Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold18
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: 4432388
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 63034 characters in sequence are not A, C, G, or T
File 3 of 27
Found at i:273737 original size:16 final size:17
Alignment explanation
Indices: 273708--273740 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
273698 CGATTTTGAG
*
273708 AATTTATTTCTTCTAGA
1 AATTGATTTCTTCTAGA
273725 AATTGATTT-TTCTAGA
1 AATTGATTTCTTCTAGA
273741 TTTTTGGAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.30, C:0.09, G:0.09, T:0.52
Consensus pattern (17 bp):
AATTGATTTCTTCTAGA
Found at i:279211 original size:19 final size:19
Alignment explanation
Indices: 279170--279243 Score: 96
Period size: 20 Copynumber: 3.8 Consensus size: 19
279160 CACACCTAGA
*
279170 TGTATCGATACATTATGCTT
1 TGTATCGATACATGAT-CTT
279190 TGTATCGATACATGATCTT
1 TGTATCGATACATGATCTT
*
279209 TGTATCGATACATGGA-CAAT
1 TGTATCGATACAT-GATC-TT
279229 TGTATCGATACATGA
1 TGTATCGATACATGA
279244 AACTGGCAGT
Statistics
Matches: 50, Mismatches: 2, Indels: 5
0.88 0.04 0.09
Matches are distributed among these distances:
19 19 0.38
20 31 0.62
ACGTcount: A:0.30, C:0.15, G:0.18, T:0.38
Consensus pattern (19 bp):
TGTATCGATACATGATCTT
Found at i:279296 original size:20 final size:20
Alignment explanation
Indices: 279271--279324 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 20
279261 CTACCACTGT
*
279271 TTGTATCGGTACATGGT-ACA
1 TTGTATCGGTACATGATGA-A
279291 TTGTATCGGTACATGATGAA
1 TTGTATCGGTACATGATGAA
*
279311 TTGTATCGATACAT
1 TTGTATCGGTACAT
279325 TGCTTCTAAC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
20 30 0.97
21 1 0.03
ACGTcount: A:0.28, C:0.13, G:0.22, T:0.37
Consensus pattern (20 bp):
TTGTATCGGTACATGATGAA
Found at i:287543 original size:13 final size:13
Alignment explanation
Indices: 287525--287549 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
287515 CATTATGTTT
287525 TGTATCGATACAA
1 TGTATCGATACAA
287538 TGTATCGATACA
1 TGTATCGATACA
287550 TGATCGTTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:287545 original size:33 final size:32
Alignment explanation
Indices: 287503--287568 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 32
287493 AAAACCCTTG
*
287503 AATGTATCGATACATTAT-GTTTTGTATCGATAC
1 AATGTATCGATACATGATCG--TTGTATCGATAC
287536 AATGTATCGATACATGATCGTTGTATCGATAC
1 AATGTATCGATACATGATCGTTGTATCGATAC
287568 A
1 A
287569 TGGACAATTA
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
32 13 0.42
33 17 0.55
34 1 0.03
ACGTcount: A:0.32, C:0.14, G:0.17, T:0.38
Consensus pattern (32 bp):
AATGTATCGATACATGATCGTTGTATCGATAC
Found at i:287642 original size:20 final size:20
Alignment explanation
Indices: 287617--287670 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 20
287607 CTACCACTGT
*
287617 TTGTATCGATACATGGT-ACA
1 TTGTATCGATACATGATGA-A
287637 TTGTATCGATACATGATGAA
1 TTGTATCGATACATGATGAA
*
287657 TTGTATCAATACAT
1 TTGTATCGATACAT
287671 TGCTTCTAAC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
20 30 0.97
21 1 0.03
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.37
Consensus pattern (20 bp):
TTGTATCGATACATGATGAA
Found at i:290332 original size:29 final size:29
Alignment explanation
Indices: 290300--290416 Score: 110
Period size: 33 Copynumber: 3.8 Consensus size: 29
290290 TGCTTGCTGG
290300 TTGCTGTTTCTTTCTTTCTTTTTGCTTAA
1 TTGCTGTTTCTTTCTTTCTTTTTGCTTAA
* * *
290329 TTGCTGTTGCTATTACTTGCTTTGCTTGC-TGA
1 TTGCTGTTTCT-TT-CTTTCTTT--TTGCTTAA
* *
290361 TTGTTGTTTCTTTCTTTCTTTTTACTTAA
1 TTGCTGTTTCTTTCTTTCTTTTTGCTTAA
290390 TTGCTATTGTTTTCTTTCTTTCTTTTT
1 TTGC---TG-TTTCTTTCTTTCTTTTT
290417 CGGTGTTTCT
Statistics
Matches: 70, Mismatches: 9, Indels: 14
0.75 0.10 0.15
Matches are distributed among these distances:
28 3 0.04
29 15 0.21
30 9 0.13
31 9 0.13
32 13 0.19
33 21 0.30
ACGTcount: A:0.08, C:0.16, G:0.12, T:0.64
Consensus pattern (29 bp):
TTGCTGTTTCTTTCTTTCTTTTTGCTTAA
Found at i:296544 original size:20 final size:20
Alignment explanation
Indices: 296502--296553 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 20
296492 CAAAGCCAAT
* *
296502 TGTATCAATACATTTAGGAA
1 TGTATCGATACATTTACGAA
**
296522 TGTATCGATACATTTACTCA
1 TGTATCGATACATTTACGAA
*
296542 TGTATTGATACA
1 TGTATCGATACA
296554 ATTTTTCAAG
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.38
Consensus pattern (20 bp):
TGTATCGATACATTTACGAA
Found at i:297692 original size:33 final size:34
Alignment explanation
Indices: 297650--297777 Score: 126
Period size: 32 Copynumber: 3.9 Consensus size: 34
297640 TCTTTTTTCA
*
297650 AAAGTCCACACAAGTTGGTGGCAACTCTTTTCTT
1 AAAGCCCACACAAGTTGGTGGCAACTCTTTTCTT
* *
297684 AAA-CCCACACAAGTTGGTGTC-A-T-TTTTTTT
1 AAAGCCCACACAAGTTGGTGGCAACTCTTTTCTT
* *
297714 AAAGCCCGCACCAGTTGGTGGCAAC-C--TTCTT
1 AAAGCCCACACAAGTTGGTGGCAACTCTTTTCTT
** *
297745 AAAAGCCTGCACAAGTTGGTGGCATCTCTTTTC
1 -AAAGCCCACACAAGTTGGTGGCAACTCTTTTC
297778 AAACCCAATA
Statistics
Matches: 76, Mismatches: 10, Indels: 15
0.75 0.10 0.15
Matches are distributed among these distances:
30 9 0.12
31 20 0.26
32 24 0.32
33 17 0.22
34 3 0.04
35 3 0.04
ACGTcount: A:0.25, C:0.25, G:0.19, T:0.31
Consensus pattern (34 bp):
AAAGCCCACACAAGTTGGTGGCAACTCTTTTCTT
Found at i:297986 original size:52 final size:52
Alignment explanation
Indices: 297878--298228 Score: 175
Period size: 52 Copynumber: 6.7 Consensus size: 52
297868 CTTCATTTTT
* * * ***
297878 AAGTCCAATGTCGCTGG-CTTCGAATCAGCACATTGGCACCCTTGT-C-ATCCAA
1 AAGTCCAATATCGCTGGCCTT-GAATTAGCACATTGGCA--CTTCTACTATCTTC
* *
297930 AAGTCCAATATTGCTGGCCTTGAATTAGCATATTGGCACTTCTACTATCTTC
1 AAGTCCAATATCGCTGGCCTTGAATTAGCACATTGGCACTTCTACTATCTTC
* * * * *
297982 AAGTCTAATGTCGCTGGGCTTGAATTAGCACATTGACACTTGTCAAAACCT-TCTTTCC
1 AAGTCCAATATCGCTGGCCTTGAATTAGCACATTGGCAC-T-TC--TA-CTATC-TT-C
* * * *
298040 AAAGTCCAATGTCGTTGGCCTTGAATTAGTACATTGGCAC-TCT-CATCATCTTT
1 -AAGTCCAATATCGCTGGCCTTGAATTAGCACATTGGCACTTCTAC-T-ATCTTC
* * * * ** *
298093 AAGTCCAATATCGTTGGCCTGGAATCAGCACATTGGCACTTTTGTTATCTTT
1 AAGTCCAATATCGCTGGCCTTGAATTAGCACATTGGCACTTCTACTATCTTC
* * * * * * *
298145 AAGCCCAATGTTGCTAG-CTGTGAATCAGCACATTGGAAACTT-T-C-ATCTTT
1 AAGTCCAATATCGCTGGCCT-TGAATTAGCACATTGG-CACTTCTACTATCTTC
** *
298195 AAGTCCAA-AGTCATTGGCCTTGAATCAGCACATT
1 AAGTCCAATA-TCGCTGGCCTTGAATTAGCACATT
298229 AGCGCATTTA
Statistics
Matches: 237, Mismatches: 42, Indels: 42
0.74 0.13 0.13
Matches are distributed among these distances:
50 34 0.14
51 5 0.02
52 136 0.57
53 12 0.05
54 4 0.02
55 2 0.01
56 5 0.02
57 4 0.02
58 1 0.00
59 34 0.14
ACGTcount: A:0.26, C:0.24, G:0.18, T:0.32
Consensus pattern (52 bp):
AAGTCCAATATCGCTGGCCTTGAATTAGCACATTGGCACTTCTACTATCTTC
Found at i:298077 original size:111 final size:111
Alignment explanation
Indices: 297929--298133 Score: 261
Period size: 111 Copynumber: 1.8 Consensus size: 111
297919 TTGTCATCCA
* * * *
297929 AAAGTCCAATATTGCTGGCCTTGAATTAGCATATTGGCACT-TC-TACTATCTTCAAGTCTAATG
1 AAAGTCCAATATCGCTGGCCTTGAATTAGCACATTGGCACTCTCAT-C-ATCTTCAAGTCCAATA
* * *
297992 TCGCTGGGCTTGAATTAGCACATTGACACTTGTCAAAACCTTCTTTCC
64 TCGCTGGCCTGGAATCAGCACATTGACACTTGTCAAAACCTTCTTTCC
* * * *
298040 AAAGTCCAATGTCGTTGGCCTTGAATTAGTACATTGGCACTCTCATCATCTTTAAGTCCAATATC
1 AAAGTCCAATATCGCTGGCCTTGAATTAGCACATTGGCACTCTCATCATCTTCAAGTCCAATATC
* *
298105 GTTGGCCTGGAATCAGCACATTGGCACTT
66 GCTGGCCTGGAATCAGCACATTGACACTT
298134 TTGTTATCTT
Statistics
Matches: 79, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
111 75 0.95
112 3 0.04
113 1 0.01
ACGTcount: A:0.26, C:0.23, G:0.18, T:0.33
Consensus pattern (111 bp):
AAAGTCCAATATCGCTGGCCTTGAATTAGCACATTGGCACTCTCATCATCTTCAAGTCCAATATC
GCTGGCCTGGAATCAGCACATTGACACTTGTCAAAACCTTCTTTCC
Found at i:298177 original size:163 final size:163
Alignment explanation
Indices: 297878--298179 Score: 365
Period size: 163 Copynumber: 1.9 Consensus size: 163
297868 CTTCATTTTT
** *
297878 AAGTCCAATGTCGCTGGCTTCGAATCAGCACATTGGCACCCTTGTCATCCAAAAGTCCAATATTG
1 AAGTCCAATGTCGCTGGCTTCGAATCAGCACATTGGCACCCTCATCATCCAAAAGTCCAATATCG
* * * * * * *
297943 CTGGCCTTGAATTAGCATATTGGCACTTCTACTATCTTCAAGTCTAATGTCGCTGGGCTTGAATT
66 CTGGCCTGGAATCAGCACATTGGCACTTCTACTATCTTCAAGCCCAATGTCGCTGAGCTTGAATC
298008 AGCACATTGACACTTGTCAAAACCTTCTTTCCA
131 AGCACATTGACACTTGTCAAAACCTTCTTTCCA
* * * * ***
298041 AAGTCCAATGTCGTTGGCCTT-GAATTAGTACATTGGCACTCTCATCATCTTTAAGTCCAATATC
1 AAGTCCAATGTCGCTGG-CTTCGAATCAGCACATTGGCACCCTCATCATCCAAAAGTCCAATATC
* * ** * *
298105 GTTGGCCTGGAATCAGCACATTGGCACTTTTGTTATCTTTAAGCCCAATGTTGCT-AGCTGTGAA
65 GCTGGCCTGGAATCAGCACATTGGCACTTCTACTATCTTCAAGCCCAATGTCGCTGAGCT-TGAA
298169 TCAGCACATTG
129 TCAGCACATTG
298180 GAAACTTTCA
Statistics
Matches: 114, Mismatches: 23, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
162 3 0.03
163 108 0.95
164 3 0.03
ACGTcount: A:0.25, C:0.24, G:0.18, T:0.32
Consensus pattern (163 bp):
AAGTCCAATGTCGCTGGCTTCGAATCAGCACATTGGCACCCTCATCATCCAAAAGTCCAATATCG
CTGGCCTGGAATCAGCACATTGGCACTTCTACTATCTTCAAGCCCAATGTCGCTGAGCTTGAATC
AGCACATTGACACTTGTCAAAACCTTCTTTCCA
Found at i:298993 original size:52 final size:50
Alignment explanation
Indices: 298875--299009 Score: 137
Period size: 52 Copynumber: 2.6 Consensus size: 50
298865 TTTGGAAAGA
* * * * * *
298875 AAATGTACCGATACATTTTTATTATATCGATACATTTTGGGTTTTGATCC
1 AAATGTATCGATACATTCTTAATGTATCAATACATTCTGGGTTTTGATCC
** * *
298925 AAATGTATTAATACATTCTTCATCGTATCAATACATTCTGGGTTTT-TTACC
1 AAATGTATCGATACATTCTTAAT-GTATCAATACATTCTGGGTTTTGAT-CC
298976 TAAATGTATCGATACATTCTTTAATGTATCAATA
1 -AAATGTATCGATACATTC-TTAATGTATCAATA
299010 TGTCTAATTA
Statistics
Matches: 68, Mismatches: 13, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
50 18 0.26
51 21 0.31
52 25 0.37
53 4 0.06
ACGTcount: A:0.31, C:0.15, G:0.11, T:0.43
Consensus pattern (50 bp):
AAATGTATCGATACATTCTTAATGTATCAATACATTCTGGGTTTTGATCC
Found at i:301404 original size:27 final size:27
Alignment explanation
Indices: 301367--301430 Score: 92
Period size: 27 Copynumber: 2.4 Consensus size: 27
301357 ATTTATCGAG
* *
301367 GATTCTTTAACCCCATTCTTCTGAGGA
1 GATTCTCTAACCCCATTCTTCTAAGGA
*
301394 GATTCTCTAACCCCATTCTTCTAAGGG
1 GATTCTCTAACCCCATTCTTCTAAGGA
*
301421 GATACTCTAA
1 GATTCTCTAA
301431 TCCTATTTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.25, C:0.27, G:0.14, T:0.34
Consensus pattern (27 bp):
GATTCTCTAACCCCATTCTTCTAAGGA
Found at i:305186 original size:13 final size:13
Alignment explanation
Indices: 305168--305193 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
305158 TACACAAAGT
305168 ATGTATCGATACA
1 ATGTATCGATACA
305181 ATGTATCGATACA
1 ATGTATCGATACA
305194 CCAAAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:305191 original size:32 final size:33
Alignment explanation
Indices: 305150--305213 Score: 103
Period size: 33 Copynumber: 2.0 Consensus size: 33
305140 TAGACAAACT
**
305150 TGTATCGATACA-CAAAGTATGTATCGATACAA
1 TGTATCGATACACCAAAAAATGTATCGATACAA
305182 TGTATCGATACACCAAAAAATGTATCGATACA
1 TGTATCGATACACCAAAAAATGTATCGATACA
305214 TTGGCTTGCA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 12 0.41
33 17 0.59
ACGTcount: A:0.42, C:0.17, G:0.14, T:0.27
Consensus pattern (33 bp):
TGTATCGATACACCAAAAAATGTATCGATACAA
Found at i:311341 original size:20 final size:21
Alignment explanation
Indices: 311272--311349 Score: 70
Period size: 20 Copynumber: 3.6 Consensus size: 21
311262 AATTTCCAAA
*
311272 ATGTATCGATACATGT-TTCT
1 ATGTATCGATACATCTATTCT
* *
311292 GTGTATCGATACATCTGGAAATTCA
1 ATGTATCGATACATCT----ATTCT
311317 ATGTATCGATACAT-TATTCT
1 ATGTATCGATACATCTATTCT
*
311337 TTGTATCGATACA
1 ATGTATCGATACA
311350 GGAGGATTAT
Statistics
Matches: 47, Mismatches: 6, Indels: 10
0.75 0.10 0.16
Matches are distributed among these distances:
20 30 0.64
24 1 0.02
25 16 0.34
ACGTcount: A:0.29, C:0.15, G:0.15, T:0.40
Consensus pattern (21 bp):
ATGTATCGATACATCTATTCT
Found at i:313847 original size:13 final size:13
Alignment explanation
Indices: 313829--313854 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
313819 TACACAAAGT
313829 ATGTATCGATACA
1 ATGTATCGATACA
313842 ATGTATCGATACA
1 ATGTATCGATACA
313855 CCAAAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:313852 original size:32 final size:33
Alignment explanation
Indices: 313811--313874 Score: 103
Period size: 33 Copynumber: 2.0 Consensus size: 33
313801 TAGCCAAACT
**
313811 TGTATCGATACA-CAAAGTATGTATCGATACAA
1 TGTATCGATACACCAAAAAATGTATCGATACAA
313843 TGTATCGATACACCAAAAAATGTATCGATACA
1 TGTATCGATACACCAAAAAATGTATCGATACA
