51, Indels: 28
0.85 0.10 0.05
Matches are distributed among these distances:
38 67 0.16
39 1 0.00
40 2 0.00
41 5 0.01
42 5 0.01
43 2 0.00
44 1 0.00
45 348 0.81
ACGTcount: A:0.30, C:0.16, G:0.23, T:0.30
Consensus pattern (45 bp):
AGTAGATCGAAGATAGCAGATCTTGTCTTCCTATATTGGCAGCGA
Found at i:41968201 original size:218 final size:214
Alignment explanation
Indices: 41967788--41968320 Score: 732
Period size: 218 Copynumber: 2.5 Consensus size: 214
41967778 GCAATAGTGG
* * * * * *
41967788 AGTAGGTCAAAGATAGCAGATCTTTTCTTCCTATGTTGGTAGCAAAGCAGATCGAAGATAACA-A
1 AGTAGATCAAAGATAGCAGATCTTGTCTTCCTATATTGGTAGCGAAGTAGATCGAAGATAGCAGA
*
41967852 ATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCAAAGATAGTAGATCTTGTCTTCCTATATTGG
66 A-CTTGTCTTCCTGTATTGGCAGCGAAGTAGATCAAAGATAGCAGATCTTGTCTTCCTATATTGG
* *
41967917 TAGCGAAGTAGATCGAATATCTTGTCTTCCTATATTGGTAGCGAAGTAGATCGAAGATAACAGAT
130 TAGCAAAGTAGATCGAATATCTTGTCTTCCTATATTGGCAGC--AGTAGAT--AAGATAACAGAT
41967982 CTTGTCTTCCTGTATTGGCAGCGA
191 CTTGTCTTCCTGTATTGGCAGCGA
* *
41968006 AGTAGATCAAAGGTAGCAGATATTGTCTTCCTATATTGGTAGCGAAGTAGATCGAAGATAGCAGA
1 AGTAGATCAAAGATAGCAGATCTTGTCTTCCTATATTGGTAGCGAAGTAGATCGAAGATAGCAGA
41968071 ACTTGTCTTCCTGTATTGGCAGCGAAGTAGATCAAAGATAGCAGATCTTGTCTTCCTATATTGGT
66 ACTTGTCTTCCTGTATTGGCAGCGAAGTAGATCAAAGATAGCAGATCTTGTCTTCCTATATTGGT
* *
41968136 AGCAAAGTAGATCGAAGATAACAGATCTTGTCTTCCTGTATTGGCAGC-GTAG-T-AGATAGCAG
131 AGCAAAGTAGATCG-A-AT-----ATCTTGTCTTCCTATATTGGCAGCAGTAGATAAGATAACAG
41968198 ATCTTGTCTTCCTGTATTGGCAGCGA
189 ATCTTGTCTTCCTGTATTGGCAGCGA
* * * *
41968224 AGTAGATCAAAGATAACAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCAAAGATAGCAGA
1 AGTAGATCAAAGATAGCAGATCTTGTCTTCCTATATTGGTAGCGAAGTAGATCGAAGATAGCAGA
* * * * *
41968289 CCTTGTCTTCCTATATCGGCAGTGAAATAGAT
66 ACTTGTCTTCCTGTATTGGCAGCGAAGTAGAT
41968321 TGAAGATACA
Statistics
Matches: 283, Mismatches: 24, Indels: 16
0.88 0.07 0.05
Matches are distributed among these distances:
218 251 0.89
219 3 0.01
220 2 0.01
221 1 0.00
222 4 0.01
225 22 0.08
ACGTcount: A:0.30, C:0.17, G:0.23, T:0.30
Consensus pattern (214 bp):
AGTAGATCAAAGATAGCAGATCTTGTCTTCCTATATTGGTAGCGAAGTAGATCGAAGATAGCAGA
ACTTGTCTTCCTGTATTGGCAGCGAAGTAGATCAAAGATAGCAGATCTTGTCTTCCTATATTGGT
AGCAAAGTAGATCGAATATCTTGTCTTCCTATATTGGCAGCAGTAGATAAGATAACAGATCTTGT
CTTCCTGTATTGGCAGCGA
Found at i:41968310 original size:128 final size:128
Alignment explanation
Indices: 41967798--41968310 Score: 693
Period size: 128 Copynumber: 4.0 Consensus size: 128
41967788 AGTAGGTCAA
* * * * * * *
41967798 AGATAGCAGATCTTTTCTTCCTATGTTGGTAGCAAAGCAGATCGAAGATAACAAATCTTGTCTTC
1 AGATAGCAGATCTTGTCTTCCTATATTGGCAGCGAAGTAGATCAAAGATAACAGATCTTGTCTTC
* * *
41967863 CTGTATTGGCAGCGAAGTAGATCAAAGATAGTAGATCTTGTCTTCCTATATTGGTAGCGAAGT
66 CTGTATTGGCAGCGAAGTAGATCAAAGATAGCAGATCTTGTCTTCCTATATTGGCAGCGTAGT
* * * * *
41967926 AGATCGAATATCTTGTCTTCCTATATTGGTAGCGAAGTAGATCGAAGATAACAGATCTTGTCTTC
1 AGATAGCAGATCTTGTCTTCCTATATTGGCAGCGAAGTAGATCAAAGATAACAGATCTTGTCTTC
* * *
41967991 CTGTATTGGCAGCGAAGTAGATCAAAGGTAGCAGATATTGTCTTCCTATATTGGTAGCGAAGTAG
66 CTGTATTGGCAGCGAAGTAGATCAAAGATAGCAGATCTTGTCTTCCTATATTGGCAGC---GTAG
41968056 AT
128 -T
* * *
41968058 CGAAGATAGCAGAACTTGTCTTCCTGTATTGGCAGCGAAGTAGATCAAAGATAGCAGATCTTGTC
1 ---AGATAGCAGATCTTGTCTTCCTATATTGGCAGCGAAGTAGATCAAAGATAACAGATCTTGTC
* * * * * *
41968123 TTCCTATATTGGTAGCAAAGTAGATCGAAGATAACAGATCTTGTCTTCCTGTATTGGCAGCGTAG
63 TTCCTGTATTGGCAGCGAAGTAGATCAAAGATAGCAGATCTTGTCTTCCTATATTGGCAGCGTAG
41968188 T
128 T
*
41968189 AGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCAAAGATAACAGATCTTGTCTTC
1 AGATAGCAGATCTTGTCTTCCTATATTGGCAGCGAAGTAGATCAAAGATAACAGATCTTGTCTTC
* *
41968254 CTGTATTGGCAGCGAAGTAGATCAAAGATAGCAGACCTTGTCTTCCTATATCGGCAG
66 CTGTATTGGCAGCGAAGTAGATCAAAGATAGCAGATCTTGTCTTCCTATATTGGCAG
41968311 TGAAATAGAT
Statistics
Matches: 339, Mismatches: 39, Indels: 14
0.86 0.10 0.04
Matches are distributed among these distances:
128 224 0.66
131 4 0.01
132 5 0.01
135 106 0.31
ACGTcount: A:0.29, C:0.17, G:0.23, T:0.31
Consensus pattern (128 bp):
AGATAGCAGATCTTGTCTTCCTATATTGGCAGCGAAGTAGATCAAAGATAACAGATCTTGTCTTC
CTGTATTGGCAGCGAAGTAGATCAAAGATAGCAGATCTTGTCTTCCTATATTGGCAGCGTAGT
Found at i:41969117 original size:20 final size:20
Alignment explanation
Indices: 41969075--41969117 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
41969065 GGGAGACAAA
* * *
41969075 AAAATACAGAGACAGATACT
1 AAAATACAGAGAAAAAGACT
*
41969095 AAAATACAGAGAAAAAGATT
1 AAAATACAGAGAAAAAGACT
41969115 AAA
1 AAA
41969118 GAGAGATACA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.63, C:0.09, G:0.14, T:0.14
Consensus pattern (20 bp):
AAAATACAGAGAAAAAGACT
Found at i:41970456 original size:13 final size:13
Alignment explanation
Indices: 41970438--41970467 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
41970428 AGCCCAAACT
41970438 CAATTACCCAACC
1 CAATTACCCAACC
41970451 CAATTACCCAACC
1 CAATTACCCAACC
41970464 CAAT
1 CAAT
41970468 AAAACTAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.40, C:0.43, G:0.00, T:0.17
Consensus pattern (13 bp):
CAATTACCCAACC
Found at i:41970647 original size:9 final size:9
Alignment explanation
Indices: 41970631--41970691 Score: 95
Period size: 9 Copynumber: 6.8 Consensus size: 9
41970621 GGTATTTTTC
41970631 GGTAATTCG
1 GGTAATTCG
*
41970640 GTTAATTCG
1 GGTAATTCG
*
41970649 GTTAATTCG
1 GGTAATTCG
*
41970658 GTTAATTCG
1 GGTAATTCG
41970667 GGTAATTCG
1 GGTAATTCG
