Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A09
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: 81831061
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 3560000 characters in sequence are not A, C, G, or T
File 79 of 259
Found at i:25534809 original size:18 final size:18
Alignment explanation
Indices: 25534759--25534814 Score: 60
Period size: 18 Copynumber: 3.1 Consensus size: 18
25534749 AAAGCCTTTG
*
25534759 AAAAGCAAAAAGAAAATGA
1 AAAAG-AAAACGAAAATGA
* *
25534778 AAAAGAAAATGAAATTGA
1 AAAAGAAAACGAAAATGA
*
25534796 AAAAGAAAGCGAAAA-GA
1 AAAAGAAAACGAAAATGA
25534813 AA
1 AA
25534815 TTTGAGAGTG
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
17 4 0.12
18 23 0.72
19 5 0.16
ACGTcount: A:0.71, C:0.04, G:0.18, T:0.07
Consensus pattern (18 bp):
AAAAGAAAACGAAAATGA
Found at i:25536324 original size:20 final size:20
Alignment explanation
Indices: 25536301--25536348 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
25536291 AGCTCCGTCC
25536301 AGCTCAACTCAGCTCATTTG
1 AGCTCAACTCAGCTCATTTG
*** **
25536321 AGCTCGTTTCAGCTTGTTTG
1 AGCTCAACTCAGCTCATTTG
25536341 AGCTCAAC
1 AGCTCAAC
25536349 CGAGCTTACT
Statistics
Matches: 20, Mismatches: 8, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.21, C:0.27, G:0.19, T:0.33
Consensus pattern (20 bp):
AGCTCAACTCAGCTCATTTG
Found at i:25537065 original size:22 final size:22
Alignment explanation
Indices: 25537014--25537079 Score: 80
Period size: 21 Copynumber: 3.0 Consensus size: 22
25537004 GGTATTTGGG
* *
25537014 AATTGGTTCGAAATAGTATGG-
1 AATTGGTACGAAATGGTATGGT
25537035 AATTGGTACGAAATGGTATGGT
1 AATTGGTACGAAATGGTATGGT
* *
25537057 ATTTGGTACGAATTGGTAATGGT
1 AATTGGTACGAAATGGT-ATGGT
25537080 TCAAAGAGGT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
21 19 0.49
22 15 0.38
23 5 0.13
ACGTcount: A:0.30, C:0.05, G:0.30, T:0.35
Consensus pattern (22 bp):
AATTGGTACGAAATGGTATGGT
Found at i:25544802 original size:20 final size:20
Alignment explanation
Indices: 25544779--25544832 Score: 54
Period size: 20 Copynumber: 2.7 Consensus size: 20
25544769 AGCTCCGTCC
25544779 AGCTCAACTCAGCTCATTTA
1 AGCTCAACTCAGCTCATTTA
*** * *
25544799 AGCTCGTTTCAGCTCGTTTG
1 AGCTCAACTCAGCTCATTTA
*
25544819 AGCTCAACTGAGCT
1 AGCTCAACTCAGCT
25544833 TACTTTCAGC
Statistics
Matches: 25, Mismatches: 9, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.22, C:0.28, G:0.19, T:0.31
Consensus pattern (20 bp):
AGCTCAACTCAGCTCATTTA
Found at i:25546548 original size:445 final size:445
Alignment explanation
Indices: 25545718--25546786 Score: 1958
Period size: 445 Copynumber: 2.4 Consensus size: 445
25545708 ATGAACATTT
*
25545718 GTTCTTGTGAGGTTGCTTTCTCTCATATCTCGTACAAGTTTCGAAAGACTTATCTGGCTTGTGCT
1 GTTCTTGTGAGGTTGCTTCCTCTCATATCTCGTACAAGTTTCGAAAGACTTATCTGGCTTGTGCT
25545783 AGTGGCGTCAATCGTCTTGTTTGAACTTATCACCAATCTTGGTGTGGCGTTCACCTATCCATCTA
66 AGTGGCGTCAATCGTCTTGTTTGAACTTATCACCAATCTTGGTGTGGCGTTCACCTATCCATCTA
*
25545848 TCCATCTTTTCACCTTAACAATATAGGAACCGAGGTGACACTTCTTAGTGTTGAATCATTCCTGA
131 TCCATCTTTTCACCTTAACAATATAGGAACCGGGGTGACACTTCTTAGTGTTGAATCATTCCTGA
* *
25545913 CGTTAAGTTCGTTTTCCATTCTCATCCTTCGAATTATTTTCTTGTTATTCCAAGCCGAGCCATTT
196 CGTTAAGTTCGTTTTCCATTCCCATCCTTCGAATTATTTTCTTGTTATTCCAAACCGAGCCATTT
*
25545978 AACCATCATCCATCTTTGCTACTAAATCGAATCTATTACTAAATTCACCCTACTTTGAAACCTTC
261 AACCATCATCCATCTTTGCTACTAAATCGAACCTATTACTAAATTCACCCTACTTTGAAACCTTC
* *
25546043 CGCTTACCCGTATCTTTTCATTCACTTCTAGTTCTAAAACCCGAAGCACGAACGACTCTCTCGAA
326 CGCTTACCCGTATCTTTACATTCACTTCTAGTTCTAAAACCCGAAGCACGAACAACTCTCTCGAA
*
25546108 CGACGATCGGGCAACTAAGTGAATTCGACTCATCATCCCGAGCCGGATCACATCA
391 CGACGATCGAGCAACTAAGTGAATTCGACTCATCATCCCGAGCCGGATCACATCA
25546163 GTTCTTGTGAGGTTGCTTCCTCTCATATCTCGTACAAGTTTCGAAAGACTTATCTGGCTTGTGCT
1 GTTCTTGTGAGGTTGCTTCCTCTCATATCTCGTACAAGTTTCGAAAGACTTATCTGGCTTGTGCT
25546228 AGTGGCGTCAATCGTCTTGTTTGAACTTATCACCAATCTTGGTGTGGCGTTCACCTATCCATCTA
66 AGTGGCGTCAATCGTCTTGTTTGAACTTATCACCAATCTTGGTGTGGCGTTCACCTATCCATCTA
*
25546293 TCCATCATTTCACCTTAACAATATAGGAACCGGGGTGACACTTCTTAGTGTTGAATCATTCCTGA
131 TCCATCTTTTCACCTTAACAATATAGGAACCGGGGTGACACTTCTTAGTGTTGAATCATTCCTGA
25546358 CGTTAAGTTCGTTTTCCATTCCCATCCTTCGAATTATTTTCTTGTTATTCCAAACCGAGCCATTT
196 CGTTAAGTTCGTTTTCCATTCCCATCCTTCGAATTATTTTCTTGTTATTCCAAACCGAGCCATTT
25546423 AACCATCATCCATCTTTGCTACTAAATCGAACCTATTACTAAATTCACCCTACTTTGAAACCTTC
261 AACCATCATCCATCTTTGCTACTAAATCGAACCTATTACTAAATTCACCCTACTTTGAAACCTTC
25546488 CGCTTACCCGTATCTTTACATTCACTTCTAGTTCTAAAACCCGAAGCACGAACAACTCTCTCGAA
326 CGCTTACCCGTATCTTTACATTCACTTCTAGTTCTAAAACCCGAAGCACGAACAACTCTCTCGAA
* * *
25546553 CTACGATCGAGCAACTAAGTGAATTTGACTCATCATCTCGAGCCGGATCACATCA
391 CGACGATCGAGCAACTAAGTGAATTCGACTCATCATCCCGAGCCGGATCACATCA
* * *
25546608 GTTCTTGTGAGGTTACTTCCTTTCATATCTCGTACAAGTTTCGAAAGACTTATCTGGGTTGTGCT
1 GTTCTTGTGAGGTTGCTTCCTCTCATATCTCGTACAAGTTTCGAAAGACTTATCTGGCTTGTGCT
* * * *
25546673 AGTGGCATCAATCATCTTGTTTGAACTTATCACCAATCTTAGTGTGGTGTTCACCTATCCATCTA
66 AGTGGCGTCAATCGTCTTGTTTGAACTTATCACCAATCTTGGTGTGGCGTTCACCTATCCATCTA
*
25546738 TCCATCTTTTCACCTTAACAATATAGGAACTGGGGTGACACTTCTTAGT
131 TCCATCTTTTCACCTTAACAATATAGGAACCGGGGTGACACTTCTTAGT
25546787 TGATACGAGC
Statistics
Matches: 603, Mismatches: 21, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
445 603 1.00
ACGTcount: A:0.24, C:0.26, G:0.15, T:0.35
Consensus pattern (445 bp):
GTTCTTGTGAGGTTGCTTCCTCTCATATCTCGTACAAGTTTCGAAAGACTTATCTGGCTTGTGCT
AGTGGCGTCAATCGTCTTGTTTGAACTTATCACCAATCTTGGTGTGGCGTTCACCTATCCATCTA
TCCATCTTTTCACCTTAACAATATAGGAACCGGGGTGACACTTCTTAGTGTTGAATCATTCCTGA
CGTTAAGTTCGTTTTCCATTCCCATCCTTCGAATTATTTTCTTGTTATTCCAAACCGAGCCATTT
AACCATCATCCATCTTTGCTACTAAATCGAACCTATTACTAAATTCACCCTACTTTGAAACCTTC
CGCTTACCCGTATCTTTACATTCACTTCTAGTTCTAAAACCCGAAGCACGAACAACTCTCTCGAA
CGACGATCGAGCAACTAAGTGAATTCGACTCATCATCCCGAGCCGGATCACATCA
Found at i:25547049 original size:30 final size:30
Alignment explanation
Indices: 25546963--25547050 Score: 79
Period size: 30 Copynumber: 2.9 Consensus size: 30
25546953 CTAGCTGACT
* * *
25546963 TTCAACTCATGAGCTAAACCTTAGCTCAAC
1 TTCAGCTCACGAGCTAAAGCTTAGCTCAAC
* * ** *
25546993 TTCAGCTTAGGAG-TTTAGCCTCAGCTCAAC
1 TTCAGCTCACGAGCTAAAG-CTTAGCTCAAC
*
25547023 TTTAGCTCACGAGCTAAAGCTTAGCTCA
1 TTCAGCTCACGAGCTAAAGCTTAGCTCA
25547051 TTTTAGTTTA