313875 TTGGCTTGCA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 12 0.41
33 17 0.59
ACGTcount: A:0.42, C:0.17, G:0.14, T:0.27
Consensus pattern (33 bp):
TGTATCGATACACCAAAAAATGTATCGATACAA
Found at i:321254 original size:32 final size:32
Alignment explanation
Indices: 321213--321279 Score: 134
Period size: 32 Copynumber: 2.1 Consensus size: 32
321203 ACATAGATAA
321213 TTTCTGCAAGTAGAAGGAACCTCTTATTAATC
1 TTTCTGCAAGTAGAAGGAACCTCTTATTAATC
321245 TTTCTGCAAGTAGAAGGAACCTCTTATTAATC
1 TTTCTGCAAGTAGAAGGAACCTCTTATTAATC
321277 TTT
1 TTT
321280 GACATGGATA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.30, C:0.18, G:0.15, T:0.37
Consensus pattern (32 bp):
TTTCTGCAAGTAGAAGGAACCTCTTATTAATC
Found at i:323677 original size:19 final size:19
Alignment explanation
Indices: 323636--323709 Score: 96
Period size: 20 Copynumber: 3.8 Consensus size: 19
323626 CACACCTAGA
*
323636 TGTATCGATACATTATGCTT
1 TGTATCGATACATGAT-CTT
323656 TGTATCGATACATGATCTT
1 TGTATCGATACATGATCTT
*
323675 TGTATCGATACATGGA-CAAT
1 TGTATCGATACAT-GATC-TT
323695 TGTATCGATACATGA
1 TGTATCGATACATGA
323710 AACTGGCAGT
Statistics
Matches: 50, Mismatches: 2, Indels: 5
0.88 0.04 0.09
Matches are distributed among these distances:
19 19 0.38
20 31 0.62
ACGTcount: A:0.30, C:0.15, G:0.18, T:0.38
Consensus pattern (19 bp):
TGTATCGATACATGATCTT
Found at i:323762 original size:20 final size:20
Alignment explanation
Indices: 323737--323790 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 20
323727 CTACCACTGT
*
323737 TTGTATCGGTACATGGT-ACA
1 TTGTATCGGTACATGATGA-A
323757 TTGTATCGGTACATGATGAA
1 TTGTATCGGTACATGATGAA
*
323777 TTGTATCGATACAT
1 TTGTATCGGTACAT
323791 TGCTTCTAAC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
20 30 0.97
21 1 0.03
ACGTcount: A:0.28, C:0.13, G:0.22, T:0.37
Consensus pattern (20 bp):
TTGTATCGGTACATGATGAA
Found at i:331927 original size:13 final size:13
Alignment explanation
Indices: 331909--331933 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
331899 ACATTATGTT
331909 TGTATCGATACAA
1 TGTATCGATACAA
331922 TGTATCGATACA
1 TGTATCGATACA
331934 TGATCGTTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:331929 original size:32 final size:32
Alignment explanation
Indices: 331888--331952 Score: 105
Period size: 32 Copynumber: 2.0 Consensus size: 32
331878 AAAACCCTTG
*
331888 AATGTATCGATACATTAT-GTTTGTATCGATAC
1 AATGTATCGATACATGATCG-TTGTATCGATAC
331920 AATGTATCGATACATGATCGTTGTATCGATAC
1 AATGTATCGATACATGATCGTTGTATCGATAC
331952 A
1 A
331953 TGGACAATTA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
32 30 0.97
33 1 0.03
ACGTcount: A:0.32, C:0.14, G:0.17, T:0.37
Consensus pattern (32 bp):
AATGTATCGATACATGATCGTTGTATCGATAC
Found at i:332026 original size:20 final size:20
Alignment explanation
Indices: 332001--332054 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 20
331991 CTACCACTGT
*
332001 TTGTATCGATACATGGT-ACA
1 TTGTATCGATACATGATGA-A
332021 TTGTATCGATACATGATGAA
1 TTGTATCGATACATGATGAA
*
332041 TTGTATCAATACAT
1 TTGTATCGATACAT
332055 TGCTTCTAAC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
20 30 0.97
21 1 0.03
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.37
Consensus pattern (20 bp):
TTGTATCGATACATGATGAA
Found at i:334747 original size:29 final size:29
Alignment explanation
Indices: 334715--334831 Score: 110
Period size: 33 Copynumber: 3.8 Consensus size: 29
334705 TGCTTGCTGG
334715 TTGCTGTTTCTTTCTTTCTTTTTGCTTAA
1 TTGCTGTTTCTTTCTTTCTTTTTGCTTAA
* * *
334744 TTGCTGTTGCTATTACTTGCTTTGCTTGC-TGA
1 TTGCTGTTTCT-TT-CTTTCTTT--TTGCTTAA
* *
334776 TTGTTGTTTCTTTCTTTCTTTTTACTTAA
1 TTGCTGTTTCTTTCTTTCTTTTTGCTTAA
334805 TTGCTATTGTTTTCTTTCTTTCTTTTT
1 TTGC---TG-TTTCTTTCTTTCTTTTT
334832 CGGTGTTTCT
Statistics
Matches: 70, Mismatches: 9, Indels: 14
0.75 0.10 0.15
Matches are distributed among these distances:
28 3 0.04
29 15 0.21
30 9 0.13
31 9 0.13
32 13 0.19
33 21 0.30
ACGTcount: A:0.08, C:0.16, G:0.12, T:0.64
Consensus pattern (29 bp):
TTGCTGTTTCTTTCTTTCTTTTTGCTTAA
Found at i:336936 original size:28 final size:28
Alignment explanation
Indices: 336905--336967 Score: 69
Period size: 25 Copynumber: 2.3 Consensus size: 28
336895 AAAAAATTTC
*
336905 AAAGAAAAGTTTAAAAAAACAAAAAAAA
1 AAAGAAAAGTGTAAAAAAACAAAAAAAA
**
336933 AAAG--AA-TGTGCAAAAACAAAAAAAA
1 AAAGAAAAGTGTAAAAAAACAAAAAAAA
336958 AAAGCAAAAG
1 AAAG-AAAAG
336968 AAACACAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
25 20 0.71
26 2 0.07
28 6 0.21
ACGTcount: A:0.75, C:0.06, G:0.11, T:0.08
Consensus pattern (28 bp):
AAAGAAAAGTGTAAAAAAACAAAAAAAA
Found at i:340963 original size:20 final size:20
Alignment explanation
Indices: 340921--340972 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 20
340911 CAAAGCCAAT
* *
340921 TGTATCAATACATTTAGGAA
1 TGTATCGATACATTTACGAA
**
340941 TGTATCGATACATTTACTCA
1 TGTATCGATACATTTACGAA
*
340961 TGTATTGATACA
1 TGTATCGATACA
340973 ATTTTTCAAG
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.38
Consensus pattern (20 bp):
TGTATCGATACATTTACGAA
Found at i:342111 original size:33 final size:34
Alignment explanation
Indices: 342069--342260 Score: 136
Period size: 31 Copynumber: 5.9 Consensus size: 34
342059 TCTTTTTTCA
*
342069 AAAGTCCACACAAGTTGGTGGCAACTCTTTTCTT
1 AAAGCCCACACAAGTTGGTGGCAACTCTTTTCTT
* *
342103 AAA-CCCACACAAGTTGGTGTC-A-T-TTTTTTT
1 AAAGCCCACACAAGTTGGTGGCAACTCTTTTCTT
* * ** *
342133 AAAGCCCGCACCAGTTGGTGGCATTTTTTTTC-T
1 AAAGCCCACACAAGTTGGTGGCAACTCTTTTCTT
* *** *
342166 AAAGCCCATACAAGTCAATGGCAAC-C-CTT-TT
1 AAAGCCCACACAAGTTGGTGGCAACTCTTTTCTT
*
342197 AAAGCCCACACAAGATGGTGGCAAC-C--TTCTT
1 AAAGCCCACACAAGTTGGTGGCAACTCTTTTCTT
** * *
342228 AAAAGCCTGCACAGGTTGGTGGCATCTCTTTTC
1 -AAAGCCCACACAAGTTGGTGGCAACTCTTTTC
342261 AAACCCACTA
Statistics
Matches: 120, Mismatches: 28, Indels: 19
0.72 0.17 0.11
Matches are distributed among these distances:
30 11 0.09
31 42 0.35
32 21 0.17
33 36 0.30
34 7 0.06
35 3 0.03
ACGTcount: A:0.27, C:0.25, G:0.18, T:0.30
Consensus pattern (34 bp):
AAAGCCCACACAAGTTGGTGGCAACTCTTTTCTT
Found at i:342152 original size:31 final size:32
Alignment explanation
Indices: 342069--342180 Score: 120
Period size: 33 Copynumber: 3.5 Consensus size: 32
342059 TCTTTTTTCA
* * *
342069 AAAGTCCACACAAGTTGGTGGCAACTCTTTTCTT
1 AAAGCCCACACAAGTTGGTGGC-A-TTTTTTTTT
*
342103 AAA-CCCACACAAGTTGGTGTCA-TTTTTTTT
1 AAAGCCCACACAAGTTGGTGGCATTTTTTTTT
* *
342133 AAAGCCCGCACCAGTTGGTGGCATTTTTTTTCT
1 AAAGCCCACACAAGTTGGTGGCATTTTTTTT-T
*
342166 AAAGCCCATACAAGT
1 AAAGCCCACACAAGT
342181 CAATGGCAAC
Statistics
Matches: 65, Mismatches: 10, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
30 9 0.14
31 16 0.25
32 8 0.12
33 29 0.45
34 3 0.05
ACGTcount: A:0.27, C:0.23, G:0.17, T:0.33
Consensus pattern (32 bp):
AAAGCCCACACAAGTTGGTGGCATTTTTTTTT
Found at i:342469 original size:52 final size:52
Alignment explanation
Indices: 342361--342711 Score: 182
Period size: 52 Copynumber: 6.7 Consensus size: 52
342351 CTTCATTTTT
* * * ***
342361 AAGTCCAATGTCGCTGG-CTTCGAATCAGCACATTGGCACCCTTGT-C-ATCCAA
1 AAGTCCAATATCGCTGGCCTT-GAATTAGCACATTGGCA--CTTCTACTATCTTC
* *
342413 AAGTCCAATATTGCTGGCCTTGAATTAGCATATTGGCACTTCTACTATCTTC
1 AAGTCCAATATCGCTGGCCTTGAATTAGCACATTGGCACTTCTACTATCTTC
* * * * * *
342465 AAGTCTAATGTCGCTGGCCTTGAATTAGCACATTGACACTTGTCAAAACCTTTTTTCC
1 AAGTCCAATATCGCTGGCCTTGAATTAGCACATTGGCAC-T-TC--TA-CTATCTT-C
* * * *
342523 AAAGTCCAATGTCGTTGGCCTTGAATTAGTACATTGGCAC-TCT-CATCATCTTT
1 -AAGTCCAATATCGCTGGCCTTGAATTAGCACATTGGCACTTCTAC-T-ATCTTC
* * * * ** *
342576 AAGTCCAATATCGTTGGCCTGGAATCAGCACATTGGCACTTTTGTTATCTTT
1 AAGTCCAATATCGCTGGCCTTGAATTAGCACATTGGCACTTCTACTATCTTC
* * * * * * *
342628 AAGCCCAATGTTGCTAG-CTGTGAATCAGCACATTGGAAACTT-T-C-ATCTTT
1 AAGTCCAATATCGCTGGCCT-TGAATTAGCACATTGG-CACTTCTACTATCTTC
** *
342678 AAGTCCAA-AGTCATTGGCCTTGAATCAGCACATT
1 AAGTCCAATA-TCGCTGGCCTTGAATTAGCACATT
342712 AGCGCATTTA
Statistics
Matches: 237, Mismatches: 44, Indels: 38
0.74 0.14 0.12
Matches are distributed among these distances:
50 34 0.14
51 5 0.02
52 137 0.58
53 12 0.05
54 5 0.02
56 3 0.01
57 5 0.02
58 1 0.00
59 35 0.15
ACGTcount: A:0.26, C:0.24, G:0.17, T:0.33
Consensus pattern (52 bp):
AAGTCCAATATCGCTGGCCTTGAATTAGCACATTGGCACTTCTACTATCTTC
Found at i:342561 original size:111 final size:111
Alignment explanation
Indices: 342412--342616 Score: 270
Period size: 111 Copynumber: 1.8 Consensus size: 111
342402 TTGTCATCCA
* * * *
342412 AAAGTCCAATATTGCTGGCCTTGAATTAGCATATTGGCACT-TC-TACTATCTTCAAGTCTAATG
1 AAAGTCCAATATCGCTGGCCTTGAATTAGCACATTGGCACTCTCAT-C-ATCTTCAAGTCCAATA
* *
342475 TCGCTGGCCTTGAATTAGCACATTGACACTTGTCAAAACCTTTTTTCC
64 TCGCTGGCCTGGAATCAGCACATTGACACTTGTCAAAACCTTTTTTCC
* * * *
342523 AAAGTCCAATGTCGTTGGCCTTGAATTAGTACATTGGCACTCTCATCATCTTTAAGTCCAATATC
1 AAAGTCCAATATCGCTGGCCTTGAATTAGCACATTGGCACTCTCATCATCTTCAAGTCCAATATC
* *
342588 GTTGGCCTGGAATCAGCACATTGGCACTT
66 GCTGGCCTGGAATCAGCACATTGACACTT
342617 TTGTTATCTT
Statistics
Matches: 80, Mismatches: 12, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
111 76 0.95
112 3 0.04
113 1 0.01
ACGTcount: A:0.26, C:0.23, G:0.17, T:0.34
Consensus pattern (111 bp):
AAAGTCCAATATCGCTGGCCTTGAATTAGCACATTGGCACTCTCATCATCTTCAAGTCCAATATC
GCTGGCCTGGAATCAGCACATTGACACTTGTCAAAACCTTTTTTCC
Found at i:342660 original size:163 final size:163
Alignment explanation
Indices: 342361--342662 Score: 365
Period size: 163 Copynumber: 1.9 Consensus size: 163
342351 CTTCATTTTT
** *
342361 AAGTCCAATGTCGCTGGCTTCGAATCAGCACATTGGCACCCTTGTCATCCAAAAGTCCAATATTG
1 AAGTCCAATGTCGCTGGCTTCGAATCAGCACATTGGCACCCTCATCATCCAAAAGTCCAATATCG
* * * * * * *
342426 CTGGCCTTGAATTAGCATATTGGCACTTCTACTATCTTCAAGTCTAATGTCGCTGGCCTTGAATT
66 CTGGCCTGGAATCAGCACATTGGCACTTCTACTATCTTCAAGCCCAATGTCGCTAGCCTTGAATC
342491 AGCACATTGACACTTGTCAAAACCTTTTTTCCA
131 AGCACATTGACACTTGTCAAAACCTTTTTTCCA
* * * * ***
342524 AAGTCCAATGTCGTTGGCCTT-GAATTAGTACATTGGCACTCTCATCATCTTTAAGTCCAATATC
1 AAGTCCAATGTCGCTGG-CTTCGAATCAGCACATTGGCACCCTCATCATCCAAAAGTCCAATATC
* * ** * *
342588 GTTGGCCTGGAATCAGCACATTGGCACTTTTGTTATCTTTAAGCCCAATGTTGCTAG-CTGTGAA
65 GCTGGCCTGGAATCAGCACATTGGCACTTCTACTATCTTCAAGCCCAATGTCGCTAGCCT-TGAA
342652 TCAGCACATTG
129 TCAGCACATTG
342663 GAAACTTTCA
Statistics
Matches: 114, Mismatches: 23, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
162 2 0.02
163 109 0.96
164 3 0.03
ACGTcount: A:0.25, C:0.24, G:0.18, T:0.33
Consensus pattern (163 bp):
AAGTCCAATGTCGCTGGCTTCGAATCAGCACATTGGCACCCTCATCATCCAAAAGTCCAATATCG
CTGGCCTGGAATCAGCACATTGGCACTTCTACTATCTTCAAGCCCAATGTCGCTAGCCTTGAATC
AGCACATTGACACTTGTCAAAACCTTTTTTCCA
Found at i:343476 original size:52 final size:50
Alignment explanation
Indices: 343358--343492 Score: 137
Period size: 52 Copynumber: 2.6 Consensus size: 50
343348 TTTGGAAAGA
* * * * * *
343358 AAATGTACCGATACATTTTTATTATATCGATACATTTTGGGTTTTGATCC
1 AAATGTATCGATACATTCTTAATGTATCAATACATTCTGGGTTTTGATCC
** * *
343408 AAATGTATTAATACATTCTTCATCGTATCAATACATTCTGGGTTTT-TTACC
1 AAATGTATCGATACATTCTTAAT-GTATCAATACATTCTGGGTTTTGAT-CC
343459 TAAATGTATCGATACATTCTTTAATGTATCAATA
1 -AAATGTATCGATACATTC-TTAATGTATCAATA
343493 TGTCTAATTA
Statistics
Matches: 68, Mismatches: 13, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
50 18 0.26
51 21 0.31
52 25 0.37
53 4 0.06
ACGTcount: A:0.31, C:0.15, G:0.11, T:0.43
Consensus pattern (50 bp):
AAATGTATCGATACATTCTTAATGTATCAATACATTCTGGGTTTTGATCC
Found at i:345888 original size:27 final size:27
Alignment explanation
Indices: 345851--345914 Score: 92
Period size: 27 Copynumber: 2.4 Consensus size: 27
345841 ATTTATCGAG
* *
345851 GATTCTTTAACCCCATTCTTCTGAGGA
1 GATTCTCTAACCCCATTCTTCTAAGGA
*
345878 GATTCTCTAACCCCATTCTTCTAAGGG
1 GATTCTCTAACCCCATTCTTCTAAGGA
*
345905 GATACTCTAA
1 GATTCTCTAA
345915 TCCTATTTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.25, C:0.27, G:0.14, T:0.34
Consensus pattern (27 bp):
GATTCTCTAACCCCATTCTTCTAAGGA
Found at i:349674 original size:13 final size:13
Alignment explanation
Indices: 349656--349681 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
349646 TACACAAAGT
349656 ATGTATCGATACA
1 ATGTATCGATACA
349669 ATGTATCGATACA
1 ATGTATCGATACA
349682 CCAAAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:349679 original size:32 final size:33
Alignment explanation
Indices: 349638--349701 Score: 103
Period size: 33 Copynumber: 2.0 Consensus size: 33
349628 TAGCCAAACT
**
349638 TGTATCGATACA-CAAAGTATGTATCGATACAA
1 TGTATCGATACACCAAAAAATGTATCGATACAA
349670 TGTATCGATACACCAAAAAATGTATCGATACA
1 TGTATCGATACACCAAAAAATGTATCGATACA