41970676 GGTAATTCG
1 GGTAATTCG
41970685 GGTAATT
1 GGTAATT
41970692 TTTAACCAAA
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 50 1.00
ACGTcount: A:0.23, C:0.10, G:0.28, T:0.39
Consensus pattern (9 bp):
GGTAATTCG
Found at i:41972948 original size:106 final size:106
Alignment explanation
Indices: 41972762--41973088 Score: 433
Period size: 106 Copynumber: 3.1 Consensus size: 106
41972752 CATCAAAAAG
*
41972762 AAACTTTCAAAATAAGGCAATATTTCGCATTTGGAAACTCGAGAAAACGTGCCCTAACGTGCTGG
1 AAACTTTCAAAATAAGGCAATATTTCGCATTTGGAAATTCGAGAAAACGTGCCCTAACGTGCTGG
* *
41972827 GTTTCGATTTCTCGTTCAACCAAATAGTCAAATATCCTTTT
66 GTTTCGATTTCTCGTTCGACCAAATAGTCAAATATCCTTTC
* * * * *
41972868 TAACTTTCAAAATAAAGCAATATTTCGCATTTGAAAATTCGAGAAAACATGCCCTAACGTGTTGG
1 AAACTTTCAAAATAAGGCAATATTTCGCATTTGGAAATTCGAGAAAACGTGCCCTAACGTGCTGG
* * **
41972933 GTTTCGATTACTCGTTTGACCAAATAGTTGAATATCCTTTC
66 GTTTCGATTTCTCGTTCGACCAAATAGTCAAATATCCTTTC
* ** * * * * *
41972974 AAAATTTCAAAACGAGGCAATGTTTTGCGTTTGGAAATTCGAGAGAACGTGCCCTAATGTGCTGG
1 AAACTTTCAAAATAAGGCAATATTTCGCATTTGGAAATTCGAGAAAACGTGCCCTAACGTGCTGG
* *
41973039 GTTTCGATTTCTCGTTCGACTAAATAGCCAAATATCCTCTT-
66 GTTTCGATTTCTCGTTCGACCAAATAGTCAAATATCCT-TTC
41973080 AAA-TTTCAA
1 AAACTTTCAA
41973089 TCTATGTCGT
Statistics
Matches: 189, Mismatches: 31, Indels: 3
0.85 0.14 0.01
Matches are distributed among these distances:
105 6 0.03
106 181 0.96
107 2 0.01
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Consensus pattern (106 bp):
AAACTTTCAAAATAAGGCAATATTTCGCATTTGGAAATTCGAGAAAACGTGCCCTAACGTGCTGG
GTTTCGATTTCTCGTTCGACCAAATAGTCAAATATCCTTTC
Found at i:41982747 original size:28 final size:28
Alignment explanation
Indices: 41982707--41982860 Score: 236
Period size: 28 Copynumber: 5.5 Consensus size: 28
41982697 TGACTTTCGA
*
41982707 CACTAAGTGTGCGATTTTAATTGTAAAG
1 CACTAAGTGTGCGAGTTTAATTGTAAAG
41982735 CACTAAGTGTGCGAGTTTAATTGTAAAG
1 CACTAAGTGTGCGAGTTTAATTGTAAAG
* *
41982763 CACTAAGTGTGCGAGTTTAATGGCAAAG
1 CACTAAGTGTGCGAGTTTAATTGTAAAG
* *
41982791 CACTAAGTGTGCGAGTTTAATGGCAAAG
1 CACTAAGTGTGCGAGTTTAATTGTAAAG
* * *
41982819 CACTAAGTGTGCGAGTTTGATTATTAAG
1 CACTAAGTGTGCGAGTTTAATTGTAAAG
41982847 CACTAAGTGTGCGA
1 CACTAAGTGTGCGA
41982861 ACTTATTAAA
Statistics
Matches: 118, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 118 1.00
ACGTcount: A:0.31, C:0.13, G:0.26, T:0.30
Consensus pattern (28 bp):
CACTAAGTGTGCGAGTTTAATTGTAAAG
Found at i:41983658 original size:70 final size:70
Alignment explanation
Indices: 41983571--41983899 Score: 500
Period size: 70 Copynumber: 4.7 Consensus size: 70
41983561 ATGTTCATGT
* *
41983571 AATTTTTATGCTTAAATGCTGTCCAATTTGTTGTATTTATGCTGCCCAAATTGTTGTATATATGC
1 AATTTTTATGCTAAAATGCTGTCCAATTTGTTGTATTTATGCTGCCCAAATTGTTGCATATATGC
*
41983636 TGTCC
66 TGTCA
* * * * *
41983641 AATTTTGATG-TAAAAATGCTG-CTCAATTTGGTATATATATGCTGCCCAAATTGTTGCACATAT
1 AATTTTTATGCT-AAAATGCTGTC-CAATTTGTTGTATTTATGCTGCCCAAATTGTTGCATATAT
41983704 GCTGTCA
64 GCTGTCA
*
41983711 AATTTTTATGCTAAAATGCTGTCCAATTTGTTGTATTTATGCTGCCCAAATTGGTGCATATATGC
1 AATTTTTATGCTAAAATGCTGTCCAATTTGTTGTATTTATGCTGCCCAAATTGTTGCATATATGC
41983776 TGTCA
66 TGTCA
41983781 AATTTTTATGCTAAAATGCTGTCCAATTTGTTGTATTTATGCTGCCCAAATTGTTGCATATATGC
1 AATTTTTATGCTAAAATGCTGTCCAATTTGTTGTATTTATGCTGCCCAAATTGTTGCATATATGC
*
41983846 TGTCC
66 TGTCA
* * * *
41983851 AATTTTTATGCTTAAATGCTGCCCAAATTGTTGTATTTATGCTGTCCAA
1 AATTTTTATGCTAAAATGCTGTCCAATTTGTTGTATTTATGCTGCCCAA
41983900 TTTTTGGTGT
Statistics
Matches: 235, Mismatches: 20, Indels: 8
0.89 0.08 0.03
Matches are distributed among these distances:
69 2 0.01
70 231 0.98
71 2 0.01
ACGTcount: A:0.26, C:0.16, G:0.16, T:0.42
Consensus pattern (70 bp):
AATTTTTATGCTAAAATGCTGTCCAATTTGTTGTATTTATGCTGCCCAAATTGTTGCATATATGC
TGTCA
Found at i:41983679 original size:47 final size:46
Alignment explanation
Indices: 41983586--41983829 Score: 132
Period size: 47 Copynumber: 5.2 Consensus size: 46
41983576 TTATGCTTAA
* *** * *
41983586 ATGCTGTCCAATTTGTTGTATTTATGCTGCCCAAATTGTTGTATAT
1 ATGCTGTCCAATTTGATGTAAAAATGCTGCCCAAATTGGTATATAT
* *
41983632 ATGCTGTCCAATTTTGATGTAAAAATGCTGCTCAATTTGGTATATAT
1 ATGCTGTCCAA-TTTGATGTAAAAATGCTGCCCAAATTGGTATATAT
* * * * * * * ** * *
41983679 ATGCTGCCCAAATTGTTGCACATATGCTG-TCAAATTTTTATGCTAAA
1 ATGCTGTCCAATTTGATGTAAAAATGCTGCCCAAATTGGTAT-AT-AT
* *** **
41983726 ATGCTGTCCAATTTGTTGTATTTATGCTGCCCAAATTGGTGCATAT
1 ATGCTGTCCAATTTGATGTAAAAATGCTGCCCAAATTGGTATATAT
* * * * * * *
41983772 ATGCTGTCAAATTTTTATGCT-AAAATGCTGTCCAATTTGTTGTATTT
1 ATGCTGTCCAA-TTTGATG-TAAAAATGCTGCCCAAATTGGTATATAT
*
41983819 ATGCTGCCCAA
1 ATGCTGTCCAA
41983830 ATTGTTGCAT
Statistics
Matches: 148, Mismatches: 44, Indels: 11
0.73 0.22 0.05
Matches are distributed among these distances:
45 9 0.06
46 36 0.24
47 95 0.64
48 8 0.05
ACGTcount: A:0.26, C:0.16, G:0.17, T:0.41
Consensus pattern (46 bp):
ATGCTGTCCAATTTGATGTAAAAATGCTGCCCAAATTGGTATATAT
Found at i:41983879 original size:47 final size:47
Alignment explanation
Indices: 41983679--41983904 Score: 192
Period size: 47 Copynumber: 4.8 Consensus size: 47
41983669 TGGTATATAT
* * *
41983679 ATGCTGCCCAAATTGTTGCACATATGCTGTCAAATTTTTATGCTAAA
1 ATGCTGCCCAAATTGTTGCATATATGCTGTCCAATTTTTATGCTTAA
* * * * * * ** * *
41983726 ATGCTGTCCAATTTGTTGTATTTATGCTGCCCAA-ATTGGTGCATAT
1 ATGCTGCCCAAATTGTTGCATATATGCTGTCCAATTTTTATGCTTAA
* * * * **
41983772 ATGCTG-TCAAATTTTTATGC-TAAAATGCTGTCCAATTTGT-TG-TATTT