Statistics
Matches: 43, Mismatches: 13, Indels: 4
0.72 0.22 0.07
Matches are distributed among these distances:
29 2 0.05
30 38 0.88
31 3 0.07
ACGTcount: A:0.28, C:0.27, G:0.16, T:0.28
Consensus pattern (30 bp):
TTCAGCTCACGAGCTAAAGCTTAGCTCAAC
Found at i:25549845 original size:23 final size:23
Alignment explanation
Indices: 25549818--25549896 Score: 97
Period size: 23 Copynumber: 3.4 Consensus size: 23
25549808 AAGAAATGAA
25549818 AGAAAAAGAAAAGAGATTGAGAG
1 AGAAAAAGAAAAGAGATTGAGAG
* *
25549841 TGAAAAAGAAAATGAGATTGA-AA
1 AGAAAAAGAAAA-GAGATTGAGAG
* * *
25549864 AGAGAATGAAAAGAGTTTGAGAG
1 AGAAAAAGAAAAGAGATTGAGAG
25549887 AGAAAAAGAA
1 AGAAAAAGAA
25549897 TGTGAACAAG
Statistics
Matches: 45, Mismatches: 9, Indels: 4
0.78 0.16 0.07
Matches are distributed among these distances:
22 7 0.16
23 30 0.67
24 8 0.18
ACGTcount: A:0.59, C:0.00, G:0.28, T:0.13
Consensus pattern (23 bp):
AGAAAAAGAAAAGAGATTGAGAG
Found at i:25549849 original size:46 final size:47
Alignment explanation
Indices: 25549798--25549896 Score: 114
Period size: 46 Copynumber: 2.1 Consensus size: 47
25549788 TGAAATCGAG
*
25549798 AAAAGAAACAAAGA-AATG-AAAGAAAAAGAAAAGAGATTGAGAGTGA
1 AAAAGAAA-AAAGAGAATGAAAAGAAAAAGAAAAGAGATTGAGAGAGA
* * * * *
25549844 AAAAG-AAAATGAGATTGAAAAGAGAATGAAAAGAGTTTGAGAGAGA
1 AAAAGAAAAAAGAGAATGAAAAGAAAAAGAAAAGAGATTGAGAGAGA
25549890 AAAAGAA
1 AAAAGAA
25549897 TGTGAACAAG
Statistics
Matches: 44, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
44 4 0.09
45 5 0.11
46 34 0.77
47 1 0.02
ACGTcount: A:0.63, C:0.01, G:0.25, T:0.11
Consensus pattern (47 bp):
AAAAGAAAAAAGAGAATGAAAAGAAAAAGAAAAGAGATTGAGAGAGA
Found at i:25549864 original size:17 final size:17
Alignment explanation
Indices: 25549825--25549872 Score: 60
Period size: 18 Copynumber: 2.8 Consensus size: 17
25549815 GAAAGAAAAA
*
25549825 GAAAAGAGATTGAGAGT
1 GAAAAGAGAATGAGAGT
* *
25549842 GAAAAAGAAAATGAGATT
1 G-AAAAGAGAATGAGAGT
25549860 GAAAAGAGAATGA
1 GAAAAGAGAATGA
25549873 AAAGAGTTTG
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
17 12 0.46
18 14 0.54
ACGTcount: A:0.56, C:0.00, G:0.29, T:0.15
Consensus pattern (17 bp):
GAAAAGAGAATGAGAGT
Found at i:25549925 original size:16 final size:18
Alignment explanation
Indices: 25549887--25549925 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
25549877 AGTTTGAGAG
25549887 AGAAAAAGAATGTGAACA
1 AGAAAAAGAATGTGAACA
*
25549905 AGAAAAAGAGTG-GAA-A
1 AGAAAAAGAATGTGAACA
25549921 AGAAA
1 AGAAA
25549926 TTAAGATAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 6 0.30
17 3 0.15
18 11 0.55
ACGTcount: A:0.64, C:0.03, G:0.26, T:0.08
Consensus pattern (18 bp):
AGAAAAAGAATGTGAACA
Found at i:25552401 original size:23 final size:22
Alignment explanation
Indices: 25552350--25552401 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 22
25552340 CCTCGTCTTT
*
25552350 TTCTTTTGTTTCTTTTTCTAAC
1 TTCTTTTCTTTCTTTTTCTAAC
25552372 -TCATTTTCTCTTCTTTCTTC-AAC
1 TTC-TTTTCT-TTCTTT-TTCTAAC
25552395 TTCTTTT
1 TTCTTTT
25552402 TCAATTTTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 2 0.08
22 5 0.20
23 13 0.52
24 5 0.20
ACGTcount: A:0.10, C:0.23, G:0.02, T:0.65
Consensus pattern (22 bp):
TTCTTTTCTTTCTTTTTCTAAC
Found at i:25556356 original size:20 final size:20
Alignment explanation
Indices: 25556333--25556380 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
25556323 AGCTCCGTCC
25556333 AGCTCAACTCAGCTCATTTG
1 AGCTCAACTCAGCTCATTTG
*** *
25556353 AGCTCGTTTCAGCTCGTTTG
1 AGCTCAACTCAGCTCATTTG
25556373 AGCTCAAC
1 AGCTCAAC
25556381 CGAGCTTACT
Statistics
Matches: 21, Mismatches: 7, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.21, C:0.29, G:0.19, T:0.31
Consensus pattern (20 bp):
AGCTCAACTCAGCTCATTTG
Found at i:25558105 original size:445 final size:445
Alignment explanation
Indices: 25557276--25558165 Score: 1636
Period size: 445 Copynumber: 2.0 Consensus size: 445
25557266 ATGAACATTT
25557276 GTTCTTGTGAGGTTGCTTCCTCTCATATCTCGTACAAGTTTCGAAAGACTTATCTGGCTTGTGCT
1 GTTCTTGTGAGGTTGCTTCCTCTCATATCTCGTACAAGTTTCGAAAGACTTATCTGGCTTGTGCT
25557341 AGTGGCGTCAATCGTCTTGTTTGAACTTATCACCAATCTTGGTGTGGCGTTCACCTATCCATCTA
66 AGTGGCGTCAATCGTCTTGTTTGAACTTATCACCAATCTTGGTGTGGCGTTCACCTATCCATCTA
*
25557406 TCCATCTTTTCACCTTAACAATATAGGAACCGAGGTGACACTTCTTAGTGTTGAATCATTCTTGA
131 TCCATCTTTTCACCTTAACAATATAGGAACCGAGGTGACACTTCTTAGTGTTGAATCATTCCTGA
*
25557471 CGTTAAGTTCGTTTTCCATTCCCATCTTTCGAATTATTTTCTTGTTATTCCAAACCGAGCCACTT
196 CGTTAAGTTCGTTTTCCATTCCCATCCTTCGAATTATTTTCTTGTTATTCCAAACCGAGCCACTT
*
25557536 AACCATCATCCATCTTTGCTACTAAATCGAATCTATTACGAAATTCACCCTACTTTGAAACCTTC
261 AACCATCATCCATCTTTGCTACTAAATCGAACCTATTACGAAATTCACCCTACTTTGAAACCTTC
* *
25557601 TGGTTACCCGTATCTTTTCATTCACTTCTAGTTCTAAAACCCGAAGCACGAACGACTCTCTCGAA
326 CGCTTACCCGTATCTTTTCATTCACTTCTAGTTCTAAAACCCGAAGCACGAACGACTCTCTCGAA
*** * *
25557666 CGGTGATCGGGCAACTAAGTGAATTTGACTCATCATCCCGAGCCGGATCACATCA
391 CGACAATCGGGCAACTAAGTGAATTCGACTCATCATCCCAAGCCGGATCACATCA
*
25557721 GTTCTTGTGAGGTTGCTTCCTCTCATATCTCGTACAAGTTTCGAAAGACTTATCTGGCTTGTGTT
1 GTTCTTGTGAGGTTGCTTCCTCTCATATCTCGTACAAGTTTCGAAAGACTTATCTGGCTTGTGCT
25557786 AGTGGCGTCAATCGTCTTGTTTGAACTTATCACCAATCTTGGTGTGGCGTTCACCTATCCATCTA
66 AGTGGCGTCAATCGTCTTGTTTGAACTTATCACCAATCTTGGTGTGGCGTTCACCTATCCATCTA
*
25557851 TCCATCTTTTCACCTTAACAATATAGGAACCGGGGTGACACTTCTTAGTGTTGAATCATTCCTGA
131 TCCATCTTTTCACCTTAACAATATAGGAACCGAGGTGACACTTCTTAGTGTTGAATCATTCCTGA
* *
25557916 CGTTAAGTTCGTTTTCCATTCCCATCCTTCGAATTATTTTCTTGTTATTCCAAATCGAGCCATTT
196 CGTTAAGTTCGTTTTCCATTCCCATCCTTCGAATTATTTTCTTGTTATTCCAAACCGAGCCACTT
*
25557981 AACCATCATCCATCTTTGCTACTAAATCGAACCTATTACTAAATTCACCCTACTTTGAAACCTTC
261 AACCATCATCCATCTTTGCTACTAAATCGAACCTATTACGAAATTCACCCTACTTTGAAACCTTC
25558046 CGCTTACCCGTATCTTTTCATTCACTTCTAGTTCTAAAACCCGAAGCACGAACGACTCTCTCGAA
326 CGCTTACCCGTATCTTTTCATTCACTTCTAGTTCTAAAACCCGAAGCACGAACGACTCTCTCGAA
*
25558111 CGACAATCGGGCAACTAAGTGAATTCGACTCATCATCTCAAGCCGGATCACATCA
391 CGACAATCGGGCAACTAAGTGAATTCGACTCATCATCCCAAGCCGGATCACATCA
25558166 ACTTTCCTTT
Statistics
Matches: 429, Mismatches: 16, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
445 429 1.00
ACGTcount: A:0.24, C:0.26, G:0.15, T:0.34
Consensus pattern (445 bp):
GTTCTTGTGAGGTTGCTTCCTCTCATATCTCGTACAAGTTTCGAAAGACTTATCTGGCTTGTGCT
