Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032249.1 Gossypioides kirkii chromosome KI_07
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: 37252039
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 2100 characters in sequence are not A, C, G, or T
File 11 of 120
Found at i:3082082 original size:28 final size:28
Alignment explanation
Indices: 3082029--3082082 Score: 65
Period size: 28 Copynumber: 1.9 Consensus size: 28
3082019 GCAGACCACT
* * *
3082029 ATCTCCACTTGCTTCTGCCACGGCCATC
1 ATCTCCACCTGCTGCTGCCACCGCCATC
3082057 ATCTCCACCTGCTGCT-CCAACCGCCA
1 ATCTCCACCTGCTGCTGCC-ACCGCCA
3082083 CTGTGGAGCA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
27 2 0.09
28 20 0.91
ACGTcount: A:0.17, C:0.46, G:0.13, T:0.24
Consensus pattern (28 bp):
ATCTCCACCTGCTGCTGCCACCGCCATC
Found at i:3082505 original size:15 final size:15
Alignment explanation
Indices: 3082485--3082577 Score: 59
Period size: 16 Copynumber: 6.3 Consensus size: 15
3082475 TGATTTTATA
*
3082485 AATATTATTAGTAAT
1 AATATTATTAATAAT
3082500 AATATTATTAATAAT
1 AATATTATTAATAAT
* *
3082515 CATAATAATTAATAAT
1 AAT-ATTATTAATAAT
* *
3082531 AGTA--ATAAAT-AT
1 AATATTATTAATAAT
* * *
3082543 -TTATAATTAATATT
1 AATATTATTAATAAT
*
3082557 AATATTAATAAATAAT
1 AATATT-ATTAATAAT
3082573 AATAT
1 AATAT
3082578 CAACCAATAA
Statistics
Matches: 59, Mismatches: 13, Indels: 11
0.71 0.16 0.13
Matches are distributed among these distances:
11 2 0.03
12 2 0.03
13 10 0.17
14 1 0.02
15 20 0.34
16 24 0.41
ACGTcount: A:0.54, C:0.01, G:0.02, T:0.43
Consensus pattern (15 bp):
AATATTATTAATAAT
Found at i:3082538 original size:19 final size:19
Alignment explanation
Indices: 3082496--3082576 Score: 69
Period size: 19 Copynumber: 4.3 Consensus size: 19
3082486 ATATTATTAG
*
3082496 TAATAAT-ATTATTAATAA
1 TAATAATAATTAATAATAA
* *
3082514 TCATAATAATTAATAATAG
1 TAATAATAATTAATAATAA
*
3082533 TAATAA-ATATTTATAATTAA
1 TAATAATA-ATTAATAA-TAA
*
3082553 TATTAAT-ATTAATAAATAA
1 TAATAATAATTAAT-AATAA
3082572 TAATA
1 TAATA
3082577 TCAACCAATA
Statistics
Matches: 49, Mismatches: 9, Indels: 9
0.73 0.13 0.13
Matches are distributed among these distances:
18 7 0.14
19 33 0.67
20 9 0.18
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.42
Consensus pattern (19 bp):
TAATAATAATTAATAATAA
Found at i:3082565 original size:12 final size:12
Alignment explanation
Indices: 3082485--3082577 Score: 66
Period size: 12 Copynumber: 7.7 Consensus size: 12
3082475 TGATTTTATA
* *
3082485 AATATTATTAGT
1 AATAATATTAAT
*
3082497 AATAATATTATT
1 AATAATATTAAT
3082509 AATAATCA-TAAT
1 AATAAT-ATTAAT
* *
3082521 AATTAATAATAGT
1 AA-TAATATTAAT
*
3082534 AATAAATATTTAT
1 AAT-AATATTAAT
3082547 AATTAATATTAAT
1 AA-TAATATTAAT
*
3082560 ATTAATA--AAT
1 AATAATATTAAT
3082570 AATAATAT
1 AATAATAT
3082578 CAACCAATAA
Statistics
Matches: 65, Mismatches: 10, Indels: 13
0.74 0.11 0.15
Matches are distributed among these distances:
10 9 0.14
12 28 0.43
13 27 0.42
14 1 0.02
ACGTcount: A:0.54, C:0.01, G:0.02, T:0.43
Consensus pattern (12 bp):
AATAATATTAAT
Found at i:3082590 original size:3 final size:3
Alignment explanation
Indices: 3082496--3082576 Score: 54
Period size: 3 Copynumber: 25.7 Consensus size: 3
3082486 ATATTATTAG
* * * * *
3082496 TAA TAA TAT TAT TAA TAA TCA TAA TAA TTAA TAA TAG TAA TAAA TAT
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA -TAA TAA TAA TAA T-AA TAA
* * *
3082543 TTA TAA TTAA TAT TAA TAT TAA TAAA TAA TAA TA
1 TAA TAA -TAA TAA TAA TAA TAA T-AA TAA TAA TA
3082577 TCAACCAATA
Statistics
Matches: 60, Mismatches: 14, Indels: 8
0.73 0.17 0.10
Matches are distributed among these distances:
3 48 0.80
4 12 0.20
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.42
Consensus pattern (3 bp):
TAA
Found at i:3083650 original size:29 final size:29
Alignment explanation
Indices: 3083607--3083685 Score: 115
Period size: 29 Copynumber: 2.7 Consensus size: 29
3083597 CAAACAGTCC
*
3083607 AAAAATTGCATTTTAACCCTAAAATTT-T
1 AAAAATTACATTTTAACCCTAAAATTTCT
3083635 AGAAAATTACATTTTAACCCTAAAATTTCT
1 A-AAAATTACATTTTAACCCTAAAATTTCT
*
3083665 AAAAATTACCATTTTTACCCT
1 AAAAATTA-CATTTTAACCCT
3083686 CGAATTTTCC
Statistics
Matches: 46, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
28 1 0.02
29 32 0.70
30 13 0.28
ACGTcount: A:0.42, C:0.18, G:0.03, T:0.38
Consensus pattern (29 bp):
AAAAATTACATTTTAACCCTAAAATTTCT
Found at i:3083727 original size:29 final size:29
Alignment explanation
Indices: 3083666--3083974 Score: 180
Period size: 29 Copynumber: 10.4 Consensus size: 29
3083656 AAAATTTCTA
*
3083666 AAAATTACCATTTTT-ACCCTCGAATTT-TCC
1 AAAA-TACCATTTTTAACCC-C-AATTTCACC
* *
3083696 AAAATCCCATTTTTAACCCCAATTTCATC
1 AAAATACCATTTTTAACCCCAATTTCACC
* *
3083725 AAAATTATCA-TTTTACCCCCAAACTTT--CC
1 AAAA-TACCATTTTTAACCCC-AA-TTTCACC
* *
3083754 AAAATTCCATTTTTAACCCCGATTTCACC
1 AAAATACCATTTTTAACCCCAATTTCACC
3083783 AAAAATTACCA-TTTT-ACCCCTGAACTTT--CC
1 -AAAA-TACCATTTTTAACCCC--AA-TTTCACC
*
3083813 AAAATACCATATTTAACCCCAATTTCACC
1 AAAATACCATTTTTAACCCCAATTTCACC
*
3083842 AAAAATTACCA-TTTT-ACCCCTGAACTTT--CT
1 -AAAA-TACCATTTTTAACCCC--AA-TTTCACC
* * *
3083872 AAAATTCCATTTTTAACCCCATTTTTACC
1 AAAATACCATTTTTAACCCCAATTTCACC
*
3083901 AAAATTACCATTTTTACCCCCGAACTTT--CC
1 AAAA-TACCATTTTTAACCCC-AA-TTTCACC
* * *
3083931 AAAATTCCATTTTTAACCTCGATTTCACC
1 AAAATACCATTTTTAACCCCAATTTCACC
3083960 AAAATTTACCATTTT
1 AAAA--TACCATTTT
3083975 GCCCTCGAGG
Statistics
Matches: 219, Mismatches: 27, Indels: 65
0.70 0.09 0.21
Matches are distributed among these distances:
27 12 0.05
28 22 0.10
29 91 0.42
30 61 0.28
31 24 0.11
32 9 0.04
ACGTcount: A:0.33, C:0.29, G:0.02, T:0.36
Consensus pattern (29 bp):
AAAATACCATTTTTAACCCCAATTTCACC
Found at i:3084000 original size:28 final size:29
Alignment explanation
Indices: 3083958--3084020 Score: 85
Period size: 28 Copynumber: 2.2 Consensus size: 29
3083948 CTCGATTTCA
*
3083958 CCAAAATTTACCATTTTGCCCTCGAGG-AT
1 CCAAAATTTACCATTTTACCCTCG-GGTAT
*
3083987 CCAAAA-TTACCATTTTACTCTCGGGTAT
1 CCAAAATTTACCATTTTACCCTCGGGTAT
3084015 CCAAAA
1 CCAAAA
3084021 GTCTCGTTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
27 2 0.06
28 23 0.74
29 6 0.19
ACGTcount: A:0.32, C:0.27, G:0.11, T:0.30
Consensus pattern (29 bp):
CCAAAATTTACCATTTTACCCTCGGGTAT
Found at i:3084002 original size:59 final size:59
Alignment explanation
Indices: 3083665--3083974 Score: 421
Period size: 59 Copynumber: 5.3 Consensus size: 59
3083655 TAAAATTTCT
* * * *
3083665 AAAAATTACCATTTTTA-CCCTCGAATTTTCCAAAATCCCATTTTTAACCCCAATTTCATC
1 AAAAATTACCA-TTTTACCCCT-GAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACC
* **
3083725 -AAAATTATCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACC
1 AAAAATTACCATTTTACCCCTGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACC
* * *
3083783 AAAAATTACCATTTTACCCCTGAACTTTCCAAAATACCATATTTAACCCCAATTTCACC
1 AAAAATTACCATTTTACCCCTGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACC
* *
3083842 AAAAATTACCATTTTACCCCTGAACTTTCTAAAATTCCATTTTTAACCCC-ATTTTTACC
1 AAAAATTACCATTTTACCCCTGAACTTTCCAAAATTCCATTTTTAACCCCGA-TTTCACC
* *
3083901 -AAAATTACCATTTTTACCCCCGAACTTTCCAAAATTCCATTTTTAACCTCGATTTCACC
1 AAAAATTACCA-TTTTACCCCTGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACC
*
3083960 AAAATTTACCATTTT
1 AAAAATTACCATTTT
3083975 GCCCTCGAGG
Statistics
Matches: 222, Mismatches: 22, Indels: 13
0.86 0.09 0.05
Matches are distributed among these distances:
58 49 0.22
59 163 0.73
60 10 0.05
ACGTcount: A:0.34, C:0.29, G:0.02, T:0.36
Consensus pattern (59 bp):
AAAAATTACCATTTTACCCCTGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACC
Found at i:3095998 original size:76 final size:76
Alignment explanation
Indices: 3095868--3096253 Score: 643
Period size: 76 Copynumber: 5.0 Consensus size: 76
3095858 ATCAGACCGC
*
3095868 AGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATGA-CACGTCTTTATCTCTGA
1 AGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGAT-ATCAAGTCTTTATCTCTGA
3095932 AATTGAAGTAAG
65 AATTGAAGTAAG
*
3095944 AGTAAGATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCTTTATCTCTCTG
1 AGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCTTTA--TCTCTG
3096009 AAATTGAAGTAAG
64 AAATTGAAGTAAG
* *
3096022 AGCAACG-TCATTTCCTATCCTCTTGAAATTGAAGTAGAG-TGGATAACACGTCTTTATCTCTGA
1 AGCAA-GATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCTTTATCTCTGA
3096085 AATTGAAGTAAG
65 AATTGAAGTAAG
3096097 AGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCTTTATCTCTGAA
1 AGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCTTTATCTCTGAA
3096162 ATTGAAGTAAG
66 ATTGAAGTAAG
* *
3096173 AGCAAGATCGTTTCCCATCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCTTTATCTCTCTG
1 AGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCTTTA--TCTCTG
3096238 AAATTGAAGTAAG
64 AAATTGAAGTAAG
3096251 AGC
1 AGC
3096254 TAGACGAAGC
Statistics
Matches: 293, Mismatches: 9, Indels: 14
0.93 0.03 0.04
Matches are distributed among these distances:
74 1 0.00
75 57 0.19
76 142 0.48
77 15 0.05
78 77 0.26
79 1 0.00
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33
Consensus pattern (76 bp):
AGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCTTTATCTCTGAA
ATTGAAGTAAG
Found at i:3096147 original size:153 final size:154
Alignment explanation
Indices: 3095868--3096350 Score: 704
Period size: 153 Copynumber: 3.1 Consensus size: 154
3095858 ATCAGACCGC
*
3095868 AGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATGACACGTCTTTATCTCTGAA
1 AGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACACGTCTTTATCTCTGAA
*
3095933 ATTGAAGTAAGAGTAAGATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCT
66 ATTGAAGTAAGAGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCT
3095998 TTATCTCTCTGAAATTGAAGTAAG
131 TTATCTCTCTGAAATTGAAGTAAG
3096022 AGCAACG-TCATTTCCTATCCTCTTGAAATTGAAGTAGAG-TGGATAACACGTCTTTATCTCTGA
1 AGCAA-GATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACACGTCTTTATCTCTGA
3096085 AATTGAAGTAAGAGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTC
65 AATTGAAGTAAGAGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTC
3096150 TTTA--TCTCTGAAATTGAAGTAAG
130 TTTATCTCTCTGAAATTGAAGTAAG
* * * *
3096173 AGCAAGATCGTTTCCCATCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCTTTATCTCTCTG
1 AGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACACGTCTTTA--TCTCTG
*
3096238 AAATTGAAGTAAGAGCTAGACGAAGCATCAAACATCATTTCCTATCCTCTTGAAATTGAAGTAAA
64 AAATTGAAGT-A-AG--AG-C-AAG--------ATCATTTCCTATCCTCTTGAAATTGAAGTAGA
*
3096303 GTTGGATAGCAAGTCTTTATCTCTCTGAAATTGAAGTAAG
115 GTTGGATATCAAGTCTTTATCTCTCTGAAATTGAAGTAAG
*
3096343 AGCTAGAT
1 AGCAAGAT
3096351 AAAGCATCAA
Statistics
Matches: 299, Mismatches: 9, Indels: 26
0.90 0.03 0.08
Matches are distributed among these distances:
150 1 0.00
151 54 0.18
152 15 0.05
153 91 0.30
154 53 0.18
155 2 0.01
156 2 0.01
158 2 0.01
159 1 0.00
160 3 0.01
168 49 0.16
170 26 0.09
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.33
Consensus pattern (154 bp):
AGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACACGTCTTTATCTCTGAA
ATTGAAGTAAGAGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCT
TTATCTCTCTGAAATTGAAGTAAG
Found at i:3096340 original size:92 final size:92
Alignment explanation
Indices: 3096183--3096447 Score: 363
Period size: 92 Copynumber: 2.9 Consensus size: 92
3096173 AGCAAGATCG
* * *
3096183 TTTCCCATCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCTTTATCTCTCTGAAATTGAAGT
1 TTTCCTATCCTCTTGAAATTGAAGTAAAGTTGGATAACAAGTCTTTATCTCTCTGAAATTGAAGT
*
3096248 AAGAGCTAGACGAAGCATCAAACATCA
66 AAGAGCTAGATGAAGCATCAAACATCA
*
3096275 TTTCCTATCCTCTTGAAATTGAAGTAAAGTTGGATAGCAAGTCTTTATCTCTCTGAAATTGAAGT
1 TTTCCTATCCTCTTGAAATTGAAGTAAAGTTGGATAACAAGTCTTTATCTCTCTGAAATTGAAGT
*
3096340 AAGAGCTAGATAAAGCATCAAACATCA
66 AAGAGCTAGATGAAGCATCAAACATCA
* * ** * * *
3096367 TTTCCTGTCCTCTTGAAGTTGTAA-TAAAGTTAGG-TAATGAGTCTTTATTTCTCTAAAATTGTA
1 TTTCCTATCCTCTTGAAATTG-AAGTAAAGTT-GGATAACAAGTCTTTATCTCTCTGAAATTGAA
* *
3096430 TTAAGAGCAAGATGAAGC
64 GTAAGAGCTAGATGAAGC
3096448 CTCGACATCA
Statistics
Matches: 155, Mismatches: 16, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
92 151 0.97
93 4 0.03
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Consensus pattern (92 bp):