1 ATGCTGCCCAAA-TTGT-TGCAT-ATATGCTGTCCAATTTTTATGCT-TAA
41983819 ATGCTGCCCAAATTGTTGCATATATGCTGTCCAATTTTTATGCTTAA
1 ATGCTGCCCAAATTGTTGCATATATGCTGTCCAATTTTTATGCTTAA
* *
41983866 ATGCTGCCCAAATTGTTGTATTTATGCTGTCCAATTTTT
1 ATGCTGCCCAAATTGTTGCATATATGCTGTCCAATTTTT
41983905 GGTGTGAAAA
Statistics
Matches: 137, Mismatches: 33, Indels: 18
0.73 0.18 0.10
Matches are distributed among these distances:
45 3 0.02
46 35 0.26
47 93 0.68
48 6 0.04
ACGTcount: A:0.25, C:0.17, G:0.16, T:0.42
Consensus pattern (47 bp):
ATGCTGCCCAAATTGTTGCATATATGCTGTCCAATTTTTATGCTTAA
Found at i:41985533 original size:15 final size:15
Alignment explanation
Indices: 41985513--41985546 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
41985503 GAGATGATTC
* *
41985513 TTTTTATTTTTTTTA
1 TTTTTATGTTTTATA
41985528 TTTTTATGTTTTATA
1 TTTTTATGTTTTATA
41985543 TTTT
1 TTTT
41985547 AAACAATTTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.15, C:0.00, G:0.03, T:0.82
Consensus pattern (15 bp):
TTTTTATGTTTTATA
Found at i:41987920 original size:31 final size:33
Alignment explanation
Indices: 41987860--41987920 Score: 81
Period size: 31 Copynumber: 1.9 Consensus size: 33
41987850 AAATAATTTA
* * *
41987860 ATTAATTTAATTTAATTAACTAATTTTTTGGTC
1 ATTAAATTAATTTAATTAAATAATATTTTGGTC
41987893 ATTAAATTAA-TT-ATTAAATAATATTTTG
1 ATTAAATTAATTTAATTAAATAATATTTTG
41987921 AGTACTAGAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 14 0.56
32 2 0.08
33 9 0.36
ACGTcount: A:0.39, C:0.03, G:0.05, T:0.52
Consensus pattern (33 bp):
ATTAAATTAATTTAATTAAATAATATTTTGGTC
Found at i:41990741 original size:17 final size:17
Alignment explanation
Indices: 41990699--41990745 Score: 62
Period size: 17 Copynumber: 2.8 Consensus size: 17
41990689 AATTCAATTT
41990699 TAATATAAAT-ATTCAA
1 TAATATAAATAATTCAA
41990715 T-ATGACTAAATAATTCAA
1 TAAT-A-TAAATAATTCAA
41990733 TAATATAAATAAT
1 TAATATAAATAAT
41990746 ATAAAATGTG
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
15 2 0.07
16 2 0.07
17 13 0.48
18 8 0.30
19 2 0.07
ACGTcount: A:0.55, C:0.06, G:0.02, T:0.36
Consensus pattern (17 bp):
TAATATAAATAATTCAA
Found at i:41991240 original size:20 final size:22
Alignment explanation
Indices: 41991207--41991247 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
41991197 AGGAAGGAGT
*
41991207 AAAAATTTTGAGGG-AAAAATA
1 AAAAAGTTTGAGGGTAAAAATA
41991228 AAAAAGTTT-AGGGTAAAAAT
1 AAAAAGTTTGAGGGTAAAAAT
41991248 GTAAAATATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.56, C:0.00, G:0.20, T:0.24
Consensus pattern (22 bp):
AAAAAGTTTGAGGGTAAAAATA
Found at i:41991285 original size:9 final size:9
Alignment explanation
Indices: 41991267--41991303 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
41991257 TATAGTTTGA
41991267 TATTCGAAT
1 TATTCGAAT
*
41991276 TATTCAAAT
1 TATTCGAAT
*
41991285 TATTCGAGT
1 TATTCGAAT
41991294 TATTCGAAT
1 TATTCGAAT
41991303 T
1 T
41991304 CGAAAACTCA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.32, C:0.11, G:0.11, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:41992914 original size:3 final size:3
Alignment explanation
Indices: 41992906--41992938 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
41992896 TTAAACACTA
41992906 CCG CCG CCG CCG CCG CCG CCG CCG CCG CCG CCG
1 CCG CCG CCG CCG CCG CCG CCG CCG CCG CCG CCG
41992939 TGGAGGAAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.00, C:0.67, G:0.33, T:0.00
Consensus pattern (3 bp):
CCG
Found at i:41997292 original size:16 final size:16
Alignment explanation
Indices: 41997271--41997301 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
41997261 AGAGACTTGT
41997271 ATAGATTGATATATTG
1 ATAGATTGATATATTG
*
41997287 ATAGATTGATGTATT
1 ATAGATTGATATATT
41997302 TACTTTTTTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.00, G:0.19, T:0.45
Consensus pattern (16 bp):
ATAGATTGATATATTG
Found at i:42000427 original size:23 final size:23
Alignment explanation
Indices: 42000377--42000429 Score: 74
Period size: 21 Copynumber: 2.4 Consensus size: 23
42000367 AAAGGAATTT
*
42000377 TGAAAGAGAGAAGTCAATAACAG
1 TGAAAGAGAGAAATCAATAACAG
*
42000400 T--AAGAGAGAAATCAATAATAG
1 TGAAAGAGAGAAATCAATAACAG
42000421 TGAAAGAGA
1 TGAAAGAGA
42000430 AAAGAAAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
21 19 0.73
23 7 0.27
ACGTcount: A:0.55, C:0.06, G:0.25, T:0.15
Consensus pattern (23 bp):
TGAAAGAGAGAAATCAATAACAG
Found at i:42001935 original size:21 final size:19
Alignment explanation
Indices: 42001911--42001961 Score: 50
Period size: 18 Copynumber: 2.6 Consensus size: 19
42001901 TTTATTTAAA
42001911 TGAATTTAATTAATTTTCTAC
1 TGAATTTAATT--TTTTCTAC
*
42001932 TGAAATT-ATTTTTTCTAC
1 TGAATTTAATTTTTTCTAC
*
42001950 TCAATTCTAATT
1 TGAATT-TAATT
42001962 CCATTAAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
18 12 0.48
19 1 0.04
20 6 0.24
21 6 0.24
ACGTcount: A:0.31, C:0.12, G:0.04, T:0.53
Consensus pattern (19 bp):
TGAATTTAATTTTTTCTAC
Found at i:42003433 original size:46 final size:46
Alignment explanation
Indices: 42003383--42003507 Score: 160
Period size: 46 Copynumber: 2.7 Consensus size: 46
42003373 TCCGAGCTTT
*
42003383 TGCATATGTTGTGGACTCGAGAATGCAAGAATAGGTTCCAAACTCC
1 TGCATATGTTGTGGACTCGAGAATACAAGAATAGGTTCCAAACTCC
* * * ** * *
42003429 TGCATATGTTGCGGACTCGGGAATACATGTTTAGGTTCCGAGCTCC
1 TGCATATGTTGTGGACTCGAGAATACAAGAATAGGTTCCAAACTCC
* *
42003475 TACATATGTTGTGGACTCGAGAATACAGGAATA
1 TGCATATGTTGTGGACTCGAGAATACAAGAATA