AGTGGCGTCAATCGTCTTGTTTGAACTTATCACCAATCTTGGTGTGGCGTTCACCTATCCATCTA
TCCATCTTTTCACCTTAACAATATAGGAACCGAGGTGACACTTCTTAGTGTTGAATCATTCCTGA
CGTTAAGTTCGTTTTCCATTCCCATCCTTCGAATTATTTTCTTGTTATTCCAAACCGAGCCACTT
AACCATCATCCATCTTTGCTACTAAATCGAACCTATTACGAAATTCACCCTACTTTGAAACCTTC
CGCTTACCCGTATCTTTTCATTCACTTCTAGTTCTAAAACCCGAAGCACGAACGACTCTCTCGAA
CGACAATCGGGCAACTAAGTGAATTCGACTCATCATCCCAAGCCGGATCACATCA
Found at i:25560770 original size:12 final size:12
Alignment explanation
Indices: 25560753--25560810 Score: 71
Period size: 12 Copynumber: 4.7 Consensus size: 12
25560743 AAGAGGAAAT
25560753 TTGAAAAAAAAA
1 TTGAAAAAAAAA
25560765 TTGAAAAAAAAA
1 TTGAAAAAAAAA
*
25560777 TCGAAAAAAAAAA
1 TTG-AAAAAAAAA
*
25560790 TTTTAAAAAAAAA
1 -TTGAAAAAAAAA
*
25560803 TCGAAAAA
1 TTGAAAAA
25560811 TCGAAGTATA
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
12 20 0.51
13 18 0.46
14 1 0.03
ACGTcount: A:0.72, C:0.03, G:0.07, T:0.17
Consensus pattern (12 bp):
TTGAAAAAAAAA
Found at i:25560785 original size:26 final size:26
Alignment explanation
Indices: 25560756--25560810 Score: 92
Period size: 26 Copynumber: 2.1 Consensus size: 26
25560746 AGGAAATTTG
25560756 AAAAAAAAATTGAAAAAAAAATCGAA
1 AAAAAAAAATTGAAAAAAAAATCGAA
* *
25560782 AAAAAAAATTTTAAAAAAAAATCGAA
1 AAAAAAAAATTGAAAAAAAAATCGAA
25560808 AAA
1 AAA
25560811 TCGAAGTATA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.76, C:0.04, G:0.05, T:0.15
Consensus pattern (26 bp):
AAAAAAAAATTGAAAAAAAAATCGAA
Found at i:25560822 original size:26 final size:26
Alignment explanation
Indices: 25560756--25560828 Score: 78
Period size: 26 Copynumber: 2.8 Consensus size: 26
25560746 AGGAAATTTG
25560756 AAAAAAAAA-T-TGAAAAAAAAATCGA
1 AAAAAAAAAGTAT-AAAAAAAAATCGA
* *
25560781 AAAAAAAAATTTTAAAAAAAAATCGA
1 AAAAAAAAAGTATAAAAAAAAATCGA
***
25560807 AAAATCGAAGTATAAAAAAAAA
1 AAAAAAAAAGTATAAAAAAAAA
25560829 GAGTGAAAAG
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
25 9 0.22
26 31 0.76
27 1 0.02
ACGTcount: A:0.74, C:0.04, G:0.07, T:0.15
Consensus pattern (26 bp):
AAAAAAAAAGTATAAAAAAAAATCGA
Found at i:25561731 original size:18 final size:18
Alignment explanation
Indices: 25561710--25561744 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
25561700 AGAAAAGAAA
25561710 ATTGA-AAAAGAAATTGAG
1 ATTGAGAAAA-AAATTGAG
25561728 ATTGAGAAAAAAATTGA
1 ATTGAGAAAAAAATTGA
25561745 AAAAGAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.57, C:0.00, G:0.20, T:0.23
Consensus pattern (18 bp):
ATTGAGAAAAAAATTGAG
Found at i:25566760 original size:30 final size:30
Alignment explanation
Indices: 25566724--25566820 Score: 97
Period size: 30 Copynumber: 3.2 Consensus size: 30
25566714 AGCTCACTCC
*
25566724 TAGCTCATA-TTCAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTCAGCTCACGAGATAAACCT
* * * * *
25566754 TAGCTCAACTTCAGCTTAGGAGTTTAATCT
1 TAGCTCAACTTCAGCTCACGAGATAAACCT
* * *
25566784 CAGCTCAACTTTAGCTCACGAGATAAAGCT
1 TAGCTCAACTTCAGCTCACGAGATAAACCT
25566814 TAGCTCA
1 TAGCTCA
25566821 TTTTAGTTTA
Statistics
Matches: 53, Mismatches: 13, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
29 1 0.02
30 52 0.98
ACGTcount: A:0.30, C:0.26, G:0.15, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTCAGCTCACGAGATAAACCT
Found at i:25571922 original size:20 final size:20
Alignment explanation
Indices: 25571899--25571952 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
25571889 AGCTAAAGTA
25571899 AGCTAAATTTAGCTCACATG
1 AGCTAAATTTAGCTCACATG
* ***
25571919 AGCTTAATTTAGCTCGTTTG
1 AGCTAAATTTAGCTCACATG
*
25571939 AGCTCAATTTAGCT
1 AGCTAAATTTAGCT
25571953 GGGAAAAACT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.28, C:0.19, G:0.17, T:0.37
Consensus pattern (20 bp):
AGCTAAATTTAGCTCACATG
Found at i:25575481 original size:13 final size:14
Alignment explanation
Indices: 25575451--25575492 Score: 59
Period size: 14 Copynumber: 3.0 Consensus size: 14
25575441 GTGGAGAGAT
25575451 CAAAAGAAAAAGAG
1 CAAAAGAAAAAGAG
*
25575465 CAAAATAAAAAGA-
1 CAAAAGAAAAAGAG
25575478 CAAAAAGAAAAAGAG
1 C-AAAAGAAAAAGAG
25575493 TGGACAAAGT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 1 0.04
14 23 0.96
ACGTcount: A:0.74, C:0.07, G:0.17, T:0.02
Consensus pattern (14 bp):
CAAAAGAAAAAGAG
Found at i:25575890 original size:30 final size:31
Alignment explanation
Indices: 25575856--25575952 Score: 103
Period size: 30 Copynumber: 3.2 Consensus size: 31
25575846 AGCTCACTCC
*
25575856 TAGCTC-ACTTTCAACTCACGAGCTAAACCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
* * ** *
25575886 TAGCTCAAC-TTCAGCTTAGGAG-TTTAGCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
25575915 TCAGCTCAACTTT-AGCTCACGAGCTAAACCT
1 T-AGCTCAACTTTCAGCTCACGAGCTAAACCT
25575946 TAGCTCA
1 TAGCTCA
25575953 TTTTAGTTTA
Statistics
Matches: 52, Mismatches: 11, Indels: 8
0.73 0.15 0.11
Matches are distributed among these distances:
29 5 0.10
30 38 0.73
31 9 0.17
ACGTcount: A:0.28, C:0.29, G:0.14, T:0.29
Consensus pattern (31 bp):
TAGCTCAACTTTCAGCTCACGAGCTAAACCT
Found at i:25578555 original size:6 final size:5
Alignment explanation
Indices: 25578531--25578587 Score: 55
Period size: 5 Copynumber: 11.0 Consensus size: 5
25578521 AAGAGAAAAT
*
25578531 AAAGA AAAGA AAAGAA AAAGCA AAAGA AGA-A AAAGAA AAAGA AATA-A
1 AAAGA AAAGA AAAG-A AAAG-A AAAGA AAAGA AAAG-A AAAGA AA-AGA
25578578 AAAGA AAAGA
1 AAAGA AAAGA
25578588 GAGGCAAGAG
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
4 4 0.09
5 24 0.55
6 16 0.36
ACGTcount: A:0.79, C:0.02, G:0.18, T:0.02
Consensus pattern (5 bp):
AAAGA
Found at i:25578580 original size:25 final size:25
Alignment explanation
Indices: 25578535--25578583 Score: 64
Period size: 27 Copynumber: 1.9 Consensus size: 25
25578525 GAAAATAAAG
25578535 AAAAGAAAAGAAAAAGCAAAAGAAGA
1 AAAAGAAAAGAAAAA-CAAAAGAAGA
*
25578561 AAAAGAAAAAGAAATA-AAAAGAA
1 AAAAG-AAAAGAAAAACAAAAGAA
25578584 AAGAGAGGCA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
25 7 0.33
26 5 0.24
27 9 0.43
ACGTcount: A:0.80, C:0.02, G:0.16, T:0.02
Consensus pattern (25 bp):
AAAAGAAAAGAAAAACAAAAGAAGA
Found at i:25580894 original size:20 final size:20
Alignment explanation
Indices: 25580849--25580894 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
25580839 GCTCGTTTCT
*
25580849 AGCTCACTCGAGCTCAAGTC