TTTCCTATCCTCTTGAAATTGAAGTAAAGTTGGATAACAAGTCTTTATCTCTCTGAAATTGAAGT
AAGAGCTAGATGAAGCATCAAACATCA
Found at i:3096724 original size:22 final size:22
Alignment explanation
Indices: 3096699--3096771 Score: 65
Period size: 22 Copynumber: 3.3 Consensus size: 22
3096689 CCAAAACCAT
*
3096699 TTTTACTTTGAAATTTAATTTA
1 TTTTAATTTGAAATTTAATTTA
* *
3096721 TTTTAATTTTAAATTTATTTTAA
1 TTTTAATTTGAAATTTAATTT-A
* * * *
3096744 ATTCAATTTTAATTTTAATTTA
1 TTTTAATTTGAAATTTAATTTA
*
3096766 ATTTAA
1 TTTTAA
3096772 ATTTAATATT
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
22 24 0.57
23 18 0.43
ACGTcount: A:0.36, C:0.03, G:0.01, T:0.60
Consensus pattern (22 bp):
TTTTAATTTGAAATTTAATTTA
Found at i:3096731 original size:6 final size:6
Alignment explanation
Indices: 3096712--3096775 Score: 64
Period size: 6 Copynumber: 11.3 Consensus size: 6
3096702 TACTTTGAAA
* * *
3096712 TTTAA- TTT-AT TTTAAT TTTAAA TTT-AT TTTAAA TTCAAT TTTAAT
1 TTTAAT TTTAAT TTTAAT TTTAAT TTTAAT TTTAAT TTTAAT TTTAAT
*
3096757 TTTAA- TTTAAT TTAAAT TT
1 TTTAAT TTTAAT TTTAAT TT
3096776 AATATTATTA
Statistics
Matches: 48, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
4 1 0.02
5 15 0.31
6 32 0.67
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (6 bp):
TTTAAT
Found at i:3096740 original size:4 final size:5
Alignment explanation
Indices: 3096710--3096778 Score: 57
Period size: 5 Copynumber: 12.6 Consensus size: 5
3096700 TTTACTTTGA
* * *
3096710 AATTT AATTT ATTTT AATTTT AAATTT ATTTT AAATTC AATTTT AATTTT
1 AATTT AATTT AATTT AA-TTT -AATTT AATTT -AATTT AA-TTT AA-TTT
3096760 AATTT AATTT AAATTT AAT
1 AATTT AATTT -AATTT AAT
3096779 ATTATTATAA
Statistics
Matches: 53, Mismatches: 6, Indels: 10
0.77 0.09 0.14
Matches are distributed among these distances:
5 27 0.51
6 24 0.45
7 2 0.04
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.59
Consensus pattern (5 bp):
AATTT
Found at i:3096752 original size:12 final size:11
Alignment explanation
Indices: 3096723--3096793 Score: 56
Period size: 11 Copynumber: 6.4 Consensus size: 11
3096713 TTAATTTATT
3096723 TTAATTTTAAA
1 TTAATTTTAAA
*
3096734 TTTATTTTAAA
1 TTAATTTTAAA
*
3096745 TTCAATTTTAATT
1 TT-AATTTTAA-A
*
3096758 TTAA-TTTAAT
1 TTAATTTTAAA
*
3096768 TTAAATTTAATA
1 TTAATTTTAA-A
*
3096780 TT-ATTATAAA
1 TTAATTTTAAA
3096790 TTAA
1 TTAA
3096794 AAAAAGAAAG
Statistics
Matches: 49, Mismatches: 6, Indels: 10
0.75 0.09 0.15
Matches are distributed among these distances:
10 8 0.16
11 28 0.57
12 11 0.22
13 2 0.04
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.56
Consensus pattern (11 bp):
TTAATTTTAAA
Found at i:3096775 original size:17 final size:15
Alignment explanation
Indices: 3096710--3096770 Score: 68
Period size: 17 Copynumber: 3.7 Consensus size: 15
3096700 TTTACTTTGA
3096710 AATTTAATTTATTTT
1 AATTTAATTTATTTT
3096725 AATTTTAAATTTATTTT
1 AA-TTT-AATTTATTTT
*
3096742 AAATTCAATTTTAATTTT
1 -AATTTAA-TTT-ATTTT
3096760 AATTTAATTTA
1 AATTTAATTTA
3096771 AATTTAATAT
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
15 3 0.08
16 8 0.21
17 21 0.54
18 7 0.18
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.61
Consensus pattern (15 bp):
AATTTAATTTATTTT
Found at i:3096778 original size:11 final size:11
Alignment explanation
Indices: 3096709--3096777 Score: 61
Period size: 11 Copynumber: 6.2 Consensus size: 11
3096699 TTTTACTTTG
3096709 AAATTTAATTT
1 AAATTTAATTT
*
3096720 -ATTTTAATTTT
1 AAATTTAA-TTT
*
3096731 AAATTTATTTT
1 AAATTTAATTT
*
3096742 AAATTCAATTTT
1 AAATTTAA-TTT
*
3096754 AATTTTAATTT
1 AAATTTAATTT
3096765 -AATTTAAATTT
1 AAATTT-AATTT
3096776 AA
1 AA
3096778 TATTATTATA
Statistics
Matches: 45, Mismatches: 8, Indels: 9
0.73 0.13 0.15
Matches are distributed among these distances:
10 10 0.22
11 20 0.44
12 15 0.33
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.58
Consensus pattern (11 bp):
AAATTTAATTT
Found at i:3096882 original size:36 final size:38
Alignment explanation
Indices: 3096820--3096893 Score: 100
Period size: 37 Copynumber: 2.0 Consensus size: 38
3096810 ATGTCTAAAG
* *
3096820 TCCAAATACATGGCCCAATTGGGCCCAAA-A-CTCAAA
1 TCCAAATACAAGGCCCAATTGAGCCCAAACACCTCAAA
3096856 TCCAACATACAAGGCCCAATT-AGCCCAAACACCTCAAA
1 TCCAA-ATACAAGGCCCAATTGAGCCCAAACACCTCAAA
3096894 CCCATTACAC
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
36 12 0.36
37 15 0.45
38 6 0.18
ACGTcount: A:0.41, C:0.34, G:0.11, T:0.15
Consensus pattern (38 bp):
TCCAAATACAAGGCCCAATTGAGCCCAAACACCTCAAA
Found at i:3097071 original size:28 final size:28
Alignment explanation
Indices: 3097018--3097071 Score: 65
Period size: 28 Copynumber: 1.9 Consensus size: 28
3097008 GCAAACCACT
* * *
3097018 ATCTCCACTTGCTTCTACCACGGCCATC
1 ATCTCCACCTGCTGCTACCACCGCCATC
3097046 ATCTCCACCTGCTGCT-CCAACCGCCA
1 ATCTCCACCTGCTGCTACC-ACCGCCA
3097072 CTGTGGAGCA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
27 2 0.09
28 20 0.91
ACGTcount: A:0.19, C:0.46, G:0.11, T:0.24
Consensus pattern (28 bp):
ATCTCCACCTGCTGCTACCACCGCCATC
Found at i:3097494 original size:15 final size:15
Alignment explanation
Indices: 3097474--3097566 Score: 59
Period size: 16 Copynumber: 6.3 Consensus size: 15
3097464 TGATTTTATA
*
3097474 AATATTATTAGTAAT
1 AATATTATTAATAAT
3097489 AATATTATTAATAAT
1 AATATTATTAATAAT
* *
3097504 CATAATAATTAATAAT
1 AAT-ATTATTAATAAT
* *
3097520 AGTA--ATAAAT-AT
1 AATATTATTAATAAT
* * *
3097532 -TTATAATTAATATT
1 AATATTATTAATAAT
*
3097546 AATATTAATAAATAAT
1 AATATT-ATTAATAAT
3097562 AATAT
1 AATAT
3097567 CAACCAATAA
Statistics
Matches: 59, Mismatches: 13, Indels: 11
0.71 0.16 0.13
Matches are distributed among these distances:
11 2 0.03
12 2 0.03
13 10 0.17
14 1 0.02
15 20 0.34
16 24 0.41
ACGTcount: A:0.54, C:0.01, G:0.02, T:0.43
Consensus pattern (15 bp):
AATATTATTAATAAT
Found at i:3097527 original size:19 final size:19
Alignment explanation
Indices: 3097485--3097565 Score: 69
Period size: 19 Copynumber: 4.3 Consensus size: 19
3097475 ATATTATTAG
*
3097485 TAATAAT-ATTATTAATAA
1 TAATAATAATTAATAATAA
* *
3097503 TCATAATAATTAATAATAG
1 TAATAATAATTAATAATAA
*
3097522 TAATAA-ATATTTATAATTAA
1 TAATAATA-ATTAATAA-TAA
*
3097542 TATTAAT-ATTAATAAATAA
1 TAATAATAATTAAT-AATAA
3097561 TAATA
1 TAATA
3097566 TCAACCAATA
Statistics
Matches: 49, Mismatches: 9, Indels: 9
0.73 0.13 0.13
Matches are distributed among these distances:
18 7 0.14
19 33 0.67
20 9 0.18
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.42
Consensus pattern (19 bp):
TAATAATAATTAATAATAA
Found at i:3097554 original size:12 final size:12
Alignment explanation
Indices: 3097474--3097566 Score: 66
Period size: 12 Copynumber: 7.7 Consensus size: 12
3097464 TGATTTTATA
* *
3097474 AATATTATTAGT
1 AATAATATTAAT
*
3097486 AATAATATTATT
1 AATAATATTAAT
3097498 AATAATCA-TAAT
1 AATAAT-ATTAAT
* *
3097510 AATTAATAATAGT
1 AA-TAATATTAAT
*
3097523 AATAAATATTTAT
1 AAT-AATATTAAT
3097536 AATTAATATTAAT
1 AA-TAATATTAAT
*
3097549 ATTAATA--AAT
1 AATAATATTAAT
3097559 AATAATAT
1 AATAATAT
3097567 CAACCAATAA
Statistics
Matches: 65, Mismatches: 10, Indels: 13
0.74 0.11 0.15
Matches are distributed among these distances:
10 9 0.14
12 28 0.43
13 27 0.42
14 1 0.02
ACGTcount: A:0.54, C:0.01, G:0.02, T:0.43
Consensus pattern (12 bp):
AATAATATTAAT
Found at i:3097579 original size:3 final size:3
Alignment explanation
Indices: 3097485--3097565 Score: 54
Period size: 3 Copynumber: 25.7 Consensus size: 3
3097475 ATATTATTAG
* * * * *
3097485 TAA TAA TAT TAT TAA TAA TCA TAA TAA TTAA TAA TAG TAA TAAA TAT
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA -TAA TAA TAA TAA T-AA TAA
* * *
3097532 TTA TAA TTAA TAT TAA TAT TAA TAAA TAA TAA TA
1 TAA TAA -TAA TAA TAA TAA TAA T-AA TAA TAA TA
3097566 TCAACCAATA
Statistics
Matches: 60, Mismatches: 14, Indels: 8
0.73 0.17 0.10
Matches are distributed among these distances:
3 48 0.80
4 12 0.20
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.42
Consensus pattern (3 bp):
TAA
Found at i:3098608 original size:28 final size:29
Alignment explanation
Indices: 3098578--3098662 Score: 109
Period size: 29 Copynumber: 2.9 Consensus size: 29
3098568 AACAGTCCAG
*
3098578 AAATTATATTTTGACCCCAAAATTTTAGA
1 AAATTACATTTTGACCCCAAAATTTTAGA
*
3098607 AAATTACATTTTGACCCCAAAATTTCCA-A
1 AAATTACATTTTGACCCCAAAATTT-TAGA
* *
3098636 AAATTACCATTTTTACCCCTAAATTTT
1 AAATTA-CATTTTGACCCCAAAATTTT
3098663 CCAAAATCCC
Statistics
Matches: 49, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
29 31 0.63
30 18 0.37
ACGTcount: A:0.39, C:0.20, G:0.04, T:0.38
Consensus pattern (29 bp):
AAATTACATTTTGACCCCAAAATTTTAGA
Found at i:3098660 original size:59 final size:58
Alignment explanation
Indices: 3098585--3098885 Score: 254
Period size: 59 Copynumber: 5.1 Consensus size: 58
3098575 CAGAAATTAT
* ** * *
3098585 ATTTTGACCCCAAAATTTTAGAAAATTACATTTTGACCCCAAAATTT-CCAAAAATTACC
1 ATTTTTACCCCAAAATTTTCCAAAATTCCATTTTAACCCC--AATTTACCAAAAATTACC
* * *
3098644 ATTTTTACCCCTAAATTTTCCAAAATCCCATTTTTAACCTCAATTTCACCAAAAATTACC
1 ATTTTTACCCCAAAATTTTCCAAAATTCCA-TTTTAACCCCAATTT-ACCAAAAATTACC
* * * *
3098704 A-TTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCTCGATTTCACCAAAAATTACC
1 ATTTTTACCCCAAAATTTTCCAAAATTCCA-TTTTAACCCCAATTT-ACCAAAAATTACC
* * * **
3098763 A-TTTTACCCTC-GAACTTTCTAAAATTCCATTTTTAACCCCAATTTCACC-AAAATTATG
1 ATTTTTACCC-CAAAATTTTCCAAAATTCCA-TTTTAACCCCAATTT-ACCAAAAATTACC
* * * * *
3098821 GTTTTTACCCTC-AAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCGAAATTTACC
1 ATTTTTACCC-CAAAATTTTCCAAAATTCCA-TTTTAACCCCAATTT-ACCAAAAATTACC
3098881 ATTTT
1 ATTTT
3098886 GCCCCATAGG
Statistics
Matches: 210, Mismatches: 26, Indels: 11
0.85 0.11 0.04
Matches are distributed among these distances:
58 12 0.06
59 166 0.79
60 32 0.15
ACGTcount: A:0.34, C:0.27, G:0.03, T:0.36
Consensus pattern (58 bp):
ATTTTTACCCCAAAATTTTCCAAAATTCCATTTTAACCCCAATTTACCAAAAATTACC
Found at i:3098695 original size:29 final size:29
Alignment explanation
Indices: 3098627--3098885 Score: 124
Period size: 30 Copynumber: 8.8 Consensus size: 29
3098617 TTGACCCCAA
* * *
3098627 AATTTC-CAAAAATTACCATTTTTACCCCTA
1 AATTTCACCAAAA-TACCATTTTTA-ACCTC
* *
3098657 AATTT-TCCAAAATCCCATTTTTAACCTC
1 AATTTCACCAAAATACCATTTTTAACCTC
* *
3098685 AATTTCACCAAAAATTACCA-TTTTACCCCC
1 AATTTCACC-AAAA-TACCATTTTTAACCTC
*
3098715 AAACTTT--CCAAAATTCCATTTTTAACCTC
1 -AA-TTTCACCAAAATACCATTTTTAACCTC
* *
3098744 GATTTCACCAAAAATTACCA-TTTTACCCTC
1 AATTTCACC-AAAA-TACCATTTTTAACCTC
* * *
3098774 GAACTTT--CTAAAATTCCATTTTTAACCCC
1 -AA-TTTCACCAAAATACCATTTTTAACCTC
*** *
3098803 AATTTCACCAAAATTATGGTTTTTACCCTC
1 AATTTCACCAAAA-TACCATTTTTAACCTC
* *
3098833 AAACTTT--CCAAAATTCCATTTTTAACCCC
1 -AA-TTTCACCAAAATACCATTTTTAACCTC
* *
3098862 GATTTCACCGAAATTTACCATTTT
1 AATTTCACC-AAA-ATACCATTTT
3098886 GCCCCATAGG
Statistics
Matches: 171, Mismatches: 35, Indels: 45
0.68 0.14 0.18
Matches are distributed among these distances:
27 9 0.05
28 20 0.12
29 55 0.32
30 57 0.33
31 21 0.12
32 9 0.05
ACGTcount: A:0.33, C:0.28, G:0.02, T:0.37
Consensus pattern (29 bp):
AATTTCACCAAAATACCATTTTTAACCTC
Found at i:3098911 original size:118 final size:118
Alignment explanation
Indices: 3098662--3098914 Score: 332
Period size: 118 Copynumber: 2.1 Consensus size: 118
3098652 CCCTAAATTT
* *
3098662 TCCAAAATCCCATTTTTAACCTCAATTTCACCAAAAATTACCATTTTACCCCCAAACTTTCCAAA
1 TCCAAAATTCCATTTTTAACCCCAATTTCACCAAAAATTACCATTTTACCCCCAAACTTTCCAAA
* **
3098727 ATTCCATTTTTAACCTCGATTTCACCAAAAATTACCATTTTACCCTCGAACTT
66 ATTCCATTTTTAACCCCGATTTCACCAAAAATTACCATTTTACCCTCGAACGA
* *** *
3098780 TCTAAAATTCCATTTTTAACCCCAATTTCACC-AAAATTATGGTTTTTACCCTCAAACTTTCCAA
1 TCCAAAATTCCATTTTTAACCCCAATTTCACCAAAAATTA-CCATTTTACCCCCAAACTTTCCAA
* * * *
3098844 AATTCCATTTTTAACCCCGATTTCACCGAAATTTACCATTTTGCCC-C-ATAGGA
65 AATTCCATTTTTAACCCCGATTTCACCAAAAATTACCATTTTACCCTCGA-ACGA
3098897 TCCAAAATTACCATTTTT
1 TCCAAAATT-CCATTTTT
3098915 CCCTCGGGTA
Statistics
Matches: 117, Mismatches: 15, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
116 1 0.01
117 17 0.15
118 99 0.85
ACGTcount: A:0.32, C:0.28, G:0.04, T:0.36
Consensus pattern (118 bp):
TCCAAAATTCCATTTTTAACCCCAATTTCACCAAAAATTACCATTTTACCCCCAAACTTTCCAAA
ATTCCATTTTTAACCCCGATTTCACCAAAAATTACCATTTTACCCTCGAACGA
Found at i:3098914 original size:59 final size:59
Alignment explanation