42003508 TTAAGCCCTG
Statistics
Matches: 65, Mismatches: 14, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
46 65 1.00
ACGTcount: A:0.28, C:0.18, G:0.26, T:0.28
Consensus pattern (46 bp):
TGCATATGTTGTGGACTCGAGAATACAAGAATAGGTTCCAAACTCC
Found at i:42007885 original size:18 final size:20
Alignment explanation
Indices: 42007850--42007892 Score: 54
Period size: 18 Copynumber: 2.2 Consensus size: 20
42007840 GTTTTTGACA
* *
42007850 TATATATTTATTATATAATT
1 TATATATTTATTAGATAAAT
42007870 TATA-ATTTATT-GATAAAT
1 TATATATTTATTAGATAAAT
42007888 TATAT
1 TATAT
42007893 GTTATATATA
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
18 9 0.45
19 7 0.35
20 4 0.20
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (20 bp):
TATATATTTATTAGATAAAT
Found at i:42007888 original size:19 final size:20
Alignment explanation
Indices: 42007850--42007892 Score: 56
Period size: 19 Copynumber: 2.2 Consensus size: 20
42007840 GTTTTTGACA
42007850 TATATATTTATTATATAATT
1 TATATATTTATTATATAATT
42007870 TATA-ATTTATTGATA-AA-T
1 TATATATTTATT-ATATAATT
42007888 TATAT
1 TATAT
42007893 GTTATATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
18 5 0.24
19 9 0.43
20 7 0.33
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (20 bp):
TATATATTTATTATATAATT
Found at i:42009134 original size:27 final size:27
Alignment explanation
Indices: 42009093--42009159 Score: 82
Period size: 27 Copynumber: 2.5 Consensus size: 27
42009083 TTTACCCTAA
*
42009093 AAATAAAATAAAAAAGATTAAAA-TAGT
1 AAATAAAATAAAAAA-ATCAAAATTAGT
* *
42009120 AATTAAAATACAAAAATCAAAATTAGT
1 AAATAAAATAAAAAAATCAAAATTAGT
*
42009147 AAATAAAGTAAAA
1 AAATAAAATAAAA
42009160 TGAATGGTGA
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
26 6 0.18
27 27 0.82
ACGTcount: A:0.69, C:0.03, G:0.06, T:0.22
Consensus pattern (27 bp):
AAATAAAATAAAAAAATCAAAATTAGT
Found at i:42009952 original size:20 final size:20
Alignment explanation
Indices: 42009931--42010044 Score: 71
Period size: 19 Copynumber: 6.0 Consensus size: 20
42009921 TATATATATT
42009931 TTTTGAAATTTTTATAATT-
1 TTTTGAAATTTTTATAATTA
* **
42009950 TTTTTAAA--AATATAA--A
1 TTTTGAAATTTTTATAATTA
*
42009966 TTTTGAAATTTTTATAAATA
1 TTTTGAAATTTTTATAATTA
* * *
42009986 TTTTG-AATTTTAAAAAATA
1 TTTTGAAATTTTTATAATTA
* *
42010005 TTTTGAATTTTTTAAAATTA
1 TTTTGAAATTTTTATAATTA
*
42010025 ATTTG-AATTATATTATAATT
1 TTTTGAAATT-T-TTATAATT
42010045 TTTGTTGAGA
Statistics
Matches: 73, Mismatches: 14, Indels: 14
0.72 0.14 0.14
Matches are distributed among these distances:
16 7 0.10
17 5 0.07
18 5 0.07
19 27 0.37
20 22 0.30
21 7 0.10
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.54
Consensus pattern (20 bp):
TTTTGAAATTTTTATAATTA
Found at i:42009963 original size:35 final size:36
Alignment explanation
Indices: 42009902--42009982 Score: 103
Period size: 35 Copynumber: 2.3 Consensus size: 36
42009892 GAAAAAAATT
* * **
42009902 AATTTTT-TAACTTTCTTTATATATATATTTTTTGA
1 AATTTTTATAACTTTCTTTAAAAATATAAATTTTGA
*
42009937 AATTTTTATAA-TTTTTTTAAAAATATAAATTTTGA
1 AATTTTTATAACTTTCTTTAAAAATATAAATTTTGA
42009972 AATTTTTATAA
1 AATTTTTATAA
42009983 ATATTTTGAA
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
35 37 0.93
36 3 0.08
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.58
Consensus pattern (36 bp):
AATTTTTATAACTTTCTTTAAAAATATAAATTTTGA
Found at i:42010017 original size:39 final size:41
Alignment explanation
Indices: 42009951--42010033 Score: 109
Period size: 39 Copynumber: 2.0 Consensus size: 41
42009941 TTTATAATTT
*
42009951 TTTTAAAAATATAAATTTTGAAATTTTTATAAA-TATTTTGAA
1 TTTTAAAAATAT-AATTTTGAAATTTTTA-AAATTAATTTGAA
*
42009993 TTTTAAAAA-AT-ATTTTGAATTTTTTAAAATTAATTTGAA
1 TTTTAAAAATATAATTTTGAAATTTTTAAAATTAATTTGAA
42010032 TT
1 TT
42010034 ATATTATAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
38 3 0.08
39 24 0.63
41 2 0.05
42 9 0.24
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (41 bp):
TTTTAAAAATATAATTTTGAAATTTTTAAAATTAATTTGAA
Found at i:42010048 original size:39 final size:38
Alignment explanation
Indices: 42009921--42010048 Score: 102
Period size: 39 Copynumber: 3.4 Consensus size: 38
42009911 ACTTTCTTTA
* ** *
42009921 TATATATATTTTTTGAAATTTTTAT-AATTTTTTTAA-
1 TATATATAATTTTTGAAATTTTTATAAATAATTTGAAT
* * *
42009957 -AAATATAAATTTTGAAATTTTTATAAATATTTTGAAT
1 TATATATAATTTTTGAAATTTTTATAAATAATTTGAAT
* * * *
42009994 TTTAAAAAATATTTTGAATTTTTTA-AAATTAATTTGAAT
1 TATATATAAT-TTTTGAAATTTTTATAAA-TAATTTGAAT
42010033 TATATTATAATTTTTG
1 TATA-TATAATTTTTG
42010049 TTGAGAGTGA
Statistics
Matches: 71, Mismatches: 15, Indels: 9
0.75 0.16 0.09
Matches are distributed among these distances:
35 21 0.30
36 9 0.13
38 7 0.10
39 30 0.42
40 4 0.06
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.55
Consensus pattern (38 bp):
TATATATAATTTTTGAAATTTTTATAAATAATTTGAAT
Found at i:42012672 original size:24 final size:24
Alignment explanation
Indices: 42012641--42012704 Score: 110
Period size: 24 Copynumber: 2.7 Consensus size: 24
42012631 GGTGATCAAC
*
42012641 AACAGCAGGAGCTGCAATATGAGG
1 AACAGCAGCAGCTGCAATATGAGG
*
42012665 AACTGCAGCAGCTGCAATATGAGG
1 AACAGCAGCAGCTGCAATATGAGG
42012689 AACAGCAGCAGCTGCA
1 AACAGCAGCAGCTGCA
42012705 TCAGCAACAG
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.36, C:0.22, G:0.30, T:0.12
Consensus pattern (24 bp):
AACAGCAGCAGCTGCAATATGAGG
Found at i:42015715 original size:3 final size:3
Alignment explanation