1 AGCTCACTCAAGCTCAAGTC
* *
25580869 AACTCACTCAAGCTCAATTC
1 AGCTCACTCAAGCTCAAGTC
25580889 AGCTCA
1 AGCTCA
25580895 ATTTTAACCC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.30, C:0.35, G:0.13, T:0.22
Consensus pattern (20 bp):
AGCTCACTCAAGCTCAAGTC
Found at i:25582466 original size:22 final size:21
Alignment explanation
Indices: 25582430--25582474 Score: 63
Period size: 22 Copynumber: 2.1 Consensus size: 21
25582420 AGAAGTGAGC
*
25582430 AAAAAAAGAAAAAAAAGTAAA
1 AAAAAAACAAAAAAAAGTAAA
*
25582451 AAAAAGAACAAAAAAAAGTGAA
1 AAAAA-AACAAAAAAAAGTAAA
25582473 AA
1 AA
25582475 GTCTTGTGAG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 5 0.24
22 16 0.76
ACGTcount: A:0.82, C:0.02, G:0.11, T:0.04
Consensus pattern (21 bp):
AAAAAAACAAAAAAAAGTAAA
Found at i:25582474 original size:10 final size:9
Alignment explanation
Indices: 25582430--25582465 Score: 54
Period size: 10 Copynumber: 3.8 Consensus size: 9
25582420 AGAAGTGAGC
25582430 AAAAAAAGA
1 AAAAAAAGA
25582439 AAAAAAAGTA
1 AAAAAAAG-A
25582449 AAAAAAAGA
1 AAAAAAAGA
25582458 ACAAAAAA
1 A-AAAAAA
25582466 AAGTGAAAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
9 10 0.40
10 15 0.60
ACGTcount: A:0.86, C:0.03, G:0.08, T:0.03
Consensus pattern (9 bp):
AAAAAAAGA
Found at i:25585234 original size:7 final size:7
Alignment explanation
Indices: 25585222--25585251 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
25585212 ATTTGTAAAG
25585222 GACTTTT
1 GACTTTT
25585229 GACTTTT
1 GACTTTT
25585236 GACTTTT
1 GACTTTT
25585243 GACTTTT
1 GACTTTT
25585250 GA
1 GA
25585252 TCATTTGAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.17, C:0.13, G:0.17, T:0.53
Consensus pattern (7 bp):
GACTTTT
Found at i:25585943 original size:9 final size:10
Alignment explanation
Indices: 25585922--25585955 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
25585912 AAAAGAGAAG
25585922 AAATTCAAAA
1 AAATTCAAAA
25585932 AAATTCAAAA
1 AAATTCAAAA
*
25585942 AAAATCGAAAA
1 AAATTC-AAAA
25585953 AAA
1 AAA
25585956 AGAAAAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 15 0.68
11 7 0.32
ACGTcount: A:0.74, C:0.09, G:0.03, T:0.15
Consensus pattern (10 bp):
AAATTCAAAA
Found at i:25586944 original size:15 final size:14
Alignment explanation
Indices: 25586921--25586968 Score: 69
Period size: 15 Copynumber: 3.3 Consensus size: 14
25586911 AAATTGAGAG
25586921 AAGAAAAAAAGAAA
1 AAGAAAAAAAGAAA
*
25586935 TAAGAGAAAAAGAAA
1 -AAGAAAAAAAGAAA
25586950 AAGAAATAAAAGAAA
1 AAGAAA-AAAAGAAA
25586965 AAGA
1 AAGA
25586969 TGAAAATGAG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
14 5 0.17
15 25 0.83
ACGTcount: A:0.79, C:0.00, G:0.17, T:0.04
Consensus pattern (14 bp):
AAGAAAAAAAGAAA
Found at i:25586950 original size:21 final size:21
Alignment explanation
Indices: 25586917--25586968 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
25586907 AATGAAATTG
*
25586917 AGAGAAGAA-AAAAAGAAATA
1 AGAGAAAAAGAAAAAGAAATA
25586937 AGAGAAAAAGAAAAAGAAATA
1 AGAGAAAAAGAAAAAGAAATA
*
25586958 AAAGAAAAAGA
1 AGAGAAAAAGA
25586969 TGAAAATGAG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
20 8 0.28
21 21 0.72
ACGTcount: A:0.77, C:0.00, G:0.19, T:0.04
Consensus pattern (21 bp):
AGAGAAAAAGAAAAAGAAATA
Found at i:25589726 original size:7 final size:7
Alignment explanation
Indices: 25589714--25589743 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
25589704 ATTTGTAAAG
25589714 GACTTTT
1 GACTTTT
25589721 GACTTTT
1 GACTTTT
25589728 GACTTTT
1 GACTTTT
25589735 GACTTTT
1 GACTTTT
25589742 GA
1 GA
25589744 TCATTTGAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.17, C:0.13, G:0.17, T:0.53
Consensus pattern (7 bp):
GACTTTT
Found at i:25591313 original size:20 final size:20
Alignment explanation
Indices: 25591267--25591313 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
25591257 AGCTCGTTTC
*
25591267 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
25591287 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
25591307 CAGCTCA
1 CAGCTCA
25591314 ATTTTAACCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:25592417 original size:20 final size:20
Alignment explanation
Indices: 25592371--25592417 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
25592361 AGCTCGTTTC
*
25592371 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
25592391 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
25592411 CAGCTCA
1 CAGCTCA
25592418 ATCTTAACCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:25593917 original size:12 final size:13
Alignment explanation
Indices: 25593900--25593946 Score: 51
Period size: 16 Copynumber: 3.5 Consensus size: 13
25593890 ACAAAAAAAT
25593900 AAAAAAATTCGAA
1 AAAAAAATTCGAA
*
25593913 AAAAAAATTGATTGAA
1 AAAAAAA-T--TCGAA
25593929 AAAAAAATTC-AA
1 AAAAAAATTCGAA
25593941 AAAAAA
1 AAAAAA
25593947 GTGAAAAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
12 8 0.28
13 8 0.28
14 1 0.03
15 1 0.03
16 11 0.38
ACGTcount: A:0.72, C:0.04, G:0.06, T:0.17
Consensus pattern (13 bp):
AAAAAAATTCGAA
Found at i:25595101 original size:48 final size:48
Alignment explanation
Indices: 25595004--25595127 Score: 155
Period size: 48 Copynumber: 2.6 Consensus size: 48
25594994 CATTGAGCGA
* * *
25595004 GAAAAGGAGAAAGAGATTGAAAAAGAAATTGAGATTGAAAAAGGATGT
1 GAAAAAGAGAAAGAAATTGAAAAAGAAATTGAGATTGAAAAAAGATGT
*
25595052 GAAAAAGAGAAAGAAATCGAAAAAGAAATTGAGATTGAACAAAAG-TGT
1 GAAAAAGAGAAAGAAATTGAAAAAGAAATTGAGATTGAA-AAAAGATGT
*
25595100 GAGGAAAA-AGAGA-AAATTGAAAAAGAAA
1 GA--AAAAGAGAAAGAAATTGAAAAAGAAA
25595128 GAAAAGACAA
Statistics
Matches: 67, Mismatches: 6, Indels: 6
0.85 0.08 0.08
Matches are distributed among these distances:
48 55 0.82
49 8 0.12
50 4 0.06
ACGTcount: A:0.59, C:0.02, G:0.26, T:0.14
Consensus pattern (48 bp):
GAAAAAGAGAAAGAAATTGAAAAAGAAATTGAGATTGAAAAAAGATGT
Found at i:25596843 original size:20 final size:20
Alignment explanation
Indices: 25596797--25596843 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
25596787 AGCTCGTTTC
*
25596797 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
25596817 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
25596837 CAGCTCA
1 CAGCTCA
25596844 ATCTTAACCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:25602199 original size:11 final size:12