Indices: 3098632--3098885 Score: 341
Period size: 59 Copynumber: 4.3 Consensus size: 59
3098622 CCCAAAATTT
* * *
3098632 CCAAAAATTACCATTTTTACCC-CTAAATTTTCCAAAATCCCATTTTTAACCTCAATTTCA
1 CCAAAAATTACCA-TTTTACCCTC-AAACTTTCCAAAATTCCATTTTTAACCCCAATTTCA
* * *
3098692 CCAAAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCTCGATTTCA
1 CCAAAAATTACCATTTTACCCTCAAACTTTCCAAAATTCCATTTTTAACCCCAATTTCA
* *
3098751 CCAAAAATTACCATTTTACCCTCGAACTTTCTAAAATTCCATTTTTAACCCCAATTTCA
1 CCAAAAATTACCATTTTACCCTCAAACTTTCCAAAATTCCATTTTTAACCCCAATTTCA
*** *
3098810 CC-AAAATTATGGTTTTTACCCTCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
1 CCAAAAATTA-CCATTTTACCCTCAAACTTTCCAAAATTCCATTTTTAACCCCAATTTCA
* *
3098869 CCGAAATTTACCATTTT
1 CCAAAAATTACCATTTT
3098886 GCCCCATAGG
Statistics
Matches: 173, Mismatches: 18, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
58 7 0.04
59 146 0.84
60 20 0.12
ACGTcount: A:0.33, C:0.28, G:0.02, T:0.36
Consensus pattern (59 bp):
CCAAAAATTACCATTTTACCCTCAAACTTTCCAAAATTCCATTTTTAACCCCAATTTCA
Found at i:3110985 original size:78 final size:76
Alignment explanation
Indices: 3110723--3111262 Score: 906
Period size: 76 Copynumber: 7.0 Consensus size: 76
3110713 ATCAGACCGC
* *
3110723 AGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACACGTCTTTATCTCTGAA
1 AGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCTTTATCTCTGAA
3110788 ATTGAAGTAAG
66 ATTGAAGTAAG
* *
3110799 AGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACACGTCTTTATCTCTGAA
1 AGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCTTTATCTCTGAA
3110864 ATTGAAGTAAG
66 ATTGAAGTAAG
*
3110875 AGTAAGATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCTTTATCTCTCTG
1 AGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCTTTA--TCTCTG
3110940 AAATTGAAGTAAG
64 AAATTGAAGTAAG
3110953 AGCAACG-TCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCTTTATCTCTCT
1 AGCAA-GATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCTTTA--TCTCT
3111017 GAAATTGAAGTAAG
63 GAAATTGAAGTAAG
* *
3111031 AGCAACG-TCATTTCCTATCCTCTTGAAATTGAAGTAGAG-TGGATAACACGTCTTTATCTCTGA
1 AGCAA-GATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCTTTATCTCTGA
3111094 AATTGAAGTAAG
65 AATTGAAGTAAG
3111106 AGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCTTTATCTCTGAA
1 AGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCTTTATCTCTGAA
3111171 ATTGAAGTAAG
66 ATTGAAGTAAG
* *
3111182 AGCAAGATCGTTTCCCATCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCTTTATCTCTCTG
1 AGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCTTTA--TCTCTG
3111247 AAATTGAAGTAAG
64 AAATTGAAGTAAG
3111260 AGC
1 AGC
3111263 TAGACGAAGC
Statistics
Matches: 447, Mismatches: 10, Indels: 12
0.95 0.02 0.03
Matches are distributed among these distances:
74 1 0.00
75 56 0.13
76 219 0.49
77 15 0.03
78 155 0.35
79 1 0.00
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.34
Consensus pattern (76 bp):
AGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCTTTATCTCTGAA
ATTGAAGTAAG
Found at i:3111349 original size:92 final size:92
Alignment explanation
Indices: 3111192--3111456 Score: 370
Period size: 92 Copynumber: 2.9 Consensus size: 92
3111182 AGCAAGATCG
* * *
3111192 TTTCCCATCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCTTTATCTCTCTGAAATTGAAGT
1 TTTCCTATCCTCTTGAAATTGAAGTAAAGTTGGATAACAAGTCTTTATCTCTCTGAAATTGAAGT
*
3111257 AAGAGCTAGACGAAGCATCAAACATCA
66 AAGAGCTAGATGAAGCATCAAACATCA
*
3111284 TTTCCTATCCTCTTGAAATTGAAGTAAAGTTGGATAGCAAGTCTTTATCTCTCTGAAATTGAAGT
1 TTTCCTATCCTCTTGAAATTGAAGTAAAGTTGGATAACAAGTCTTTATCTCTCTGAAATTGAAGT
*
3111349 AAGAGCTAGATAAAGCATCAAACATCA
66 AAGAGCTAGATGAAGCATCAAACATCA
* * * ** * * * *
3111376 TTTCCTGTCCTCTTGAAGTTGTAA-TAAAGTTGGGTAATGAGTCTTTATTTCTCTAAAATTGTAT
1 TTTCCTATCCTCTTGAAATTG-AAGTAAAGTTGGATAACAAGTCTTTATCTCTCTGAAATTGAAG
*
3111440 TAAGAGCAAGATGAAGC
65 TAAGAGCTAGATGAAGC
3111457 CTCGACATCA
Statistics
Matches: 155, Mismatches: 17, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
92 153 0.99
93 2 0.01
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Consensus pattern (92 bp):
TTTCCTATCCTCTTGAAATTGAAGTAAAGTTGGATAACAAGTCTTTATCTCTCTGAAATTGAAGT
AAGAGCTAGATGAAGCATCAAACATCA
Found at i:3111729 original size:5 final size:5
Alignment explanation
Indices: 3111719--3111787 Score: 57
Period size: 5 Copynumber: 12.6 Consensus size: 5
3111709 TTTACTTTGA
* * *
3111719 AATTT AATTT ATTTT AATTTT AAATTT AAATTA AATTCA AATTT AATTT
1 AATTT AATTT AATTT AA-TTT -AATTT -AATTT AATT-T AATTT AATTT
3111768 GAATTT AATTT AAATTT AAT
1 -AATTT AATTT -AATTT AAT
3111788 ATTATTATAA
Statistics
Matches: 55, Mismatches: 4, Indels: 10
0.80 0.06 0.14
Matches are distributed among these distances:
5 27 0.49
6 26 0.47
7 2 0.04
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.54
Consensus pattern (5 bp):
AATTT
Found at i:3111752 original size:17 final size:16
Alignment explanation
Indices: 3111719--3111783 Score: 53
Period size: 17 Copynumber: 4.0 Consensus size: 16
3111709 TTTACTTTGA
**
3111719 AATTT-AATTTATTTT
1 AATTTAAATTTAAATT
3111734 AATTTTAAATTTAAATT
1 AA-TTTAAATTTAAATT
* *
3111751 AAATTCAAATTTAATTT
1 -AATTTAAATTTAAATT
3111768 GAATTT-AATTTAAATT
1 -AATTTAAATTTAAATT
3111784 TAATATTATT
Statistics
Matches: 40, Mismatches: 7, Indels: 5
0.77 0.13 0.10
Matches are distributed among these distances:
15 2 0.05
16 12 0.30
17 24 0.60
18 2 0.05
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.54
Consensus pattern (16 bp):
AATTTAAATTTAAATT
Found at i:3111784 original size:11 final size:11
Alignment explanation
Indices: 3111719--3111787 Score: 77
Period size: 11 Copynumber: 6.3 Consensus size: 11
3111709 TTTACTTTGA
3111719 AATTT-AATTT
1 AATTTAAATTT
* *
3111729 ATTTTAATTTT
1 AATTTAAATTT
*
3111740 AAATTTAAATTA
1 -AATTTAAATTT
*
3111752 AATTCAAATTT
1 AATTTAAATTT
*
3111763 AATTTGAATTT
1 AATTTAAATTT
3111774 AATTTAAATTT
1 AATTTAAATTT
3111785 AAT
1 AAT
3111788 ATTATTATAA
Statistics
Matches: 47, Mismatches: 10, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
10 4 0.09
11 35 0.74
12 8 0.17
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.54
Consensus pattern (11 bp):
AATTTAAATTT
Found at i:3111785 original size:6 final size:6
Alignment explanation
Indices: 3111718--3111786 Score: 67
Period size: 6 Copynumber: 12.3 Consensus size: 6
3111708 TTTTACTTTG
* * *
3111718 AAATTT -AATTT -ATTTT AATTTT AAATTT AAA-TT AAATTC AAATTT
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT
*
3111763 -AATTT GAATTT -AATTT AAATTT AA
1 AAATTT AAATTT AAATTT AAATTT AA
3111787 TATTATTATA
Statistics
Matches: 55, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
5 24 0.44
6 31 0.56
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.52
Consensus pattern (6 bp):
AAATTT
Found at i:3111802 original size:22 final size:21
Alignment explanation
Indices: 3111719--3111803 Score: 73
Period size: 22 Copynumber: 3.9 Consensus size: 21
3111709 TTTACTTTGA
** *
3111719 AATTTAATTTATTTTAATTTT
1 AATTTAATTTAAATTAAATTT
*
3111740 AAATTTAAATTAAATTCAAATTT
1 -AATTTAATTTAAATT-AAATTT
*
3111763 AATTTGAATTTAATTTAAATTT
1 AATTT-AATTTAAATTAAATTT
3111785 AATATT-ATTATAAATTAAA
1 AAT-TTAATT-TAAATTAAA
3111804 AAAAGAAAGT
Statistics
Matches: 52, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
21 3 0.06
22 34 0.65
23 15 0.29
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.52
Consensus pattern (21 bp):
AATTTAATTTAAATTAAATTT
Found at i:3112506 original size:15 final size:15
Alignment explanation
Indices: 3112483--3112574 Score: 50
Period size: 13 Copynumber: 6.3 Consensus size: 15
3112473 TGATTTTATA
*
3112483 AATACTATTAGTAAT
1 AATACTATTAATAAT
*
3112498 AATATTATTAATAAT
1 AATACTATTAATAAT
*
3112513 CATA--A-TAATTAAT
1 AATACTATTAA-TAAT
* *
3112526 AATACTAATAAATATT
1 AATACT-ATTAATAAT
* *
3112542 TATA--ATTAATACT
1 AATACTATTAATAAT
*
3112555 AATACTAATAAATAAT
1 AATACT-ATTAATAAT
3112571 AATA
1 AATA
3112575 TCAACCAATA
Statistics
Matches: 57, Mismatches: 12, Indels: 15
0.68 0.14 0.18
Matches are distributed among these distances:
12 3 0.05
13 18 0.32
15 16 0.28
16 18 0.32
17 2 0.04
ACGTcount: A:0.54, C:0.05, G:0.01, T:0.39
Consensus pattern (15 bp):
AATACTATTAATAAT
Found at i:3112534 original size:16 final size:16
Alignment explanation
Indices: 3112506--3112574 Score: 65
Period size: 16 Copynumber: 4.5 Consensus size: 16
3112496 ATAATATTAT
*
3112506 TAATAAT-CATAATAAT
1 TAATAATAC-TAATAAA
3112522 TAATAATACTAATAAA
1 TAATAATACTAATAAA
* *
3112538 T-AT-TTA-TAATTAA
1 TAATAATACTAATAAA
*
3112551 TACTAATACTAATAAA
1 TAATAATACTAATAAA
3112567 TAATAATA
1 TAATAATA
3112575 TCAACCAATA
Statistics
Matches: 42, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
13 7 0.17
14 3 0.07
15 4 0.10
16 27 0.64
17 1 0.02
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.38
Consensus pattern (16 bp):
TAATAATACTAATAAA
Found at i:3112536 original size:19 final size:19
Alignment explanation
Indices: 3112494--3112571 Score: 59
Period size: 19 Copynumber: 3.9 Consensus size: 19
3112484 ATACTATTAG
* *
3112494 TAATAAT-ATTATTAATAA
1 TAATAATAATTAATAATAC
*
3112512 TCATAATAATTAATAATAC
1 TAATAATAATTAATAATAC
*
3112531 TAATAAATATTTATAATTAATAC
1 TAAT-AATA-AT-TAA-TAATAC
* *
3112554 TAATACTAATAAATAATA
1 TAATAATAATTAATAATA
3112572 ATATCAACCA
Statistics
Matches: 47, Mismatches: 8, Indels: 9
0.73 0.12 0.14
Matches are distributed among these distances:
18 6 0.13
19 17 0.36
20 6 0.13
21 2 0.04
22 6 0.13
23 10 0.21
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.40
Consensus pattern (19 bp):
TAATAATAATTAATAATAC
Found at i:3112586 original size:29 final size:29
Alignment explanation
Indices: 3112523--3112587 Score: 69
Period size: 29 Copynumber: 2.2 Consensus size: 29
3112513 CATAATAATT
* * * *
3112523 AATAATACTAATAAATATTTATAATTAAT
1 AATAATACTAATAAATAATAATAATCAAC
*
3112552 ACTAATACTAATAAATAATAAT-ATCAACC
1 AATAATACTAATAAATAATAATAATCAA-C
3112581 AATAATA
1 AATAATA
3112588 AAAAAAAGAG
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
28 4 0.14
29 25 0.86
ACGTcount: A:0.57, C:0.09, G:0.00, T:0.34
Consensus pattern (29 bp):
AATAATACTAATAAATAATAATAATCAAC
Found at i:3112588 original size:3 final size:3
Alignment explanation
Indices: 3112494--3112574 Score: 54
Period size: 3 Copynumber: 25.7 Consensus size: 3
3112484 ATACTATTAG
* * * * *
3112494 TAA TAA TAT TAT TAA TAA TCA TAA TAA TTAA TAA TAC TAA TAAA TAT
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA -TAA TAA TAA TAA T-AA TAA
* * *
3112541 TTA TAA TTAA TAC TAA TAC TAA TAAA TAA TAA TA
1 TAA TAA -TAA TAA TAA TAA TAA T-AA TAA TAA TA
3112575 TCAACCAATA
Statistics
Matches: 60, Mismatches: 14, Indels: 8
0.73 0.17 0.10
Matches are distributed among these distances:
3 48 0.80
4 12 0.20
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.40
Consensus pattern (3 bp):
TAA
Found at i:3113639 original size:30 final size:28
Alignment explanation
Indices: 3113606--3113893 Score: 164
Period size: 29 Copynumber: 9.9 Consensus size: 28
3113596 TTTGACCCCA
3113606 AAATTTCCAAAAATTACCATTTTTACCCT
1 AAATTTCC-AAAATTACCATTTTTACCCT
*
3113635 AAAATTTTCCAAAA-TCCCATTTTTAACCC-
1 -AAA-TTTCCAAAATTACCATTTTT-ACCCT
** *
3113664 CGATTTCATCAAAATTACCA-TTTTACCCCC
1 AAATTTC--CAAAATTACCATTTTTA-CCCT
3113694 AAACTTTCCAAAATT-CCATTTTTAACCCT
1 AAA-TTTCCAAAATTACCATTTTT-ACCCT
*
3113723 -AATTTCACTAAAAATTACCA-TTTTACCCCC
1 AAATTTC-C--AAAATTACCATTTTTA-CCCT
* * *
3113753 GAACTTCCAAAATT-CCATTTTTAACCT
1 AAATTTCCAAAATTACCATTTTTACCCT
* *
3113780 CGATTTTACCAAAATTACCATTTTTACCCT
1 -AAATTT-CCAAAATTACCATTTTTACCCT
*
3113810 CGAACTTTCCAAAATT-CCATTTTTAACCC-
1 --AAATTTCCAAAATTACCATTTTT-ACCCT
** *
3113839 CGATTTCACCAAAACTACCATTTTTACCCT
1 AAATTT--CCAAAATTACCATTTTTACCCT
* *
3113869 CGAACTTTCCAAAATT-CTATTTTTA
1 --AAATTTCCAAAATTACCATTTTTA
3113894 ACCCCGATTT
Statistics
Matches: 204, Mismatches: 26, Indels: 57
0.71 0.09 0.20
Matches are distributed among these distances:
27 16 0.08
28 23 0.11
29 71 0.35
30 70 0.34
31 21 0.10
32 3 0.01
ACGTcount: A:0.33, C:0.28, G:0.02, T:0.36
Consensus pattern (28 bp):
AAATTTCCAAAATTACCATTTTTACCCT
Found at i:3113702 original size:58 final size:59
Alignment explanation
Indices: 3113615--3113930 Score: 415
Period size: 59 Copynumber: 5.4 Consensus size: 59