Indices: 42015707--42015739 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
42015697 ACAAGCGGGG
*
42015707 GAA GAA GAA GAA GAA GAA GAA GAA GAA GTA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
42015740 ACCTTGGAGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.64, C:0.00, G:0.33, T:0.03
Consensus pattern (3 bp):
GAA
Found at i:42024278 original size:8 final size:7
Alignment explanation
Indices: 42024248--42024278 Score: 53
Period size: 7 Copynumber: 4.3 Consensus size: 7
42024238 TTTTAAAAAT
42024248 ATTTTAA
1 ATTTTAA
42024255 ATTTTAA
1 ATTTTAA
42024262 ATTTTAA
1 ATTTTAA
42024269 ATTCTTAA
1 ATT-TTAA
42024277 AT
1 AT
42024279 AAATCTAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 17 0.74
8 6 0.26
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (7 bp):
ATTTTAA
Found at i:42027798 original size:23 final size:23
Alignment explanation
Indices: 42027772--42027815 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
42027762 ACAAAATCCT
42027772 GATGAAACTATTATACCAAATGA
1 GATGAAACTATTATACCAAATGA
42027795 GATGAAACTATTATACCAAAT
1 GATGAAACTATTATACCAAAT
42027816 TAAGTTTCCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.48, C:0.14, G:0.11, T:0.27
Consensus pattern (23 bp):
GATGAAACTATTATACCAAATGA
Found at i:42032411 original size:16 final size:16
Alignment explanation
Indices: 42032392--42032455 Score: 69
Period size: 16 Copynumber: 4.0 Consensus size: 16
42032382 TATATGTATA
42032392 TAATAATTATTAAAAT
1 TAATAATTATTAAAAT
*
42032408 TAATAATTATTACAA-
1 TAATAATTATTAAAAT
*
42032423 TATTAA-TATTAAAATT
1 TAATAATTATTAAAA-T
*
42032439 TAATAATAATATAAAAT
1 TAATAATTAT-TAAAAT
42032456 ATATAATGAC
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
14 7 0.18
15 5 0.13
16 19 0.49
17 3 0.08
18 5 0.13
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (16 bp):
TAATAATTATTAAAAT
Found at i:42033014 original size:20 final size:20
Alignment explanation
Indices: 42032989--42033026 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
42032979 ATTTCAACCA
42032989 GTATAATAATAAATAATAAT
1 GTATAATAATAAATAATAAT
* *
42033009 GTATAATGATAATTAATA
1 GTATAATAATAAATAATA
42033027 TATTATGTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.55, C:0.00, G:0.08, T:0.37
Consensus pattern (20 bp):
GTATAATAATAAATAATAAT
Found at i:42034414 original size:10 final size:9
Alignment explanation
Indices: 42034388--42034413 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
42034378 TCATCTACTA
42034388 ATAAAAAAC
1 ATAAAAAAC
42034397 ATAAAAAAC
1 ATAAAAAAC
42034406 ATAAAAAA
1 ATAAAAAA
42034414 AGAAAAGAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.81, C:0.08, G:0.00, T:0.12
Consensus pattern (9 bp):
ATAAAAAAC
Found at i:42038718 original size:15 final size:16
Alignment explanation
Indices: 42038693--42038722 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
42038683 AACTATCATC
42038693 AAACTAATGATGATGT
1 AAACTAATGATGATGT
42038709 AAAC-AATGATGATG
1 AAACTAATGATGATG
42038723 CAATTAATGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.47, C:0.07, G:0.20, T:0.27
Consensus pattern (16 bp):
AAACTAATGATGATGT
Found at i:42038731 original size:15 final size:15
Alignment explanation
Indices: 42038692--42038734 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
42038682 AAACTATCAT
42038692 CAAACTAATGATGATG
1 CAAA-TAATGATGATG
* *
42038708 TAAACAATGATGATG
1 CAAATAATGATGATG
*
42038723 CAATTAATGATG
1 CAAATAATGATG
42038735 GAAGCAACCA
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
15 19 0.86
16 3 0.14
ACGTcount: A:0.44, C:0.09, G:0.19, T:0.28
Consensus pattern (15 bp):
CAAATAATGATGATG
Found at i:42039529 original size:15 final size:15
Alignment explanation
Indices: 42039509--42039537 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
42039499 TAGTGGCTAG
42039509 TGGCTAGTGGCTCTA
1 TGGCTAGTGGCTCTA
42039524 TGGCTAGTGGCTCT
1 TGGCTAGTGGCTCT
42039538 TAATTTAGCA
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:0.10, C:0.21, G:0.34, T:0.34
Consensus pattern (15 bp):
TGGCTAGTGGCTCTA
Found at i:42043225 original size:31 final size:29
Alignment explanation
Indices: 42043190--42043261 Score: 71
Period size: 28 Copynumber: 2.5 Consensus size: 29
42043180 ACATATACGT
42043190 ATATACATATATAAGCA-ATTATATAATAATA
1 ATATACATATATAAGCATA-TATAT-ATAA-A
*
42043221 ATATA-ATAT-GAAGCATATATATATAAA
1 ATATACATATATAAGCATATATATATAAA
*
42043248 ATTTACATA-ATAAG
1 ATATACATATATAAG
42043262 TATAAACAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 9
0.74 0.06 0.19
Matches are distributed among these distances:
27 5 0.14
28 10 0.29
29 10 0.29
30 5 0.14
31 5 0.14
ACGTcount: A:0.54, C:0.06, G:0.06, T:0.35
Consensus pattern (29 bp):
ATATACATATATAAGCATATATATATAAA
Found at i:42044333 original size:17 final size:17
Alignment explanation
Indices: 42044311--42044343 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
42044301 ATTATTTTTG
42044311 GGCTT-GTTGGGTATTTA
1 GGCTTGGTT-GGTATTTA
42044328 GGCTTGGTTGGTATTT
1 GGCTTGGTTGGTATTT
42044344 GTGTTAGGCT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 12 0.80
18 3 0.20
ACGTcount: A:0.09, C:0.06, G:0.36, T:0.48
Consensus pattern (17 bp):
GGCTTGGTTGGTATTTA
Found at i:42047046 original size:5 final size:5
Alignment explanation
Indices: 42047038--42047085 Score: 53
Period size: 5 Copynumber: 9.0 Consensus size: 5
42047028 AAATTTGCAC
42047038 ATTTT ATTTT ATTTTT ATTTT -TCCTTCT ATTTT ATTTT ATTTT ATTTT