Alignment explanation
Indices: 25602167--25602197 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
25602157 TTGAGAGAAC
25602167 TTGAAAAAGCCT
1 TTGAAAAAGCCT
25602179 TTGAAAAAGCCT
1 TTGAAAAAGCCT
25602191 TTGAAAA
1 TTGAAAA
25602198 GCAAAAAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.45, C:0.13, G:0.16, T:0.26
Consensus pattern (12 bp):
TTGAAAAAGCCT
Found at i:25602234 original size:30 final size:30
Alignment explanation
Indices: 25602200--25602281 Score: 94
Period size: 30 Copynumber: 2.7 Consensus size: 30
25602190 TTTGAAAAGC
*
25602200 AAAAAGAAAATGAAAATGAAA-ATGAGATTG
1 AAAAAGAAAATGAAAA-GAAATATGAGAGTG
* * *
25602230 AAAAAGAGAACGAAAAGAAATCTGAGAGTG
1 AAAAAGAAAATGAAAAGAAATATGAGAGTG
*
25602260 AAAAAGAAGATGAAAAAGAAAT
1 AAAAAGAAAATG-AAAAGAAAT
25602282 TGAAACAAAA
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
29 4 0.09
30 30 0.70
31 9 0.21
ACGTcount: A:0.63, C:0.02, G:0.22, T:0.12
Consensus pattern (30 bp):
AAAAAGAAAATGAAAAGAAATATGAGAGTG
Found at i:25605581 original size:30 final size:29
Alignment explanation
Indices: 25605487--25605582 Score: 77
Period size: 30 Copynumber: 3.2 Consensus size: 29
25605477 AGCTAAACTG
* *
25605487 AGCTC-ACTTTCAACTCACGAGCTAAACCTT
1 AGCTCAACTTT-AGCTCACGAG-TAAAGCTT
* * * ** *
25605517 AGCTCAACTTCAGCTTAGGAGTTTAGCCTC
1 AGCTCAACTTTAGCTCACGAGTAAAG-CTT
25605547 AGCTCAACTTTAGCTCACGAGATAAAGCTT
1 AGCTCAACTTTAGCTCACGAG-TAAAGCTT
25605577 AGCTCA
1 AGCTCA
25605583 TTTTAGTTTA
Statistics
Matches: 49, Mismatches: 14, Indels: 6
0.71 0.20 0.09
Matches are distributed among these distances:
29 2 0.04
30 40 0.82
31 7 0.14
ACGTcount: A:0.29, C:0.28, G:0.16, T:0.27
Consensus pattern (29 bp):
AGCTCAACTTTAGCTCACGAGTAAAGCTT
Found at i:25608749 original size:12 final size:12
Alignment explanation
Indices: 25608734--25608764 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
25608724 TTCTTTTTGC
25608734 TTTTCAAAGGCT
1 TTTTCAAAGGCT
25608746 TTTTCAAAGGCT
1 TTTTCAAAGGCT
25608758 TTTTCAA
1 TTTTCAA
25608765 GTTCTCTCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.26, C:0.16, G:0.13, T:0.45
Consensus pattern (12 bp):
TTTTCAAAGGCT
Found at i:25608834 original size:6 final size:5
Alignment explanation
Indices: 25608812--25608873 Score: 56
Period size: 5 Copynumber: 12.0 Consensus size: 5
25608802 CTCTTGCCTC
* *
25608812 TCTTT TCTTT T-TATT TCATTT TCTTT TCTTC TC-TT GCTTTT TCTTTT
1 TCTTT TCTTT TCT-TT TC-TTT TCTTT TCTTT TCTTT TC-TTT TC-TTT
25608859 TCTTT TCTTT TCTTT
1 TCTTT TCTTT TCTTT
25608874 ATTTTCTCTT
Statistics
Matches: 48, Mismatches: 4, Indels: 10
0.77 0.06 0.16
Matches are distributed among these distances:
4 3 0.06
5 31 0.65
6 13 0.27
7 1 0.02
ACGTcount: A:0.03, C:0.19, G:0.02, T:0.76
Consensus pattern (5 bp):
TCTTT
Found at i:25608846 original size:26 final size:25
Alignment explanation
Indices: 25608812--25608879 Score: 82
Period size: 26 Copynumber: 2.6 Consensus size: 25
25608802 CTCTTGCCTC
25608812 TCTTTTCTTTTTATTTCATTTTCTTT
1 TCTTTTCTTTTT-TTTCATTTTCTTT
* * *
25608838 TCTTCTCTTGCTTTTTCTTTTTCTTT
1 TCTTTTCTT-TTTTTTCATTTTCTTT
*
25608864 TCTTTTCTTTATTTTC
1 TCTTTTCTTTTTTTTC
25608880 TCTTTACAAG
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
25 5 0.14
26 28 0.80
27 2 0.06
ACGTcount: A:0.04, C:0.19, G:0.01, T:0.75
Consensus pattern (25 bp):
TCTTTTCTTTTTTTTCATTTTCTTT
Found at i:25608846 original size:31 final size:30
Alignment explanation
Indices: 25608810--25608885 Score: 77
Period size: 31 Copynumber: 2.5 Consensus size: 30
25608800 GCCTCTTGCC
25608810 TCTCTTTTCTTTTTATTTCATTTTCTTTTCT
1 TCTCTTTTCTTTTTATTTC-TTTTCTTTTCT
25608841 TCTCTTGCTT-TTTCTT-TTTCTTTTCTTTTCT
1 TCTCTT--TTCTTT-TTATTTCTTTTCTTTTCT
* *
25608872 T-TATTTTCTCTTTA
1 TCTCTTTTCTTTTTA
25608886 CAAGAATGTA
Statistics
Matches: 38, Mismatches: 2, Indels: 12
0.73 0.04 0.23
Matches are distributed among these distances:
28 4 0.11
29 2 0.05
30 3 0.08
31 18 0.47
32 7 0.18
33 4 0.11
ACGTcount: A:0.05, C:0.20, G:0.01, T:0.74
Consensus pattern (30 bp):
TCTCTTTTCTTTTTATTTCTTTTCTTTTCT
Found at i:25609811 original size:12 final size:11
Alignment explanation
Indices: 25609794--25609824 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
25609784 TATACTTCGA
25609794 TTTTTTTAATT
1 TTTTTTTAATT
*
25609805 TTTTTTTGATT
1 TTTTTTTAATT
25609816 TTTTTTTAA
1 TTTTTTTAA
25609825 AATTTCGAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.16, C:0.00, G:0.03, T:0.81
Consensus pattern (11 bp):
TTTTTTTAATT
Found at i:25609924 original size:10 final size:10
Alignment explanation
Indices: 25609911--25609952 Score: 57
Period size: 10 Copynumber: 4.1 Consensus size: 10
25609901 TTTTCGGATT
25609911 TTTTTTTCAA
1 TTTTTTTCAA
*
25609921 TTTTTTTTAA
1 TTTTTTTCAA
*
25609931 TTTTTTTCAT
1 TTTTTTTCAA
25609941 TTTTTTTACAA
1 TTTTTTT-CAA
25609952 T
1 T
25609953 ACCGTAATAC
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
10 24 0.89
11 3 0.11
ACGTcount: A:0.19, C:0.07, G:0.00, T:0.74
Consensus pattern (10 bp):
TTTTTTTCAA
Found at i:25609936 original size:19 final size:19
Alignment explanation
Indices: 25609911--25609948 Score: 67
Period size: 19 Copynumber: 1.9 Consensus size: 19
25609901 TTTTCGGATT
25609911 TTTTTTTCAATTTTTTTTAA
1 TTTTTTTC-ATTTTTTTTAA
25609931 TTTTTTTCATTTTTTTTA
1 TTTTTTTCATTTTTTTTA
25609949 CAATACCGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.16, C:0.05, G:0.00, T:0.79
Consensus pattern (19 bp):
TTTTTTTCATTTTTTTTAA
Found at i:25609946 original size:12 final size:11
Alignment explanation
Indices: 25609896--25609947 Score: 54
Period size: 11 Copynumber: 4.7 Consensus size: 11
25609886 GAATACAAAC
25609896 TTTTTTTTTCGGA
1 TTTTTTTTTC--A
25609909 TTTTTTTTTCA
1 TTTTTTTTTCA
*
25609920 ATTTTTTTT-A
1 TTTTTTTTTCA
*
25609930 -ATTTTTTTCA
1 TTTTTTTTTCA
25609940 TTTTTTTT
1 TTTTTTTT
25609948 ACAATACCGT
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
9 7 0.21
10 2 0.06
11 15 0.44
13 10 0.29
ACGTcount: A:0.12, C:0.06, G:0.04, T:0.79
Consensus pattern (11 bp):
TTTTTTTTTCA
Found at i:25611146 original size:17 final size:16
Alignment explanation
Indices: 25611087--25611146 Score: 50
Period size: 17 Copynumber: 3.6 Consensus size: 16
25611077 GAGACAGCCA
* *
25611087 CCATACATGCATTTAAG
1 CCATTCATGCATTT-AT