3113605 AAAATTTCCA
*** * *
3113615 AAAATTACCATTTTTACCCTAAAATTTTCCAAAATCCCATTTTTAACCCCGATTTCATC
1 AAAATTACCATTTTTACCCCCGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCATC
* ** *
3113674 AAAATTACCA-TTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCCTAATTTCACTA
1 AAAATTACCATTTTTACCCCCGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA-TC
* * *
3113733 AAAATTACCA-TTTTACCCCCGAAC-TTCCAAAATTCCATTTTTAACCTCGATTTTACC
1 AAAATTACCATTTTTACCCCCGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCATC
* *
3113790 AAAATTACCATTTTTACCCTCGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACC
1 AAAATTACCATTTTTACCCCCGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCATC
* * *
3113849 AAAACTACCATTTTTACCCTCGAACTTTCCAAAATTCTATTTTTAACCCCGATTTCATC
1 AAAATTACCATTTTTACCCCCGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCATC
* *
3113908 GAAATTTACCA-TTTTGCCCCCGA
1 -AAAATTACCATTTTTACCCCCGA
3113931 GGATCCAAAA
Statistics
Matches: 229, Mismatches: 24, Indels: 8
0.88 0.09 0.03
Matches are distributed among these distances:
57 10 0.04
58 80 0.35
59 131 0.57
60 8 0.03
ACGTcount: A:0.32, C:0.29, G:0.03, T:0.36
Consensus pattern (59 bp):
AAAATTACCATTTTTACCCCCGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCATC
Found at i:3113913 original size:29 final size:28
Alignment explanation
Indices: 3113640--3113905 Score: 208
Period size: 29 Copynumber: 9.2 Consensus size: 28
3113630 ACCCTAAAAT
*
3113640 TTTC-CAAAATCCCATTTTTAACCCCGA
1 TTTCACAAAATTCCATTTTTAACCCCGA
* *
3113667 TTTCATCAAAATTACCA-TTTTACCCCCAAA
1 TTTCA-CAAAATT-CCATTTTTAACCCC-GA
**
3113697 CTTTC-CAAAATTCCATTTTTAACCCTAA
1 -TTTCACAAAATTCCATTTTTAACCCCGA
*
3113725 TTTCACTAAAAATTACCA-TTTTACCCCCGAA
1 TTTCAC--AAAATT-CCATTTTTAACCCCG-A
* *
3113756 CTTC-CAAAATTCCATTTTTAACCTCGA
1 TTTCACAAAATTCCATTTTTAACCCCGA
*
3113783 TTTTACCAAAATTACCATTTTT-ACCCTCGAA
1 TTTCA-CAAAATT-CCATTTTTAACCC-CG-A
3113814 CTTTC-CAAAATTCCATTTTTAACCCCGA
1 -TTTCACAAAATTCCATTTTTAACCCCGA
*
3113842 TTTCACCAAAACTACCATTTTT-ACCCTCGAA
1 TTTCA-CAAAA-TTCCATTTTTAACCC-CG-A
*
3113873 CTTTC-CAAAATTCTATTTTTAACCCCGA
1 -TTTCACAAAATTCCATTTTTAACCCCGA
3113901 TTTCA
1 TTTCA
3113906 TCGAAATTTA
Statistics
Matches: 194, Mismatches: 18, Indels: 53
0.73 0.07 0.20
Matches are distributed among these distances:
27 22 0.11
28 23 0.12
29 69 0.36
30 60 0.31
31 13 0.07
32 7 0.04
ACGTcount: A:0.32, C:0.30, G:0.03, T:0.36
Consensus pattern (28 bp):
TTTCACAAAATTCCATTTTTAACCCCGA
Found at i:3113963 original size:27 final size:28
Alignment explanation
Indices: 3113913--3113967 Score: 94
Period size: 28 Copynumber: 2.0 Consensus size: 28
3113903 TCATCGAAAT
3113913 TTACCATTTTGCCCCCGAGGATCCAAAA
1 TTACCATTTTGCCCCCGAGGATCCAAAA
*
3113941 TTACCATTTTGCCCCCG-GTATCCAAAA
1 TTACCATTTTGCCCCCGAGGATCCAAAA
3113968 GTCTCATTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
27 9 0.35
28 17 0.65
ACGTcount: A:0.27, C:0.33, G:0.13, T:0.27
Consensus pattern (28 bp):
TTACCATTTTGCCCCCGAGGATCCAAAA
Found at i:3113975 original size:27 final size:28
Alignment explanation
Indices: 3113914--3113977 Score: 87
Period size: 27 Copynumber: 2.3 Consensus size: 28
3113904 CATCGAAATT
*
3113914 TACCATTTTGCCCCCGAGGATCCAAAAT
1 TACCATTTTGCCCCCGAGGATCCAAAAG
*
3113942 TACCATTTTGCCCCCG-GTATCCAAAAG
1 TACCATTTTGCCCCCGAGGATCCAAAAG
3113969 T-CTCATTTT
1 TAC-CATTTT
3113978 CAACCTCGAT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
26 1 0.03
27 16 0.48
28 16 0.48
ACGTcount: A:0.25, C:0.31, G:0.12, T:0.31
Consensus pattern (28 bp):
TACCATTTTGCCCCCGAGGATCCAAAAG
Found at i:3115367 original size:23 final size:24
Alignment explanation
Indices: 3115336--3115383 Score: 64
Period size: 26 Copynumber: 2.0 Consensus size: 24
3115326 TGTAAATAAA
3115336 AAAATATCTC-TAGAG-ATTTTTT
1 AAAATATCTCTTAGAGAATTTTTT
3115358 AAAATAATCTCTTTAGAGAATTTTTT
1 AAAAT-ATCTC-TTAGAGAATTTTTT
3115384 TCTCTACAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 5 0.23
23 5 0.23
25 5 0.23
26 7 0.32
ACGTcount: A:0.38, C:0.08, G:0.08, T:0.46
Consensus pattern (24 bp):
AAAATATCTCTTAGAGAATTTTTT
Found at i:3115374 original size:25 final size:26
Alignment explanation
Indices: 3115332--3115383 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 26
3115322 AAGTTGTAAA
3115332 TAAAAAAATATCTCTAGAG-ATTTTT
1 TAAAAAAATATCTCTAGAGAATTTTT
* * *
3115357 TAAAATAATCTCTTTAGAGAATTTTT
1 TAAAAAAATATCTCTAGAGAATTTTT
3115383 T
1 T
3115384 TCTCTACAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
25 16 0.70
26 7 0.30
ACGTcount: A:0.40, C:0.08, G:0.08, T:0.44
Consensus pattern (26 bp):
TAAAAAAATATCTCTAGAGAATTTTT
Found at i:3115620 original size:37 final size:35
Alignment explanation
Indices: 3115574--3115642 Score: 86
Period size: 37 Copynumber: 1.9 Consensus size: 35
3115564 ACTTTAATAA
*
3115574 TAAATTAATA-AAATACTATTAAAATAAGTATTAAAT
1 TAAATTAATATAAA-ACTATTAAAAGAA-TATTAAAT
*
3115610 TAAATTTAATATTAAACTATTAAAAGAATATTA
1 TAAA-TTAATATAAAACTATTAAAAGAATATTA
3115643 TTTTTGGAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
36 9 0.31
37 18 0.62
38 2 0.07
ACGTcount: A:0.57, C:0.03, G:0.03, T:0.38
Consensus pattern (35 bp):
TAAATTAATATAAAACTATTAAAAGAATATTAAAT
Found at i:3115624 original size:68 final size:69
Alignment explanation
Indices: 3115490--3115624 Score: 191
Period size: 68 Copynumber: 2.0 Consensus size: 69
3115480 TAATTAAACT
* * * * *
3115490 TAATCACTTTAATATTAAATTAACATAATATTTATCAAGATAAATATTAGATTAAATTTAATATT
1 TAATCACTTTAATAATAAATTAACAAAATATCTATCAAAATAAATATTAAATTAAATTTAATATT
3115555 AAGA
66 AAGA
* * *
3115559 TAATCACTTTAATAATAAATTAATAAAATA-CTATTAAAATAAGTATTAAATTAAATTTAATATT
1 TAATCACTTTAATAATAAATTAACAAAATATCTATCAAAATAAATATTAAATTAAATTTAATATT
3115623 AA
66 AA
3115625 ACTATTAAAA
Statistics
Matches: 58, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
68 31 0.53
69 27 0.47
ACGTcount: A:0.52, C:0.05, G:0.03, T:0.40
Consensus pattern (69 bp):
TAATCACTTTAATAATAAATTAACAAAATATCTATCAAAATAAATATTAAATTAAATTTAATATT
AAGA
Found at i:3120560 original size:108 final size:108
Alignment explanation
Indices: 3120330--3120566 Score: 293
Period size: 108 Copynumber: 2.2 Consensus size: 108
3120320 ATAAATAGTA
* * * *
3120330 GCAAATA-CAGTTGGTTTATCCAATTAGAGTTGGGTTCACTATTTAATTCATCAGTTATCTGAAT
1 GCAAATATC-GTTGGTTTATCCAACTAGAGCTGGGCTCACTACTTAATTCATCAGTTATCTGAAT
*
3120394 AGTGCTTGACACATATTCATCGGTTTATCCGACAGGCGCTGGGT
65 AGTGCTTGACACATATTCATCGGTTTATCCGACAGGCGCTGGGC
* * *
3120438 TCAAATATCGTTGGTTTATCCAACTAGAGCTGGGCTCACTACTTAATTCGTCAGTTTATCTGACT
1 GCAAATATCGTTGGTTTATCCAACTAGAGCTGGGCTCACTACTTAATTCATCAG-TTATCTGAAT
** *
3120503 AGTG-TTGGACACATATTTGTCGGTTTATCCGACTA-GCGTTGGGC
65 AGTGCTT-GACACATATTCATCGGTTTATCCGAC-AGGCGCTGGGC
* *
3120547 GCAAA-CTCTTTGGTTTATCC
1 GCAAATATCGTTGGTTTATCC
3120567 GTTAGGCATC
Statistics
Matches: 111, Mismatches: 14, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
108 61 0.55
109 49 0.44
110 1 0.01
ACGTcount: A:0.24, C:0.19, G:0.21, T:0.36
Consensus pattern (108 bp):
GCAAATATCGTTGGTTTATCCAACTAGAGCTGGGCTCACTACTTAATTCATCAGTTATCTGAATA
GTGCTTGACACATATTCATCGGTTTATCCGACAGGCGCTGGGC
Found at i:3126271 original size:42 final size:42
Alignment explanation
Indices: 3126222--3126442 Score: 345
Period size: 42 Copynumber: 5.2 Consensus size: 42
3126212 GGTATAAGTA
* * * *
3126222 TTCCTTTAAACATAATCTCATTCTCATCCCAAGACATGAGTC
1 TTCCTTTAAACATATTCTCATGCTCATTCCGAGACATGAGTC
* *
3126264 TTCCTTTAAACATAATCTCATCCTCA-TCACGAGACATGAGTC
1 TTCCTTTAAACATATTCTCATGCTCATTC-CGAGACATGAGTC
3126306 TTCCTTTTTAAACATATTCTCATGCTCATTCCGAGACATGAGTC
1 TTCC--TTTAAACATATTCTCATGCTCATTCCGAGACATGAGTC
3126350 TTCCTTTAAACATATTCTCATGCTCATTCCGAGACATGAGTC
1 TTCCTTTAAACATATTCTCATGCTCATTCCGAGACATGAGTC
3126392 TTCCTTTAAACATATTCTCATGCTCATTCCGAGACATGAGTC
1 TTCCTTTAAACATATTCTCATGCTCATTCCGAGACATGAGTC
3126434 TTCCATTTA
1 TTCC-TTTA
3126443 TAGGTCAAGT
Statistics
Matches: 169, Mismatches: 5, Indels: 9
0.92 0.03 0.05
Matches are distributed among these distances:
41 1 0.01
42 125 0.74
43 4 0.02
44 37 0.22
45 2 0.01
ACGTcount: A:0.28, C:0.27, G:0.10, T:0.36
Consensus pattern (42 bp):
TTCCTTTAAACATATTCTCATGCTCATTCCGAGACATGAGTC
Found at i:3126328 original size:86 final size:84
Alignment explanation
Indices: 3126222--3126442 Score: 345
Period size: 86 Copynumber: 2.6 Consensus size: 84
3126212 GGTATAAGTA
* * * *
3126222 TTCCTTTAAACATAATCTCATTCTCATCCCAAGACATGAGTCTTCCTTTAAACATAATCTCATCC
1 TTCCTTTAAACATATTCTCATGCTCATTCCGAGACATGAGTCTTCCTTTAAACATAATCTCATCC
3126287 TCA-TCACGAGACATGAGTC
66 TCATTC-CGAGACATGAGTC
*
3126306 TTCCTTTTTAAACATATTCTCATGCTCATTCCGAGACATGAGTCTTCCTTTAAACATATTCTCAT
1 TTCC--TTTAAACATATTCTCATGCTCATTCCGAGACATGAGTCTTCCTTTAAACATAATCTCAT
*
3126371 GCTCATTCCGAGACATGAGTC
64 CCTCATTCCGAGACATGAGTC
3126392 TTCCTTTAAACATATTCTCATGCTCATTCCGAGACATGAGTCTTCCATTTA
1 TTCCTTTAAACATATTCTCATGCTCATTCCGAGACATGAGTCTTCC-TTTA
3126443 TAGGTCAAGT
Statistics
Matches: 127, Mismatches: 6, Indels: 7
0.91 0.04 0.05
Matches are distributed among these distances:
84 46 0.36
85 4 0.03
86 75 0.59
87 2 0.02
ACGTcount: A:0.28, C:0.27, G:0.10, T:0.36
Consensus pattern (84 bp):
TTCCTTTAAACATATTCTCATGCTCATTCCGAGACATGAGTCTTCCTTTAAACATAATCTCATCC
TCATTCCGAGACATGAGTC
Found at i:3126362 original size:128 final size:125
Alignment explanation
Indices: 3126177--3126437 Score: 371
Period size: 128 Copynumber: 2.1 Consensus size: 125
3126167 TAGGTTCATA
* **
3126177 AGTCTTCCTTTTTAAACAATCTTATGCTCTACCGAGGTATAAGTATTCCTTTAAACATAATCTCA
1 AGTCTTCCTTTTTAAACAATCTCATGCTCTACCGAGACATAAGTATTCCTTTAAACATAATCTCA
*
3126242 TTCTCATCCCAAGACATGAGTCTTCCTTTAAACATAATCTCATCCTCA-TCACGAGACATG
66 TGCTCATCCCAAGACATGAGTCTTCCTTTAAACATAATCTCATCCTCATTC-CGAGACATG
* * * *
3126302 AGTCTTCCTTTTTAAACATATTCTCATGCTCATTCCGAGACATGAGTCTTCCTTTAAACATATTC
1 AGTCTTCCTTTTTAAACA-A-TCTCATGCTC-TACCGAGACATAAGTATTCCTTTAAACATAATC
* * * *
3126367 TCATGCTCATTCCGAGACATGAGTCTTCCTTTAAACATATTCTCATGCTCATTCCGAGACATG
63 TCATGCTCATCCCAAGACATGAGTCTTCCTTTAAACATAATCTCATCCTCATTCCGAGACATG
3126430 AGTCTTCC
1 AGTCTTCC
3126438 ATTTATAGGT
Statistics
Matches: 120, Mismatches: 12, Indels: 5
0.88 0.09 0.04
Matches are distributed among these distances:
125 18 0.15
126 1 0.01
127 9 0.08
128 90 0.75
129 2 0.02
ACGTcount: A:0.28, C:0.26, G:0.11, T:0.36
Consensus pattern (125 bp):
AGTCTTCCTTTTTAAACAATCTCATGCTCTACCGAGACATAAGTATTCCTTTAAACATAATCTCA
TGCTCATCCCAAGACATGAGTCTTCCTTTAAACATAATCTCATCCTCATTCCGAGACATG
Found at i:3130652 original size:17 final size:17
Alignment explanation
Indices: 3130630--3130664 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
3130620 CAAAAGTCTC
3130630 TGTACTCTTTTGAAAGG
1 TGTACTCTTTTGAAAGG
3130647 TGTACTCTTTTGAAAGG
1 TGTACTCTTTTGAAAGG
3130664 T
1 T
3130665 AAAATTTAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.23, C:0.11, G:0.23, T:0.43
Consensus pattern (17 bp):
TGTACTCTTTTGAAAGG
Found at i:3131517 original size:23 final size:23
Alignment explanation
Indices: 3131459--3131518 Score: 59
Period size: 23 Copynumber: 2.6 Consensus size: 23
3131449 TTTTCATATT
* *
3131459 TTTATTTTTTCAAAAAAAAATAG
1 TTTATTTTTTTAAAAAAAAATAA
* **
3131482 GTTATTTGCTTAAAATAAAAA-AA
1 TTTATTTTTTTAAAA-AAAAATAA
3131505 TTTATTTTTTTAAA
1 TTTATTTTTTTAAA
3131519 TGTATGTACT
Statistics
Matches: 28, Mismatches: 8, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
23 23 0.82
24 5 0.18
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.47
Consensus pattern (23 bp):
TTTATTTTTTTAAAAAAAAATAA
Found at i:3131709 original size:13 final size:12
Alignment explanation
Indices: 3131676--3131709 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
3131666 ACCAATTTTA
3131676 AATTTTTTTAAT
1 AATTTTTTTAAT
*
3131688 ATTTTTTTTAAT
1 AATTTTTTTAAT
3131700 AATTTATTTT
1 AATTT-TTTT
3131710 CTTTGAACCA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
12 15 0.79
13 4 0.21
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (12 bp):
AATTTTTTTAAT
Found at i:3136400 original size:23 final size:21
Alignment explanation
Indices: 3136386--3136428 Score: 70
Period size: 20 Copynumber: 2.1 Consensus size: 21
3136376 ACACCATCTT
3136386 TATCCAACCCAACACACCA-A
1 TATCCAACCCAACACACCATA
*
3136406 TATCCAACCCTACACACCATA
1 TATCCAACCCAACACACCATA
3136427 TA
1 TA
3136429 GTGTCGGTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 18 0.86