349702 TTGGCTTGCA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 12 0.41
33 17 0.59
ACGTcount: A:0.42, C:0.17, G:0.14, T:0.27
Consensus pattern (33 bp):
TGTATCGATACACCAAAAAATGTATCGATACAA
Found at i:358268 original size:20 final size:19
Alignment explanation
Indices: 358222--358276 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 19
358212 AAAACCCTTA
358222 AAAGTATCGATATACA-ATTC
1 AAAGTATCG--ATACATATTC
358242 AAAGTATCGATACATATTGC
1 AAAGTATCGATACATATT-C
*
358262 AATGTATCGATACAT
1 AAAGTATCGATACAT
358277 GAAAAAGATG
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
18 5 0.16
19 3 0.09
20 24 0.75
ACGTcount: A:0.42, C:0.15, G:0.13, T:0.31
Consensus pattern (19 bp):
AAAGTATCGATACATATTC
Found at i:358365 original size:13 final size:13
Alignment explanation
Indices: 358347--358372 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
358337 TACACAAAGT
358347 ATGTATCGATACA
1 ATGTATCGATACA
358360 ATGTATCGATACA
1 ATGTATCGATACA
358373 CCAAAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:358370 original size:32 final size:33
Alignment explanation
Indices: 358329--358392 Score: 103
Period size: 33 Copynumber: 2.0 Consensus size: 33
358319 TAGCCAAACT
**
358329 TGTATCGATACA-CAAAGTATGTATCGATACAA
1 TGTATCGATACACCAAAAAATGTATCGATACAA
358361 TGTATCGATACACCAAAAAATGTATCGATACA
1 TGTATCGATACACCAAAAAATGTATCGATACA
358393 TTGGCTTGCA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 12 0.41
33 17 0.59
ACGTcount: A:0.42, C:0.17, G:0.14, T:0.27
Consensus pattern (33 bp):
TGTATCGATACACCAAAAAATGTATCGATACAA
Found at i:365787 original size:32 final size:32
Alignment explanation
Indices: 365746--365812 Score: 134
Period size: 32 Copynumber: 2.1 Consensus size: 32
365736 ACATAGATAA
365746 TTTCTGCAAGTAGAAGGAACCTCTTATTAATC
1 TTTCTGCAAGTAGAAGGAACCTCTTATTAATC
365778 TTTCTGCAAGTAGAAGGAACCTCTTATTAATC
1 TTTCTGCAAGTAGAAGGAACCTCTTATTAATC
365810 TTT
1 TTT
365813 GACATGGATA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.30, C:0.18, G:0.15, T:0.37
Consensus pattern (32 bp):
TTTCTGCAAGTAGAAGGAACCTCTTATTAATC
Found at i:373017 original size:8 final size:8
Alignment explanation
Indices: 372999--373054 Score: 57
Period size: 7 Copynumber: 7.4 Consensus size: 8
372989 AAGAAAAATA
372999 TTTTA-AT
1 TTTTATAT
373006 TTTTATAT
1 TTTTATAT
*
373014 TTTTA-AA
1 TTTTATAT
*
373021 TTTAATA-
1 TTTTATAT
373028 TTTTA-AT
1 TTTTATAT
373035 TTTTATAT
1 TTTTATAT
373043 TTTTAATAT
1 TTTT-ATAT
373052 TTT
1 TTT
373055 AGTAAATGAA
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
6 1 0.02
7 19 0.46
8 14 0.34
9 7 0.17
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (8 bp):
TTTTATAT
Found at i:373019 original size:15 final size:15
Alignment explanation
Indices: 372999--373055 Score: 80
Period size: 15 Copynumber: 3.8 Consensus size: 15
372989 AAGAAAAATA
372999 TTTTAATTTTTATAT
1 TTTTAATTTTTATAT
* *
373014 TTTTAAATTTAATA-
1 TTTTAATTTTTATAT
373028 TTTTAATTTTTATAT
1 TTTTAATTTTTATAT
373043 TTTTAATATTTTA
1 TTTTAAT-TTTTA
373056 GTAAATGAAG
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
14 12 0.33
15 19 0.53
16 5 0.14
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (15 bp):
TTTTAATTTTTATAT
Found at i:373024 original size:21 final size:21
Alignment explanation
Indices: 373000--373055 Score: 69
Period size: 21 Copynumber: 2.6 Consensus size: 21
372990 AGAAAAATAT
373000 TTTAAT-TTTTATATTTTTAAA
1 TTTAATATTTTA-ATTTTTAAA
*
373021 TTTAATATTTTAATTTTTATATT
1 TTTAATATTTTAATTTTTA-A-A
373044 TTTAATATTTTA
1 TTTAATATTTTA
373056 GTAAATGAAG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
21 13 0.42
22 6 0.19
23 12 0.39
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (21 bp):
TTTAATATTTTAATTTTTAAA
Found at i:373028 original size:29 final size:30
Alignment explanation
Indices: 372995--373053 Score: 111
Period size: 29 Copynumber: 2.0 Consensus size: 30
372985 GTGAAAGAAA
372995 AATATTTTAATTTTTATATTTTTAA-ATTT
1 AATATTTTAATTTTTATATTTTTAATATTT
373024 AATATTTTAATTTTTATATTTTTAATATTT
1 AATATTTTAATTTTTATATTTTTAATATTT
373054 TAGTAAATGA
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
29 25 0.86
30 4 0.14
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (30 bp):
AATATTTTAATTTTTATATTTTTAATATTT
Found at i:373055 original size:8 final size:8
Alignment explanation
Indices: 372995--373055 Score: 62
Period size: 8 Copynumber: 8.1 Consensus size: 8
372985 GTGAAAGAAA
372995 AATATTTT
1 AATATTTT
373003 AAT-TTTT
1 AATATTTT
373010 -ATATTTTT
1 AATA-TTTT
373018 AA-A-TTT
1 AATATTTT
373024 AATATTTT
1 AATATTTT
373032 AAT-TTTT
1 AATATTTT
373039 -ATATTTTT
1 AATA-TTTT
373047 AATATTTT
1 AATATTTT
373055 A
1 A
373056 GTAAATGAAG
Statistics
Matches: 45, Mismatches: 0, Indels: 16
0.74 0.00 0.26
Matches are distributed among these distances:
6 9 0.20
7 9 0.20
8 23 0.51
9 4 0.09
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (8 bp):
AATATTTT
Found at i:373120 original size:19 final size:19
Alignment explanation
Indices: 373074--373122 Score: 57
Period size: 18 Copynumber: 2.6 Consensus size: 19
373064 AGAAAATTGG
373074 TTAATGATATTAAAAAAGAT
1 TTAAT-ATATTAAAAAAGAT
*
373094 TTAA-ATATTAATAAA-AT
1 TTAATATATTAAAAAAGAT
373111 ATTAATATATTA
1 -TTAATATATTA
373123 TGTGATATGA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
17 2 0.08
18 14 0.54
19 6 0.23
20 4 0.15
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.41
Consensus pattern (19 bp):
TTAATATATTAAAAAAGAT
Found at i:374949 original size:151 final size:152
Alignment explanation
Indices: 374710--375024 Score: 437
Period size: 152 Copynumber: 2.1 Consensus size: 152
374700 AGACCCTAGA
374710 GGACTT-AAAAA-GATGAAAACAAACCTACTCTTAATTCGTACTTTCGGCATAGAAGCGGGCCCG
1 GGACTTGAAAAAGGATGAAAACAAACCTACTCTTAATTCGTACTTTCGGCATAGAAGCGGGCCCG
** *
374773 ATAGTTTTATAGGACTAGATTTTCGA-AAATATGCAAACATATCCCTAAGGTTTA-CTATCGACT
66 ATAGTTTTATAGGACTAGAGCTTCGAGAAATATACAAACATATCCCTAAGGTTTATC-ATCGACT
*** *
374836 TAGAAGTGCTTGGTGATCTTAAG
130 TAGAAGTGCCCAGTGATCCTAAG
* ** *
374859 GGACTTGAAAAAGGGTGAAAACAAACCTACT-TCTAATTCGTACCTTT-GGTGTAGAAGCGGATC
1 GGACTTGAAAAAGGATGAAAACAAACCTACTCT-TAATTCGTA-CTTTCGGCATAGAAGCGG-GC
*
374922 CCGATAGTTTTATAGGACTAG-GCTTCGAGAAATATACAAACATATCCTTAAGGTTTATCATCGA
63 CCGATAGTTTTATAGGACTAGAGCTTCGAGAAATATACAAACATATCCCTAAGGTTTATCATCGA
374986 CTTAGAAGTGCCCAGTGATCCTAAG
128 CTTAGAAGTGCCCAGTGATCCTAAG
375011 GGACTTGAAAAAGG
1 GGACTTGAAAAAGG
375025 TTGCAAAGAG
Statistics
Matches: 147, Mismatches: 12, Indels: 11
0.86 0.07 0.06
Matches are distributed among these distances:
149 6 0.04
150 6 0.04
151 42 0.29
152 92 0.63
153 1 0.01
ACGTcount: A:0.34, C:0.17, G:0.21, T:0.28
Consensus pattern (152 bp):
GGACTTGAAAAAGGATGAAAACAAACCTACTCTTAATTCGTACTTTCGGCATAGAAGCGGGCCCG
ATAGTTTTATAGGACTAGAGCTTCGAGAAATATACAAACATATCCCTAAGGTTTATCATCGACTT
AGAAGTGCCCAGTGATCCTAAG
Found at i:376130 original size:19 final size:19
Alignment explanation
Indices: 376106--376167 Score: 54
Period size: 19 Copynumber: 3.2 Consensus size: 19
376096 TTTTGAATTT
376106 CAAACAATTTGTATCGATA
1 CAAACAATTTGTATCGATA
**
376125 CAAACAGTAACTGTATCGATA
1 CAAACA--ATTTGTATCGATA
* *
376146 CATA-AGTGTTGTATCGATA
1 CAAACAAT-TTGTATCGATA
376165 CAA
1 CAA
376168 TGTATCAATA
Statistics
Matches: 33, Mismatches: 7, Indels: 6
0.72 0.15 0.13
Matches are distributed among these distances:
19 18 0.55
20 1 0.03
21 14 0.42
ACGTcount: A:0.40, C:0.16, G:0.15, T:0.29
Consensus pattern (19 bp):
CAAACAATTTGTATCGATA
Found at i:376179 original size:32 final size:32
Alignment explanation
Indices: 376136--376198 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
376126 AAACAGTAAC
*
376136 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCAATACATAAGTGTTGTATCGATACAA
376168 TGTATCAATACATAAGTGTTGTATCGATACA
1 TGTATCAATACATAAGTGTTGTATCGATACA
376199 TAAGTTTTGT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.17, T:0.35
Consensus pattern (32 bp):
TGTATCAATACATAAGTGTTGTATCGATACAA
Found at i:376192 original size:19 final size:19
Alignment explanation
Indices: 376136--376217 Score: 104
Period size: 19 Copynumber: 4.6 Consensus size: 19
376126 AAACAGTAAC
376136 TGTATCGATACATAAGTGT
1 TGTATCGATACATAAGTGT
376155 TGTATCGATAC--AA----
1 TGTATCGATACATAAGTGT
*
376168 TGTATCAATACATAAGTGT
1 TGTATCGATACATAAGTGT
*
376187 TGTATCGATACATAAGTTT
1 TGTATCGATACATAAGTGT
376206 TGTATCGATACA
1 TGTATCGATACA
376218 ATGTATCGCT
Statistics
Matches: 54, Mismatches: 3, Indels: 12
0.78 0.04 0.17
Matches are distributed among these distances:
13 10 0.19
15 2 0.04
17 2 0.04
19 40 0.74
ACGTcount: A:0.34, C:0.12, G:0.17, T:0.37
Consensus pattern (19 bp):
TGTATCGATACATAAGTGT
Found at i:376289 original size:13 final size:13
Alignment explanation
Indices: 376271--376295 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
376261 TTACTCAATG
376271 TATCGATACATTA
1 TATCGATACATTA
376284 TATCGATACATT
1 TATCGATACATT
376296 GATCTTTTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.08, T:0.40
Consensus pattern (13 bp):
TATCGATACATTA
Found at i:380442 original size:13 final size:13
Alignment explanation
Indices: 380424--380448 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
380414 CAAAGATCAG
380424 TGTATCGATACAA
1 TGTATCGATACAA
380437 TGTATCGATACA
1 TGTATCGATACA
380449 TTTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:380526 original size:33 final size:33
Alignment explanation
Indices: 380489--380555 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
380479 AGTAGCTTAA
380489 ATTGTATCGATACAAAAAAGTATGTATCGATAC
1 ATTGTATCGATACAAAAAAGTATGTATCGATAC
* ***
380522 ATTGTATCGATACAACATTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAGTATGTATCGATAC
380555 A
1 A
380556 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.39, C:0.13, G:0.13, T:0.34
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAGTATGTATCGATAC
Found at i:380529 original size:13 final size:13
Alignment explanation
Indices: 380511--380535 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
380501 CAAAAAAGTA
380511 TGTATCGATACAT
1 TGTATCGATACAT
380524 TGTATCGATACA
1 TGTATCGATACA
380536 ACATTTTATG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:382282 original size:51 final size:51
Alignment explanation
Indices: 382217--382356 Score: 174
Period size: 51 Copynumber: 2.7 Consensus size: 51
382207 ATTTTTCATC
* * * * *
382217 TCGGGGATACTCCAA-TCCCGGTTTCATTTCCAAGACATCAATTTTTCTTAA
1 TCGGGGATACTCCAACT-CCGATTTCATTTCCAAAACACCAATTTTCCATAA
* * *
382268 TCGGGGATACTCCAACTCCGATTTTATTTCTAAAACACCCATTTTCCATAA
1 TCGGGGATACTCCAACTCCGATTTCATTTCCAAAACACCAATTTTCCATAA
* *
382319 TCGGGGATACTCCAACTTCGATTTTATTTCCAAAACAC
1 TCGGGGATACTCCAACTCCGATTTCATTTCCAAAACAC
382357 TGACTTTTTA
Statistics
Matches: 78, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
51 77 0.99
52 1 0.01
ACGTcount: A:0.28, C:0.26, G:0.12, T:0.34
Consensus pattern (51 bp):
TCGGGGATACTCCAACTCCGATTTCATTTCCAAAACACCAATTTTCCATAA
Found at i:382372 original size:51 final size:51
Alignment explanation
Indices: 382217--382385 Score: 171
Period size: 51 Copynumber: 3.3 Consensus size: 51
382207 ATTTTTCATC
* * * * * * **
382217 TCGGGGATACTCCAA-TCCCGGTTTCATTTCCAAGACATCAATTTTTCTTAA
1 TCGGGGATACTCCAACT-CCGATTTTATTTCCAAAACACCCATTTTCCACAA
* *
382268 TCGGGGATACTCCAACTCCGATTTTATTTCTAAAACACCCATTTTCCATAA
1 TCGGGGATACTCCAACTCCGATTTTATTTCCAAAACACCCATTTTCCACAA
* ** *
382319 TCGGGGATACTCCAACTTCGATTTTATTTCCAAAACACTGACTTTT-TACAA
1 TCGGGGATACTCCAACTCCGATTTTATTTCCAAAACACCCA-TTTTCCACAA
*
382370 TCGGAGATACTCCAAC
1 TCGGGGATACTCCAAC
382386 CCTCGTTATT
Statistics
Matches: 101, Mismatches: 15, Indels: 4
0.84 0.12 0.03
Matches are distributed among these distances:
51 96 0.95
52 5 0.05
ACGTcount: A:0.28, C:0.26, G:0.12, T:0.33
Consensus pattern (51 bp):
TCGGGGATACTCCAACTCCGATTTTATTTCCAAAACACCCATTTTCCACAA
Found at i:382548 original size:79 final size:80
Alignment explanation
Indices: 382325--382699 Score: 344
Period size: 79 Copynumber: 4.8 Consensus size: 80
382315 ATAATCGGGG
* * * * * * *
382325 ATACTCCAACTTC-GATTTTATTTCCAAAACACTGACTTTTT-ACAATCGGAGATACTCCAACCC
1 ATACTCCAACCTCTGGTTTTATTTCTAAAACA-TCAATTTTTCATAATCGGGGATACTCCAACCC
* *
382388 TCGTTATTTCCCAGGGG
65 -CGTTATTTCCGAGGGA
* *
382405 ACACTCCAACC-CTGGTTTTATTTCTAAAACATCAATTTTTC---ATCGGGGATACTCCAGCCCC
1 ATACTCCAACCTCTGGTTTTATTTCTAAAACATCAATTTTTCATAATCGGGGATACTCCAACCCC
382466 GTTATTTCCGAGGGA
66 GTTATTTCCGAGGGA
* * * * * *
382481 ATACTCTAACCTC-GGCTTTATTT-TCAAAATATTAATTTCTCATAATCGGGGATACTCCAAACC
1 ATACTCCAACCTCTGGTTTTATTTCT-AAAACATCAATTTTTCATAATCGGGGATACTCCAACCC
* *
382544 CGTTATTTTCGTCGGG-