25611104 CCATTCATGCATTCTAT
1 CCATTCATGCATT-TAT
*
25611121 -CATCCCATGCATTTGAT
1 CCAT-TCATGCATTT-AT
25611138 CCATTCATG
1 CCATTCATG
25611147 GACTAGCCTT
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
16 4 0.11
17 27 0.77
18 4 0.11
ACGTcount: A:0.27, C:0.28, G:0.10, T:0.35
Consensus pattern (16 bp):
CCATTCATGCATTTAT
Found at i:25611577 original size:30 final size:29
Alignment explanation
Indices: 25611537--25611639 Score: 100
Period size: 30 Copynumber: 3.4 Consensus size: 29
25611527 CGAGTTTAAA
*
25611537 CTAAAATGAGCTAAGCTTTAGCTCGTGAG
1 CTAAATTGAGCTAAGCTTTAGCTCGTGAG
* * * * *
25611566 CTAAAGTTGAGCTGAGGC-TAAACTCCTAAG
1 CTAAA-TTGAGCT-AAGCTTTAGCTCGTGAG
*
25611596 CTGAAATTGAGCTAAGGTTTAGCTCGTGAG
1 CT-AAATTGAGCTAAGCTTTAGCTCGTGAG
25611626 CTAAATATGAGCTA
1 CTAAAT-TGAGCTA
25611640 GGAGTGAGCT
Statistics
Matches: 57, Mismatches: 12, Indels: 9
0.73 0.15 0.12
Matches are distributed among these distances:
29 11 0.19
30 40 0.70
31 6 0.11
ACGTcount: A:0.32, C:0.17, G:0.24, T:0.27
Consensus pattern (29 bp):
CTAAATTGAGCTAAGCTTTAGCTCGTGAG
Found at i:25613348 original size:14 final size:14
Alignment explanation
Indices: 25613329--25613367 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
25613319 GAATGGAATT
*
25613329 GTAGGAACGAAAGG
1 GTAGGAACAAAAGG
25613343 GTAGGAACAAAAGG
1 GTAGGAACAAAAGG
* *
25613357 ATATGAACAAA
1 GTAGGAACAAA
25613368 TTGGTCGGTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.51, C:0.08, G:0.31, T:0.10
Consensus pattern (14 bp):
GTAGGAACAAAAGG
Found at i:25623170 original size:63 final size:65
Alignment explanation
Indices: 25623036--25623170 Score: 154
Period size: 67 Copynumber: 2.1 Consensus size: 65
25623026 TATGAACTTG
*
25623036 ATTTAATAGATGCTTCTTTAAATAAACTAGTTACTAGGATAATTTAGTGATGCATGAGTTAAAGT
1 ATTTAATAGATGCTTCTTTAAATAAACTAGTTACTAGGATAA--TAGTGATGCATAAGTTAAAGT
25623101 TC
64 TC
* * *
25623103 ATTTAATA-ATGCTTCTATTAATTAAACTAGTTGCT-GGATTAA-A-TGATGCATAAGTGT-TAG
1 ATTTAATAGATGCTTCT-TTAAATAAACTAGTTACTAGGA-TAATAGTGATGCATAAGT-TAAAG
25623163 TTC
63 TTC
25623166 ATTTA
1 ATTTA
25623171 TTTAAGTTAG
Statistics
Matches: 61, Mismatches: 4, Indels: 10
0.81 0.05 0.13
Matches are distributed among these distances:
63 21 0.34
64 2 0.03
66 11 0.18
67 27 0.44
ACGTcount: A:0.35, C:0.09, G:0.16, T:0.41
Consensus pattern (65 bp):
ATTTAATAGATGCTTCTTTAAATAAACTAGTTACTAGGATAATAGTGATGCATAAGTTAAAGTTC
Found at i:25624209 original size:39 final size:35
Alignment explanation
Indices: 25624122--25624194 Score: 137
Period size: 35 Copynumber: 2.1 Consensus size: 35
25624112 TTCAATCCAT
*
25624122 TTTTGTTTCTTACCATTTCGAACTAAAATAAATTC
1 TTTTGTTTCTTACCATTTCGAACTAAAATAAATAC
25624157 TTTTGTTTCTTACCATTTCGAACTAAAATAAATAC
1 TTTTGTTTCTTACCATTTCGAACTAAAATAAATAC
25624192 TTT
1 TTT
25624195 CTTTTACATC
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.32, C:0.16, G:0.05, T:0.47
Consensus pattern (35 bp):
TTTTGTTTCTTACCATTTCGAACTAAAATAAATAC
Found at i:25624662 original size:10 final size:10
Alignment explanation
Indices: 25624649--25624684 Score: 63
Period size: 10 Copynumber: 3.6 Consensus size: 10
25624639 AACTCAATTC
25624649 AGCTCATTTG
1 AGCTCATTTG
25624659 AGCTCATTTG
1 AGCTCATTTG
*
25624669 AGCTCGTTTG
1 AGCTCATTTG
25624679 AGCTCA
1 AGCTCA
25624685 ACCGAGCTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 24 1.00
ACGTcount: A:0.19, C:0.22, G:0.22, T:0.36
Consensus pattern (10 bp):
AGCTCATTTG
Found at i:25624664 original size:20 final size:20
Alignment explanation
Indices: 25624641--25624685 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
25624631 CTCCGTCCAA
25624641 CTCAATTCAGCTCATTTGAG
1 CTCAATTCAGCTCATTTGAG
* * *
25624661 CTCATTTGAGCTCGTTTGAG
1 CTCAATTCAGCTCATTTGAG
25624681 CTCAA
1 CTCAA
25624686 CCGAGCTTAC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.22, C:0.24, G:0.18, T:0.36
Consensus pattern (20 bp):
CTCAATTCAGCTCATTTGAG
Found at i:25624691 original size:20 final size:20
Alignment explanation
Indices: 25624649--25624692 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
25624639 AACTCAATTC
***
25624649 AGCTCATTTGAGCTCATTTG
1 AGCTCATTTGAGCTCAACCG
*
25624669 AGCTCGTTTGAGCTCAACCG
1 AGCTCATTTGAGCTCAACCG
25624689 AGCT
1 AGCT
25624693 TACTTTCAAC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.20, C:0.25, G:0.23, T:0.32
Consensus pattern (20 bp):
AGCTCATTTGAGCTCAACCG
Found at i:25629895 original size:13 final size:12
Alignment explanation
Indices: 25629877--25629932 Score: 96
Period size: 12 Copynumber: 4.7 Consensus size: 12
25629867 TCGGTATTGT
25629877 AAAAAAAAATTC
1 AAAAAAAAATTC
25629889 AAAAAAAAATTC
1 AAAAAAAAATTC
25629901 GAAAAAAAAATTC
1 -AAAAAAAAATTC
25629914 -AAAAAAAATTC
1 AAAAAAAAATTC
25629925 AAAAAAAA
1 AAAAAAAA
25629933 GTTTGTATTC
Statistics
Matches: 42, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
11 11 0.26
12 19 0.45
13 12 0.29
ACGTcount: A:0.77, C:0.07, G:0.02, T:0.14
Consensus pattern (12 bp):
AAAAAAAAATTC
Found at i:25632719 original size:40 final size:40
Alignment explanation
Indices: 25632619--25632843 Score: 285
Period size: 40 Copynumber: 5.7 Consensus size: 40
25632609 GCTCCTCGTT
* * ** *
25632619 CAAATGCCTTCGGGACATAGCCCGGATTTAGTAACTCACA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCA
*
25632659 C-AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCA
25632698 CAAATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCA
*
25632738 CGAATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCA
* * * * * *
25632778 CGAATGCCTTCGGAACTTAATCCGGATATATTC-ACTTAGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTA-ACAAC-TCGCA
*
25632819 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGA
25632844 CAGCATTCAA
Statistics
Matches: 167, Mismatches: 15, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
39 35 0.21
40 124 0.74
41 8 0.05
ACGTcount: A:0.29, C:0.29, G:0.20, T:0.23
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCA
Found at i:25651372 original size:55 final size:53
Alignment explanation
Indices: 25651242--25651374 Score: 142
Period size: 55 Copynumber: 2.5 Consensus size: 53
25651232 AGGATACCAA
* * **
25651242 GTAAGACAATGCCAAGGCATGGCATTGGTAAGTTTTATAAGGCAAGGAAATCAT
1 GTAAGACAATGCCAAGGCATGGCATTGATAACTACTATAAGGCAA-GAAATCAT