21 3 0.14
ACGTcount: A:0.42, C:0.42, G:0.00, T:0.16
Consensus pattern (21 bp):
TATCCAACCCAACACACCATA
Found at i:3136822 original size:12 final size:12
Alignment explanation
Indices: 3136807--3136834 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
3136797 CCCTTGTGTA
3136807 ACACACAGTCTG
1 ACACACAGTCTG
3136819 ACACACAGTCTG
1 ACACACAGTCTG
3136831 ACAC
1 ACAC
3136835 CCACCCGTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.36, C:0.36, G:0.14, T:0.14
Consensus pattern (12 bp):
ACACACAGTCTG
Found at i:3141900 original size:17 final size:17
Alignment explanation
Indices: 3141880--3141939 Score: 68
Period size: 17 Copynumber: 3.4 Consensus size: 17
3141870 TCAACATGAT
3141880 TAAATAATTCAATAATA
1 TAAATAATTCAATAATA
* *
3141897 TAAATAATACAA-AATG
1 TAAATAATTCAATAATA
3141913 TGAAATTTAATTCAATAATA
1 T-AAA--TAATTCAATAATA
3141933 TAAATAA
1 TAAATAA
3141940 CAGACATAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
16 4 0.11
17 17 0.49
19 10 0.29
20 4 0.11
ACGTcount: A:0.58, C:0.05, G:0.03, T:0.33
Consensus pattern (17 bp):
TAAATAATTCAATAATA
Found at i:3143536 original size:311 final size:311
Alignment explanation
Indices: 3142973--3143597 Score: 1250
Period size: 311 Copynumber: 2.0 Consensus size: 311
3142963 CACTTAATAA
3142973 CCTCTATATTGCCAACAACTTCTTGACCCAATGACAAGAGCATTATGTTGGAGGCATGAGCGCTT
1 CCTCTATATTGCCAACAACTTCTTGACCCAATGACAAGAGCATTATGTTGGAGGCATGAGCGCTT
3143038 GGGTTCAATCCCAAGCAACCCCATTCCCCTCCCTCAATTATAAAAAAAACCCTCTATATCACGGT
66 GGGTTCAATCCCAAGCAACCCCATTCCCCTCCCTCAATTATAAAAAAAACCCTCTATATCACGGT
3143103 TTAAACTATAATTACGAAAGAGATGGTGAGTTTTGTGGAGTTGGTTGGGGTGTATCTTGTGAAGT
131 TTAAACTATAATTACGAAAGAGATGGTGAGTTTTGTGGAGTTGGTTGGGGTGTATCTTGTGAAGT
3143168 TTGGAGCGGTTAATGATCGAGATAGGATCCTAAATCTAGCCCCGTGACTGTTTGACCAACATTTA
196 TTGGAGCGGTTAATGATCGAGATAGGATCCTAAATCTAGCCCCGTGACTGTTTGACCAACATTTA
3143233 TTCTCGATGGTGCCTTTTGTAAGGGATAAAATACATGTGTTTAATCTTGTC
261 TTCTCGATGGTGCCTTTTGTAAGGGATAAAATACATGTGTTTAATCTTGTC
3143284 CCTCTATATTGCCAACAACTTCTTGACCCAATGACAAGAGCATTATGTTGGAGGCATGAGCGCTT
1 CCTCTATATTGCCAACAACTTCTTGACCCAATGACAAGAGCATTATGTTGGAGGCATGAGCGCTT
3143349 GGGTTCAATCCCAAGCAACCCCATTCCCCTCCCTCAATTATAAAAAAAACCCTCTATATCACGGT
66 GGGTTCAATCCCAAGCAACCCCATTCCCCTCCCTCAATTATAAAAAAAACCCTCTATATCACGGT
3143414 TTAAACTATAATTACGAAAGAGATGGTGAGTTTTGTGGAGTTGGTTGGGGTGTATCTTGTGAAGT
131 TTAAACTATAATTACGAAAGAGATGGTGAGTTTTGTGGAGTTGGTTGGGGTGTATCTTGTGAAGT
3143479 TTGGAGCGGTTAATGATCGAGATAGGATCCTAAATCTAGCCCCGTGACTGTTTGACCAACATTTA
196 TTGGAGCGGTTAATGATCGAGATAGGATCCTAAATCTAGCCCCGTGACTGTTTGACCAACATTTA
3143544 TTCTCGATGGTGCCTTTTGTAAGGGATAAAATACATGTGTTTAATCTTGTC
261 TTCTCGATGGTGCCTTTTGTAAGGGATAAAATACATGTGTTTAATCTTGTC
3143595 CCT
1 CCT
3143598 TTTTGGATTA
Statistics
Matches: 314, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
311 314 1.00
ACGTcount: A:0.28, C:0.20, G:0.21, T:0.31
Consensus pattern (311 bp):
CCTCTATATTGCCAACAACTTCTTGACCCAATGACAAGAGCATTATGTTGGAGGCATGAGCGCTT
GGGTTCAATCCCAAGCAACCCCATTCCCCTCCCTCAATTATAAAAAAAACCCTCTATATCACGGT
TTAAACTATAATTACGAAAGAGATGGTGAGTTTTGTGGAGTTGGTTGGGGTGTATCTTGTGAAGT
TTGGAGCGGTTAATGATCGAGATAGGATCCTAAATCTAGCCCCGTGACTGTTTGACCAACATTTA
TTCTCGATGGTGCCTTTTGTAAGGGATAAAATACATGTGTTTAATCTTGTC
Found at i:3151728 original size:17 final size:17
Alignment explanation
Indices: 3151629--3151733 Score: 66
Period size: 17 Copynumber: 5.5 Consensus size: 17
3151619 CTAATTTTAG
*
3151629 ATTTTAAATTTTAAATTC
1 ATTTTAAA-TTTAAATTT
*
3151647 ATTTTAAGTTTAAATTT
1 ATTTTAAATTTAAATTT
*
3151664 ATTGTAAATTTAAGCTTATTT
1 ATTTTAAATTTAA----ATTT
* *
3151685 AGCTTATTTCGAGTTTAAATTT
1 A---T-TTT-AAATTTAAATTT
3151707 ATTTTAAATTTAAATTT
1 ATTTTAAATTTAAATTT
3151724 ATTTTGAAAT
1 ATTTT-AAAT
3151734 AAAATTTAAA
Statistics
Matches: 68, Mismatches: 9, Indels: 20
0.70 0.09 0.21
Matches are distributed among these distances:
17 34 0.50
18 14 0.21
19 1 0.01
21 5 0.07
22 5 0.07
24 1 0.01
25 2 0.03
26 6 0.09
ACGTcount: A:0.35, C:0.04, G:0.07, T:0.54
Consensus pattern (17 bp):
ATTTTAAATTTAAATTT
Found at i:3151738 original size:17 final size:17
Alignment explanation
Indices: 3151701--3151741 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
3151691 TTTCGAGTTT
*
3151701 AAATTTATTTTAAATTT
1 AAATTTATTTTAAATTA
3151718 AAATTTATTTTGAAA-TA
1 AAATTTATTTT-AAATTA
3151735 AAATTTA
1 AAATTTA
3151742 AATTTAAAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 19 0.86
18 3 0.14
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.51
Consensus pattern (17 bp):
AAATTTATTTTAAATTA
Found at i:3153574 original size:29 final size:29
Alignment explanation
Indices: 3153506--3153860 Score: 149
Period size: 30 Copynumber: 12.1 Consensus size: 29
3153496 CCCAAGAAGT
* * * * *
3153506 CCCTGAACTATCTAGAAATCATATTTTAA
1 CCCTGAACTTTCTAAAAATTACATTTTTA
*
3153535 CCCCCGAACTTTCTAAAAATTACATTTTTA
1 -CCCTGAACTTTCTAAAAATTACATTTTTA
* * * *
3153565 CCCTTAACTTTC-CAAAATTTCATTTTAA
1 CCCTGAACTTTCTAAAAATTACATTTTTA
3153593 CCCTGAACCTTTC-AAAAATTACCA-TTTTA
1 CCCTGAA-CTTTCTAAAAATTA-CATTTTTA
* * *
3153622 CCCCCGGA-TGTT-TAAAAATTTCATTTTTA
1 -CCCTGAACT-TTCTAAAAATTACATTTTTA
* * * * *
3153651 ACCTCAAACCTTCCAAAAATCACCA-TTTTA
1 CCCT-GAACTTTCTAAAAATTA-CATTTTTA
* * *
3153681 CCCCCGAACATT-TAAAAATTTCATTTTTA
1 -CCCTGAACTTTCTAAAAATTACATTTTTA
* * *
3153710 ACCTCGAACCTTCAAAAAATTACCA-TTTTA
1 CCCT-GAACTTTCTAAAAATTA-CATTTTTA
* * * *
3153740 CCCTTAAATGTCTAAAAATTCCATTTTTA
1 CCCTGAACTTTCTAAAAATTACATTTTTA
* * *
3153769 ACCTCGAACCTTC-CAAAATTACCA-TTTTA
1 CCCT-GAACTTTCTAAAAATTA-CATTTTTA
* * *
3153798 CCCCCCGAACATT-TAAAAATTCCATTTTTA
1 --CCCTGAACTTTCTAAAAATTACATTTTTA
* * *
3153828 ACCTCGAACCTTCCAAAAATTACCA-TTTTA
1 CCCT-GAACTTTCTAAAAATTA-CATTTTTA
3153858 CCC
1 CCC
3153861 CCGGGCATCC
Statistics
Matches: 237, Mismatches: 63, Indels: 50
0.68 0.18 0.14
Matches are distributed among these distances:
28 32 0.14
29 97 0.41
30 98 0.41
31 10 0.04
ACGTcount: A:0.35, C:0.27, G:0.04, T:0.35
Consensus pattern (29 bp):
CCCTGAACTTTCTAAAAATTACATTTTTA
Found at i:3153589 original size:28 final size:28
Alignment explanation
Indices: 3153528--3153857 Score: 145
Period size: 29 Copynumber: 11.2 Consensus size: 28
3153518 TAGAAATCAT
*
3153528 ATTTTAACCCCCGAACTTTCTAAAAATTAC
1 ATTTTAA-CCCTGAACTTTC-AAAAATTAC
* * * *
3153558 ATTTTTACCCTTAACTTTCCAAAATTTC
1 ATTTTAACCCTGAACTTTCAAAAATTAC
3153586 ATTTTAACCCTGAACCTTTCAAAAATTACC
1 ATTTTAACCCTGAA-CTTTCAAAAATTA-C
* * * * *
3153616 ATTTTACCCCCGGA-TGTTTAAAAATTTC
1 ATTTTAACCCTGAACT-TTCAAAAATTAC
* * *
3153644 ATTTTTAA-CCTCAAACCTTCCAAAAATCACC
1 A-TTTTAACCCT-GAA-CTTTCAAAAATTA-C
* * *
3153675 ATTTTACCCCCGAACATTT-AAAAATTTC
1 ATTTTAACCCTGAAC-TTTCAAAAATTAC
*
3153703 ATTTTTAA-CCTCGAACCTTCAAAAAATTACC
1 A-TTTTAACCCT-GAACTTTC-AAAAATTA-C
* * * *
3153734 ATTTT-ACCCTTAAATGTCTAAAAATTCC
1 ATTTTAACCCTGAACTTTC-AAAAATTAC
* *
3153762 ATTTTTAA-CCTCGAACCTTCCAAAATTACC
1 A-TTTTAACCCT-GAACTTTCAAAAATTA-C
* * *
3153792 ATTTTACCCCCCGAACATTT-AAAAATTCC
1 ATTTTA-ACCCTGAAC-TTTCAAAAATTAC
*
3153821 ATTTTTAA-CCTCGAACCTTCCAAAAATTACC
1 A-TTTTAACCCT-GAA-CTTTCAAAAATTA-C
3153852 ATTTTA
1 ATTTTA
3153858 CCCCCGGGCA
Statistics
Matches: 219, Mismatches: 53, Indels: 56
0.67 0.16 0.17
Matches are distributed among these distances:
28 34 0.16
29 89 0.41
30 83 0.38
31 13 0.06
ACGTcount: A:0.35, C:0.26, G:0.03, T:0.35
Consensus pattern (28 bp):
ATTTTAACCCTGAACTTTCAAAAATTAC
Found at i:3153876 original size:59 final size:59
Alignment explanation
Indices: 3153578--3153863 Score: 402
Period size: 59 Copynumber: 4.9 Consensus size: 59
3153568 TTAACTTTCC
* * **
3153578 AAAATTTCA-TTTTAACC-CTGAACCTTTCAAAAATTACCATTTTACCCCCGGATGTTTA
1 AAAATTTCATTTTTAACCTC-GAACCTTCCAAAAATTACCATTTTACCCCCGAACATTTA
* *
3153636 AAAATTTCATTTTTAACCTCAAACCTTCCAAAAATCACCATTTTACCCCCGAACATTTA
1 AAAATTTCATTTTTAACCTCGAACCTTCCAAAAATTACCATTTTACCCCCGAACATTTA
* **
3153695 AAAATTTCATTTTTAACCTCGAACCTTCAAAAAATTACCATTTTA-CCCTTAA-ATGTCTA
1 AAAATTTCATTTTTAACCTCGAACCTTCCAAAAATTACCATTTTACCCCCGAACAT-T-TA
*
3153754 AAAATTCCATTTTTAACCTCGAACCTTCC-AAAATTACCATTTTACCCCCCGAACATTTA
1 AAAATTTCATTTTTAACCTCGAACCTTCCAAAAATTACCATTTTA-CCCCCGAACATTTA
*
3153813 AAAATTCCATTTTTAACCTCGAACCTTCCAAAAATTACCATTTTACCCCCG
1 AAAATTTCATTTTTAACCTCGAACCTTCCAAAAATTACCATTTTACCCCCG
3153864 GGCATCCAAA
Statistics
Matches: 205, Mismatches: 15, Indels: 15
0.87 0.06 0.06
Matches are distributed among these distances:
57 2 0.01
58 30 0.15
59 149 0.73
60 22 0.11
61 2 0.01
ACGTcount: A:0.35, C:0.27, G:0.04, T:0.34
Consensus pattern (59 bp):
AAAATTTCATTTTTAACCTCGAACCTTCCAAAAATTACCATTTTACCCCCGAACATTTA
Found at i:3154369 original size:2 final size:2
Alignment explanation
Indices: 3154362--3154392 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
3154352 CAAGTTCTCA
3154362 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3154393 CAAATGATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3155822 original size:30 final size:31
Alignment explanation
Indices: 3155771--3155828 Score: 75
Period size: 30 Copynumber: 1.9 Consensus size: 31
3155761 ACAATTGAAC
3155771 TTAAATTATAAAATCTAAAAAA-TACAAAAA
1 TTAAATTATAAAATCTAAAAAAGTACAAAAA
* *
3155801 TTAAATT-TTAAATTTATAAAAAGTACAA
1 TTAAATTATAAAATCTA-AAAAAGTACAA
3155829 CAACTTACAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 7 0.29
30 12 0.50
31 5 0.21
ACGTcount: A:0.60, C:0.05, G:0.02, T:0.33
Consensus pattern (31 bp):
TTAAATTATAAAATCTAAAAAAGTACAAAAA
Found at i:3156633 original size:13 final size:13
Alignment explanation
Indices: 3156615--3156639 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3156605 AATATAATAA
3156615 AATATTAAAAATT
1 AATATTAAAAATT
3156628 AATATTAAAAAT
1 AATATTAAAAAT
3156640 GATAATTTTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (13 bp):
AATATTAAAAATT
Found at i:3157102 original size:5 final size:5
Alignment explanation
Indices: 3157094--3157146 Score: 56
Period size: 5 Copynumber: 10.2 Consensus size: 5
3157084 TTTTCTTTTT
3157094 TTATA TTATA TTATA TTAT- TATATTA TTATA TTAT- TATATTA TTATA
1 TTATA TTATA TTATA TTATA T-TA-TA TTATA TTATA T-TA-TA TTATA
3157141 TTATA T
1 TTATA T
3157147 ATACCAAAAA
Statistics
Matches: 42, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
4 2 0.05
5 32 0.76
6 6 0.14
7 2 0.05
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (5 bp):
TTATA
Found at i:3157113 original size:8 final size:8
Alignment explanation
Indices: 3157102--3157148 Score: 87
Period size: 8 Copynumber: 6.0 Consensus size: 8
3157092 TTTTATATTA
3157102 TATTATAT
1 TATTATAT
3157110 TATTATAT
1 TATTATAT
3157118 TATTATAT
1 TATTATAT
3157126 TATTATAT
1 TATTATAT
3157134 TATTATAT
1 TATTATAT
3157142 TA-TATAT
1 TATTATAT
3157149 ACCAAAAAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 1
0.98 0.00 0.03
Matches are distributed among these distances:
7 5 0.13
8 34 0.87
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (8 bp):
TATTATAT
Found at i:3157483 original size:12 final size:12
Alignment explanation
Indices: 3157466--3157492 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
3157456 ATAACTCTTA
3157466 TTTTATTATTAT
1 TTTTATTATTAT
3157478 TTTTATTATTAT
1 TTTTATTATTAT
3157490 TTT
1 TTT
3157493 AGAGGCATTT
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:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (12 bp):
TTTTATTATTAT
Found at i:3160927 original size:15 final size:15
Alignment explanation
Indices: 3160907--3160948 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
3160897 AGTTTTTAAA
*
3160907 TTTGAAAACTAAAAT
1 TTTGAAAACTAAAAG
3160922 TTTGAAAA-TAAAAG
1 TTTGAAAACTAAAAG
**
3160936 TAAGAAAACTAAA
1 TTTGAAAACTAAA
3160949 TTCCTAATAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
14 11 0.48
15 12 0.52
ACGTcount: A:0.60, C:0.05, G:0.10, T:0.26
Consensus pattern (15 bp):
TTTGAAAACTAAAAG
Found at i:3169197 original size:6 final size:6
Alignment explanation
Indices: 3169186--3169233 Score: 96
Period size: 6 Copynumber: 8.0 Consensus size: 6
3169176 ATATATATAC
3169186 ATTTAT ATTTAT ATTTAT ATTTAT ATTTAT ATTTAT ATTTAT ATTTAT
1 ATTTAT ATTTAT ATTTAT ATTTAT ATTTAT ATTTAT ATTTAT ATTTAT
3169234 CGATGTAAAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 42 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (6 bp):
ATTTAT
Found at i:3176566 original size:41 final size:42