65 CGTTATTTCCG-AGGGA
* *
382560 ATACTCCAA-CTCTGGTTTTATTTCTAAAACATCAATTTTTCATAATCGGGAATACTCCAATCCC
1 ATACTCCAACCTCTGGTTTTATTTCTAAAACATCAATTTTTCATAATCGGGGATACTCCAACCCC
*
382624 GTTATTTCC-AAGGA
66 GTTATTTCCGAGGGA
* * * * * * *
382638 GATACTCCAACC-CCGATTTTATTT-TCAAAATACCGATTTTTTATAATCAGGGATACTCCAAC
1 -ATACTCCAACCTCTGGTTTTATTTCT-AAAACATCAATTTTTCATAATCGGGGATACTCCAAC
382700 TCTATTTCTT
Statistics
Matches: 242, Mismatches: 39, Indels: 29
0.78 0.13 0.09
Matches are distributed among these distances:
75 1 0.00
76 45 0.19
77 20 0.08
78 4 0.02
79 142 0.59
80 30 0.12
ACGTcount: A:0.28, C:0.25, G:0.13, T:0.34
Consensus pattern (80 bp):
ATACTCCAACCTCTGGTTTTATTTCTAAAACATCAATTTTTCATAATCGGGGATACTCCAACCCC
GTTATTTCCGAGGGA
Found at i:382684 original size:158 final size:155
Alignment explanation
Indices: 382322--382698 Score: 459
Period size: 158 Copynumber: 2.4 Consensus size: 155
382312 TCCATAATCG
* * * * * * *
382322 GGGATACTCCAACTTCGATTTTATTTCCAAAACACTGACTTTTTACAATCGGAGATACTCCAACC
1 GGGATACTCCAACCTCGATTTTATTTTCAAAATACTGATTTTTTATAATCGGGGATACTCCAAAC
*
382387 CTCGTTATTTCCCAGGGGACACTCCAACCCTGGTTTTATTTCTAAAACATCAATTTTTCATCGGG
66 CTCGTTATTTCCCACGGGACACTCCAACCCTGGTTTTATTTCTAAAACATCAATTTTTCATCGGG
* * *
382452 GATACTCCAGCCCCGTTATTTCCGA
131 AATACTCCAACCCCGTTATTTCCAA
* ** * * * *
382477 GGGAATACTCTAACCTCGGCTTTATTTTCAAAATATTAATTTCTCATAATCGGGGATACTCCAAA
1 GGG-ATACTCCAACCTCGATTTTATTTTCAAAATACTGATTTTTTATAATCGGGGATACTCCAAA
* ** * *
382542 CC-CGTTATTTTCGTCGGGATACTCCAACTCTGGTTTTATTTCTAAAACATCAATTTTTCATAAT
65 CCTCGTTATTTCCCACGGGACACTCCAACCCTGGTTTTATTTCTAAAACATCAATTTTTC---AT
*
382606 CGGGAATACTCCAATCCCGTTATTTCCAA
127 CGGGAATACTCCAACCCCGTTATTTCCAA
* * *
382635 GGAGATACTCCAACCCCGATTTTATTTTCAAAATACCGATTTTTTATAATCAGGGATACTCCAA
1 GG-GATACTCCAACCTCGATTTTATTTTCAAAATACTGATTTTTTATAATCGGGGATACTCCAA
382699 CTCTATTTCT
Statistics
Matches: 183, Mismatches: 34, Indels: 7
0.82 0.15 0.03
Matches are distributed among these distances:
155 54 0.30
156 49 0.27
158 79 0.43
159 1 0.01
ACGTcount: A:0.28, C:0.25, G:0.13, T:0.34
Consensus pattern (155 bp):
GGGATACTCCAACCTCGATTTTATTTTCAAAATACTGATTTTTTATAATCGGGGATACTCCAAAC
CTCGTTATTTCCCACGGGACACTCCAACCCTGGTTTTATTTCTAAAACATCAATTTTTCATCGGG
AATACTCCAACCCCGTTATTTCCAA
Found at i:384563 original size:13 final size:13
Alignment explanation
Indices: 384545--384571 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
384535 GATACATGGC
384545 ACAATGTATCGAT
1 ACAATGTATCGAT
384558 ACAATGTATCGAT
1 ACAATGTATCGAT
384571 A
1 A
384572 TATGAAGAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ACAATGTATCGAT
Found at i:385717 original size:18 final size:18
Alignment explanation
Indices: 385694--385740 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
385684 GGGAAGGAAA
*
385694 TATTTTTTTTACTTTATT-
1 TATTTTTTTTA-GTTATTC
*
385712 TATTTTATTTAGTTATTC
1 TATTTTTTTTAGTTATTC
*
385730 TTTTTTTTTTA
1 TATTTTTTTTA
385741 ATTTTTAAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
17 5 0.21
18 19 0.79
ACGTcount: A:0.17, C:0.04, G:0.02, T:0.77
Consensus pattern (18 bp):
TATTTTTTTTAGTTATTC
Found at i:386293 original size:109 final size:110
Alignment explanation
Indices: 386170--386619 Score: 454
Period size: 109 Copynumber: 4.1 Consensus size: 110
386160 CGTATGTTAT
* *
386170 TTTATGACCCTAGAC-TAGCTTATTTCGAGGCCAATCCCTTGGTGCTTGAATACTATGTAATTTA
1 TTTATGACTCTAGACATAACTTATTTCGAGGCCAATCCCTTGGTGCTTGAATACTATGTAATTTA
*
386234 TATGAAAAAATGAATTATCCTATATAAAGGGCATTTGTACGCCAT
66 TATGAAAAAATGAATTATCCTATATAAAGGGCATTTGTACGCCAC
* * * *
386279 TTTATGACTTTAGACAATAACTTATTTCAAGGCTAATCCCTTGGTGCTTGAATACTATGTAACTT
1 TTTATGACTCTAGAC-ATAACTTATTTCGAGGCCAATCCCTTGGTGCTTGAATACTATGTAATTT
** *
386344 ATGCG-AAAAATGGATTATCCTATATAAAGGG----TGTACGCCAC
65 ATATGAAAAAATGAATTATCCTATATAAAGGGCATTTGTACGCCAC
* * * * * *
386385 TTTATAACTCTAGACAGTAATTTATTTCGGGGCCAATCTCTTGGTGCTCGAATA-TCACGTAA-T
1 TTTATGACTCTAGACA-TAACTTATTTCGAGGCCAATCCCTTGGTGCTTGAATACT-ATGTAATT
* * * * **
386448 T-TATGCAAAAATTGAATTATTCTATAT-AAGGGCGTTTTTTTGCCAC
64 TATATG-AAAAAATGAATTATCCTATATAAAGGGCATTTGTACGCCAC
* * * * * * * * *
386494 TTTATAACTCTAGATAATTACCTATTTTGAGACTAATCCCTTGGTGCCTGATTACTATGTAATTT
1 TTTATGACTCTAGA-CATAACTTATTTCGAGGCCAATCCCTTGGTGCTTGAATACTATGTAATTT
* * ** *
386559 AT-TCAAAAAATGAATTATCTTATATAAAGGGCATTCATACGCTAC
65 ATATGAAAAAATGAATTATCCTATATAAAGGGCATTTGTACGCCAC
386604 TTTATGACTCTAGACA
1 TTTATGACTCTAGACA
386620 ATGACCTATT
Statistics
Matches: 274, Mismatches: 52, Indels: 30
0.77 0.15 0.08
Matches are distributed among these distances:
104 2 0.01
105 9 0.03
106 75 0.27
109 84 0.31
110 56 0.20
111 48 0.18
ACGTcount: A:0.31, C:0.17, G:0.15, T:0.36
Consensus pattern (110 bp):
TTTATGACTCTAGACATAACTTATTTCGAGGCCAATCCCTTGGTGCTTGAATACTATGTAATTTA
TATGAAAAAATGAATTATCCTATATAAAGGGCATTTGTACGCCAC
Found at i:386430 original size:106 final size:107
Alignment explanation
Indices: 386188--386695 Score: 448
Period size: 109 Copynumber: 4.7 Consensus size: 107
386178 CCTAGACTAG
**
386188 CTTATTTCGAGGCCAATCCCTTGGTGCTTGAATACTATGTAATTTATATGAAAAAATGAATTATC
1 CTTATTTCGAGGCCAATCCCTTGGTGCTTGAATACTATGTAATTTATGCG-AAAAATGAATTATC
* * *
386253 CTATATAAAGGGCATTTGTACGCCATTTTATGACTTTAGACAATAA
65 CTATATAAAGGG---TTGTACGCCACTTTATAACTCTAGACAATAA
* * * *
386299 CTTATTTCAAGGCTAATCCCTTGGTGCTTGAATACTATGTAACTTATGCGAAAAATGGATTATCC
1 CTTATTTCGAGGCCAATCCCTTGGTGCTTGAATACTATGTAATTTATGCGAAAAATGAATTATCC
*
386364 TATATAAAGGG-TGTACGCCACTTTATAACTCTAGACAGTAA
66 TATATAAAGGGTTGTACGCCACTTTATAACTCTAGACAATAA
* * * * *
386405 TTTATTTCGGGGCCAATCTCTTGGTGCTCGAATA-TCACGTAATTTATGC-AAAAATTGAATTAT
1 CTTATTTCGAGGCCAATCCCTTGGTGCTTGAATACT-ATGTAATTTATGCGAAAAA-TGAATTAT
* * * ** * *
386468 TCTATATAAGGGCGTTTTTTTGCCACTTTATAACTCTAGATAATTA
64 CCTATATAAAGG-G-TTGTACGCCACTTTATAACTCTAGACAATAA
* * * * * * * * *
386514 CCTATTTTGAGACTAATCCCTTGGTGCCTGATTACTATGTAATTTATTCAAAAAATGAATTATCT
1 CTTATTTCGAGGCCAATCCCTTGGTGCTTGAATACTATGTAATTTATGCGAAAAATGAATTATCC
* * * *
386579 TATATAAAGGGCATTCATACGCTACTTTATGACTCTAGACAATGA
66 TATATAAAGGG--TT-GTACGCCACTTTATAACTCTAGACAATAA
* * * * * * *** * * ** *
386624 CCTATTTTGGGGTCAATCCCTTAGTTCCCAAATACCATTTAATTCGTGCG-AAAATGAATTATCT
1 CTTATTTCGAGGCCAATCCCTTGGTGCTTGAATACTATGTAATTTATGCGAAAAATGAATTATCC
386688 TATATAAA
66 TATATAAA
386696 AAGCATTCGT
Statistics
Matches: 323, Mismatches: 65, Indels: 20
0.79 0.16 0.05
Matches are distributed among these distances:
105 6 0.02
106 82 0.25
107 1 0.00
108 1 0.00
109 100 0.31
110 88 0.27
111 45 0.14
ACGTcount: A:0.32, C:0.17, G:0.15, T:0.36
Consensus pattern (107 bp):
CTTATTTCGAGGCCAATCCCTTGGTGCTTGAATACTATGTAATTTATGCGAAAAATGAATTATCC
TATATAAAGGGTTGTACGCCACTTTATAACTCTAGACAATAA
Found at i:386585 original size:215 final size:217
Alignment explanation
Indices: 386189--386589 Score: 522
Period size: 215 Copynumber: 1.9 Consensus size: 217
386179 CTAGACTAGC
* *
386189 TTATTTCGAGGCCAATCCCTTGGTGCTTGAATACTATGTAATTTATATGAAAAAATGAATTATCC
1 TTATTTCGAGGCCAATCCCTTGGTGCTCGAATACTACGTAATTTATATGAAAAAATGAATTATCC
* * * * *
386254 TATATAAAGGGCATTTGTACGCCATTTTATGACTTTAGACAATAACTTATTTCAAGGCTAATCCC
66 TATATAAAGGGCATTTGTACGCCACTTTATAACTCTAGACAATAACCTATTTCAAGACTAATCCC
* * *
386319 TTGGTGCTTGAATACTATGTAACTTATGCGAAAAATGGATTATCCTATATAAAGGGTGTACGCCA
131 TTGGTGCCTGAATACTATGTAACTTATGCAAAAAATGAATTATCCTATATAAAGGGTGTACGCCA
386384 CTTTATAACTCTAGACAGTAAT
196 CTTTATAACTCTAGACAGTAAT
* * *
386406 TTATTTCGGGGCCAATCTCTTGGTGCTCGAATA-TCACGTAA-TT-TATGCAAAAATTGAATTAT
1 TTATTTCGAGGCCAATCCCTTGGTGCTCGAATACT-ACGTAATTTATATG-AAAAAATGAATTAT
* * * ** * * **
386468 TCTATAT-AAGGGCGTTTTTTTGCCACTTTATAACTCTAGATAATTACCTATTTTGAGACTAATC
64 CCTATATAAAGGGCATTTGTACGCCACTTTATAACTCTAGACAATAACCTATTTCAAGACTAATC
* * * *
386532 CCTTGGTGCCTGATTACTATGTAATTTATTCAAAAAATGAATTATCTTATATAAAGGG
129 CCTTGGTGCCTGAATACTATGTAACTTATGCAAAAAATGAATTATCCTATATAAAGGG
386590 CATTCATACG
Statistics
Matches: 156, Mismatches: 26, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
215 99 0.63
216 22 0.14
217 35 0.22
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.37
Consensus pattern (217 bp):
TTATTTCGAGGCCAATCCCTTGGTGCTCGAATACTACGTAATTTATATGAAAAAATGAATTATCC
TATATAAAGGGCATTTGTACGCCACTTTATAACTCTAGACAATAACCTATTTCAAGACTAATCCC
TTGGTGCCTGAATACTATGTAACTTATGCAAAAAATGAATTATCCTATATAAAGGGTGTACGCCA
CTTTATAACTCTAGACAGTAAT
Found at i:386776 original size:109 final size:109
Alignment explanation
Indices: 386565--386776 Score: 264
Period size: 109 Copynumber: 1.9 Consensus size: 109
386555 ATTTATTCAA
** * *
386565 AAAATGAATTATCTTATATAAAGGGCATTCATACGCTACTTTATGACTCTAGACAATGACCTATT
1 AAAATGAATTATCTTATATAAAAAGCATTCATACGCTAATTTATGACTCTAGACAATGAACTATT
* * * **
386630 TTGGGGTCAATCCCTTAGTTCCCAAATACCATTTAATTCGTGCG
66 TCGGGATCAATCCCTTAGTACCCAAATACCACGTAATTCGTGCG
* *
386674 AAAATGAATTATCTTATATAAAAAGCATTCGTACG-TCAATTTATGACTTTAGACAATGAACTAT
1 AAAATGAATTATCTTATATAAAAAGCATTCATACGCT-AATTTATGACTCTAGACAATGAACTAT
* * * * *
386738 TTCGGGATTAATCTCTTAGTACTCGAATACTACGTAATT
65 TTCGGGATCAATCCCTTAGTACCCAAATACCACGTAATT
386777 AATGCAATTA
Statistics
Matches: 86, Mismatches: 16, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
108 1 0.01
109 85 0.99
ACGTcount: A:0.34, C:0.17, G:0.14, T:0.35
Consensus pattern (109 bp):
AAAATGAATTATCTTATATAAAAAGCATTCATACGCTAATTTATGACTCTAGACAATGAACTATT
TCGGGATCAATCCCTTAGTACCCAAATACCACGTAATTCGTGCG
Found at i:387066 original size:19 final size:19
Alignment explanation
Indices: 387044--387081 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
387034 AATATTTTAT
387044 TTTTA-TTATATTAAAAATA
1 TTTTATTTA-ATTAAAAATA
387063 TTTTATTTAATTAAAAATA
1 TTTTATTTAATTAAAAATA
387082 AATAAACAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 15 0.83
20 3 0.17
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
TTTTATTTAATTAAAAATA
Found at i:387083 original size:25 final size:26
Alignment explanation
Indices: 387029--387083 Score: 60
Period size: 25 Copynumber: 2.2 Consensus size: 26
387019 TTATATTTTT
* * *
387029 TAAACAATATTTTATTTTTATTATAT
1 TAAACAATATTTTATTTTAATTAAAA
387055 TAAA-AATATTTTA-TTTAATTAAAAA
1 TAAACAATATTTTATTTTAATT-AAAA
387080 TAAA
1 TAAA
387084 TAAACAAGTG
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
24 6 0.24
25 15 0.60
26 4 0.16
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (26 bp):
TAAACAATATTTTATTTTAATTAAAA
Found at i:387715 original size:20 final size:20
Alignment explanation
Indices: 387690--387746 Score: 78
Period size: 20 Copynumber: 2.9 Consensus size: 20
387680 TTTTACCAAG
387690 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * *
387710 ATGTATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
*
387730 ATGTATTGATACATTTT
1 ATGTATCGATACATTTT
387747 GCCTTTTTTA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.44
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:387836 original size:51 final size:52
Alignment explanation
Indices: 387710--387843 Score: 218
Period size: 52 Copynumber: 2.6 Consensus size: 52
387700 ACATTTTTCA
*
387710 ATGTATCGATACATGTATGAATGTATTGATACATTTTGCCTTTTTTACCCAG
1 ATGTATCGATACATGTATGAATGTATCGATACATTTTGCCTTTTTTACCCAG
*
387762 ATGTATCGATACATGTATGAATGTATCGATACATTTTGTC-TTTTTACCCAG
1 ATGTATCGATACATGTATGAATGTATCGATACATTTTGCCTTTTTTACCCAG
*
387813 ATGTATCGATACATTGAAT-AATGTATCGATA
1 ATGTATCGATACA-TGTATGAATGTATCGATA
387844 TACTAGTTAA
Statistics
Matches: 78, Mismatches: 3, Indels: 3
0.93 0.04 0.04
Matches are distributed among these distances:
51 36 0.46
52 42 0.54
ACGTcount: A:0.30, C:0.14, G:0.16, T:0.40
Consensus pattern (52 bp):
ATGTATCGATACATGTATGAATGTATCGATACATTTTGCCTTTTTTACCCAG
Found at i:401727 original size:1 final size:1
Alignment explanation
Indices: 401721--401777 Score: 51
Period size: 1 Copynumber: 57.0 Consensus size: 1
401711 CTTTCGTATG
* * * * * * *
401721 AAAAAAAACAAAAAGAAAACAAAAAATAAAAAAACAAAAACAAAAACAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
401778 CTAAGAAAAT
Statistics
Matches: 42, Mismatches: 14, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
1 42 1.00
ACGTcount: A:0.88, C:0.09, G:0.02, T:0.02
Consensus pattern (1 bp):
A
Found at i:401739 original size:6 final size:6
Alignment explanation
Indices: 401724--401856 Score: 73
Period size: 6 Copynumber: 21.8 Consensus size: 6
401714 TCGTATGAAA
* * *
401724 AAAAAC AAAAAG AAAACAA AAAATAA AAAAAC AAAAAC AAAAAC AAAAA-
1 AAAAAC AAAAAC AAAA-AC AAAA-AC AAAAAC AAAAAC AAAAAC AAAAAC
* * * *
401773 AAAAAC TAAGAAA- ATAAAC AAGAAC ACCAAA- AAAACC AAAAAC --AAA-
1 AAAAAC -AA-AAAC AAAAAC AAAAAC A-AAAAC AAAAAC AAAAAC AAAAAC