* * *
25651296 GTAAGACAATGTCAAGACATGGCATTGATAAACTACTATAAGGCAA-ATATCCCAT
1 GTAAGACAATGCCAAGGCATGGCATTGAT-AACTACTATAAGGCAAGAAAT--CAT
* *
25651351 GTAAGACCATCCCAAGGCATGGCA
1 GTAAGACAATGCCAAGGCATGGCA
25651375 ATGGTGAGTT
Statistics
Matches: 65, Mismatches: 11, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
53 3 0.05
54 26 0.40
55 36 0.55
ACGTcount: A:0.38, C:0.18, G:0.22, T:0.22
Consensus pattern (53 bp):
GTAAGACAATGCCAAGGCATGGCATTGATAACTACTATAAGGCAAGAAATCAT
Found at i:25659173 original size:40 final size:40
Alignment explanation
Indices: 25659090--25659392 Score: 396
Period size: 40 Copynumber: 7.6 Consensus size: 40
25659080 TTGAATGCTG
* * * * * *
25659090 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTATTAAA
* * * * *
25659130 TCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTATTAAA
25659170 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
25659210 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
*
25659250 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
*
25659290 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* * *
25659330 TCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* * *
25659369 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
25659393 TGAACGAGGA
Statistics
Matches: 241, Mismatches: 19, Indels: 7
0.90 0.07 0.03
Matches are distributed among these distances:
39 35 0.15
40 198 0.82
41 8 0.03
ACGTcount: A:0.24, C:0.20, G:0.28, T:0.27
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
Found at i:25666529 original size:40 final size:40
Alignment explanation
Indices: 25666446--25666748 Score: 396
Period size: 40 Copynumber: 7.6 Consensus size: 40
25666436 TTGAATGCTG
* * * * * *
25666446 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTATTAAA
* * * * *
25666486 TCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTATTAAA
25666526 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
25666566 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
*
25666606 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
*
25666646 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* * *
25666686 TCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* * *
25666725 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
25666749 TGAACGAGGA
Statistics
Matches: 241, Mismatches: 19, Indels: 7
0.90 0.07 0.03
Matches are distributed among these distances:
39 35 0.15
40 198 0.82
41 8 0.03
ACGTcount: A:0.24, C:0.20, G:0.28, T:0.27
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
Found at i:25669024 original size:15 final size:15
Alignment explanation
Indices: 25669004--25669034 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
25668994 GAATGTGAGC
*
25669004 AAATTAATTTTTTTT
1 AAATTAATTATTTTT
25669019 AAATTAATTATTTTT
1 AAATTAATTATTTTT
25669034 A
1 A
25669035 TGCCCCGAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (15 bp):
AAATTAATTATTTTT
Found at i:25672414 original size:43 final size:42
Alignment explanation
Indices: 25672313--25672457 Score: 148
Period size: 43 Copynumber: 3.4 Consensus size: 42
25672303 CTTAGATATG
* * *
25672313 GTCTTACATGTTATCACATACCGATGCCACTGTCCCAGACAGT
1 GTCTTACATGTAATCACATAACGATGCCAATGTCCCAGACA-T
* * * * *
25672356 GTCTCACACGAAATCATATAACGGTGCCAATGTCCCAGACAT
1 GTCTTACATGTAATCACATAACGATGCCAATGTCCCAGACAT
* * *
25672398 GATCTTACAAGTAATCACA-ATACAATGCTAATGTCCCAGACAT
1 G-TCTTACATGTAATCACATA-ACGATGCCAATGTCCCAGACAT
25672441 GGTCTTACATGTAATCA
1 -GTCTTACATGTAATCA
25672458 TATCTCGATA
Statistics
Matches: 83, Mismatches: 16, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
42 3 0.04
43 79 0.95
44 1 0.01
ACGTcount: A:0.32, C:0.26, G:0.15, T:0.26
Consensus pattern (42 bp):
GTCTTACATGTAATCACATAACGATGCCAATGTCCCAGACAT
Found at i:25674226 original size:29 final size:29
Alignment explanation
Indices: 25674180--25674248 Score: 120
Period size: 29 Copynumber: 2.4 Consensus size: 29
25674170 CACATGGTTT
* *
25674180 GGCACATGGGCGTTTATGGCCATTTTTAG
1 GGCACACGGGCGTGTATGGCCATTTTTAG
25674209 GGCACACGGGCGTGTATGGCCATTTTTAG
1 GGCACACGGGCGTGTATGGCCATTTTTAG
25674238 GGCACACGGGC
1 GGCACACGGGC
25674249 TAGCCACATG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 38 1.00
ACGTcount: A:0.17, C:0.22, G:0.35, T:0.26
Consensus pattern (29 bp):
GGCACACGGGCGTGTATGGCCATTTTTAG
Found at i:25676319 original size:28 final size:28
Alignment explanation
Indices: 25676287--25676351 Score: 103
Period size: 28 Copynumber: 2.3 Consensus size: 28
25676277 ATTTACTAGA
*
25676287 ATACCCCTATGTATGCAAAATTACCATT
1 ATACCCCTATGTATGCAAAATGACCATT
* *
25676315 ATACCTCTATGTATGCAAAATGACCTTT
1 ATACCCCTATGTATGCAAAATGACCATT
25676343 ATACCCCTA
1 ATACCCCTA
25676352 GGGTTAATTT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.34, C:0.26, G:0.08, T:0.32
Consensus pattern (28 bp):
ATACCCCTATGTATGCAAAATGACCATT
Found at i:25676514 original size:27 final size:27
Alignment explanation
Indices: 25676456--25676537 Score: 112
Period size: 28 Copynumber: 3.0 Consensus size: 27
25676446 AGGAAGCGTC
25676456 CTGGTGGCTA-TGCCACAAATTATCTGTT
1 CTGGTGGC-ACTGCCACAAA-TATCTGTT
* *
25676484 CTGGTGGCCCTGCCACATATATCTGTT
1 CTGGTGGCACTGCCACAAATATCTGTT
25676511 CTGGTGGCACTGCCACAAAATATCTGT
1 CTGGTGGCACTGCCAC-AAATATCTGT
25676538 ATCAGGTGAC
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
27 23 0.48
28 25 0.52
ACGTcount: A:0.21, C:0.26, G:0.22, T:0.32
Consensus pattern (27 bp):
CTGGTGGCACTGCCACAAATATCTGTT
Found at i:25676564 original size:55 final size:56
Alignment explanation
Indices: 25676456--25676570 Score: 128
Period size: 55 Copynumber: 2.1 Consensus size: 56
25676446 AGGAAGCGTC
* * * *
25676456 CTGGTGGCTATGCCACAAATTATCTGTTCTGGTGGCCCTGCCACATATATCTGT-T
1 CTGGTGGCTATGCCACAAAATATCTGTTCAGGTGACCCTACCACATATATCTGTAT
* * *
25676511 CTGGTGGC-ACTGCCACAAAATATCTGTATCAGGTGACTCTATCACAT-TTTCTGTAT
1 CTGGTGGCTA-TGCCACAAAATATCTGT-TCAGGTGACCCTACCACATATATCTGTAT
25676567 CTGG
1 CTGG
25676571 CAGCCATGCT
Statistics
Matches: 50, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
54 1 0.02
55 30 0.60
56 19 0.38
ACGTcount: A:0.21, C:0.24, G:0.21, T:0.34
Consensus pattern (56 bp):
CTGGTGGCTATGCCACAAAATATCTGTTCAGGTGACCCTACCACATATATCTGTAT
Found at i:25683009 original size:28 final size:28