1 ATTTT ATTTT A-TTTT ATTTT AT--TT-T ATTTT ATTTT ATTTT ATTTT
42047086 GCAGGTAGAC
Statistics
Matches: 38, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
4 1 0.03
5 26 0.68
6 9 0.24
7 1 0.03
8 1 0.03
ACGTcount: A:0.17, C:0.06, G:0.00, T:0.77
Consensus pattern (5 bp):
ATTTT
Found at i:42047452 original size:11 final size:11
Alignment explanation
Indices: 42047438--42047476 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
42047428 TAGCTTTTAC
42047438 AAAAAAAAATG
1 AAAAAAAAATG
*
42047449 -AAAAAAAACG
1 AAAAAAAAATG
*
42047459 AGAAAAAAATG
1 AAAAAAAAATG
42047470 AAAAAAA
1 AAAAAAA
42047477 TAAATAATAC
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
10 9 0.39
11 14 0.61
ACGTcount: A:0.82, C:0.03, G:0.10, T:0.05
Consensus pattern (11 bp):
AAAAAAAAATG
Found at i:42047454 original size:10 final size:10
Alignment explanation
Indices: 42047439--42047476 Score: 58
Period size: 10 Copynumber: 3.7 Consensus size: 10
42047429 AGCTTTTACA
42047439 AAAAAAAATG
1 AAAAAAAATG
*
42047449 AAAAAAAACG
1 AAAAAAAATG
42047459 AGAAAAAAATG
1 A-AAAAAAATG
42047470 AAAAAAA
1 AAAAAAA
42047477 TAAATAATAC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
10 16 0.64
11 9 0.36
ACGTcount: A:0.82, C:0.03, G:0.11, T:0.05
Consensus pattern (10 bp):
AAAAAAAATG
Found at i:42049672 original size:12 final size:12
Alignment explanation
Indices: 42049655--42049679 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
42049645 TTGCCACCCC
42049655 ATATCTGTTTGA
1 ATATCTGTTTGA
42049667 ATATCTGTTTGA
1 ATATCTGTTTGA
42049679 A
1 A
42049680 GAACAGTCAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.28, C:0.08, G:0.16, T:0.48
Consensus pattern (12 bp):
ATATCTGTTTGA
Found at i:42058411 original size:21 final size:21
Alignment explanation
Indices: 42058385--42058424 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
42058375 TCTCCTTGGC
42058385 AAGTGGGA-ATCGCGATACCCA
1 AAGT-GGATATCGCGATACCCA
42058406 AAGTGGATATCGCGATACC
1 AAGTGGATATCGCGATACC
42058425 ACTCGATTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 3 0.17
21 15 0.83
ACGTcount: A:0.33, C:0.23, G:0.28, T:0.17
Consensus pattern (21 bp):
AAGTGGATATCGCGATACCCA
Found at i:42059695 original size:16 final size:16
Alignment explanation
Indices: 42059671--42059702 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
42059661 ACGAATAGAT
*
42059671 ATACTTATTTAAATAA
1 ATACCTATTTAAATAA
42059687 ATACCTATTTAAATAA
1 ATACCTATTTAAATAA
42059703 TCATATTACT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.50, C:0.09, G:0.00, T:0.41
Consensus pattern (16 bp):
ATACCTATTTAAATAA
Found at i:42061405 original size:5 final size:5
Alignment explanation
Indices: 42061395--42061424 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
42061385 TTATGTTCAC
42061395 GGGAA GGGAA GGGAA GGGAA GGG-A GGGAA G
1 GGGAA GGGAA GGGAA GGGAA GGGAA GGGAA G
42061425 AATACAAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
4 4 0.17
5 20 0.83
ACGTcount: A:0.37, C:0.00, G:0.63, T:0.00
Consensus pattern (5 bp):
GGGAA
Found at i:42065863 original size:15 final size:15
Alignment explanation
Indices: 42065843--42065873 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
42065833 ACACAGATAT
42065843 CCAACCTAAGGTTCG
1 CCAACCTAAGGTTCG
*
42065858 CCAACCTGAGGTTCG
1 CCAACCTAAGGTTCG
42065873 C
1 C
42065874 AAATGGGTTC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.23, C:0.35, G:0.23, T:0.19
Consensus pattern (15 bp):
CCAACCTAAGGTTCG
Found at i:42071377 original size:17 final size:17
Alignment explanation
Indices: 42071350--42071395 Score: 56
Period size: 17 Copynumber: 2.7 Consensus size: 17
42071340 CCGATATAAT
* * *
42071350 AAATATATTTATTTTTT
1 AAATATTTTTAATTTTA
*
42071367 AAATTTTTTTAATTTTA
1 AAATATTTTTAATTTTA
42071384 AAATATTTTTAA
1 AAATATTTTTAA
42071396 AATACTTTTT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
AAATATTTTTAATTTTA
Found at i:42071434 original size:21 final size:21
Alignment explanation
Indices: 42071387--42071434 Score: 51
Period size: 22 Copynumber: 2.2 Consensus size: 21
42071377 AATTTTAAAA
* * **
42071387 TATTTTTAAAATACTTTTTTT
1 TATTTTAAAAATAATTTTTGG
42071408 TAATTTTAAAAATAATTTTTGG
1 T-ATTTTAAAAATAATTTTTGG
42071430 TATTT
1 TATTT
42071435 ATTAAAAAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 5 0.23
22 17 0.77
ACGTcount: A:0.33, C:0.02, G:0.04, T:0.60
Consensus pattern (21 bp):
TATTTTAAAAATAATTTTTGG
Found at i:42072978 original size:194 final size:194
Alignment explanation
Indices: 42072631--42073008 Score: 465
Period size: 194 Copynumber: 1.9 Consensus size: 194
42072621 TTACGTACTC
* * * * *
42072631 TGTAACACCCTAGGAAAATTCCACATTGGCAAAGCATGGGAGAGACCTGCGTATATACAGGGGTA
1 TGTAACACCCTAGGAAAATTCCACATCGGCAAAACACGGGAGAGACCTGCGTATATAAAGGAGTA
* ** * ***
42072696 GTAACACTTAAGTGGAAAGAGGCCTTTTGAGGGTCTATGACCTTTTCCAAGAACAAAGTTATGAG
66 GCAACACTTAAGTGGAAAGAGGCCTTTTGAGGGTCTATGACCGCTCCCAAGAACAAAACCATGAG
* * * *
42072761 GGCCATGTGCGCTCAAGGCGGACAATATCTTACCGGGATGGGTGTTGGCTATGAAATTTATCAA
131 GGCCATGTGCACCCAAAGCGGACAATATCTTACCAGGATGGGTGTTGGCTATGAAATTTATCAA
* * * *
42072825 TGTAACACCCTAGGCAAA-TCTCACATCGGTAAAACACGGGAGGGACCTGGGCTATATAAAGGAG
1 TGTAACACCCTAGGAAAATTC-CACATCGGCAAAACACGGGAGAGACCTGCG-TATATAAAGGAG
* * * **
42072889 TAGCAACACTTTAA-TGGAAATAGGCCTTTTGGGGGTGTATGGGCGCTCCCAAGAACAAAACCAT
64 TAGCAACAC-TTAAGTGGAAAGAGGCCTTTTGAGGGTCTATGACCGCTCCCAAGAACAAAACCAT
* *