401819 AAAAAC AAAAA- AAGAAAC AAAAAAC AAACAAAC AAAAA
1 AAAAAC AAAAAC AA-AAAC -AAAAAC -AA-AAAC AAAAA
401857 AAGGGTTCAT
Statistics
Matches: 101, Mismatches: 12, Indels: 28
0.72 0.09 0.20
Matches are distributed among these distances:
4 3 0.03
5 15 0.15
6 50 0.50
7 24 0.24
8 9 0.09
ACGTcount: A:0.81, C:0.14, G:0.03, T:0.02
Consensus pattern (6 bp):
AAAAAC
Found at i:401745 original size:12 final size:11
Alignment explanation
Indices: 401721--401858 Score: 93
Period size: 12 Copynumber: 11.7 Consensus size: 11
401711 CTTTCGTATG
401721 AAAAAAAACAAA
1 AAAAAAAAC-AA
*
401733 AAGAAAACAAAAA
1 AA-AAAA-AACAA
401746 ATAAAAAAACAA
1 A-AAAAAAACAA
401758 AAACAAAAACAA
1 AAA-AAAAACAA
401770 AAAAAAAACTAA
1 AAAAAAAAC-AA
*
401782 GAAAATAAAC--
1 -AAAAAAAACAA
* * *
401792 AAGAACACCAA
1 AAAAAAAACAA
401803 AAAAACCAAA-AA
1 AAAAA--AAACAA
401815 CAAAAAAAACAA
1 -AAAAAAAACAA
401827 AAAAAGAAACAA
1 AAAAA-AAACAA
*
401839 AAAACAAACAA
1 AAAAAAAACAA
401850 ACAAAAAAA
1 A-AAAAAAA
401859 GGGTTCATAT
Statistics
Matches: 100, Mismatches: 12, Indels: 28
0.71 0.09 0.20
Matches are distributed among these distances:
9 5 0.05
11 27 0.27
12 40 0.40
13 25 0.25
14 3 0.03
ACGTcount: A:0.82, C:0.13, G:0.03, T:0.02
Consensus pattern (11 bp):
AAAAAAAACAA
Found at i:401754 original size:15 final size:15
Alignment explanation
Indices: 401736--401857 Score: 87
Period size: 15 Copynumber: 8.3 Consensus size: 15
401726 AAACAAAAAG
401736 AAAACAAAAAATA-AA
1 AAAACAAAAAA-ACAA
401751 AAAAC--AAAAAC-A
1 AAAACAAAAAAACAA
401763 AAAACAAAAAAA-AA
1 AAAACAAAAAAACAA
* *
401777 ACTAAGAAAATAAACAA
1 A-AAACAAAA-AAACAA
* *
401794 GAACACCAAAAAAACCA
1 -AA-AACAAAAAAACAA
*
401811 AAAACAAAAAAA-AC
1 AAAACAAAAAAACAA
*
401825 AAAA-AAAGAAACAA
1 AAAACAAAAAAACAA
*
401839 AAAACAAACAAACAA
1 AAAACAAAAAAACAA
401854 AAAA
1 AAAA
401858 AGGGTTCATA
Statistics
Matches: 84, Mismatches: 12, Indels: 22
0.71 0.10 0.19
Matches are distributed among these distances:
12 7 0.08
13 10 0.12
14 16 0.19
15 33 0.39
16 5 0.06
17 7 0.08
18 6 0.07
ACGTcount: A:0.81, C:0.14, G:0.02, T:0.02
Consensus pattern (15 bp):
AAAACAAAAAAACAA
Found at i:401756 original size:26 final size:26
Alignment explanation
Indices: 401721--401858 Score: 106
Period size: 26 Copynumber: 5.2 Consensus size: 26
401711 CTTTCGTATG
*
401721 AAAAAAAACAAAAA-GAAAACAAAAA
1 AAAAAAAACAAAAACAAAAACAAAAA
401746 ATAAAAAAACAAAAACAAAAACAAAAA
1 A-AAAAAAACAAAAACAAAAACAAAAA
* * **
401773 AAAAACTAAGAAAATAAACAAGAAC--ACC
1 AAAAA--AA-ACAA-AAACAAAAACAAAAA
*
401801 AAAAAAACCAAAAACAAAAA-AAACAA
1 AAAAAAAACAAAAACAAAAACAAA-AA
* *
401827 AAAAAGAAACAAAAA-ACAAACAAACA
1 AAAAA-AAACAAAAACAAAAACAAAAA
401853 AAAAAA
1 AAAAAA
401859 GGGTTCATAT
Statistics
Matches: 89, Mismatches: 13, Indels: 22
0.72 0.10 0.18
Matches are distributed among these distances:
24 8 0.09
25 5 0.06
26 34 0.38
27 22 0.25
28 8 0.09
29 3 0.03
30 9 0.10
ACGTcount: A:0.82, C:0.13, G:0.03, T:0.02
Consensus pattern (26 bp):
AAAAAAAACAAAAACAAAAACAAAAA
Found at i:401859 original size:27 final size:26
Alignment explanation
Indices: 401721--401858 Score: 124
Period size: 27 Copynumber: 5.2 Consensus size: 26
401711 CTTTCGTATG
401721 AAAAAAAACAAAAAGA-AAACAAA-AA
1 AAAAAAAACAAAAA-ACAAACAAACAA
401746 ATAAAAAAAC-AAAAAC-AA-AAACAA
1 A-AAAAAAACAAAAAACAAACAAACAA
* *
401770 AAAAAAAACTAAGAAAATAAACAAGAACAC
1 AAAAAAAAC-AA-AAAACAAAC-A-AACAA
* * *
401800 CAAAAAAACCAAAAACAAAAAAAACAA
1 AAAAAAAACAAAAAAC-AAACAAACAA
401827 AAAAAGAAACAAAAAACAAACAAACAA
1 AAAAA-AAACAAAAAACAAACAAACAA
401854 AAAAA
1 AAAAA
401859 GGGTTCATAT
Statistics
Matches: 91, Mismatches: 10, Indels: 22
0.74 0.08 0.18
Matches are distributed among these distances:
23 11 0.12
24 6 0.07
25 6 0.07
26 12 0.13
27 24 0.26
28 15 0.16
29 5 0.05
30 12 0.13
ACGTcount: A:0.82, C:0.13, G:0.03, T:0.02
Consensus pattern (26 bp):
AAAAAAAACAAAAAACAAACAAACAA
Found at i:403141 original size:28 final size:28
Alignment explanation
Indices: 403107--403581 Score: 448
Period size: 28 Copynumber: 16.5 Consensus size: 28
403097 TGTTCATCTC
403107 TTCAAAGCCCACAAGTCAGTGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
**
403135 TTCAAAGCCCACAAGTCAGTGGCATATT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
*
403163 TTTAAAGCCCACAAGTCAGTGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
403191 TTCAAAGCCCACAAGTCAGTGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* * * *
403219 TTCAAAGCCCACAAGTCAATGGTACCCC
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* * *
403247 TTCAAAGCTCATAAGTTAGTGGCATTCCCTT
1 TTCAAAGCCCACAAGTCAGTGGCA-T-CC-T
* *** * *
403278 TTTAAAGCCTGTAAGTCGGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
** * *
403306 TTTGAAGCCCACACAAGTCGGTGGCAACTCTT
1 TTCAAAG-CC-CACAAGTCAGTGGC-A-TCCT
*
403338 TTCAAAGCCCACAAGTCAATGGCAT-CT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
** * *
403365 CTTCAAAAAACCACAAGTTAGCGGCATCCT
1 -TTC-AAAGCCCACAAGTCAGTGGCATCCT
*
403395 TTCAAAGCCCACAAGTCAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
*
403423 TTCAAAGCCCACAAGTCAATGGCATACCCT
1 TTCAAAGCCCACAAGTCAGTGGCAT--CCT
* *
403453 TTCAAAGCCCACATAAATCAGTGGCACCCT
1 TTCAAAGCCCAC--AAGTCAGTGGCATCCT
* * *
403483 TCCAAAGCCCACAAGTCAGTGGTACCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* * * * *
403511 TTCAAAGCCCACAAGTTAATGGTACCCC
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* *
403539 TTCAAAGCCTACAAGTTAGTGGCATCCTCT
1 TTCAAAGCCCACAAGTCAGTGGCAT-C-CT
*
403569 TTTAAAGCCCACA
1 TTCAAAGCCCACA
403582 CAAGTTAGTG
Statistics
Matches: 367, Mismatches: 64, Indels: 30
0.80 0.14 0.07
Matches are distributed among these distances:
27 1 0.00
28 234 0.64
29 26 0.07
30 68 0.19
31 21 0.06
32 17 0.05
ACGTcount: A:0.30, C:0.30, G:0.17, T:0.23
Consensus pattern (28 bp):
TTCAAAGCCCACAAGTCAGTGGCATCCT
Found at i:410929 original size:33 final size:33
Alignment explanation
Indices: 410883--410947 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 33
410873 CGTTGGACAC
* *
410883 AATGTATCGATACAATTCTTC-ATGTATCGATAT
1 AATGTATCAATAC-ATTCTCCTATGTATCGATAT
*
410916 AATGTATCAATACATTGTCCTATGTATCGATA
1 AATGTATCAATACATTCTCCTATGTATCGATA
410948 CATTTCACTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
32 5 0.18
33 23 0.82
ACGTcount: A:0.34, C:0.15, G:0.12, T:0.38
Consensus pattern (33 bp):
AATGTATCAATACATTCTCCTATGTATCGATAT
Found at i:411038 original size:13 final size:13
Alignment explanation
Indices: 411020--411046 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
411010 TAATGAGCAT
411020 GTATCGATACAAG
1 GTATCGATACAAG
411033 GTATCGATACAAG
1 GTATCGATACAAG
411046 G
1 G
411047 CATAATATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.15, G:0.26, T:0.22
Consensus pattern (13 bp):
GTATCGATACAAG
Found at i:414016 original size:79 final size:78
Alignment explanation
Indices: 413914--414430 Score: 488
Period size: 79 Copynumber: 6.5 Consensus size: 78
413904 AAATTTAATA
* * * *
413914 TTTTGGAGATAAAAACAGGGTTGGAGTACTCCCTC-AGAAATAATGGGGTTGAAGTATCCCCAAT
1 TTTTGGAAATAAAATCAGGGTTGGAGTA-TCCCTCGA-AAATAACGGGGTTGGAGTATCCCCAAT
* *
413978 GGTGGAAAATCGATG
64 TGTGGAAAATTGATG
* * * * * * * *
413993 TTCTGAAAATAAAATCAAGGTTGGAGTATCTCCTCAAAAATAACAGGGTCGGATTATCCCCGATT
1 TTTTGGAAATAAAATCAGGGTTGGAGTATC-CCTCGAAAATAACGGGGTTGGAGTATCCCCAATT
*
414058 ATGGAAAATT-AGTG
65 GTGGAAAATTGA-TG
* * *
414072 TTTTGGAAATAAAATCGGGGTTGGAGTATCTCCTCGAAAATAATGAGGTTGGAGTATCCCCAATT
1 TTTTGGAAATAAAATCAGGGTTGGAGTATC-CCTCGAAAATAACGGGGTTGGAGTATCCCCAATT
*
414137 GTGGAAAATTGGTG
65 GTGGAAAATTGATG
* * * *
414151 TTTTGGAAATAAAATCGGGGTTAGAGTATCCTTTCGAAAATAACGGGGTTGGAGTATCCCCGATT
1 TTTTGGAAATAAAATCAGGGTTGGAGTATCC-CTCGAAAATAACGGGGTTGGAGTATCCCCAATT
*
414216 GT-GAAGAATTGGTG
65 GTGGAA-AATTGATG
* * * * ** **
414230 TCTTGAAAATAAAA-CCGAGGTTAGAGTATTTTCTCGAAAATAACGGGGTTAAAGTATCCCCAAT
1 TTTTGGAAATAAAATCAG-GGTTGGAGTA-TCCCTCGAAAATAACGGGGTTGGAGTATCCCCAAT
*
414294 TGTGAAAAATT-AGTG
64 TGTGGAAAATTGA-TG
* * * *
414309 TTTTGGAAATAAAAT-AGGGGTTGGAGTATCCCTTTGGAAATAACGAGGTTGGAGTATCCCAAAT
1 TTTTGGAAATAAAATCA-GGGTTGGAGTATCCC-TCGAAAATAACGGGGTTGGAGTATCCCCAAT
* *
414373 TGTGAAAAATTGGTG
64 TGTGGAAAATTGATG
* * * *
414388 TTTTGGAAATAAAACCGGGGTTAGAGTATCTCCTCGGAAATAA
1 TTTTGGAAATAAAATCAGGGTTGGAGTATC-CCTCGAAAATAA
414431 AAACATGAAT
Statistics
Matches: 362, Mismatches: 60, Indels: 32
0.80 0.13 0.07
Matches are distributed among these distances:
78 11 0.03
79 344 0.95
80 7 0.02
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.29
Consensus pattern (78 bp):
TTTTGGAAATAAAATCAGGGTTGGAGTATCCCTCGAAAATAACGGGGTTGGAGTATCCCCAATTG
TGGAAAATTGATG
Found at i:414209 original size:158 final size:158
Alignment explanation
Indices: 413914--414430 Score: 603
Period size: 158 Copynumber: 3.3 Consensus size: 158
413904 AAATTTAATA
* * * *
413914 TTTTGGAGATAAAAACAGGGTTGGAGTA-CTCCCTC-AGAAATAATGGGGTTGAAGTATCCCCAA
1 TTTTGGAAATAAAACCGGGGTTAGAGTATCT-CCTCGA-AAATAATGGGGTTGAAGTATCCCCAA
* * * * * ** * * *
413977 TGGTGGAAAATCGATGTTCTGAAAATAAAATCAAGGTTGGAGTAT-CTCCTCAAAAATAACAGGG
64 TTGTGGAAAATTGGTGTTTTGGAAATAAAATCGGGGTTGGAGTATCCT-TTCGAAAATAACGGGG
* * * *
414041 TCGGATTATCCCCGATTATGGAAAATTAGTG
128 TTGGAGTATCCCCGATTGTGGAAAATTGGTG
* * * *
414072 TTTTGGAAATAAAATCGGGGTTGGAGTATCTCCTCGAAAATAATGAGGTTGGAGTATCCCCAATT
1 TTTTGGAAATAAAACCGGGGTTAGAGTATCTCCTCGAAAATAATGGGGTTGAAGTATCCCCAATT
*
414137 GTGGAAAATTGGTGTTTTGGAAATAAAATCGGGGTTAGAGTATCCTTTCGAAAATAACGGGGTTG
66 GTGGAAAATTGGTGTTTTGGAAATAAAATCGGGGTTGGAGTATCCTTTCGAAAATAACGGGGTTG
414202 GAGTATCCCCGATTGT-GAAGAATTGGTG
131 GAGTATCCCCGATTGTGGAA-AATTGGTG
* * * * * * *
414230 TCTTGAAAATAAAACCGAGGTTAGAGTATTTTCTCGAAAATAACGGGGTTAAAGTATCCCCAATT
1 TTTTGGAAATAAAACCGGGGTTAGAGTATCTCCTCGAAAATAATGGGGTTGAAGTATCCCCAATT
* * * * *
414295 GTGAAAAATTAGTGTTTTGGAAATAAAATAGGGGTTGGAGTATCCCTTT-GGAAATAACGAGGTT
66 GTGGAAAATTGGTGTTTTGGAAATAAAATCGGGGTTGGAGTAT-CCTTTCGAAAATAACGGGGTT
** *
414359 GGAGTATCCCAAATTGTGAAAAATTGGTG
130 GGAGTATCCCCGATTGTGGAAAATTGGTG
*
414388 TTTTGGAAATAAAACCGGGGTTAGAGTATCTCCTCGGAAATAA
1 TTTTGGAAATAAAACCGGGGTTAGAGTATCTCCTCGAAAATAA
414431 AAACATGAAT
Statistics
Matches: 307, Mismatches: 46, Indels: 12
0.84 0.13 0.03
Matches are distributed among these distances:
157 3 0.01
158 292 0.95
159 12 0.04
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.29
Consensus pattern (158 bp):
TTTTGGAAATAAAACCGGGGTTAGAGTATCTCCTCGAAAATAATGGGGTTGAAGTATCCCCAATT
GTGGAAAATTGGTGTTTTGGAAATAAAATCGGGGTTGGAGTATCCTTTCGAAAATAACGGGGTTG
GAGTATCCCCGATTGTGGAAAATTGGTG
Found at i:414331 original size:237 final size:237
Alignment explanation
Indices: 413951--414417 Score: 643
Period size: 237 Copynumber: 2.0 Consensus size: 237
413941 ACTCCCTCAG
* * *
413951 AAATAATGGGGTTGAAGTATCCCCAATGGTGGAAAATCGATGTTCTGAAAATAAAATCAAGGTTG
1 AAATAACGGGGTTGAAGTATCCCCAATGGTGGAAAATCGATGTTCTGAAAATAAAACCAAGGTTA
** * * *
414016 GAGTATCTCCTCAAAAATAACAGGGTCGGATTATCCCCGATTATGGAAAATTAGTGTTTTGGAAA
66 GAGTATCTCCTCAAAAATAACAGGGTCAAAGTATCCCCAATTATGAAAAATTAGTGTTTTGGAAA
* * * *
414081 TAAAATCGGGGTTGGAGTATCTCC-TCGAAAATAATGAGGTTGGAGTATCCCCAATTGTGGAAAA
131 TAAAATAGGGGTTGGAGTATC-CCTTCGAAAATAACGAGGTTGGAGTATCCCAAATTGTGAAAAA
*
414145 TTGGTGTTTTGGAAATAAAATCGGGGTTAGAGTATCCTTTCGA
195 TTGGTGTTTTGGAAATAAAACCGGGGTTAGAGTATCCTTTCGA
* * * * * *
414188 AAATAACGGGGTTGGAGTATCCCCGATTGT-GAAGAATTGGTG-TCTTGAAAATAAAACCGAGGT
1 AAATAACGGGGTTGAAGTATCCCCAATGGTGGAA-AATCGATGTTC-TGAAAATAAAACCAAGGT
* * * * * *
414251 TAGAGTATTTTCTCGAAAATAACGGGGTTAAAGTATCCCCAATTGTGAAAAATTAGTGTTTTGGA
64 TAGAGTATCTCCTCAAAAATAACAGGGTCAAAGTATCCCCAATTATGAAAAATTAGTGTTTTGGA
* *
414316 AATAAAATAGGGGTTGGAGTATCCCTTTGGAAATAACGAGGTTGGAGTATCCCAAATTGTGAAAA
129 AATAAAATAGGGGTTGGAGTATCCCTTCGAAAATAACGAGGTTGGAGTATCCCAAATTGTGAAAA
414381 ATTGGTGTTTTGGAAATAAAACCGGGGTTAGAGTATC
194 ATTGGTGTTTTGGAAATAAAACCGGGGTTAGAGTATC
414418 TCCTCGGAAA
Statistics
Matches: 200, Mismatches: 27, Indels: 6
0.86 0.12 0.03
Matches are distributed among these distances:
236 7 0.04
237 193 0.96
ACGTcount: A:0.34, C:0.12, G:0.25, T:0.29
Consensus pattern (237 bp):
AAATAACGGGGTTGAAGTATCCCCAATGGTGGAAAATCGATGTTCTGAAAATAAAACCAAGGTTA
GAGTATCTCCTCAAAAATAACAGGGTCAAAGTATCCCCAATTATGAAAAATTAGTGTTTTGGAAA
TAAAATAGGGGTTGGAGTATCCCTTCGAAAATAACGAGGTTGGAGTATCCCAAATTGTGAAAAAT
TGGTGTTTTGGAAATAAAACCGGGGTTAGAGTATCCTTTCGA
Found at i:416801 original size:30 final size:30
Alignment explanation
Indices: 416767--416859 Score: 98
Period size: 30 Copynumber: 3.4 Consensus size: 30
416757 AAAACTGCTT
416767 GAATGTATCGATACATCTAAGTAAAACCTA
1 GAATGTATCGATACATCTAAGTAAAACCTA
*
416797 GAATGTATCGAT--A-C-AA-T-GAA-C--