Alignment explanation
Indices: 3176492--3176574 Score: 116
Period size: 42 Copynumber: 2.0 Consensus size: 42
3176482 AATGGAATAG
3176492 ATTATTAAAAATCACAATTTTTTTAAAAGAATATATCCGTTC
1 ATTATTAAAAATCACAATTTTTTTAAAAGAATATATCCGTTC
* * *
3176534 ATTATTAAAAATCA-TATTTTTCTTTAAA-AATATATCGGTTC
1 ATTATTAAAAATCACAATTTTT-TTAAAAGAATATATCCGTTC
3176575 TTAATTTTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
41 18 0.49
42 19 0.51
ACGTcount: A:0.41, C:0.11, G:0.05, T:0.43
Consensus pattern (42 bp):
ATTATTAAAAATCACAATTTTTTTAAAAGAATATATCCGTTC
Found at i:3181012 original size:42 final size:42
Alignment explanation
Indices: 3180898--3181036 Score: 134
Period size: 42 Copynumber: 3.3 Consensus size: 42
3180888 AGCGCGTCAG
* *
3180898 TTGGACGTGCTTTCTGCACAGTTGGCAAGAAAGCTCGTCCAG
1 TTGGACGAGCTTTCTGCACAGTTGGCAAGAAAGCTCGTCCAA
* * * * * * * **
3180940 CTAGACAAGCTGTCCGCATAATTGTTAAGAAAGCTCGTCCAA
1 TTGGACGAGCTTTCTGCACAGTTGGCAAGAAAGCTCGTCCAA
* * * *
3180982 TTGGGCGAGCTTTCTACACAGTTGGCAAGAAAGCACGTCTAA
1 TTGGACGAGCTTTCTGCACAGTTGGCAAGAAAGCTCGTCCAA
*
3181024 TTGAACGAGCTTT
1 TTGGACGAGCTTT
3181037 TATTGATATG
Statistics
Matches: 71, Mismatches: 26, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
42 71 1.00
ACGTcount: A:0.27, C:0.22, G:0.24, T:0.26
Consensus pattern (42 bp):
TTGGACGAGCTTTCTGCACAGTTGGCAAGAAAGCTCGTCCAA
Found at i:3190435 original size:25 final size:25
Alignment explanation
Indices: 3190381--3190429 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
3190371 AATAATATAA
* *
3190381 ATTATTATTTAATTAGTATTATATT
1 ATTATTATTTAACTAATATTATATT
3190406 ATTATTA-TTAACTAATATATATAT
1 ATTATTATTTAACTAATAT-TATAT
3190430 GTTTATATGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 9 0.43
25 12 0.57
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (25 bp):
ATTATTATTTAACTAATATTATATT
Found at i:3192747 original size:31 final size:29
Alignment explanation
Indices: 3192707--3192773 Score: 71
Period size: 31 Copynumber: 2.2 Consensus size: 29
3192697 ATCTCAAAAC
* *
3192707 TATATATGAACTTTGGTTTAATGTGCAATTG
1 TATACATGAACTTTGATTT--TGTGCAATTG
* * *
3192738 TATACATGAATTTTGATTTTGTGTAATTT
1 TATACATGAACTTTGATTTTGTGCAATTG
3192767 TATACAT
1 TATACAT
3192774 AAAATTTTGA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
29 15 0.48
31 16 0.52
ACGTcount: A:0.30, C:0.06, G:0.15, T:0.49
Consensus pattern (29 bp):
TATACATGAACTTTGATTTTGTGCAATTG
Found at i:3192760 original size:29 final size:30
Alignment explanation
Indices: 3192728--3192786 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 30
3192718 TTTGGTTTAA
*
3192728 TGTGCAATTGTATACAT-GAATTTTGATTT
1 TGTGCAATTGTATACATAAAATTTTGATTT
* *
3192757 TGTGTAATTTTATACATAAAATTTTGATTT
1 TGTGCAATTGTATACATAAAATTTTGATTT
3192787 GATCCAATTC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 15 0.58
30 11 0.42
ACGTcount: A:0.31, C:0.05, G:0.14, T:0.51
Consensus pattern (30 bp):
TGTGCAATTGTATACATAAAATTTTGATTT
Found at i:3193007 original size:29 final size:30
Alignment explanation
Indices: 3192929--3193008 Score: 74
Period size: 31 Copynumber: 2.7 Consensus size: 30
3192919 GATTTAATCA
**
3192929 AAATTAAAGTTTAAAT-TATATATTTAAACC
1 AAATTAAAGTTT-AATGTATATAACTAAACC
* * * *
3192959 ACAATTAGAGTTTCACGTATATAACTACACC
1 A-AATTAAAGTTTAATGTATATAACTAAACC
3192990 AAATTAAAGTTT-ATGTATA
1 AAATTAAAGTTTAATGTATA
3193009 ATTTTGAAAT
Statistics
Matches: 40, Mismatches: 8, Indels: 5
0.75 0.15 0.09
Matches are distributed among these distances:
29 6 0.15
30 12 0.30
31 22 0.55
ACGTcount: A:0.45, C:0.11, G:0.07, T:0.36
Consensus pattern (30 bp):
AAATTAAAGTTTAATGTATATAACTAAACC
Found at i:3193281 original size:29 final size:30
Alignment explanation
Indices: 3193228--3193297 Score: 88
Period size: 29 Copynumber: 2.3 Consensus size: 30
3193218 TAAATAAAAT
3193228 TATACATGAACTATGATTTAATGTGCAATTA
1 TATACATGAACTATGATTT-ATGTGCAATTA
* * * *
3193259 TATATATGAACTTTGATTT-TGTGTAATTT
1 TATACATGAACTATGATTTATGTGCAATTA
3193288 TATACATGAA
1 TATACATGAA
3193298 ATTTTCATTT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
29 17 0.50
31 17 0.50
ACGTcount: A:0.36, C:0.07, G:0.13, T:0.44
Consensus pattern (30 bp):
TATACATGAACTATGATTTATGTGCAATTA
Found at i:3194376 original size:31 final size:30
Alignment explanation
Indices: 3194339--3194422 Score: 107
Period size: 31 Copynumber: 2.8 Consensus size: 30
3194329 GATTAAATTA
* *
3194339 AAATTAAAATTTCAAATATACATTTGAACC
1 AAATTAAAATTTCATATATACAATTGAACC
* * *
3194369 ATAATTAAAATTTCATGTATATAATTGTACC
1 A-AATTAAAATTTCATATATACAATTGAACC
3194400 AAATTAAAA-TTCATATATACAAT
1 AAATTAAAATTTCATATATACAAT
3194423 AACACATTAA
Statistics
Matches: 46, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
29 12 0.26
30 9 0.20
31 25 0.54
ACGTcount: A:0.49, C:0.11, G:0.04, T:0.37
Consensus pattern (30 bp):
AAATTAAAATTTCATATATACAATTGAACC
Found at i:3195753 original size:361 final size:361
Alignment explanation
Indices: 3195089--3195812 Score: 1385
Period size: 361 Copynumber: 2.0 Consensus size: 361
3195079 CACAACATCA
3195089 GTCACCAATGGTGGTGAGTCTGAAGGTTCAGCCCCAACTACCAATGTGCTGCAAACTCATCTTCC
1 GTCACCAATGGTGGTGAGTCTGAAGGTTCAGCCCCAACTACCAATGTGCTGCAAACTCATCTTCC
3195154 TATAGTCCGGCGAACCTTGCAGCTAATACACAGATCCCGAGTCTGCTAAAGGAGAATGACGCTGA
66 TATAGTCCGGCGAACCTTGCAGCTAATACACAGATCCCGAGTCTGCTAAAGGAGAATGACGCTGA
3195219 GTACCTCCATTTGTGTGGATTCATAATACCTAGTAAATGTAAAGGCTAATCTTCAAATTATGGAC
131 GTACCTCCATTTGTGTGGATTCATAATACCTAGTAAATGTAAAGGCTAATCTTCAAATTATGGAC
*
3195284 ATTTTTATTCAACAAAAACTGTTAAATTTCACAGGGCGTATATGTATTGGTTGTGAACCATAATG
196 ATTTTTATTCAACAAAAACAGTTAAATTTCACAGGGCGTATATGTATTGGTTGTGAACCATAATG
3195349 AGGCCATAATCTAATGCTAGTTCACATCATATTCTCAACAATATATACTCCTCAGCAATGAAAAT
261 AGGCCATAATCTAATGCTAGTTCACATCATATTCTCAACAATATATACTCCTCAGCAATGAAAAT
* *
3195414 GGTCATATTTAAAAAAAAATAAGAAAAAAGCTTGGG
326 GGTCACATTTAAAAAAAAATAAGAAAAAAGCATGGG
*
3195450 GTCACCAATGGTGGTGAGTCTGAAGGTTCAGCCCCAACTACCAATTTGCTGCAAACTCATCTTCC
1 GTCACCAATGGTGGTGAGTCTGAAGGTTCAGCCCCAACTACCAATGTGCTGCAAACTCATCTTCC
* *
3195515 TATAGTCCGGTGAACCTTGCAGCTAATACACAGATCCTGAGTCTGCTAAAGGAGAATGACGCTGA
66 TATAGTCCGGCGAACCTTGCAGCTAATACACAGATCCCGAGTCTGCTAAAGGAGAATGACGCTGA
3195580 GTACCTCCATTTGTGTGGATTCATAATACCTAGTAAATGTAAAGGCTAATCTTCAAATTATGGAC
131 GTACCTCCATTTGTGTGGATTCATAATACCTAGTAAATGTAAAGGCTAATCTTCAAATTATGGAC
3195645 ATTTTTATTCAACAAAAACAGTTAAATTTCACAGGGCGTATATGTATTGGTTGTGAACCATAATG
196 ATTTTTATTCAACAAAAACAGTTAAATTTCACAGGGCGTATATGTATTGGTTGTGAACCATAATG
*
3195710 AGGCCATAATCTAATGCTAGTTCACATCATATTCTCGACAATATATACTCCTCAGCAATGAAAAT
261 AGGCCATAATCTAATGCTAGTTCACATCATATTCTCAACAATATATACTCCTCAGCAATGAAAAT
3195775 GGTCACATTTAAAAAAAAATAAGAAAAAAGCATGGG
326 GGTCACATTTAAAAAAAAATAAGAAAAAAGCATGGG
3195811 GT
1 GT
3195813 GAGAGAGGCT
Statistics
Matches: 356, Mismatches: 7, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
361 356 1.00
ACGTcount: A:0.34, C:0.19, G:0.18, T:0.28
Consensus pattern (361 bp):
GTCACCAATGGTGGTGAGTCTGAAGGTTCAGCCCCAACTACCAATGTGCTGCAAACTCATCTTCC
TATAGTCCGGCGAACCTTGCAGCTAATACACAGATCCCGAGTCTGCTAAAGGAGAATGACGCTGA
GTACCTCCATTTGTGTGGATTCATAATACCTAGTAAATGTAAAGGCTAATCTTCAAATTATGGAC
ATTTTTATTCAACAAAAACAGTTAAATTTCACAGGGCGTATATGTATTGGTTGTGAACCATAATG
AGGCCATAATCTAATGCTAGTTCACATCATATTCTCAACAATATATACTCCTCAGCAATGAAAAT
GGTCACATTTAAAAAAAAATAAGAAAAAAGCATGGG
Found at i:3197467 original size:21 final size:21
Alignment explanation
Indices: 3197441--3197480 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
3197431 CAAAACGACG
*
3197441 TAGTTTTGTCTTTTAATTTAA
1 TAGTTTTGACTTTTAATTTAA
3197462 TAGTTTTGACTTTTAATTT
1 TAGTTTTGACTTTTAATTT
3197481 TAGAAAAGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.23, C:0.05, G:0.10, T:0.62
Consensus pattern (21 bp):
TAGTTTTGACTTTTAATTTAA
Found at i:3197524 original size:70 final size:70
Alignment explanation
Indices: 3197354--3197517 Score: 274
Period size: 70 Copynumber: 2.3 Consensus size: 70
3197344 AATGGGTAAA
* * *
3197354 CATTTATCAAAAAGGCATAGTTTTGTCTTTTAACTTAATAGTTTTGACTTTTAATTTTAGAAAAT
1 CATTTATCAAAAAGACGTAGTTTTGTCTTTTAACTTAATAGTTTTGACTTTTAATTTTAGAAAAG
3197419 ATAAG
66 ATAAG
* *
3197424 CATTTATCAAAACGACGTAGTTTTGTCTTTTAATTTAATAGTTTTGACTTTTAATTTTAGAAAAG
1 CATTTATCAAAAAGACGTAGTTTTGTCTTTTAACTTAATAGTTTTGACTTTTAATTTTAGAAAAG
3197489 ATAAG
66 ATAAG
*
3197494 CATTTATCAAAATGACGTAGTTTT
1 CATTTATCAAAAAGACGTAGTTTT
3197518 TCCTTTTTTT
Statistics
Matches: 88, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
70 88 1.00
ACGTcount: A:0.35, C:0.09, G:0.12, T:0.44
Consensus pattern (70 bp):
CATTTATCAAAAAGACGTAGTTTTGTCTTTTAACTTAATAGTTTTGACTTTTAATTTTAGAAAAG
ATAAG
Found at i:3197898 original size:19 final size:19
Alignment explanation
Indices: 3197858--3197919 Score: 63
Period size: 20 Copynumber: 3.2 Consensus size: 19
3197848 AAAACACAAA
*
3197858 ATTTAGAATTTTTATAAA-T
1 ATTTAGAA-TTTTAAAAATT
3197877 ATTTAGAATTTTAAAAATT
1 ATTTAGAATTTTAAAAATT
* * *
3197896 ATTTTCGATTTTTGAAAATT
1 A-TTTAGAATTTTAAAAATT
3197916 ATTT
1 ATTT
3197920 TGATTATTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
18 8 0.22
19 13 0.35
20 16 0.43
ACGTcount: A:0.39, C:0.02, G:0.06, T:0.53
Consensus pattern (19 bp):
ATTTAGAATTTTAAAAATT
Found at i:3197913 original size:20 final size:19
Alignment explanation
Indices: 3197865--3197924 Score: 68
Period size: 20 Copynumber: 3.2 Consensus size: 19
3197855 AAAATTTAGA
* *
3197865 ATTTTTATAAA-TATTTAG
1 ATTTTTAAAAATTATTTTG
*
3197883 AATTTTAAAAATTATTTTCG
1 ATTTTTAAAAATTATTTT-G
*
3197903 ATTTTTGAAAATTATTTTG
1 ATTTTTAAAAATTATTTTG
3197922 ATT
1 ATT
3197925 ATTTTGTAAT
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
18 9 0.26
19 9 0.26
20 17 0.49
ACGTcount: A:0.37, C:0.02, G:0.07, T:0.55
Consensus pattern (19 bp):
ATTTTTAAAAATTATTTTG
Found at i:3205269 original size:7 final size:7
Alignment explanation
Indices: 3205257--3205282 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
3205247 GGGAACTAAA
3205257 AAAAAAT
1 AAAAAAT
3205264 AAAAAAT
1 AAAAAAT
3205271 AAAAAAT
1 AAAAAAT
3205278 AAAAA
1 AAAAA
3205283 TTTAATTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (7 bp):
AAAAAAT
Found at i:3206560 original size:30 final size:30
Alignment explanation
Indices: 3206525--3206741 Score: 190
Period size: 30 Copynumber: 7.3 Consensus size: 30
3206515 CATTAAAATC
* * * *
3206525 GGGTCAAATTCAAATTTTTAAAAACTTTAA
1 GGGTCAAATTTAAATTTTTAGAAAGTTTAG
** *
3206555 GGGTCAAATCAAAATTTTTAGAAAGTTTGG
1 GGGTCAAATTTAAATTTTTAGAAAGTTTAG
*
3206585 GGGTCAAA-TTAGAATTTTTAGAAA-TTTTG
1 GGGTCAAATTTA-AATTTTTAGAAAGTTTAG
* * * *
3206614 ATGGTTAAATTTGAATTTCTAGAAAGTTTAG
1 -GGGTCAAATTTAAATTTTTAGAAAGTTTAG
* * *
3206645 GGGTTAAATTTGAATTTTTAGAAAATTT-G
1 GGGTCAAATTTAAATTTTTAGAAAGTTTAG
* * * *
3206674 GGGTTAAATTTGAATTTTTAGAAA-ATTCG
1 GGGTCAAATTTAAATTTTTAGAAAGTTTAG
* *
3206703 ATGGTCAAATTGAAATTTTTAGAAAGTTTAG
1 -GGGTCAAATTTAAATTTTTAGAAAGTTTAG
3206734 GGGTCAAA
1 GGGTCAAA
3206742 AAACAATTTT
Statistics
Matches: 155, Mismatches: 25, Indels: 14
0.80 0.13 0.07
Matches are distributed among these distances:
28 2 0.01
29 31 0.20
30 113 0.73
31 9 0.06
ACGTcount: A:0.37, C:0.05, G:0.20, T:0.39
Consensus pattern (30 bp):
GGGTCAAATTTAAATTTTTAGAAAGTTTAG
Found at i:3206713 original size:59 final size:58
Alignment explanation
Indices: 3206567--3206737 Score: 191
Period size: 59 Copynumber: 2.9 Consensus size: 58
3206557 GTCAAATCAA
* * * *
3206567 AATTTTTAGAAAGTTTGGGGGTCAAATTAGAATTTTTAGAAATTTTGATGGTTAAATTTG
1 AATTTTTAGAAAG-TTGAGGGTCAAATTTGAATTTTTAGAAAATTTG-GGGTTAAATTTG
* * *
3206627 AATTTCTAGAAAGTTTAGGGGTTAAATTTGAATTTTTAGAAAATTTGGGGTTAAATTTG
1 AATTTTTAGAAAGTTGA-GGGTCAAATTTGAATTTTTAGAAAATTTGGGGTTAAATTTG
* * *
3206686 AATTTTTAGAAAATTCGATGGTCAAA-TTGAAATTTTTAGAAAGTTTAGGGGT
1 AATTTTTAGAAAGTT-GAGGGTCAAATTTG-AATTTTTAGAAAATTT-GGGGT
3206738 CAAAAAACAA
Statistics
Matches: 94, Mismatches: 13, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
58 3 0.03
59 47 0.50
60 44 0.47
ACGTcount: A:0.35, C:0.02, G:0.22, T:0.42
Consensus pattern (58 bp):
AATTTTTAGAAAGTTGAGGGTCAAATTTGAATTTTTAGAAAATTTGGGGTTAAATTTG
Found at i:3206750 original size:89 final size:89
Alignment explanation
Indices: 3206526--3206751 Score: 258
Period size: 89 Copynumber: 2.5 Consensus size: 89
3206516 ATTAAAATCG
* * * * * *
3206526 GGTCAAATTCAAATTTTTAAAAACTTTAAGGGTCAAATCAAAATTTTTAGAAAGTTTGGGGGTCA