42072953 GA-GGCCATGTGCACCCAAAGCGGACAATATTTTACCAGGCTGGGTGTTGGCTATGA
128 GAGGGCCATGTGCACCCAAAGCGGACAATATCTTACCAGGATGGGTGTTGGCTATGA
42073009 CATACTCCAT
Statistics
Matches: 154, Mismatches: 27, Indels: 6
0.82 0.14 0.03
Matches are distributed among these distances:
193 2 0.01
194 89 0.58
195 59 0.38
196 4 0.03
ACGTcount: A:0.30, C:0.20, G:0.27, T:0.23
Consensus pattern (194 bp):
TGTAACACCCTAGGAAAATTCCACATCGGCAAAACACGGGAGAGACCTGCGTATATAAAGGAGTA
GCAACACTTAAGTGGAAAGAGGCCTTTTGAGGGTCTATGACCGCTCCCAAGAACAAAACCATGAG
GGCCATGTGCACCCAAAGCGGACAATATCTTACCAGGATGGGTGTTGGCTATGAAATTTATCAA
Found at i:42074291 original size:26 final size:26
Alignment explanation
Indices: 42074254--42074305 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 26
42074244 GTCCGTTCAT
*
42074254 GGTCCTCTGACCAACTCAAATTCAAG
1 GGTCCTCTGACCAACTCAAACTCAAG
* *
42074280 GGTCCT-TCGACCCACTTAAACTCAAG
1 GGTCCTCT-GACCAACTCAAACTCAAG
42074306 CTCGCTAGGG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
25 1 0.05
26 21 0.95
ACGTcount: A:0.29, C:0.33, G:0.15, T:0.23
Consensus pattern (26 bp):
GGTCCTCTGACCAACTCAAACTCAAG
Found at i:42075330 original size:20 final size:21
Alignment explanation
Indices: 42075305--42075348 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
42075295 AATTTTTAAA
42075305 AATAGT-AGAAGATTCTTCTC
1 AATAGTCAGAAGATTCTTCTC
* *
42075325 AATAGTCAGAGGATTTTTCTC
1 AATAGTCAGAAGATTCTTCTC
42075346 AAT
1 AAT
42075349 CGAAAAAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 6 0.29
21 15 0.71
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.36
Consensus pattern (21 bp):
AATAGTCAGAAGATTCTTCTC
Found at i:42082426 original size:31 final size:31
Alignment explanation
Indices: 42082387--42082466 Score: 117
Period size: 31 Copynumber: 2.6 Consensus size: 31
42082377 TTATTGTAAG
*
42082387 GCATGGAAATTGAAGCAATAA-GGAGGTATAA
1 GCATGGAAATTGAAGCAATAACGG-GGAATAA
*
42082418 TCATGGAAATTGAAGCAATAACGGGGAATAA
1 GCATGGAAATTGAAGCAATAACGGGGAATAA
*
42082449 GCATAGAAATTGAAGCAA
1 GCATGGAAATTGAAGCAA
42082467 ATGAAAAATA
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
31 42 0.95
32 2 0.05
ACGTcount: A:0.46, C:0.09, G:0.26, T:0.19
Consensus pattern (31 bp):
GCATGGAAATTGAAGCAATAACGGGGAATAA
Found at i:42084721 original size:6 final size:6
Alignment explanation
Indices: 42084712--42084742 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
42084702 TCGGCGTCGG
*
42084712 CTTCGT CTTCGT CTTCGT CTTCTT CTTCGT C
1 CTTCGT CTTCGT CTTCGT CTTCGT CTTCGT C
42084743 ATCCTCATCT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.00, C:0.35, G:0.13, T:0.52
Consensus pattern (6 bp):
CTTCGT
Found at i:42084809 original size:24 final size:23
Alignment explanation
Indices: 42084741--42084809 Score: 75
Period size: 24 Copynumber: 2.9 Consensus size: 23
42084731 TTCTTCTTCG
**
42084741 TCATCCTCATCTTCATCCCCATCT
1 TCATCCTCATCTTCA-CTTCATCT
*
42084765 CCATCCTCATCTTCACTTTCATCT
1 TCATCCTCATCTTCAC-TTCATCT
*
42084789 TCATCTTCATCTTCAGCTTCA
1 TCATCCTCATCTTCA-CTTCA
42084810 GGCTCAGTCT
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
23 1 0.03
24 36 0.95
25 1 0.03
ACGTcount: A:0.17, C:0.41, G:0.01, T:0.41
Consensus pattern (23 bp):
TCATCCTCATCTTCACTTCATCT
Found at i:42084810 original size:6 final size:6
Alignment explanation
Indices: 42084741--42084809 Score: 68
Period size: 6 Copynumber: 11.5 Consensus size: 6
42084731 TTCTTCTTCG
* * * * *
42084741 TCATCC TCATCT TCATCC CCATCT CCATCC TCATCT TCA-CTT TCATCT
1 TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCATC-T TCATCT
*
42084789 TCATCT TCATCT TCAGCT TCA
1 TCATCT TCATCT TCATCT TCA
42084810 GGCTCAGTCT
Statistics
Matches: 53, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
5 1 0.02
6 51 0.96
7 1 0.02
ACGTcount: A:0.17, C:0.41, G:0.01, T:0.41
Consensus pattern (6 bp):
TCATCT
Found at i:42089816 original size:15 final size:15
Alignment explanation
Indices: 42089796--42089830 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
42089786 TTGTTGTTAG
* *
42089796 GTTTTCTTTTAATTT
1 GTTTTCATTCAATTT
42089811 GTTTTCATTCAATTT
1 GTTTTCATTCAATTT
42089826 GTTTT
1 GTTTT
42089831 TGTTTCTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.14, C:0.09, G:0.09, T:0.69
Consensus pattern (15 bp):
GTTTTCATTCAATTT
Found at i:42091272 original size:9 final size:10
Alignment explanation
Indices: 42091245--42091308 Score: 53
Period size: 9 Copynumber: 6.3 Consensus size: 10
42091235 ATTCAATAGT
*
42091245 TTTTATAA-C
1 TTTTATAATA
42091254 TTTTATAATA
1 TTTTATAATA
42091264 TTTTA-AATA
1 TTTTATAATA
*
42091273 TTTTAT-ATG
1 TTTTATAATA
42091282 TTTGTATAAAATA
1 TTT-TAT--AATA
42091295 TTTTAATAATA
1 TTTT-ATAATA
42091306 TTT
1 TTT
42091309 ATGATTGTTT
Statistics
Matches: 45, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
9 22 0.49
10 8 0.18
11 7 0.16
12 1 0.02
13 7 0.16
ACGTcount: A:0.38, C:0.02, G:0.03, T:0.58
Consensus pattern (10 bp):
TTTTATAATA
Found at i:42091400 original size:24 final size:24
Alignment explanation
Indices: 42091349--42091400 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
42091339 TGATTTTTAT
* *
42091349 AATTTTTATGACCTTTATATATAC
1 AATTTTTATGACCTTTATAGATAA
*
42091373 AATTTTTATGACTTTTACTAGA-AA
1 AATTTTTATGACCTTTA-TAGATAA
42091397 AATT
1 AATT
42091401 CATGATTTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 21 0.88
25 3 0.12
ACGTcount: A:0.37, C:0.10, G:0.06, T:0.48
Consensus pattern (24 bp):
AATTTTTATGACCTTTATAGATAA