1 GAATGTATCGATACATCTAAGTAAAACCTA
*
416818 -AATGTATCGATACATCTAGGTAAAACCTA
1 GAATGTATCGATACATCTAAGTAAAACCTA
416847 GAATGTATCGATA
1 GAATGTATCGATA
416860 TAATGAACAA
Statistics
Matches: 50, Mismatches: 3, Indels: 20
0.68 0.04 0.27
Matches are distributed among these distances:
20 11 0.22
22 1 0.02
23 2 0.04
24 3 0.06
25 2 0.04
26 4 0.08
27 2 0.04
28 1 0.02
30 24 0.48
ACGTcount: A:0.42, C:0.15, G:0.16, T:0.27
Consensus pattern (30 bp):
GAATGTATCGATACATCTAAGTAAAACCTA
Found at i:416843 original size:50 final size:50
Alignment explanation
Indices: 416768--416881 Score: 201
Period size: 50 Copynumber: 2.3 Consensus size: 50
416758 AAACTGCTTG
416768 AATGTATCGATACATCTAAGTAAAACCTAGAATGTATCGATACAATGAAC
1 AATGTATCGATACATCTAAGTAAAACCTAGAATGTATCGATACAATGAAC
* *
416818 AATGTATCGATACATCTAGGTAAAACCTAGAATGTATCGATATAATGAAC
1 AATGTATCGATACATCTAAGTAAAACCTAGAATGTATCGATACAATGAAC
*
416868 AATGTATCAATACA
1 AATGTATCGATACA
416882 AATTGTGGAT
Statistics
Matches: 61, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
50 61 1.00
ACGTcount: A:0.44, C:0.15, G:0.14, T:0.27
Consensus pattern (50 bp):
AATGTATCGATACATCTAAGTAAAACCTAGAATGTATCGATACAATGAAC
Found at i:417272 original size:3 final size:3
Alignment explanation
Indices: 417264--417304 Score: 64
Period size: 3 Copynumber: 13.7 Consensus size: 3
417254 GCATTCGATT
* *
417264 TTA TTA TTA TTA TTA TTA TTA TTA TTG TTG TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
417305 TTTTTGGGCA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.27, C:0.00, G:0.05, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:417599 original size:42 final size:42
Alignment explanation
Indices: 417494--417624 Score: 137
Period size: 42 Copynumber: 3.1 Consensus size: 42
417484 CTTTGAGGAC
*
417494 AAAGGAAA-AAGAGTACG-CCTTGCTCTTCGAGGACAAAAGTAA
1 AAAGGAAATAA-AGTACGTCC-TGCTCTTTGAGGACAAAAGTAA
*
417536 AGAAGGAAATCAAATGT--GTCCTACTCTTTGAGGACAAAAG-AGA
1 A-AAGGAAAT-AAA-GTACGTCCTGCTCTTTGAGGACAAAAGTA-A
* *
417579 AAAGGAAATAAAGTACGTCCTGCTCTTTGAGGACAAAGGGAA
1 AAAGGAAATAAAGTACGTCCTGCTCTTTGAGGACAAAAGTAA
417621 AAAG
1 AAAG
417625 AAAGGAAGCG
Statistics
Matches: 76, Mismatches: 4, Indels: 18
0.78 0.04 0.18
Matches are distributed among these distances:
40 2 0.03
41 3 0.04
42 36 0.47
43 28 0.37
44 3 0.04
45 4 0.05
ACGTcount: A:0.43, C:0.15, G:0.24, T:0.18
Consensus pattern (42 bp):
AAAGGAAATAAAGTACGTCCTGCTCTTTGAGGACAAAAGTAA
Found at i:417639 original size:41 final size:42
Alignment explanation
Indices: 417553--417653 Score: 114
Period size: 41 Copynumber: 2.4 Consensus size: 42
417543 AATCAAATGT
* * * *
417553 GTCCTACTCTTTGAGGACAAAAGAGAAAAGGAAATAAAGTAC
1 GTCCTGCTCTTTGAGGACAAAAGAGAAAAAGAAAGAAAGCAC
* * *
417595 GTCCTGCTCTTTGAGGAC-AAAGGGAAAAAGAAAGGAAGCGC
1 GTCCTGCTCTTTGAGGACAAAAGAGAAAAAGAAAGAAAGCAC
* *
417636 GTCCTGCTATTTGGGGAC
1 GTCCTGCTCTTTGAGGAC
417654 TAGAAGGTGC
Statistics
Matches: 50, Mismatches: 9, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
41 33 0.66
42 17 0.34
ACGTcount: A:0.36, C:0.17, G:0.28, T:0.20
Consensus pattern (42 bp):
GTCCTGCTCTTTGAGGACAAAAGAGAAAAAGAAAGAAAGCAC
Found at i:417835 original size:61 final size:62
Alignment explanation
Indices: 417710--417840 Score: 153
Period size: 61 Copynumber: 2.1 Consensus size: 62
417700 CTACTCTTTA
* * *
417710 AGGATT-AAAAGGTGCCACCAGTTCGTATGAGCTTTAAAAAGGAAAGATGTCTTGCTCTTTG
1 AGGATTGAAAAGGTGCCACCACTTCGTATGAGCTTTAAAAAGGAAAGATATCTTGCTCTTCG
* * *
417771 AGGATTGAAAA-GTGCCACCACCTT-GTGTGGGCTTT-AAAAGGAAAAGGTATCTTGCTCTTCG
1 AGGATTGAAAAGGTGCCACCA-CTTCGTATGAGCTTTAAAAAGG-AAAGATATCTTGCTCTTCG
*
417832 AGGACTGAA
1 AGGATTGAA
417841 GGATAAAAGG
Statistics
Matches: 60, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
60 6 0.10
61 48 0.80
62 6 0.10
ACGTcount: A:0.31, C:0.16, G:0.26, T:0.27
Consensus pattern (62 bp):
AGGATTGAAAAGGTGCCACCACTTCGTATGAGCTTTAAAAAGGAAAGATATCTTGCTCTTCG
Found at i:418799 original size:7 final size:7
Alignment explanation
Indices: 418784--418838 Score: 58
Period size: 7 Copynumber: 7.6 Consensus size: 7
418774 AAACAGGTTC
418784 TTTTCTT
1 TTTTCTT
*
418791 TTCTCTT
1 TTTTCTT
418798 TTTTCTT
1 TTTTCTT
418805 TTTTCTT
1 TTTTCTT
*
418812 TTTGCATT
1 TTTTC-TT
418820 TTTT-TT
1 TTTTCTT
418826 GTTGTTCTT
1 -TT-TTCTT
418835 TTTT
1 TTTT
418839 GTTTCATTTT
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
6 2 0.05
7 27 0.68
8 9 0.22
9 2 0.05
ACGTcount: A:0.02, C:0.13, G:0.05, T:0.80
Consensus pattern (7 bp):
TTTTCTT
Found at i:425080 original size:33 final size:33
Alignment explanation
Indices: 425043--425109 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
425033 TTCAATGATT
425043 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
425076 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
425109 T
1 T
425110 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:425081 original size:13 final size:13
Alignment explanation
Indices: 425063--425087 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
425053 CATAAAATGT
425063 TGTATCGATACAA
1 TGTATCGATACAA
425076 TGTATCGATACA
1 TGTATCGATACA
425088 TATTTTTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:425168 original size:13 final size:13
Alignment explanation
Indices: 425150--425174 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
425140 ATTACTCAAA
425150 TGTATCGATACAT
1 TGTATCGATACAT
425163 TGTATCGATACA
1 TGTATCGATACA
425175 CTGATCTTTG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:425276 original size:52 final size:52
Alignment explanation
Indices: 425183--425306 Score: 207
Period size: 52 Copynumber: 2.4 Consensus size: 52
425173 CACTGATCTT
*
425183 TGTATCGATACATGCAGGC-AATTTGCCCAGATGTATCGATACA-TTTTAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATT-AAA
425234 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
*
425286 TGTATCGATACATGCAAGCAA
1 TGTATCGATACATGCAGGCAA
425307 CTTTTCATAT
Statistics
Matches: 69, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
51 19 0.28
52 47 0.68
53 3 0.04
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
Found at i:432728 original size:4 final size:4
Alignment explanation
Indices: 432719--432749 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
432709 AAACAAAACA
*
432719 AAAT AAAT AAAT GAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
432750 CACCTCAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:434813 original size:78 final size:78
Alignment explanation
Indices: 434707--434907 Score: 215
Period size: 78 Copynumber: 2.6 Consensus size: 78
434697 AATAATGGGG
* * * * *
434707 TTGGAGTATCCCCTTGAAAATAATGGGGTTGGAGTATCCCCGGTTGTGAAAAATCGATGA-TTAG
1 TTGGAGTAT-CCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAAAAATCAAT-ATTTAG
*
434771 GAAATAAAATCAGGA
64 GAAATAAAACCAGGA
* * *
434786 TTGGAGTATCCCTCGAAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAATATTTTGGA
1 TTGGAGTATCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAAAAATCAATATTTAGGA
* * *
434851 AATAAAGCCGGGG
66 AATAAAACCAGGA
* * ** *
434864 TTAGAGTATCCACTCGGAGGTAACGGGATTGGAGTATCCCCGAT
1 TTGGAGTATCC-CTCGAAAATAACGGGGTTGGAGTATCCCCGAT
434908 GAAATAACGA
Statistics
Matches: 102, Mismatches: 18, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
77 1 0.01
78 65 0.64
79 36 0.35
ACGTcount: A:0.32, C:0.15, G:0.27, T:0.26
Consensus pattern (78 bp):
TTGGAGTATCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAAAAATCAATATTTAGGA
AATAAAACCAGGA
Found at i:434976 original size:108 final size:106
Alignment explanation
Indices: 434783--434982 Score: 240
Period size: 107 Copynumber: 1.9 Consensus size: 106
434773 AATAAAATCA
* * *
434783 GGATTGGAGTATCCCTCGAAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAATATTTT
1 GGATTGGAGTATCCCTCGAAAATAACGAGGTTGGAGTATACCCAATTATGAAAAATCAATATTTT
* * *
434848 GGAAATAAAGCCGGGGTTAGAGTATCCACTCGGAGGTAACG
66 GGAAATAAAACCAGAGTTAGAGTATCCACTCGGAGGTAACG
* * * *** *
434889 GGATTGGAGTATCCC-CGATGAAATAACGAGGTTGGAGTATACTCGATTGTGAAAAATTGGTGTT
1 GGATTGGAGTATCCCTCGA--AAATAACGAGGTTGGAGTATACCCAATTATGAAAAATCAAT-AT
*
434953 TTTGGAAATAAAATCAGAGTTAGAGTATCC
63 TTTGGAAATAAAACCAGAGTTAGAGTATCC
434983 CCGATTAAAA
Statistics
Matches: 77, Mismatches: 14, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
105 3 0.04
106 15 0.19
107 32 0.42
108 27 0.35
ACGTcount: A:0.33, C:0.14, G:0.27, T:0.27
Consensus pattern (106 bp):
GGATTGGAGTATCCCTCGAAAATAACGAGGTTGGAGTATACCCAATTATGAAAAATCAATATTTT
GGAAATAAAACCAGAGTTAGAGTATCCACTCGGAGGTAACG
Found at i:434988 original size:52 final size:51
Alignment explanation
Indices: 434918--435575 Score: 367
Period size: 51 Copynumber: 12.6 Consensus size: 51
434908 GAAATAACGA
* * * *
434918 GGTTGGAGTATACTCGATTGTGAAAAATTGGTGTTTTTGGAAATAAAATCAG
1 GGTTGGAGTATCCCCGATTGTGAAAAATTGGTG-TTTTGGAAATAAAACCGG
* * *** *
434970 AGTTAGAGTATCCCCGATTAAAAGAAAATTGGTGTTTTGAAAATAAAACCGG
1 GGTTGGAGTATCCCCGATTGTGA-AAAATTGGTGTTTTGGAAATAAAACCGG
* * * *
435022 GGTTGGAGTATCCCCGATTGTGGAAAATTAGTGTTTTAGAAATAACACCGG
1 GGTTGGAGTATCCCCGATTGTGAAAAATTGGTGTTTTGGAAATAAAACCGG
* * *** * * *
435073 GGTTGGAGTATCCCCGATTATGAGAAATCAATATTTTGGGAATAAAGCCGG
1 GGTTGGAGTATCCCCGATTGTGAAAAATTGGTGTTTTGGAAATAAAACCGG
* *** * * * *
435124 GGTTGGAGTATCCCCTCGGA-GGT-AACGGGGTTGGAGTATCCTCGATGAAAT--AA-TGA
1 GGTTGGAGTAT-CCC-C-GATTGTGAA--AAATTGGTGT-T--TTG--GAAATAAAACCGG
* * * *
435180 GGTTGGAGTATCCTCGATTGTGAAAAATTGGTGTTTTTAGAAATAAAATCAG
1 GGTTGGAGTATCCCCGATTGTGAAAAATTGGTG-TTTTGGAAATAAAACCGG
* ** * * *
435232 AGTTGGAGTATCCCCGATTAAAGGAAAATTGGTGTTTTGAAAATAAAACCGA
1 GGTTGGAGTATCCCCGATT-GTGAAAAATTGGTGTTTTGGAAATAAAACCGG
* * *
435284 GGTTGGAGTATCCCCGATTGTGGAAAATTAGTGTTTTAGAAATAAAACCGG
1 GGTTGGAGTATCCCCGATTGTGAAAAATTGGTGTTTTGGAAATAAAACCGG
* * * *** * * *
435335 GGTTGGAGTTTCCCCGATTATGAGAAATCAATATTTTGGAAATAAAGCTGG
1 GGTTGGAGTATCCCCGATTGTGAAAAATTGGTGTTTTGGAAATAAAACCGG
* * *** * * ***** * *
435386 GGTTTGAGTATCCCCTCGGA-GGT-AACGGGGTTGGAGTATCCCCGATGAAATAACGA
1 GGTTGGAGTAT-CCC-C-GATTGTGAA--AAATTGGTGTTTTGGAAAT-AAA-ACCGG
* * *
435442 GGTTGGAGTATCCTCGATTGTGAAAAATTGGTGTTTTTGGAAATAAAATCGA
1 GGTTGGAGTATCCCCGATTGTGAAAAATTGGTG-TTTTGGAAATAAAACCGG
* ** * * *
435494 AGTTGGAGTATCCCCGATTAAAGGAAAATTGGTGTTTTGAAAATAAAATCGG
1 GGTTGGAGTATCCCCGATT-GTGAAAAATTGGTGTTTTGGAAATAAAACCGG
* *
435546 GGTTGGAGTATCCCCGATTATGAACAATTG
1 GGTTGGAGTATCCCCGATTGTGAAAAATTG
435576 AGAAACTTAA
Statistics
Matches: 445, Mismatches: 132, Indels: 59
0.70 0.21 0.09
Matches are distributed among these distances:
49 5 0.01
51 163 0.37
52 159 0.36
53 54 0.12
54 22 0.05
55 12 0.03
56 23 0.05
57 3 0.01
59 4 0.01
ACGTcount: A:0.32, C:0.12, G:0.27, T:0.29
Consensus pattern (51 bp):
GGTTGGAGTATCCCCGATTGTGAAAAATTGGTGTTTTGGAAATAAAACCGG
Found at i:435273 original size:262 final size:262
Alignment explanation
Indices: 434808--435564 Score: 1345
Period size: 262 Copynumber: 2.9 Consensus size: 262
434798 TCGAAAATAA
*
434808 CGGGGTTGGAGTATCCCCAATTATGAGAAATCAATATTTTGGAAATAAAGCCGGGGTTAGAGTAT
1 CGGGGTTGGAGTATCCCCGATTATGAGAAATCAATATTTTGGAAATAAAGCCGGGGTTAGAGTAT
* * *
434873 CCACTCGGAGGTAACGGGATTGGAGTATCCCCGATGAAATAACGAGGTTGGAGTATACTCGATTG
66 CCCCTCGGAGGTAACGGGGTTGGAGTATCCCCGATGAAATAACGAGGTTGGAGTATCCTCGATTG
* *
434938 TGAAAAATTGGTGTTTTTGGAAATAAAATCAGAGTTAGAGTATCCCCGATTAAAAGAAAATTGGT
131 TGAAAAATTGGTGTTTTTGGAAATAAAATCAGAGTTGGAGTATCCCCGATTAAAGGAAAATTGGT
*
435003 GTTTTGAAAATAAAACCGGGGTTGGAGTATCCCCGATTGTGGAAAATTAGTGTTTTAGAAATAAC
196 GTTTTGAAAATAAAACCGGGGTTGGAGTATCCCCGATTGTGGAAAATTAGTGTTTTAGAAATAAA
435068 AC
261 AC
* *
435070 CGGGGTTGGAGTATCCCCGATTATGAGAAATCAATATTTTGGGAATAAAGCCGGGGTTGGAGTAT
1 CGGGGTTGGAGTATCCCCGATTATGAGAAATCAATATTTTGGAAATAAAGCCGGGGTTAGAGTAT
* *
435135 CCCCTCGGAGGTAACGGGGTTGGAGTATCCTCGATGAAATAATGAGGTTGGAGTATCCTCGATTG
66 CCCCTCGGAGGTAACGGGGTTGGAGTATCCCCGATGAAATAACGAGGTTGGAGTATCCTCGATTG
*
435200 TGAAAAATTGGTGTTTTTAGAAATAAAATCAGAGTTGGAGTATCCCCGATTAAAGGAAAATTGGT
131 TGAAAAATTGGTGTTTTTGGAAATAAAATCAGAGTTGGAGTATCCCCGATTAAAGGAAAATTGGT
*
435265 GTTTTGAAAATAAAACCGAGGTTGGAGTATCCCCGATTGTGGAAAATTAGTGTTTTAGAAATAAA
196 GTTTTGAAAATAAAACCGGGGTTGGAGTATCCCCGATTGTGGAAAATTAGTGTTTTAGAAATAAA
435330 AC
261 AC
* * *
435332 CGGGGTTGGAGTTTCCCCGATTATGAGAAATCAATATTTTGGAAATAAAGCTGGGGTTTGAGTAT
1 CGGGGTTGGAGTATCCCCGATTATGAGAAATCAATATTTTGGAAATAAAGCCGGGGTTAGAGTAT
435397 CCCCTCGGAGGTAACGGGGTTGGAGTATCCCCGATGAAATAACGAGGTTGGAGTATCCTCGATTG
66 CCCCTCGGAGGTAACGGGGTTGGAGTATCCCCGATGAAATAACGAGGTTGGAGTATCCTCGATTG
435462 TGAAAAATTGGTGTTTTTGGAAATAAAATC-GAAGTTGGAGTATCCCCGATTAAAGGAAAATTGG
131 TGAAAAATTGGTGTTTTTGGAAATAAAATCAG-AGTTGGAGTATCCCCGATTAAAGGAAAATTGG
*