1 GGTCAAATTGAAATTTTTAGAAAGTTTAGGGGTCAAA-AAAAATTTTTAGAAAATTTGGGGGTCA
* *
3206591 AATTAGAATTTTTAGAAATTTTGAT
65 AATTAGAATTTTTAGAAAATTCGAT
* * * *** *
3206616 GGTTAAATTTG-AATTTCTAGAAAGTTTAGGGGTTAAATTTGAATTTTTAGAAAATTT-GGGGTT
1 GGTCAAA-TTGAAATTTTTAGAAAGTTTAGGGGTCAAA-AAAAATTTTTAGAAAATTTGGGGGTC
*
3206679 AAATTTGAATTTTTAGAAAATTCGAT
64 AAATTAGAATTTTTAGAAAATTCGAT
3206705 GGTCAAATTGAAATTTTTAGAAAGTTTAGGGGTCAAAAAACAATTTT
1 GGTCAAATTGAAATTTTTAGAAAGTTTAGGGGTCAAAAAA-AATTTT
3206752 AAAATAAAAT
Statistics
Matches: 112, Mismatches: 21, Indels: 7
0.80 0.15 0.05
Matches are distributed among these distances:
88 3 0.03
89 64 0.57
90 43 0.38
91 2 0.02
ACGTcount: A:0.38, C:0.05, G:0.19, T:0.39
Consensus pattern (89 bp):
GGTCAAATTGAAATTTTTAGAAAGTTTAGGGGTCAAAAAAAATTTTTAGAAAATTTGGGGGTCAA
ATTAGAATTTTTAGAAAATTCGAT
Found at i:3208427 original size:40 final size:40
Alignment explanation
Indices: 3208382--3208532 Score: 137
Period size: 40 Copynumber: 3.8 Consensus size: 40
3208372 ATTGGATTGT
*
3208382 TTCAATCT-ACCTCATGGTCAGGGTAAGAGATCTGATGGTC
1 TTCAATCTGACCTC-TGGTCAGGGTAAAAGATCTGATGGTC
* * *
3208422 TTCAATCTGCCCTCTTGTTAGGGTAAAAGATCTGATGGTC
1 TTCAATCTGACCTCTGGTCAGGGTAAAAGATCTGATGGTC
* * * * *
3208462 TTCAATCTGCCCTCTGATTAGGG-AAAGAGATCAGATGATC
1 TTCAATCTGACCTCTGGTCAGGGTAAA-AGATCTGATGGTC
* * * *
3208502 TTTAATTTG-CCTTCTGTTTAGGGTAAAAGAT
1 TTCAATCTGACC-TCTGGTCAGGGTAAAAGAT
3208533 TGGATTACTT
Statistics
Matches: 96, Mismatches: 11, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
39 5 0.05
40 84 0.88
41 7 0.07
ACGTcount: A:0.26, C:0.18, G:0.23, T:0.34
Consensus pattern (40 bp):
TTCAATCTGACCTCTGGTCAGGGTAAAAGATCTGATGGTC
Found at i:3208667 original size:50 final size:49
Alignment explanation
Indices: 3208613--3208756 Score: 155
Period size: 50 Copynumber: 2.9 Consensus size: 49
3208603 CAGGAGTATA
*
3208613 AGATTCGTCTTTGCGACTTCAATCTGCCCCTCTACAGCTTTAGGTGAATG
1 AGATTCGCCTTTGCG-CTTCAATCTGCCCCTCTACAGCTTTAGGTGAATG
* * * * *
3208663 AGATTCGCCGTTGCGGCTTCAATCTACCCCTTTACAGCTTTAAGTGTATG
1 AGATTCGCCTTTGC-GCTTCAATCTGCCCCTCTACAGCTTTAGGTGAATG
* ** *
3208713 AGATTTGCCATTTTG-GCTTCAATCTGTTCCTCTACAACTTTAGG
1 AGATTCGCC--TTTGCGCTTCAATCTGCCCCTCTACAGCTTTAGG
3208757 GGTATAAGAC
Statistics
Matches: 77, Mismatches: 14, Indels: 6
0.79 0.14 0.06
Matches are distributed among these distances:
50 73 0.95
51 1 0.01
52 3 0.04
ACGTcount: A:0.20, C:0.25, G:0.19, T:0.36
Consensus pattern (49 bp):
AGATTCGCCTTTGCGCTTCAATCTGCCCCTCTACAGCTTTAGGTGAATG
Found at i:3209634 original size:50 final size:50
Alignment explanation
Indices: 3209561--3209660 Score: 121
Period size: 50 Copynumber: 2.0 Consensus size: 50
3209551 ATCTCCTTAG
** * *
3209561 GCTTCGAGACGCCCTTTGCGGGTTTTCATCTCATCCTACCTT-TTTTTTTT
1 GCTTCGAGACGCCCTTTAAGGGTTTTCAACTCAACCT-CCTTCTTTTTTTT
* * *
3209611 GCTTTGAGTCGCCCTTTAAGGGTTTTCAACTCAACCTCTTTCTTTTTTTT
1 GCTTCGAGACGCCCTTTAAGGGTTTTCAACTCAACCTCCTTCTTTTTTTT
3209661 TAGGCGAAGT
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
49 3 0.07
50 39 0.93
ACGTcount: A:0.12, C:0.26, G:0.15, T:0.47
Consensus pattern (50 bp):
GCTTCGAGACGCCCTTTAAGGGTTTTCAACTCAACCTCCTTCTTTTTTTT
Found at i:3214644 original size:21 final size:20
Alignment explanation
Indices: 3214618--3214671 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 20
3214608 GGAGTTTTTG
3214618 GTATCGGTAG-ATGCATGACTT
1 GTATCGGTAGAAT-CAT-ACTT
3214639 GTATCGGTAGAAATCATACTT
1 GTATCGGTAG-AATCATACTT
*
3214660 GTATCGGAAGAA
1 GTATCGGTAGAA
3214672 CTAGCACAAG
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
20 2 0.07
21 23 0.77
22 3 0.10
23 2 0.07
ACGTcount: A:0.31, C:0.13, G:0.26, T:0.30
Consensus pattern (20 bp):
GTATCGGTAGAATCATACTT
Found at i:3216538 original size:58 final size:58
Alignment explanation
Indices: 3216469--3216588 Score: 206
Period size: 58 Copynumber: 2.1 Consensus size: 58
3216459 AAAAGGAGTT
*
3216469 GTTTATGAGTGTTATTT-AGGAATAAAATTATATTTGGGTTTAAAAATATTTGGGTTTA
1 GTTTATGAGTGTT-TTTGAAGAATAAAATTATATTTGGGTTTAAAAATATTTGGGTTTA
*
3216527 GTTTATGAGTGTTTTTGAAGAATGAAATTATATTTGGGTTTAAAAATATTTGGGTTTA
1 GTTTATGAGTGTTTTTGAAGAATAAAATTATATTTGGGTTTAAAAATATTTGGGTTTA
3216585 GTTT
1 GTTT
3216589 GTTGATGGGT
Statistics
Matches: 59, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
57 3 0.05
58 56 0.95
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (58 bp):
GTTTATGAGTGTTTTTGAAGAATAAAATTATATTTGGGTTTAAAAATATTTGGGTTTA
Found at i:3216844 original size:36 final size:35
Alignment explanation
Indices: 3216766--3216854 Score: 124
Period size: 35 Copynumber: 2.5 Consensus size: 35
3216756 TTTGAATTCG
* * *
3216766 AAAATTAAAGTCGATTCAAAATCGAAATTCGAAAA
1 AAAATTCAACTCGATTCAAAATCGAAATTCAAAAA
* *
3216801 AAAATTCAACTTGATTCAAACTCGAAATTCAAAAA
1 AAAATTCAACTCGATTCAAAATCGAAATTCAAAAA
3216836 AAATATTCAACTCGATTCA
1 AAA-ATTCAACTCGATTCA
3216855 TTTAACTCGA
Statistics
Matches: 47, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
35 33 0.70
36 14 0.30
ACGTcount: A:0.51, C:0.16, G:0.08, T:0.26
Consensus pattern (35 bp):
AAAATTCAACTCGATTCAAAATCGAAATTCAAAAA
Found at i:3223220 original size:30 final size:28
Alignment explanation
Indices: 3223185--3223369 Score: 108
Period size: 29 Copynumber: 6.3 Consensus size: 28
3223175 CATTAAAACC
3223185 GGGTCAAATTTGAATTTTTGAAAACTTTAA
1 GGGTCAAATTTGAATTTTTGAAAA-TTT-A
* * *
3223215 AGGTCAAA--TCAATTTTTTTGGAAAGTTTA
1 GGGTCAAATTTGAA--TTTTT-GAAAATTTA
* *
3223244 GGGTCAAATTGGAATTTTT-AGAAATATGA
1 GGGTCAAATTTGAATTTTTGA-AAAT-TTA
* * * *
3223273 GGGTTAAATTGGAATTTCTAAAAAGTTTA
1 GGGTCAAATTTGAATTTTTGAAAA-TTTA
* *
3223302 AGGTTAAATTTGAATTTTTGGAAAATTTAA
1 GGGTCAAATTTGAATTTTT-GAAAATTT-A
* *
3223332 GGGTTAAA-TTGAAATTTTTAGAAAGTTTA
1 GGGTCAAATTTG-AATTTTT-GAAAATTTA
3223361 GGGTTCAAA
1 GGG-TCAAA
3223370 AAATAATTTT
Statistics
Matches: 123, Mismatches: 19, Indels: 26
0.73 0.11 0.15
Matches are distributed among these distances:
27 1 0.01
28 6 0.05
29 63 0.51
30 47 0.38
31 6 0.05
ACGTcount: A:0.37, C:0.04, G:0.20, T:0.39
Consensus pattern (28 bp):
GGGTCAAATTTGAATTTTTGAAAATTTA
Found at i:3223261 original size:29 final size:29
Alignment explanation
Indices: 3223229--3223369 Score: 140
Period size: 29 Copynumber: 4.8 Consensus size: 29
3223219 CAAATCAATT
*
3223229 TTTTTGGAAAGTTTAGGGTCAAATTGGAA
1 TTTTTAGAAAGTTTAGGGTCAAATTGGAA
* *
3223258 TTTTTAGAAA-TATGAGGGTTAAATTGGAA
1 TTTTTAGAAAGT-TTAGGGTCAAATTGGAA
* * * * *
3223287 TTTCTAAAAAGTTTAAGGTTAAATTTGAA
1 TTTTTAGAAAGTTTAGGGTCAAATTGGAA
* * * *
3223316 TTTTTGGAAAATTTAAGGGTTAAATTGAAA
1 TTTTTAGAAAGTTT-AGGGTCAAATTGGAA
3223346 TTTTTAGAAAGTTTAGGGTTCAAA
1 TTTTTAGAAAGTTTAGGG-TCAAA
3223370 AAATAATTTT
Statistics
Matches: 90, Mismatches: 18, Indels: 7
0.78 0.16 0.06
Matches are distributed among these distances:
28 1 0.01
29 60 0.67
30 29 0.32
ACGTcount: A:0.37, C:0.02, G:0.21, T:0.40
Consensus pattern (29 bp):
TTTTTAGAAAGTTTAGGGTCAAATTGGAA
Found at i:3223357 original size:59 final size:58
Alignment explanation
Indices: 3223185--3223365 Score: 186
Period size: 59 Copynumber: 3.1 Consensus size: 58
3223175 CATTAAAACC
* * * * * *
3223185 GGGTCAAATTTGAATTTTTGAAAACTTTAAAGGTCAAA-TCAATTTTTTTGGAAAGTTTA
1 GGGTTAAATTTGAATTTTTGAAAA-TTTAAGGGTTAAATTGAA-ATTTTTAGAAAGTTTA
* * * * * * *
3223244 GGGTCAAATTGGAATTTTT-AGAAATATGAGGGTTAAATTGGAATTTCTAAAAAGTTTA
1 GGGTTAAATTTGAATTTTTGA-AAATTTAAGGGTTAAATTGAAATTTTTAGAAAGTTTA
*
3223302 AGGTTAAATTTGAATTTTTGGAAAATTTAAGGGTTAAATTGAAATTTTTAGAAAGTTTA
1 GGGTTAAATTTGAATTTTT-GAAAATTTAAGGGTTAAATTGAAATTTTTAGAAAGTTTA
3223361 GGGTT
1 GGGTT
3223366 CAAAAAATAA
Statistics
Matches: 98, Mismatches: 20, Indels: 8
0.78 0.16 0.06
Matches are distributed among these distances:
58 38 0.39
59 59 0.60
60 1 0.01
ACGTcount: A:0.36, C:0.03, G:0.20, T:0.40
Consensus pattern (58 bp):
GGGTTAAATTTGAATTTTTGAAAATTTAAGGGTTAAATTGAAATTTTTAGAAAGTTTA
Found at i:3236269 original size:22 final size:23
Alignment explanation
Indices: 3236244--3236291 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
3236234 AAATTTATTT
* *
3236244 AATTCATTTATGTTCA-TGAATA
1 AATTAATTTATATTCATTGAATA
*
3236266 AATTAATTTATATTCATTTAATA
1 AATTAATTTATATTCATTGAATA
3236289 AAT
1 AAT
3236292 CGTTTAAAGT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
22 14 0.64
23 8 0.36
ACGTcount: A:0.42, C:0.06, G:0.04, T:0.48
Consensus pattern (23 bp):
AATTAATTTATATTCATTGAATA
Found at i:3243597 original size:8 final size:8
Alignment explanation
Indices: 3243584--3243613 Score: 60
Period size: 8 Copynumber: 3.8 Consensus size: 8
3243574 TTCCTCTTGT
3243584 TTTTTTTA
1 TTTTTTTA
3243592 TTTTTTTA
1 TTTTTTTA
3243600 TTTTTTTA
1 TTTTTTTA
3243608 TTTTTT
1 TTTTTT
3243614 GAAGAAGAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.10, C:0.00, G:0.00, T:0.90
Consensus pattern (8 bp):
TTTTTTTA
Found at i:3281612 original size:32 final size:33
Alignment explanation
Indices: 3281557--3281623 Score: 118
Period size: 32 Copynumber: 2.1 Consensus size: 33
3281547 AAACAATCAG
*
3281557 ATGCATAACTTTTAGAGTTATCAATTCTATTAT
1 ATGCATAACTTTTAGAGTTATCAACTCTATTAT
3281590 ATGCATAACTTTT-GAGTTATCAACTCTATTAT
1 ATGCATAACTTTTAGAGTTATCAACTCTATTAT
3281622 AT
1 AT
3281624 TCCTTCCGTC
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 20 0.61
33 13 0.39
ACGTcount: A:0.33, C:0.13, G:0.09, T:0.45
Consensus pattern (33 bp):
ATGCATAACTTTTAGAGTTATCAACTCTATTAT
Found at i:3286333 original size:18 final size:17
Alignment explanation
Indices: 3286312--3286411 Score: 110
Period size: 18 Copynumber: 5.6 Consensus size: 17
3286302 TTAAACCAAT
*
3286312 TTTAAGATTTATTTTAAG
1 TTTAA-ATTTATTTTAAA
* *
3286330 TTTAAATTGATTTTTGAA
1 TTTAAATTTA-TTTTAAA
3286348 TTTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
*
3286365 TTTAAATTTTGTTTTAAAA
1 TTTAAA-TTTATTTT-AAA
*
3286384 TTTAAATTTAATTTAAA
1 TTTAAATTTATTTTAAA
*
3286401 TTTAGATTTAT
1 TTTAAATTTAT
3286412 ATATGAATTT
Statistics
Matches: 69, Mismatches: 10, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
17 28 0.41
18 32 0.46
19 9 0.13
ACGTcount: A:0.37, C:0.00, G:0.06, T:0.57
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:3286357 original size:6 final size:6
Alignment explanation
Indices: 3286346--3286424 Score: 63
Period size: 6 Copynumber: 13.3 Consensus size: 6
3286336 TTGATTTTTG
* * **
3286346 AATTTA AATTT- ATTTTA AATTTA AATTTT GTTTTAA AATTTA AATTT-
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTT-A AATTTA AATTTA
* * * *
3286393 AATTTA AATTTA GATTTA TATATG AATTTA AA
1 AATTTA AATTTA AATTTA AATTTA AATTTA AA
3286425 ACTTATTATA
Statistics
Matches: 55, Mismatches: 15, Indels: 6
0.72 0.20 0.08
Matches are distributed among these distances:
5 9 0.16
6 43 0.78
7 3 0.05
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.53
Consensus pattern (6 bp):
AATTTA
Found at i:3288530 original size:29 final size:28
Alignment explanation
Indices: 3288498--3288559 Score: 79
Period size: 28 Copynumber: 2.2 Consensus size: 28
3288488 AAATTTTTAT
* *
3288498 TTTTGACCCCAAAACTTTCAAAATTACCA
1 TTTTGACCCCAAAA-GTCCAAAATTACCA
* *
3288527 TTTTGCCCCCGAAAGTCCAAAATTACCA
1 TTTTGACCCCAAAAGTCCAAAATTACCA
3288555 TTTTG
1 TTTTG
3288560 CCTCAGAGTA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
28 17 0.59
29 12 0.41
ACGTcount: A:0.32, C:0.27, G:0.08, T:0.32
Consensus pattern (28 bp):
TTTTGACCCCAAAAGTCCAAAATTACCA
Found at i:3293743 original size:5 final size:5
Alignment explanation
Indices: 3293720--3293783 Score: 69
Period size: 5 Copynumber: 12.6 Consensus size: 5
3293710 TGAATAAAAG
* *
3293720 AAGAA AAAAA AAGGAAA AAGAA AAGAGA AA-AA GAGAA AAGAA AAGAA
1 AAGAA AAGAA AA-G-AA AAGAA AAGA-A AAGAA AAGAA AAGAA AAGAA
3293767 AAGAA AA-AA AAGAA AAG
1 AAGAA AAGAA AAGAA AAG
3293784 GAGAGGTTGA
Statistics
Matches: 50, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
4 6 0.12
5 36 0.72
6 4 0.08
7 4 0.08
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (5 bp):
AAGAA
Found at i:3293751 original size:25 final size:25
Alignment explanation
Indices: 3293715--3293785 Score: 85
Period size: 25 Copynumber: 2.8 Consensus size: 25
3293705 TTCAATGAAT
3293715 AAAAGAAGAAAAA-AAAAGGAAAAAG
1 AAAAGAA-AAAAAGAAAAGGAAAAAG
3293740 AAAAGAGAAAAAGAGAAAA-G-AAAAG
1 AAAAGA-AAAAA-AGAAAAGGAAAAAG
3293765 AAAAGAAAAAAAAGAAAAGGA
1 AAAAG-AAAAAAAGAAAAGGA
3293786 GAGGTTGAAG