Found at i:42094846 original size:21 final size:21
Alignment explanation
Indices: 42094802--42094840 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
42094792 ATATGTGTTT
42094802 TATTTATAATATAATTATTAA
1 TATTTATAATATAATTATTAA
*
42094823 TATTTAT-ATTTAATTATT
1 TATTTATAATATAATTATT
42094841 TTATATCTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
TATTTATAATATAATTATTAA
Found at i:42101706 original size:13 final size:13
Alignment explanation
Indices: 42101688--42101714 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
42101678 CAAGCTGCTC
42101688 AAATCAAAATCAA
1 AAATCAAAATCAA
42101701 AAATCAAAATCAA
1 AAATCAAAATCAA
42101714 A
1 A
42101715 TCCCCTTTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.70, C:0.15, G:0.00, T:0.15
Consensus pattern (13 bp):
AAATCAAAATCAA
Found at i:42101980 original size:5 final size:5
Alignment explanation
Indices: 42101967--42102004 Score: 67
Period size: 5 Copynumber: 7.6 Consensus size: 5
42101957 GAATAAAACA
*
42101967 AAGAG AAGAA AAGAG AAGAG AAGAG AAGAG AAGAG AAG
1 AAGAG AAGAG AAGAG AAGAG AAGAG AAGAG AAGAG AAG
42102005 CGTAACGGCG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
5 31 1.00
ACGTcount: A:0.63, C:0.00, G:0.37, T:0.00
Consensus pattern (5 bp):
AAGAG
Found at i:42106376 original size:3 final size:3
Alignment explanation
Indices: 42106368--42106426 Score: 63
Period size: 3 Copynumber: 20.0 Consensus size: 3
42106358 ATATGTAGGT
42106368 ATA ATA ATA ATA ATA TATA AT- ATA ATA ATA A-A ATTA ATA ATA ATA
1 ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA A-TA ATA ATA ATA
42106413 A-A ATTA ATA A-A ATA
1 ATA A-TA ATA ATA ATA
42106427 GACTAAAAAC
Statistics
Matches: 49, Mismatches: 0, Indels: 14
0.78 0.00 0.22
Matches are distributed among these distances:
2 8 0.16
3 34 0.69
4 7 0.14
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:42106395 original size:24 final size:22
Alignment explanation
Indices: 42106368--42106426 Score: 73
Period size: 24 Copynumber: 2.5 Consensus size: 22
42106358 ATATGTAGGT
*
42106368 ATAATAATAATAATATATAATATA
1 ATAATAA-AATAATA-ATAATAAA
42106392 ATAATAAAATTAATAATAATAAA
1 ATAATAAAA-TAATAATAATAAA
42106415 ATTAATAAAATA
1 A-TAATAAAATA
42106427 GACTAAAAAC
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
23 12 0.38
24 20 0.62
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (22 bp):
ATAATAAAATAATAATAATAAA
Found at i:42109584 original size:36 final size:35
Alignment explanation
Indices: 42109516--42109598 Score: 89
Period size: 36 Copynumber: 2.3 Consensus size: 35
42109506 AAAGGCCTAG
*
42109516 AAATAATATAAATAAATCAATAAATAAAATCAATAT
1 AAATAATAAAAATAAATCAATAAATAAAATCAA-AT
* *
42109552 ACATAATAAAAAT-AATCACATACAA-AATATCAAAT
1 AAATAATAAAAATAAATCA-ATA-AATAAAATCAAAT
*
42109587 AAATCATAAAAA
1 AAATAATAAAAA
42109599 ACAATTCTTT
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
35 17 0.43
36 21 0.52
37 2 0.05
ACGTcount: A:0.66, C:0.10, G:0.00, T:0.24
Consensus pattern (35 bp):
AAATAATAAAAATAAATCAATAAATAAAATCAAAT
Found at i:42115733 original size:25 final size:24
Alignment explanation
Indices: 42115665--42115733 Score: 61
Period size: 25 Copynumber: 2.9 Consensus size: 24
42115655 GTATACATAC
* * *
42115665 ATATATATACA-AAGATAAATATA
1 ATATATATAAATAAAATAAAAATA
* *
42115688 ATATATATAGATTATAA-AAAAATA
1 ATATATATA-AATAAAATAAAAATA
42115712 ATTATATATAAATAAAATAAAA
1 A-TATATATAAATAAAATAAAA
42115734 TAAAAATAAT
Statistics
Matches: 35, Mismatches: 7, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
23 9 0.26
24 12 0.34
25 14 0.40
ACGTcount: A:0.64, C:0.01, G:0.03, T:0.32
Consensus pattern (24 bp):
ATATATATAAATAAAATAAAAATA
Found at i:42123340 original size:13 final size:14
Alignment explanation
Indices: 42123322--42123355 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
42123312 GCGATTTTTA
42123322 AATTTTTTATATT-
1 AATTTTTTATATTG
*
42123335 AATTTTTTATTTTG
1 AATTTTTTATATTG
42123349 AATTTTT
1 AATTTTT
42123356 AGAATTATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 12 0.63
14 7 0.37
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (14 bp):
AATTTTTTATATTG
Found at i:42129011 original size:2 final size:2
Alignment explanation
Indices: 42129004--42129051 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
42128994 GTAAGGGTTA
42129004 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
42129046 AT AT AT
1 AT AT AT
42129052 TGTTTTTAAA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:42135757 original size:8 final size:8
Alignment explanation
Indices: 42135738--42135767 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
42135728 CTAACTAGAA
42135738 TAAATA-T
1 TAAATATT
42135745 TAAATATT
1 TAAATATT
42135753 TAAATATT
1 TAAATATT
42135761 TAAATAT
1 TAAATAT
42135768 AAATTTAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 6 0.27
8 16 0.73
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (8 bp):
TAAATATT
Found at i:42135775 original size:12 final size:11
Alignment explanation
Indices: 42135758--42135796 Score: 51
Period size: 12 Copynumber: 3.4 Consensus size: 11
42135748 ATATTTAAAT
42135758 ATTTAAATATAA
1 ATTTAAA-ATAA
42135770 ATTTAAAATATA
1 ATTTAAAATA-A
*
42135782 TTTTAAAATAA
1 ATTTAAAATAA
42135793 ATTT
1 ATTT
42135797 CTTTGTACCA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
11 7 0.29
12 17 0.71
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (11 bp):
ATTTAAAATAA
Done.