435526 TGTTTTGAAAATAAAATCGGGGTTGGAGTATCCCCGATT
195 TGTTTTGAAAATAAAACCGGGGTTGGAGTATCCCCGATT
435565 ATGAACAATT
Statistics
Matches: 472, Mismatches: 22, Indels: 2
0.95 0.04 0.00
Matches are distributed among these distances:
261 1 0.00
262 471 1.00
ACGTcount: A:0.32, C:0.13, G:0.27, T:0.29
Consensus pattern (262 bp):
CGGGGTTGGAGTATCCCCGATTATGAGAAATCAATATTTTGGAAATAAAGCCGGGGTTAGAGTAT
CCCCTCGGAGGTAACGGGGTTGGAGTATCCCCGATGAAATAACGAGGTTGGAGTATCCTCGATTG
TGAAAAATTGGTGTTTTTGGAAATAAAATCAGAGTTGGAGTATCCCCGATTAAAGGAAAATTGGT
GTTTTGAAAATAAAACCGGGGTTGGAGTATCCCCGATTGTGGAAAATTAGTGTTTTAGAAATAAA
AC
Found at i:438005 original size:19 final size:18
Alignment explanation
Indices: 437981--438042 Score: 64
Period size: 19 Copynumber: 3.7 Consensus size: 18
437971 AGCGATACAT
437981 TGTATCGATACAAAACTTA
1 TGTATCGATAC-AAACTTA
438000 TGTATCGATAC--A---A
1 TGTATCGATACAAACTTA
438013 TGTATCG-TACAACACTTA
1 TGTATCGATACAA-ACTTA
438031 TGTATCGATACA
1 TGTATCGATACA
438043 TTTACGGTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 14
0.72 0.00 0.28
Matches are distributed among these distances:
12 3 0.08
13 8 0.22
15 1 0.03
16 1 0.03
18 8 0.22
19 15 0.42
ACGTcount: A:0.37, C:0.18, G:0.13, T:0.32
Consensus pattern (18 bp):
TGTATCGATACAAACTTA
Found at i:438030 original size:31 final size:32
Alignment explanation
Indices: 437973--438042 Score: 115
Period size: 31 Copynumber: 2.2 Consensus size: 32
437963 AGCATCGTAG
*
437973 CGATACATTGTATCGATACAAAACTTATGTAT
1 CGATACAATGTATCGATACAAAACTTATGTAT
*
438005 CGATACAATGTATCG-TACAACACTTATGTAT
1 CGATACAATGTATCGATACAAAACTTATGTAT
438036 CGATACA
1 CGATACA
438043 TTTACGGTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
31 22 0.61
32 14 0.39
ACGTcount: A:0.37, C:0.19, G:0.13, T:0.31
Consensus pattern (32 bp):
CGATACAATGTATCGATACAAAACTTATGTAT
Found at i:439525 original size:79 final size:79
Alignment explanation
Indices: 439377--439547 Score: 193
Period size: 79 Copynumber: 2.2 Consensus size: 79
439367 ATTTTAATAT
* * * *
439377 TTTGGAGATAAAAACAGGATCGGAGTACCCTCTCAGAAATAACGGGATTGAAGTATCCCCAATGG
1 TTTGGAAATAAAAACAGGATCGGAGTACCCTATCAAAAATAACGGGATTGAAGTATCCCCAATGA
439442 TGAAAAATCGA-TGC
66 TGAAAAAT-GAGTGC
* * * * * * *
439456 TTTGGAAATAAAATCAGGGAT-GGAGTATCCTATCAAAAATAACGGGGTTGGAGTATCCTCGATT
1 TTTGGAAATAAAAACA-GGATCGGAGTACCCTATCAAAAATAACGGGATTGAAGTATCCCCAATG
* *
439520 ATGAAAAATTAGTGT
65 ATGAAAAATGAGTGC
439535 TTTGGAAATAAAA
1 TTTGGAAATAAAA
439548 CCGGGGTTAG
Statistics
Matches: 77, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
78 1 0.01
79 72 0.94
80 4 0.05
ACGTcount: A:0.38, C:0.13, G:0.23, T:0.26
Consensus pattern (79 bp):
TTTGGAAATAAAAACAGGATCGGAGTACCCTATCAAAAATAACGGGATTGAAGTATCCCCAATGA
TGAAAAATGAGTGC
Found at i:439570 original size:51 final size:51
Alignment explanation
Indices: 439498--439617 Score: 177
Period size: 51 Copynumber: 2.4 Consensus size: 51
439488 TCAAAAATAA
*
439498 CGGGGTTGGAGTATCCTCGATTATGAAAAATTAGTGTTTTGGAAATAAAAC
1 CGGGGTTGGAGTATCCCCGATTATGAAAAATTAGTGTTTTGGAAATAAAAC
* * * * *
439549 CGGGGTTAGAGTATCCCCGATTGTGAAAAGTTGGTGTTTTGGAAATAAAAT
1 CGGGGTTGGAGTATCCCCGATTATGAAAAATTAGTGTTTTGGAAATAAAAC
*
439600 CGGGGTTGGACTATCCCC
1 CGGGGTTGGAGTATCCCC
439618 TCAGAAATAA
Statistics
Matches: 61, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
51 61 1.00
ACGTcount: A:0.28, C:0.13, G:0.28, T:0.30
Consensus pattern (51 bp):
CGGGGTTGGAGTATCCCCGATTATGAAAAATTAGTGTTTTGGAAATAAAAC
Found at i:439615 original size:130 final size:130
Alignment explanation
Indices: 439428--439693 Score: 345
Period size: 130 Copynumber: 2.0 Consensus size: 130
439418 ACGGGATTGA
* *
439428 AGTATCCCCAATGGTGAAAAATCGATGCTTTGGAAATAAAATCAGGGATGGAGTATCCTATCAAA
1 AGTATCCCCAATGGTGAAAAATCGATGCTTTGGAAATAAAATCAGGGATGGACTATCCCATCAAA
* * *
439493 AATAACGGGGTTGGAGTATC-CTCGATTATGAAAAATTAGTGTTTTGGAAATAAAACCGGGGTTA
66 AATAACAGGGTTGGAGTATCTC-CGATTATGAAAAATTAGTGTCTTCGAAATAAAACCGGGGTTA
439557 G
130 G
* * * * * * * * * *
439558 AGTATCCCCGATTGTGAAAAGTTGGTGTTTTGGAAATAAAATCGGGGTTGGACTATCCCCTCAGA
1 AGTATCCCCAATGGTGAAAAATCGATGCTTTGGAAATAAAATCAGGGATGGACTATCCCATCAAA
* * **
439623 AATAACAGGGTTGGAGTATCTCCGATTGTGAAAAATTGGTGTCTTCGAAATAAAATTGGGGTTAG
66 AATAACAGGGTTGGAGTATCTCCGATTATGAAAAATTAGTGTCTTCGAAATAAAACCGGGGTTAG
439688 AGTATC
1 AGTATC
439694 TCCTCGAAAA
Statistics
Matches: 116, Mismatches: 19, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
130 115 0.99
131 1 0.01
ACGTcount: A:0.33, C:0.13, G:0.26, T:0.29
Consensus pattern (130 bp):
AGTATCCCCAATGGTGAAAAATCGATGCTTTGGAAATAAAATCAGGGATGGACTATCCCATCAAA
AATAACAGGGTTGGAGTATCTCCGATTATGAAAAATTAGTGTCTTCGAAATAAAACCGGGGTTAG
Found at i:439640 original size:79 final size:78
Alignment explanation
Indices: 439551--440969 Score: 1062
Period size: 79 Copynumber: 18.0 Consensus size: 78
439541 AATAAAACCG
* * *
439551 GGGTTAGAGTATCCCCGATTGTGAAAAGTTGGTGTTTTGGAAATAAAATCGGGGTTGGACTATCC
1 GGGTTAGAGTATCCCCGATTGTGAAAAATTGGTGTCTTGGAAATAAAA-CGGGGTTGGAGTATCC
439616 CCTCAGAAATAACA
65 CCTCAGAAATAACA
* * * * * *
439630 GGGTTGGAGTATCTCCGATTGTGAAAAATTGGTGTCTTCGAAATAAAATTGGGGTTAGAGTATCT
1 GGGTTAGAGTATCCCCGATTGTGAAAAATTGGTGTCTTGGAAATAAAA-CGGGGTTGGAGTATCC
**
439695 CCTC-GAAAATAATG
65 CCTCAG-AAATAACA
* * * *
439709 GGGTTTGAGTATCCCCGATTATGAAAAATTGGTGTCTTGGAAATAAAACCGGGTTGAAGTATCCC
1 GGGTTAGAGTATCCCCGATTGTGAAAAATTGGTGTCTTGGAAATAAAACGGGGTTGGAGTATCCC
*
439774 TTCAGAAATAAC-
66 CTCAGAAATAACA
* * * * *
439786 GCAGTTAGAGTATCCCCGATTGTTAAAATTTGGTGTTTTAGAAATAAAACTGGGGTTGGAGTATC
1 G-GGTTAGAGTATCCCCGATTGTGAAAAATTGGTGTCTTGGAAATAAAAC-GGGGTTGGAGTATC
*
439851 TCCTCAGAAATAAC-
64 CCCTCAGAAATAACA
* * * ** * *
439865 GGGATTGGAGTATCCCCAATTGT-AAAAATTTGGTGTTTTAAAAATAAAACCGGAGTTAGAGTAT
1 GGG-TTAGAGTATCCCCGATTGTGAAAAA-TTGGTGTCTTGGAAATAAAA-CGGGGTTGGAGTAT
*
439929 CCCCTCAGAAATAATA
63 CCCCTCAGAAATAACA
* * * *
439945 GGGTTGGAGTATCCCCGATTGTGAAAAATTAGTGTTTTGGAAATAAAATCGGGGTTTGAGTATCC
1 GGGTTAGAGTATCCCCGATTGTGAAAAATTGGTGTCTTGGAAATAAAA-CGGGGTTGGAGTATCC
* *
440010 CCTCAAAAATAACG
65 CCTCAGAAATAACA
* * *
440024 GGGTTGGAGTATCCCCGATTGTGGAAAATTGGTGTCTTGGAAATAAAACCGGGGTTGAAGTATCC
1 GGGTTAGAGTATCCCCGATTGTGAAAAATTGGTGTCTTGGAAATAAAA-CGGGGTTGGAGTATCC
* *
440089 GCTCGGAAATAACA
65 CCTCAGAAATAACA
* * * * * * *
440103 AGGTTGGAGTATCCTCAATTGTGAAAAATTGGTGTCTTGAAAATAAAATTGAGGTTGGAGTATCC
1 GGGTTAGAGTATCCCCGATTGTGAAAAATTGGTGTCTTGGAAATAAAA-CGGGGTTGGAGTATCC
440168 CCT-AGGAAATAACA
65 CCTCA-GAAATAACA
* *
440182 GGGTTAGAGTATCTCCGATTGTGAAAAATTGGTGTCTTGGAAATAAAACCGGGGTTGGAGTATCT
1 GGGTTAGAGTATCCCCGATTGTGAAAAATTGGTGTCTTGGAAATAAAA-CGGGGTTGGAGTATCC
* *
440247 CCTAAAAAATAACA
65 CCTCAGAAATAACA
* *
440261 GGGTTAGAGTATCCCTGATTGTGAAAAATTGGTGTCTTGGAAATAAAACCGGGGTTAGAGTATCC
1 GGGTTAGAGTATCCCCGATTGTGAAAAATTGGTGTCTTGGAAATAAAA-CGGGGTTGGAGTATCC
*
440326 CCT-TGAAAATAAC-
65 CCTCAG-AAATAACA
* * ** * *
440339 GAGATTAGAGTATCCTCGATTGTG--GGATTGGAGTATCCCTT--AAAAAATAACGGGGTTGGAG
1 G-GGTTAGAGTATCCCCGATTGTGAAAAATT-G-GTGT--CTTGGAAATAA-AACGGGGTTGGAG
* **
440400 TAT-CCCTAATTGTGAAA-AATT
60 TATCCCCTCA----GAAATAACA
* * *** * ** * * * ** * * * * * *
440421 GGTGTCTTGGAAATAAAACCG---GGGTTAGAGT-ATCCCCTCGAAA-ATAACGAGATTAGAGTA
1 GG-G--TTAG-AGTATCCCCGATTGTGAAAAATTGGTGTCTTGGAAATAAAACGGGGTTGGAGTA
* **
440481 T-CCCTGATTGTGAAA-AATT
62 TCCCCTCA----GAAATAACA
* * * ** * * * * * *
440500 GGTGTCTTGGAAATAAAGCCGGGGTTG-G----AGT-ATCTCCT-CAAA-AATAACGGGGTTGGA
1 GG-G--TTAG-AGT--ATCCCCGATTGTGAAAAATTGGTGTCTTGGAAATAA-AACGGGGTTGGA
*
440557 GTATCCCCTC-GAAAATAACG
59 GTATCCCCTCAG-AAATAACA
* * *
440577 GGGTTAGAGCATCCCCGATTGTGAAAAATTGGTGTTTTGGAAATAAAACTGGGGTTGGAGTATCT
1 GGGTTAGAGTATCCCCGATTGTGAAAAATTGGTGTCTTGGAAATAAAAC-GGGGTTGGAGTATCC
* *
440642 GCTCGGAAATAACA
65 CCTCAGAAATAACA
* * *
440656 GGGTTAGAGTATCCCCGATTGTGAAAAATTAGTGTCTTGGAAATAAAATCGAGGTTAGAGTATCC
1 GGGTTAGAGTATCCCCGATTGTGAAAAATTGGTGTCTTGGAAATAAAA-CGGGGTTGGAGTATCC
440721 CCTC-GAAAATAACA
65 CCTCAG-AAATAACA
* * * * *
440735 AGGTTGGAGTATCCCCGATTATGAAAAATTAGTGTCTTGAAAATAAAACCGGGGTTGGAGTATCC
1 GGGTTAGAGTATCCCCGATTGTGAAAAATTGGTGTCTTGGAAATAAAA-CGGGGTTGGAGTATCC
* *
440800 CCTCAGACATAACG
65 CCTCAGAAATAACA
* * * * * ** *
440814 GGGTTAGAGTATTCCCAATTATGAAAAATTGATGTTTTAAAAATAAAACTGGGGTTAGAGTATCC
1 GGGTTAGAGTATCCCCGATTGTGAAAAATTGGTGTCTTGGAAATAAAAC-GGGGTTGGAGTATCC
*
440879 CCTCAGAAATAACG
65 CCTCAGAAATAACA
* * * *
440893 GGGTTAGAGTATCTCTGATTGTGAAAAATTGGTGTTTTGAAAATAAAACCGGGGTTGGAGTATCC
1 GGGTTAGAGTATCCCCGATTGTGAAAAATTGGTGTCTTGGAAATAAAA-CGGGGTTGGAGTATCC
*
440958 CCTCGGAAATAA
65 CCTCAGAAATAA
440970 AAACATGAAT
Statistics
Matches: 1100, Mismatches: 184, Indels: 112
0.79 0.13 0.08
Matches are distributed among these distances:
71 7 0.01
72 1 0.00
73 1 0.00
74 3 0.00
75 1 0.00
76 6 0.01
77 11 0.01
78 85 0.08
79 932 0.85
80 21 0.02
81 12 0.01
82 6 0.01
83 2 0.00
84 7 0.01
85 5 0.00
ACGTcount: A:0.33, C:0.14, G:0.25, T:0.28
Consensus pattern (78 bp):
GGGTTAGAGTATCCCCGATTGTGAAAAATTGGTGTCTTGGAAATAAAACGGGGTTGGAGTATCCC
CTCAGAAATAACA
Found at i:440370 original size:130 final size:130
Alignment explanation
Indices: 440236--440492 Score: 446
Period size: 130 Copynumber: 2.0 Consensus size: 130
440226 AAAACCGGGG
*
440236 TTGGAGTATCTCC-TAAAAAATAACAGGGTTAGAGTATCCCTGATTGTGAAAAATTGGTGTCTTG
1 TTGGAGTATC-CCTTAAAAAATAACAGGGTTAGAGTATCCCTAATTGTGAAAAATTGGTGTCTTG
*
440300 GAAATAAAACCGGGGTTAGAGTATCCCCTTGAAAATAACGAGATTAGAGTAT-CCTCGATTGTGG
65 GAAATAAAACCGGGGTTAGAGTATCCCCTCGAAAATAACGAGATTAGAGTATCCCT-GATTGTGG
440364 GA
129 GA
* *
440366 TTGGAGTATCCCTTAAAAAATAACGGGGTTGGAGTATCCCTAATTGTGAAAAATTGGTGTCTTGG
1 TTGGAGTATCCCTTAAAAAATAACAGGGTTAGAGTATCCCTAATTGTGAAAAATTGGTGTCTTGG
440431 AAATAAAACCGGGGTTAGAGTATCCCCTCGAAAATAACGAGATTAGAGTATCCCTGATTGTG
66 AAATAAAACCGGGGTTAGAGTATCCCCTCGAAAATAACGAGATTAGAGTATCCCTGATTGTG
440493 AAAAATTGGT
Statistics
Matches: 121, Mismatches: 4, Indels: 4
0.94 0.03 0.03
Matches are distributed among these distances:
129 2 0.02
130 116 0.96
131 3 0.02
ACGTcount: A:0.33, C:0.14, G:0.25, T:0.28
Consensus pattern (130 bp):
TTGGAGTATCCCTTAAAAAATAACAGGGTTAGAGTATCCCTAATTGTGAAAAATTGGTGTCTTGG
AAATAAAACCGGGGTTAGAGTATCCCCTCGAAAATAACGAGATTAGAGTATCCCTGATTGTGGGA
Found at i:440414 original size:209 final size:209
Alignment explanation
Indices: 440157--440562 Score: 609
Period size: 209 Copynumber: 1.9 Consensus size: 209
440147 AAAATTGAGG
** *
440157 TTGGAGTATCCCCTAGGAAATAACAGGGTTAGAGTATCTCCGATTGTGAAAAATTGGTGTCTTGG
1 TTGGAGTATCCCCTAAAAAATAACAGGGTTAGAGTATCTCCAATTGTGAAAAATTGGTGTCTTGG
* * *
440222 AAATAAAACCGGGGTTGGAGTATCTCCTAAAAAATAAC-AGGGTTAGAGTATCCCTGATTGTGAA
66 AAATAAAACCGGGGTTAGAGTATCCCCTAAAAAATAACGA-GATTAGAGTATCCCTGATTGTGAA
**
440286 AAATTGGTGTCTTGGAAATAAAACCGGGGTTAGAGTATCCCCTTGAAAATAACGAGATTAGAGTA
130 AAATTGGTGTCTTGGAAATAAAACCGGGGTTAGAGTATCCCCTCAAAAATAACGAGATTAGAGTA
440351 TCCTCGATTGTGGGA
195 TCCTCGATTGTGGGA
* * *
440366 TTGGAGTATCCCTTAAAAAATAACGGGGTTGGAGTATC-CCTAATTGTGAAAAATTGGTGTCTTG
1 TTGGAGTATCCCCTAAAAAATAACAGGGTTAGAGTATCTCC-AATTGTGAAAAATTGGTGTCTTG
**
440430 GAAATAAAACCGGGGTTAGAGTATCCCCTCGAAAATAACGAGATTAGAGTATCCCTGATTGTGAA
65 GAAATAAAACCGGGGTTAGAGTATCCCCTAAAAAATAACGAGATTAGAGTATCCCTGATTGTGAA
* * * * * *
440495 AAATTGGTGTCTTGGAAATAAAGCCGGGGTTGGAGTATCTCCTCAAAAATAACGGGGTTGGAGTA
130 AAATTGGTGTCTTGGAAATAAAACCGGGGTTAGAGTATCCCCTCAAAAATAACGAGATTAGAGTA
440560 TCC
195 TCC
440563 CCTCGAAAAT
Statistics
Matches: 176, Mismatches: 19, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
208 2 0.01
209 173 0.98
210 1 0.01
ACGTcount: A:0.32, C:0.14, G:0.26, T:0.28
Consensus pattern (209 bp):
TTGGAGTATCCCCTAAAAAATAACAGGGTTAGAGTATCTCCAATTGTGAAAAATTGGTGTCTTGG
AAATAAAACCGGGGTTAGAGTATCCCCTAAAAAATAACGAGATTAGAGTATCCCTGATTGTGAAA
AATTGGTGTCTTGGAAATAAAACCGGGGTTAGAGTATCCCCTCAAAAATAACGAGATTAGAGTAT
CCTCGATTGTGGGA
Found at i:440552 original size:28 final size:28
Alignment explanation
Indices: 440519--440592 Score: 112
Period size: 28 Copynumber: 2.6 Consensus size: 28
440509 GAAATAAAGC
*
440519 CGGGGTTGGAGTATCTCCTCAAAAATAA
1 CGGGGTTGGAGTATCCCCTCAAAAATAA
*
440547 CGGGGTTGGAGTATCCCCTCGAAAATAA
1 CGGGGTTGGAGTATCCCCTCAAAAATAA
* *
440575 CGGGGTTAGAGCATCCCC
1 CGGGGTTGGAGTATCCCC
440593 GATTGTGAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 42 1.00
ACGTcount: A:0.27, C:0.23, G:0.28, T:0.22
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCTCAAAAATAA
Found at i:440559 original size:107 final size:107
Alignment explanation
Indices: 440440--440671 Score: 356
Period size: 107 Copynumber: 2.2 Consensus size: 107
440430 GAAATAAAAC
* *
440440 CGGGGTTAGAGTATCCCCTCGAAAATAACGAGATTAGAGTATCCCTGATTGTGAAAAATTGGTGT