Statistics
Matches: 40, Mismatches: 0, Indels: 11
0.78 0.00 0.22
Matches are distributed among these distances:
24 6 0.15
25 26 0.65
26 4 0.10
27 4 0.10
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (25 bp):
AAAAGAAAAAAAGAAAAGGAAAAAG
Found at i:3293756 original size:15 final size:13
Alignment explanation
Indices: 3293715--3293783 Score: 63
Period size: 13 Copynumber: 5.4 Consensus size: 13
3293705 TTCAATGAAT
3293715 AAAAGAAGAAAAA-
1 AAAAGAA-AAAAAG
*
3293728 AAAAG-GAAAAAG
1 AAAAGAAAAAAAG
*
3293740 AAAAGAGAAAAAG
1 AAAAGAAAAAAAG
* *
3293753 AGAA-AAGAAAAG
1 AAAAGAAAAAAAG
3293765 AAAAGAAAAAAAAG
1 AAAAG-AAAAAAAG
3293779 AAAAG
1 AAAAG
3293784 GAGAGGTTGA
Statistics
Matches: 46, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
11 5 0.11
12 14 0.30
13 15 0.33
14 12 0.26
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (13 bp):
AAAAGAAAAAAAG
Found at i:3293781 original size:32 final size:32
Alignment explanation
Indices: 3293715--3293787 Score: 85
Period size: 32 Copynumber: 2.2 Consensus size: 32
3293705 TTCAATGAAT
* *
3293715 AAAAGAAGAAAAAAAAAGGAAAAAGAAAAGAGA
1 AAAAG-AGAAAAAAAAAGGAAAAAAAAAAAAGA
*
3293748 AAAAGAGAAAAGAAAA-GAAAAGAAAAAAAAGA
1 AAAAGAGAAAAAAAAAGGAAAA-AAAAAAAAGA
*
3293780 AAAGGAGA
1 AAAAGAGA
3293788 GGTTGAAGTG
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
31 5 0.14
32 25 0.71
33 5 0.14
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (32 bp):
AAAAGAGAAAAAAAAAGGAAAAAAAAAAAAGA
Found at i:3295068 original size:50 final size:50
Alignment explanation
Indices: 3294986--3295170 Score: 151
Period size: 50 Copynumber: 3.7 Consensus size: 50
3294976 TCAACATCAT
* **
3294986 AAAATACAATGGGAAAGATCTAAGACCACAACGACAGATCCAGTACCGCA
1 AAAATACAAAGGGAAAGATCTAAGACCACAACGGTAGATCCAGTACCGCA
* * * * *
3295036 AAAATACAACAGGGAAAGGTCTAAG-TCGCAACGGTAGA-CCGTGTACCTCA
1 AAAATACAA-AGGGAAAGATCTAAGACCACAACGGTAGATCC-AGTACCGCA
* * * * * * *
3295086 AAGACACGACGGGAAAGATCTAAGACCGCAATGGTGGATCCAGTACCGCA
1 AAAATACAAAGGGAAAGATCTAAGACCACAACGGTAGATCCAGTACCGCA
* * * *
3295136 AAGATACTAAAAGGAAAGGTCTAAG-TCACAACGGT
1 AAAATAC-AAAGGGAAAGATCTAAGACCACAACGGT
3295171 GGACCGTGTA
Statistics
Matches: 104, Mismatches: 26, Indels: 10
0.74 0.19 0.07
Matches are distributed among these distances:
49 15 0.14
50 61 0.59
51 28 0.27
ACGTcount: A:0.41, C:0.22, G:0.23, T:0.14
Consensus pattern (50 bp):
AAAATACAAAGGGAAAGATCTAAGACCACAACGGTAGATCCAGTACCGCA
Found at i:3295169 original size:100 final size:99
Alignment explanation
Indices: 3294996--3295285 Score: 377
Period size: 100 Copynumber: 2.9 Consensus size: 99
3294986 AAAATACAAT
* * * * * *
3294996 GGGAAAGATCTAAGACCACAACGACAGATCCAGTACCGCAAAAATACAACAGGGAAAGGTCTAAG
1 GGGAAAGATCTAAGACCGCAATGGCGGATCCAGTACCGCAAAGATACAA-AAGGAAAGGTCTAAG
3295061 TCGCAACGGTAGACCGTGTACCTCAAAGACACGAC
65 TCGCAACGGTAGACCGTGTACCTCAAAGACACGAC
*
3295096 GGGAAAGATCTAAGACCGCAATGGTGGATCCAGTACCGCAAAGATACTAAAAGGAAAGGTCTAAG
1 GGGAAAGATCTAAGACCGCAATGGCGGATCCAGTACCGCAAAGATAC-AAAAGGAAAGGTCTAAG
* * *
3295161 TCACAACGGTGGACCGTGTACCTCAAAAGGCACGAC
65 TCGCAACGGTAGACCGTGTACCTC-AAAGACACGAC
* * * *
3295197 GGGAAAGATCTAA-ATCGTAATGGCGGATCCAATACCGCAAAGATACAAAAAGGAAATGTCTAAG
1 GGGAAAGATCTAAGACCGCAATGGCGGATCCAGTACCGCAAAGATAC-AAAAGGAAAGGTCTAAG
* *
3295261 TCGTAACGG-CGAACCGTGTACCTCA
65 TCGCAACGGTAG-ACCGTGTACCTCA
3295286 GAAGCAGGAA
Statistics
Matches: 168, Mismatches: 19, Indels: 7
0.87 0.10 0.04
Matches are distributed among these distances:
99 2 0.01
100 141 0.84
101 25 0.15
ACGTcount: A:0.38, C:0.22, G:0.24, T:0.15
Consensus pattern (99 bp):
GGGAAAGATCTAAGACCGCAATGGCGGATCCAGTACCGCAAAGATACAAAAGGAAAGGTCTAAGT
CGCAACGGTAGACCGTGTACCTCAAAGACACGAC
Found at i:3295172 original size:50 final size:49
Alignment explanation
Indices: 3295022--3295269 Score: 176
Period size: 50 Copynumber: 5.0 Consensus size: 49
3295012 CACAACGACA
* *
3295022 GATCCAGTACCGCAAAAATACAACAGGGAAAGGTCTAAGTCGCAACGGTA
1 GATCCAGTACCGCAAAGATACAA-AGGGAAAGGTCTAAGTCGCAACGGTG
* * * * * * * *
3295072 GA-CCGTGTACCTCAAAGACACGACGGGAAAGATCTAAGACCGCAATGGTG
1 GATCC-AGTACCGCAAAGATACAAAGGGAAAGGTCTAAG-TCGCAACGGTG
* *
3295122 GATCCAGTACCGCAAAGATACTAAAAGGAAAGGTCTAAGTCACAACGGTG
1 GATCCAGTACCGCAAAGATAC-AAAGGGAAAGGTCTAAGTCGCAACGGTG
* * ** * * * * * * *
3295172 GA-CCGTGTACCTCAAAAGGCACGACGGGAAAGATCTAAATCGTAATGGCG
1 GATCC-AGTACCGC-AAAGATACAAAGGGAAAGGTCTAAGTCGCAACGGTG
* * * *
3295222 GATCCAATACCGCAAAGATACAAAAAGGAAATGTCTAAGTCGTAACGG
1 GATCCAGTACCGCAAAGATAC-AAAGGGAAAGGTCTAAGTCGCAACGG
3295270 CGAACCGTGT
Statistics
Matches: 145, Mismatches: 45, Indels: 16
0.70 0.22 0.08
Matches are distributed among these distances:
49 23 0.16
50 99 0.68
51 23 0.16
ACGTcount: A:0.38, C:0.21, G:0.25, T:0.15
Consensus pattern (49 bp):
GATCCAGTACCGCAAAGATACAAAGGGAAAGGTCTAAGTCGCAACGGTG
Found at i:3296333 original size:206 final size:204
Alignment explanation
Indices: 3295901--3296426 Score: 774
Period size: 206 Copynumber: 2.6 Consensus size: 204
3295891 ATACACAAAT
* * * * *
3295901 AGTGAGGCGGTCATCTTCCTGATGAGATACAGAGAAGTATACCAACTC-AA-T-GCTCAAATACG
1 AGTGAGGCGGTCATCTTCCTGATGAGACACTGAGAAGAAGACCAAATCAAACTAGCTC-AATACG
3295963 AGCAAATCTTTGAACCCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAATGGT
65 AGCAAATCTTTGAACCCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAATGGT
* * *
3296028 TAGCTTCCTGATAAGATACAGAGAAGTGGACCAAATTCGTCTTCTTGAGGAGATCCAGAGAAGCG
130 TAGCTTCCTGATAAGACACAGAGAAGTGGACCAAATTCGTCTTCCTAAGGAGATCCAGAGAAGCG
3296093 AATTAAAACA
195 AATTAAAACA
* * * *
3296103 AGTGATGTGGTCATATTCCTGATGAGACACTGAGAAGAAGACCAAATCAAACCTAGGCTCAATGC
1 AGTGAGGCGGTCATCTTCCTGATGAGACACTGAGAAGAAGACCAAATCAAA-CTA-GCTCAATAC
** *
3296168 GAGCAAATCTTCAAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGG
64 GAGCAAATCTTTGAACCCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAATGG
* * *
3296233 TTAGCTTCCTGATGAGACACAGAGAAGTGGATCAGATTCGTCTTCCTAAGGAGATCCAGAGAAGC
129 TTAGCTTCCTGATAAGACACAGAGAAGTGGACCAAATTCGTCTTCCTAAGGAGATCCAGAGAAGC
3296298 GAATTAAAACA
194 GAATTAAAACA
* *
3296309 A-TCGAGGCGGTCATCTTTCTGATGAGACACTGAGAAGAAGACCAAATCAAAACAACGCTCAATA
1 AGT-GAGGCGGTCATCTTCCTGATGAGACACTGAGAAGAAGACCAAATC-AAACTA-GCTCAATA
*
3296373 CGAGCAAATCTTTGAA-CCCAGCTTCCTGATGAGACAGTGAGAAGCAGGTCGAAG
63 CGAGCAAATCTTTGAACCCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAG
3296427 TCAACGAAAC
Statistics
Matches: 288, Mismatches: 29, Indels: 11
0.88 0.09 0.03
Matches are distributed among these distances:
202 40 0.14
203 2 0.01
205 38 0.13
206 201 0.70
207 7 0.02
ACGTcount: A:0.36, C:0.20, G:0.23, T:0.21
Consensus pattern (204 bp):
AGTGAGGCGGTCATCTTCCTGATGAGACACTGAGAAGAAGACCAAATCAAACTAGCTCAATACGA
GCAAATCTTTGAACCCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAATGGTT
AGCTTCCTGATAAGACACAGAGAAGTGGACCAAATTCGTCTTCCTAAGGAGATCCAGAGAAGCGA
ATTAAAACA
Found at i:3296799 original size:18 final size:17
Alignment explanation
Indices: 3296778--3296877 Score: 110
Period size: 18 Copynumber: 5.6 Consensus size: 17
3296768 TTAAACCCAT
*
3296778 TTTAAGATTTATTTTAAG
1 TTTAA-ATTTATTTTAAA
* *
3296796 TTTAAATTGATTTTTGAA
1 TTTAAATTTA-TTTTAAA
3296814 TTTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
*
3296831 TTTAAATTTTGTTTTAAAA
1 TTTAAA-TTTATTTT-AAA
*
3296850 TTTAAATTTAATTTAAA
1 TTTAAATTTATTTTAAA
*
3296867 TTTAGATTTAT
1 TTTAAATTTAT
3296878 ATATGAATTT
Statistics
Matches: 69, Mismatches: 10, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
17 28 0.41
18 32 0.46
19 9 0.13
ACGTcount: A:0.37, C:0.00, G:0.06, T:0.57
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:3296823 original size:6 final size:6
Alignment explanation
Indices: 3296812--3296890 Score: 63
Period size: 6 Copynumber: 13.3 Consensus size: 6
3296802 TTGATTTTTG
* * **
3296812 AATTTA AATTT- ATTTTA AATTTA AATTTT GTTTTAA AATTTA AATTT-
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTT-A AATTTA AATTTA
* * * *
3296859 AATTTA AATTTA GATTTA TATATG AATTTA AA
1 AATTTA AATTTA AATTTA AATTTA AATTTA AA
3296891 ACTTATTATA
Statistics
Matches: 55, Mismatches: 15, Indels: 6
0.72 0.20 0.08
Matches are distributed among these distances:
5 9 0.16
6 43 0.78
7 3 0.05
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.53
Consensus pattern (6 bp):
AATTTA
Found at i:3299822 original size:59 final size:58
Alignment explanation
Indices: 3299759--3300221 Score: 549
Period size: 59 Copynumber: 7.9 Consensus size: 58
3299749 AAAATTCAGA
* * * * * * *
3299759 GTTAAAAATGGGATTTTAGAAGGTCCAGGAGTAAAATGGTAATTTTTAGTAAAATCAAG
1 GTTAAAAATGGGATTTTGGAAAGTTCGGGGGTAAAATGGTAA-TTTTGGTAAAATCGAG
* * * * *
3299818 GTT-AAAACGAGG-TTTTAGAGAGTTCGAGGGTAAAATGGTAATTTTGGTGAAATCG-G
1 GTTAAAAATG-GGATTTTGGAAAGTTCGGGGGTAAAATGGTAATTTTGGTAAAATCGAG
* * * *
3299874 GGTCAAAATGGGATTTTGG-AAGATTTGGGGGTAAAATGGTAATTTTGGTGAAATCGAG
1 GTTAAAAATGGGATTTTGGAAAG-TTCGGGGGTAAAATGGTAATTTTGGTAAAATCGAG
* * *
3299932 GTTAAAAATAGGATTTTGGAAAGTTCGGGGGTAAAATGGTAAATTTGGTGAAATC-AGG
1 GTTAAAAATGGGATTTTGGAAAGTTCGGGGGTAAAATGGTAATTTTGGTAAAATCGA-G
* * *
3299990 GTTAAAAATGGGATTTTAGAAAGTTTGGGGGTAAAATGGTAATTTTTGGTGAAATCGAG
1 GTTAAAAATGGGATTTTGGAAAGTTCGGGGGTAAAATGGTAA-TTTTGGTAAAATCGAG
* *
3300049 ATTAAAAATGGGATTTTGGAAAGTTCGGGAGTAAAATGGTAATTTTTGGTAAAATCGAG
1 GTTAAAAATGGGATTTTGGAAAGTTCGGGGGTAAAATGGTAA-TTTTGGTAAAATCGAG
* * *
3300108 GTTAAAAATGGGATTATGGAAAGTTTGGGGGTAAAATGGTAACTTTTGGTAAAATCGGG
1 GTTAAAAATGGGATTTTGGAAAGTTCGGGGGTAAAATGGTAA-TTTTGGTAAAATCGAG
* * *
3300167 GTTAAAAATGGGATTTTGGAAAATTTGGGGGTAAAATGGTAACTTTTGGTGAAAT
1 GTTAAAAATGGGATTTTGGAAAGTTCGGGGGTAAAATGGTAA-TTTTGGTAAAAT
3300222 AAGCCAAAAC
Statistics
Matches: 356, Mismatches: 39, Indels: 18
0.86 0.09 0.04
Matches are distributed among these distances:
56 7 0.02
57 53 0.15
58 115 0.32
59 180 0.51
60 1 0.00
ACGTcount: A:0.35, C:0.03, G:0.30, T:0.32
Consensus pattern (58 bp):
GTTAAAAATGGGATTTTGGAAAGTTCGGGGGTAAAATGGTAATTTTGGTAAAATCGAG
Found at i:3300000 original size:30 final size:29
Alignment explanation
Indices: 3299849--3300000 Score: 75
Period size: 29 Copynumber: 5.2 Consensus size: 29
3299839 GTTCGAGGGT
* * *
3299849 AAAATGGTAATTTTGGTGAAATCGGGGTC
1 AAAATGGTAAATTTGGTGAAATCGGGTTA
* * * ** * *
3299878 AAAATGG-GATTTTGGAAGATTTGGGGGT-
1 AAAATGGTAAATTTGG-TGAAATCGGGTTA
*
3299906 AAAATGGTAATTTTGGTGAAATCGAGGTTA
1 AAAATGGTAAATTTGGTGAAATCG-GGTTA
* *
3299936 AAAATAGG---ATTTTG-GAAAGTTCGGGGGT-
1 AAAAT-GGTAAATTTGGTGAAA--TC-GGGTTA
3299964 AAAATGGTAAATTTGGTGAAATCAGGGTTA
1 AAAATGGTAAATTTGGTGAAATC-GGGTTA
3299994 AAAATGG
1 AAAATGG
3300001 GATTTTAGAA
Statistics
Matches: 93, Mismatches: 17, Indels: 25
0.69 0.13 0.19
Matches are distributed among these distances:
27 6 0.06
28 27 0.29
29 36 0.39
30 18 0.19
31 6 0.06
ACGTcount: A:0.35, C:0.03, G:0.32, T:0.30
Consensus pattern (29 bp):
AAAATGGTAAATTTGGTGAAATCGGGTTA
Found at i:3300055 original size:30 final size:30
Alignment explanation
Indices: 3300021--3300114 Score: 88
Period size: 30 Copynumber: 3.2 Consensus size: 30
3300011 AGTTTGGGGG
3300021 TAAAATGGTAATTTTTGGTGAAATCGAGAT
1 TAAAATGGTAATTTTTGGTGAAATCGAGAT
* * *
3300051 TAAAAATGG-GA-TTTT-G-GAAAGTTCGGGAG
1 T-AAAATGGTAATTTTTGGTGAAA--TCGAGAT
* *
3300080 TAAAATGGTAATTTTTGGTAAAATCGAGGT
1 TAAAATGGTAATTTTTGGTGAAATCGAGAT
3300110 TAAAA
1 TAAAA
3300115 ATGGGATTAT
Statistics
Matches: 49, Mismatches: 8, Indels: 14
0.69 0.11 0.20
Matches are distributed among these distances:
27 4 0.08
28 8 0.16
29 11 0.22
30 15 0.31
31 8 0.16
32 3 0.06
ACGTcount: A:0.38, C:0.03, G:0.26, T:0.33
Consensus pattern (30 bp):
TAAAATGGTAATTTTTGGTGAAATCGAGAT
Found at i:3300057 original size:31 final size:31
Alignment explanation
Indices: 3300022--3300118 Score: 96
Period size: 31 Copynumber: 3.2 Consensus size: 31
3300012 GTTTGGGGGT
3300022 AAAATGGTAATTTTTGGTGAAATCGAGATTA
1 AAAATGGTAATTTTTGGTGAAATCGAGATTA
* * *
3300053 AAAATGG-GA-TTTT-G-GAAAGTTCGGGAGT-
1 AAAATGGTAATTTTTGGTGAAA--TCGAGATTA
* *
3300081 AAAATGGTAATTTTTGGTAAAATCGAGGTTA
1 AAAATGGTAATTTTTGGTGAAATCGAGATTA
3300112 AAAATGG
1 AAAATGG
3300119 GATTATGGAA
Statistics
Matches: 51, Mismatches: 8, Indels: 14
0.70 0.11 0.19
Matches are distributed among these distances:
27 4 0.08
28 8 0.16
29 11 0.22
30 10 0.20
31 15 0.29
32 3 0.06
ACGTcount: A:0.38, C:0.03, G:0.27, T:0.32
Consensus pattern (31 bp):
AAAATGGTAATTTTTGGTGAAATCGAGATTA
Done.