1 CGGGGTTAGAGTATCCCCTCGAAAATAACGAGATTAGAGCATCCCCGATTGTGAAAAATTGGTGT
*
440505 CTTGGAAATAAAGCCGGGGTTGGAGTATCTCCTCAAAAATAA
66 CTTGGAAATAAAACCGGGGTTGGAGTATCTCCTCAAAAATAA
* * *
440547 CGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTAGAGCATCCCCGATTGTGAAAAATTGGTGT
1 CGGGGTTAGAGTATCCCCTCGAAAATAACGAGATTAGAGCATCCCCGATTGTGAAAAATTGGTGT
* * * **
440612 TTTGGAAATAAAACTGGGGTTGGAGTATCTGCTCGGAAATAA
66 CTTGGAAATAAAACCGGGGTTGGAGTATCTCCTCAAAAATAA
*
440654 CAGGGTTAGAGTATCCCC
1 CGGGGTTAGAGTATCCCC
440672 GATTGTGAAA
Statistics
Matches: 112, Mismatches: 13, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
107 112 1.00
ACGTcount: A:0.30, C:0.16, G:0.28, T:0.26
Consensus pattern (107 bp):
CGGGGTTAGAGTATCCCCTCGAAAATAACGAGATTAGAGCATCCCCGATTGTGAAAAATTGGTGT
CTTGGAAATAAAACCGGGGTTGGAGTATCTCCTCAAAAATAA
Found at i:440600 original size:186 final size:186
Alignment explanation
Indices: 440366--440750 Score: 538
Period size: 186 Copynumber: 2.1 Consensus size: 186
440356 GATTGTGGGA
* * * *
440366 TTGGAGTATCCCTTAAAAAATAACGGGGTTGGAGTATCCCTAATTGTGAAAAATTGGTGTCTTGG
1 TTGGAGTATCCCCTAAAAAATAACGGGGTTAGAGCATCCCCAATTGTGAAAAATTGGTGTCTTGG
*
440431 AAATAAAACCGGGGTTAGAGTATCCCCTCGAAAATAAC-GAGATTAGAGTATCCCTGATTGTGAA
66 AAATAAAACCGGGGTTAGAGTATCCCCTCGAAAATAACAG-GATTAGAGTATCCCCGATTGTGAA
* * * * * **
440495 AAATTGGTGTCTTGGAAATAAAGCCGGGGTTGGAGTATCTCCTCAAAAATAACGGGG
130 AAATTAGTGTCTTGGAAATAAAACCGAGGTTAGAGTATCCCCTCAAAAATAACAAGG
** * *
440552 TTGGAGTATCCCCTCGAAAATAACGGGGTTAGAGCATCCCCGATTGTGAAAAATTGGTGTTTTGG
1 TTGGAGTATCCCCTAAAAAATAACGGGGTTAGAGCATCCCCAATTGTGAAAAATTGGTGTCTTGG
* * ** * *
440617 AAATAAAACTGGGGTTGGAGTATCTGCTCGGAAATAACAGGGTTAGAGTATCCCCGATTGTGAAA
66 AAATAAAACCGGGGTTAGAGTATCCCCTCGAAAATAACAGGATTAGAGTATCCCCGATTGTGAAA
* *
440682 AATTAGTGTCTTGGAAATAAAATCGAGGTTAGAGTATCCCCTCGAAAATAACAAGG
131 AATTAGTGTCTTGGAAATAAAACCGAGGTTAGAGTATCCCCTCAAAAATAACAAGG
440738 TTGGAGTATCCCC
1 TTGGAGTATCCCC
440751 GATTATGAAA
Statistics
Matches: 174, Mismatches: 24, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
186 173 0.99
187 1 0.01
ACGTcount: A:0.32, C:0.15, G:0.26, T:0.27
Consensus pattern (186 bp):
TTGGAGTATCCCCTAAAAAATAACGGGGTTAGAGCATCCCCAATTGTGAAAAATTGGTGTCTTGG
AAATAAAACCGGGGTTAGAGTATCCCCTCGAAAATAACAGGATTAGAGTATCCCCGATTGTGAAA
AATTAGTGTCTTGGAAATAAAACCGAGGTTAGAGTATCCCCTCAAAAATAACAAGG
Found at i:443387 original size:20 final size:20
Alignment explanation
Indices: 443362--443416 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
443352 TAAAACCCAG
443362 AATGTATCGATACAA-GAAAC
1 AATGTATCGATACAATG-AAC
*
443382 AATGTATCAATACAATGAAC
1 AATGTATCGATACAATGAAC
*
443402 AATGCATCGATACAA
1 AATGTATCGATACAA
443417 ATTGTAGAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
20 30 0.97
21 1 0.03
ACGTcount: A:0.49, C:0.16, G:0.13, T:0.22
Consensus pattern (20 bp):
AATGTATCGATACAATGAAC
Found at i:444290 original size:13 final size:13
Alignment explanation
Indices: 444271--444310 Score: 62
Period size: 13 Copynumber: 3.1 Consensus size: 13
444261 ATAGTAACCC
444271 ATGTATCGATACA
1 ATGTATCGATACA
* *
444284 TTGTATCCATACA
1 ATGTATCGATACA
444297 ATGTATCGATACA
1 ATGTATCGATACA
444310 A
1 A
444311 AGAACATTGT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.38, C:0.17, G:0.12, T:0.33
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:453557 original size:81 final size:82
Alignment explanation
Indices: 453472--453641 Score: 195
Period size: 81 Copynumber: 2.1 Consensus size: 82
453462 AACTAGTTTC
* * ** * * * *
453472 GGTCTTGACAGA-AGGTACGGACCTAAACTTAAGGGACTTGGTTTTTAAAGAAAGTAAGAAACCT
1 GGTCTTGACAAACAGGTACAGACCTAAACTTAAAAGACTCGATTTCTAAAGAAAGTAAAAAACCT
453536 AAACTAAAACTAG-ACTT
66 AAACT-AAACTAGAACTT
* * * *
453553 GGTCTCGA-AAACAGGTATAGACCTAAGCTTAAAAGACTCGATTTCTACAGAAAGTAAAAAACCT
1 GGTCTTGACAAACAGGTACAGACCTAAACTTAAAAGACTCGATTTCTAAAGAAAGTAAAAAACCT
453617 AAACTAAACTAGAACTT
66 AAACTAAACTAGAACTT
453634 -GTCTTGAC
1 GGTCTTGAC
453642 GAAAGATACA
Statistics
Matches: 73, Mismatches: 13, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
80 15 0.21
81 58 0.79
ACGTcount: A:0.41, C:0.17, G:0.18, T:0.24
Consensus pattern (82 bp):
GGTCTTGACAAACAGGTACAGACCTAAACTTAAAAGACTCGATTTCTAAAGAAAGTAAAAAACCT
AAACTAAACTAGAACTT
Found at i:458507 original size:354 final size:352
Alignment explanation
Indices: 457855--458558 Score: 1099
Period size: 354 Copynumber: 2.0 Consensus size: 352
457845 CGCACGATCA
*
457855 AAAAATGTAGTTTTGAGGCCAATATCGAATAAAAAAGACGAATATTCAAGAAAATGGTTTCTAAG
1 AAAAATGTAGTTTTAAGGCCAATATCGAATAAAAAAGACGAATATTCAAGAAAATGGTTTCTAAG
*
457920 TATTTCCTTGTCAAATTTTGGAAATTCATTTTTGCAGATGATATCACATCAAATTTATCATTTTT
66 TATTTCCTTGTCAAATTTTGGAAATTCATTTTTGCAAATGATATCACATCAAATTTATCATTTTT
* * * *
457985 TGGAATTTTTCAAGATTTTTTGAAAAATTTAAGAAGTTGATCGTCCCATATTTTTATCGATACCT
131 TGGAATTTTTCAAGATTTTTTGAAAAATATAAGAAGTTGATCATCCCATACTTTTATCGATACAT
* *
458050 ATGCAGTATTTATGCCGATATGCACTTTAAAAAATCAAAAATATTTATAAAAACCATATTCGCAT
196 ATGCAGTATTTATGCCGATATGCACTTCAAAAAATAAAAAATATTTATAAAAACCATATTCGCAT
* *
458115 TTTATATCACAATGTGTCAATTTCTCAGTTTTACTAATTAATTTTAAATTTTTCACTATACCGCG
261 TTTATACCACAATGTGTCAATTTCTCAATTTTACTAATTAATTTTAAATTTTTCACTATACCGCG
* **
458180 AATTCCTGTGTGCAAAATTTTTTATAC
326 AATTCCTATGCACAAAATTTTTTATAC
* * *
458207 AAAAGTGTAGTTTTAAGGCCAATATCGGATTAAAAAGACGAATATTCAAGAAAAATTGGTTTCTA
1 AAAAATGTAGTTTTAAGGCCAATATCGAATAAAAAAGACGAATATTCAAG-AAAA-TGGTTTCTA
* *
458272 AGTATTTCCTTGTCAAATTTTGGAAATTTATTTTTGCAAATGATATCACATCAAATTTCTCATTT
64 AGTATTTCCTTGTCAAATTTTGGAAATTCATTTTTGCAAATGATATCACATCAAATTTATCATTT
* **
458337 TTTGGAATTTTTTAAGATTTTTTTGAAAAA-ATAAGAAGTTGATCATCGTATACTTTTATCGATA
129 TTTGGAATTTTTCAAGA-TTTTTTGAAAAATATAAGAAGTTGATCATCCCATACTTTTATCGATA
* * *
458401 CATGTGTAGTATTTATG-CGATATGTACTTCAAAAAATAAAAAATATTTATAAAAACCAATATT-
193 CATATGCAGTATTTATGCCGATATGCACTTCAAAAAATAAAAAATATTTATAAAAACC-ATATTC
* * *
458464 GACATTTTATACCACAATGTGTTAATTTGTCAATTTTACTAATTAATTTTGAATTTTTCACTATA
257 G-CATTTTATACCACAATGTGTCAATTTCTCAATTTTACTAATTAATTTTAAATTTTTCACTATA
458529 CCGCGAATTCCTATGCACAAAATTTTTTAT
321 CCGCGAATTCCTATGCACAAAATTTTTTAT
458559 TGAAATTTGT
Statistics
Matches: 320, Mismatches: 27, Indels: 8
0.90 0.08 0.02
Matches are distributed among these distances:
352 46 0.14
353 42 0.13
354 220 0.69
355 12 0.04
ACGTcount: A:0.36, C:0.12, G:0.12, T:0.40
Consensus pattern (352 bp):
AAAAATGTAGTTTTAAGGCCAATATCGAATAAAAAAGACGAATATTCAAGAAAATGGTTTCTAAG
TATTTCCTTGTCAAATTTTGGAAATTCATTTTTGCAAATGATATCACATCAAATTTATCATTTTT
TGGAATTTTTCAAGATTTTTTGAAAAATATAAGAAGTTGATCATCCCATACTTTTATCGATACAT
ATGCAGTATTTATGCCGATATGCACTTCAAAAAATAAAAAATATTTATAAAAACCATATTCGCAT
TTTATACCACAATGTGTCAATTTCTCAATTTTACTAATTAATTTTAAATTTTTCACTATACCGCG
AATTCCTATGCACAAAATTTTTTATAC
Found at i:460714 original size:20 final size:21
Alignment explanation
Indices: 460677--460726 Score: 84
Period size: 20 Copynumber: 2.4 Consensus size: 21
460667 CTACAGCTTA
460677 TATCGATACAACAAGTGAATG
1 TATCGATACAACAAGTGAATG
*
460698 TATCGATAC-ATAAGTGAATG
1 TATCGATACAACAAGTGAATG
460718 TATCGATAC
1 TATCGATAC
460727 TGGACCTTGT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
20 19 0.68
21 9 0.32
ACGTcount: A:0.40, C:0.14, G:0.18, T:0.28
Consensus pattern (21 bp):
TATCGATACAACAAGTGAATG
Found at i:460849 original size:51 final size:50
Alignment explanation
Indices: 460764--460882 Score: 168
Period size: 50 Copynumber: 2.4 Consensus size: 50
460754 TTTGGAAAGA
* *
460764 AAATTTATTGATACATT-TTTAATGTATCAATACATTTTGGGTTTTGATCC
1 AAATGTATTGATACATTCTTTAATGTATCAATACATTCT-GGTTTTGATCC
* *
460814 AAATGTATTGATACATTCTTTATTGTATCGATACATTCTGGTTTTGATCC
1 AAATGTATTGATACATTCTTTAATGTATCAATACATTCTGGTTTTGATCC
**
460864 AAATGTATCAATACATTCT
1 AAATGTATTGATACATTCT
460883 GGATTTTTGA
Statistics
Matches: 62, Mismatches: 6, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
50 44 0.71
51 18 0.29
ACGTcount: A:0.30, C:0.13, G:0.12, T:0.45
Consensus pattern (50 bp):
AAATGTATTGATACATTCTTTAATGTATCAATACATTCTGGTTTTGATCC
Found at i:460878 original size:30 final size:31
Alignment explanation
Indices: 460837--460914 Score: 122
Period size: 32 Copynumber: 2.5 Consensus size: 31
460827 CATTCTTTAT
*
460837 TGTATCGATACATTCTGG-TTTTGATCCAAA
1 TGTATCGATACATTCTGGATTTTGACCCAAA
*
460867 TGTATCAATACATTCTGGATTTTTGACCCAAA
1 TGTATCGATACATTCTGGA-TTTTGACCCAAA
460899 TGTATCGATACATTCT
1 TGTATCGATACATTCT
460915 TCAATATATC
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
30 17 0.40
32 26 0.60
ACGTcount: A:0.28, C:0.18, G:0.14, T:0.40
Consensus pattern (31 bp):
TGTATCGATACATTCTGGATTTTGACCCAAA
Found at i:467290 original size:21 final size:20
Alignment explanation
Indices: 467264--467302 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
467254 GTTGGGACCT
467264 TGTATCGATACATTCTAGAAA
1 TGTATCGATACATT-TAGAAA
467285 TGTATCGATACATTTAGA
1 TGTATCGATACATTTAGA
467303 TAAAAATGCA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.36, C:0.13, G:0.15, T:0.36
Consensus pattern (20 bp):
TGTATCGATACATTTAGAAA
Found at i:468734 original size:158 final size:158
Alignment explanation
Indices: 468572--468870 Score: 408
Period size: 158 Copynumber: 1.9 Consensus size: 158
468562 TGAAAAATCG
* **
468572 ATATTTT-AGAAATAAAAA-AGGGGTTAGAGTAT-CCCTACAGAAATAACGGGGTTGGAGTATTT
1 ATATTTTGA-AAATAAAAATA-GAGTTAGAGTATGCCCT-CAGAAATAACGGGGTTGGAGTATCC
** * *
468634 TCGAGATGAAAATTTTAATATTTTGGAAATAAAAACGGGGTTAGAGTAACCCCTCAAAAATAACA
63 TCGAGATGAAAAACTTAATATTTTGAAAATAAAAACGGAGTTAGAGTAACCCCTCAAAAATAACA
468699 GAGT-TGGAGTATCCCTAAGATGAAAATTTTA
128 GAGTAT-GAGTATCCCTAAGATGAAAATTTTA
* **
468730 ATATTTTGAAAATAAAAATAGAGTTGGAGTATGCCCTTGGAAATAACGGGGTTGGAGTATCCTCG
1 ATATTTTGAAAATAAAAATAGAGTTAGAGTATGCCCTCAGAAATAACGGGGTTGGAGTATCCTCG
* * * *
468795 AGATGAAAAACTTAATATTTTGAAAATAAAAATGGAGTTGGAGTATCCCCTCAAAAATAACAGGG
66 AGATGAAAAACTTAATATTTTGAAAATAAAAACGGAGTTAGAGTAACCCCTCAAAAATAACAGAG
468860 TATGAGTATCC
131 TATGAGTATCC
468871 TCTCGAAAAT
Statistics
Matches: 123, Mismatches: 14, Indels: 8
0.85 0.10 0.06
Matches are distributed among these distances:
158 116 0.94
159 7 0.06
ACGTcount: A:0.40, C:0.11, G:0.21, T:0.28
Consensus pattern (158 bp):
ATATTTTGAAAATAAAAATAGAGTTAGAGTATGCCCTCAGAAATAACGGGGTTGGAGTATCCTCG
AGATGAAAAACTTAATATTTTGAAAATAAAAACGGAGTTAGAGTAACCCCTCAAAAATAACAGAG
TATGAGTATCCCTAAGATGAAAATTTTA
Found at i:468869 original size:28 final size:28
Alignment explanation
Indices: 468835--468900 Score: 80
Period size: 28 Copynumber: 2.4 Consensus size: 28
468825 AATGGAGTTG
468835 GAGTATCCCCTCAAAAATAACAGGG-TA
1 GAGTATCCCCTCAAAAATAACAGGGTTA
* * **
468862 TGAGTATCCTCTCGAAAATAATGGGGTTA
1 -GAGTATCCCCTCAAAAATAACAGGGTTA
468891 GAGTATCCCC
1 GAGTATCCCC
468901 GATGGATAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
28 30 0.94
29 2 0.06
ACGTcount: A:0.33, C:0.21, G:0.21, T:0.24
Consensus pattern (28 bp):
GAGTATCCCCTCAAAAATAACAGGGTTA
Found at i:468871 original size:79 final size:79
Alignment explanation
Indices: 468572--468872 Score: 340
Period size: 79 Copynumber: 3.8 Consensus size: 79
468562 TGAAAAATCG
* * * * **
468572 ATATTTT-AGAAATAAAAAAGGGGTTAGAGTAT-CCCTACAGAAATAACGGGGTTGGAGTATTTT
1 ATATTTTGA-AAATAAAAATGGAGTTAGAGTATCCCCT-CAAAAATAACAGGGTTGGAGTATCCT
468635 CGAGATGAAAATTTTA
64 CGAGATGAAAATTTTA
* * * * *
468651 ATATTTTGGAAATAAAAACGGGGTTAGAGTAACCCCTCAAAAATAACAGAGTTGGAGTATCC-CT
1 ATATTTTGAAAATAAAAATGGAGTTAGAGTATCCCCTCAAAAATAACAGGGTTGGAGTATCCTC-
*
468715 AAGATGAAAATTTTA
65 GAGATGAAAATTTTA
* * * *** *
468730 ATATTTTGAAAATAAAAATAGAGTTGGAGTATGCCCTTGGAAATAACGGGGTTGGAGTATCCTCG
1 ATATTTTGAAAATAAAAATGGAGTTAGAGTATCCCCTCAAAAATAACAGGGTTGGAGTATCCTCG
**
468795 AGATGAAAAACTTA
66 AGATGAAAATTTTA
*
468809 ATATTTTGAAAATAAAAATGGAGTTGGAGTATCCCCTCAAAAATAACAGGGTAT-GAGTATCCTC
1 ATATTTTGAAAATAAAAATGGAGTTAGAGTATCCCCTCAAAAATAACAGGGT-TGGAGTATCCTC
468873 TCGAAAATAA
Statistics
Matches: 187, Mismatches: 30, Indels: 10
0.82 0.13 0.04
Matches are distributed among these distances:
78 1 0.01
79 180 0.96
80 6 0.03
ACGTcount: A:0.40, C:0.11, G:0.21, T:0.28
Consensus pattern (79 bp):
ATATTTTGAAAATAAAAATGGAGTTAGAGTATCCCCTCAAAAATAACAGGGTTGGAGTATCCTCG
AGATGAAAATTTTA
Found at i:470160 original size:4 final size:4
Alignment explanation
Indices: 470151--470187 Score: 60
Period size: 4 Copynumber: 9.8 Consensus size: 4
470141 ATGACACTGA
470151 AAAG AAAG AAAG -AAG -AAG AAAG AAAG AAAG AAAG AAA
1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAA
470188 TACATGGTGA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 6 0.19
4 26 0.81
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (4 bp):
AAAG
Done.