Alignment explanation
Indices: 25682977--25683041 Score: 94
Period size: 28 Copynumber: 2.3 Consensus size: 28
25682967 ATTTACTAGA
* *
25682977 ATACCCCTATGTATTCAAAATTACCATT
1 ATACCCCTATGTATGCAAAATGACCATT
* *
25683005 ATACCTCTATGTATGCAAAATGACCTTT
1 ATACCCCTATGTATGCAAAATGACCATT
25683033 ATACCCCTA
1 ATACCCCTA
25683042 GGGTTAATTT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.34, C:0.26, G:0.06, T:0.34
Consensus pattern (28 bp):
ATACCCCTATGTATGCAAAATGACCATT
Found at i:25683205 original size:27 final size:27
Alignment explanation
Indices: 25683147--25683236 Score: 128
Period size: 28 Copynumber: 3.2 Consensus size: 27
25683137 AGGAAGCGTC
25683147 CTGGTGGCTA-TGCCACAAATTATCTGTT
1 CTGGTGGC-ACTGCCACAAA-TATCTGTT
*
25683175 CTGGTGGCCCTGCCACAAATATCTGTT
1 CTGGTGGCACTGCCACAAATATCTGTT
25683202 CTGGTGGCACTGCCACAAAATATCTGTAT
1 CTGGTGGCACTGCCAC-AAATATCTGT-T
25683231 CTGGTG
1 CTGGTG
25683237 ACTCTGTCAC
Statistics
Matches: 57, Mismatches: 2, Indels: 5
0.89 0.03 0.08
Matches are distributed among these distances:
27 23 0.40
28 27 0.47
29 7 0.12
ACGTcount: A:0.21, C:0.24, G:0.23, T:0.31
Consensus pattern (27 bp):
CTGGTGGCACTGCCACAAATATCTGTT
Found at i:25683255 original size:55 final size:56
Alignment explanation
Indices: 25683147--25683261 Score: 137
Period size: 55 Copynumber: 2.1 Consensus size: 56
25683137 AGGAAGCGTC
* *
25683147 CTGGTGGCTATGCCACAAATTATCTGTTCTGGTGGCCCTGCCACAAATATCTGT-T
1 CTGGTGGCTATGCCACAAAATATCTGTTCTGGTGACCCTGCCACAAATATCTGTAT
* * * *
25683202 CTGGTGGC-ACTGCCACAAAATATCTGTATCTGGTGACTCTGTCAC-ATTTTCTGTAT
1 CTGGTGGCTA-TGCCACAAAATATCTGT-TCTGGTGACCCTGCCACAAATATCTGTAT
25683258 CTGG
1 CTGG
25683262 CAGCCATGCT
Statistics
Matches: 51, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
54 1 0.02
55 31 0.61
56 19 0.37
ACGTcount: A:0.20, C:0.24, G:0.22, T:0.34
Consensus pattern (56 bp):
CTGGTGGCTATGCCACAAAATATCTGTTCTGGTGACCCTGCCACAAATATCTGTAT
Found at i:25684641 original size:20 final size:20
Alignment explanation
Indices: 25684605--25684642 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
25684595 AAATTTATGT
*
25684605 TAAGTAAATGGACTGGTAAG
1 TAAGTAAATGGAATGGTAAG
25684625 TAAGTAAA-GGAAATGGTA
1 TAAGTAAATGG-AATGGTA
25684643 CACAGTTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 2 0.12
20 14 0.88
ACGTcount: A:0.45, C:0.03, G:0.29, T:0.24
Consensus pattern (20 bp):
TAAGTAAATGGAATGGTAAG
Found at i:25685824 original size:20 final size:20
Alignment explanation
Indices: 25685790--25685830 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
25685780 CCCTGCAATT
*
25685790 TGAAAAATTTCATATTTTTC
1 TGAAAAATTTCATATGTTTC
25685810 TGAAAAA-TTCTATATGTTTC
1 TGAAAAATTTC-ATATGTTTC
25685830 T
1 T
25685831 AACTTAGTCC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 3 0.16
20 16 0.84
ACGTcount: A:0.34, C:0.10, G:0.07, T:0.49
Consensus pattern (20 bp):
TGAAAAATTTCATATGTTTC
Found at i:25687762 original size:48 final size:48
Alignment explanation
Indices: 25687686--25687959 Score: 261
Period size: 48 Copynumber: 5.7 Consensus size: 48
25687676 GGTGACATGT
**
25687686 GAGCCAGTGTAAGACCATGTTTGAAACATGGCATCGACAATGTAATGA
1 GAGCCAGTGTAAGACCATGTTTGGGACATGGCATCGACAATGTAATGA
* *
25687734 GAGCCAGTGTAAGACCATGTTTGGAACATGGCATCGGCAATGTAATGA
1 GAGCCAGTGTAAGACCATGTTTGGGACATGGCATCGACAATGTAATGA
* * * * * * * *
25687782 GAGTCAGTGCAAGGCCATGTCTGGGACATGGTATCGGCATTG-ATATGT
1 GAGCCAGTGTAAGACCATGTTTGGGACATGGCATCGACAATGTA-ATGA
* * *
25687830 GCGCTAGTGTAAGACCAT-TTCTGGGACATGGCATCAGCCACAT-T-ATGA
1 GAGCCAGTGTAAGACCATGTT-TGGGACATGGCATC-GACA-ATGTAATGA
* * * *
25687878 GAGCCAGCGTAAGACCATGTATGGGACATGGCATCTACATTG-AGATGA
1 GAGCCAGTGTAAGACCATGTTTGGGACATGGCATCGACAATGTA-ATGA
* * * *
25687926 GAGCTAGAGTAAGACCATGTCTAGGACATGGCAT
1 GAGCCAGTGTAAGACCATGTTTGGGACATGGCAT
25687960 TGGCAAATTC
Statistics
Matches: 186, Mismatches: 31, Indels: 18
0.79 0.13 0.08
Matches are distributed among these distances:
46 1 0.01
47 4 0.02
48 176 0.95
49 4 0.02
50 1 0.01
ACGTcount: A:0.30, C:0.18, G:0.28, T:0.23
Consensus pattern (48 bp):
GAGCCAGTGTAAGACCATGTTTGGGACATGGCATCGACAATGTAATGA
Found at i:25687944 original size:144 final size:144
Alignment explanation
Indices: 25687682--25687956 Score: 335
Period size: 144 Copynumber: 1.9 Consensus size: 144
25687672 TTTGGGTGAC
*
25687682 ATGTGAGCCAGTGTAAGACCATGTTTGAAACATGGCATCGACAATGTAATGAGAGCCAGTGTAAG
1 ATGTGAGCCAGTGTAAGACCATGTTTGAAACATGGCATCGACAATGTAATGAGAGCCAGCGTAAG
* * * * *
25687747 ACCATGTTTGGAACATGGCATCGGCAATGTAATGAGAGTCAGTGCAAGGCCATGTCTGGGACATG
66 ACCATGTATGGAACATGGCATCGACAATGTAATGAGAGTCAGAGCAAGACCATGTCTAGGACATG
25687812 GTATCGGCATTGAT
131 GTATCGGCATTGAT
* * ** *
25687826 ATGTGCGCTAGTGTAAGACCAT-TTCTGGGACATGGCATCAGCCACAT-T-ATGAGAGCCAGCGT
1 ATGTGAGCCAGTGTAAGACCATGTT-TGAAACATGGCATC-GACA-ATGTAATGAGAGCCAGCGT
* * * *
25687888 AAGACCATGTATGGGACATGGCATCTACATTG-AGATGAGAG-CTAGAGTAAGACCATGTCTAGG
63 AAGACCATGTATGGAACATGGCATCGACAATGTA-ATGAGAGTC-AGAGCAAGACCATGTCTAGG
25687951 ACATGG
126 ACATGG
25687957 CATTGGCAAA
Statistics
Matches: 111, Mismatches: 15, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
143 4 0.04
144 101 0.91
145 4 0.04
146 2 0.02
ACGTcount: A:0.30, C:0.18, G:0.29, T:0.24
Consensus pattern (144 bp):
ATGTGAGCCAGTGTAAGACCATGTTTGAAACATGGCATCGACAATGTAATGAGAGCCAGCGTAAG
ACCATGTATGGAACATGGCATCGACAATGTAATGAGAGTCAGAGCAAGACCATGTCTAGGACATG
GTATCGGCATTGAT
Found at i:25689975 original size:40 final size:40
Alignment explanation
Indices: 25689919--25690136 Score: 357
Period size: 40 Copynumber: 5.5 Consensus size: 40
25689909 CAGATGATAA
25689919 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
25689959 TCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
25689999 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGCTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
25690039 CCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
25690079 CCGGGCTAAGTCCCGAAGGCATTTGAGCGAGTAACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
25690119 -CTGGCTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
25690137 TACTTGGTTT
Statistics
Matches: 166, Mismatches: 12, Indels: 1
0.93 0.07 0.01
Matches are distributed among these distances:
39 16 0.10
40 150 0.90
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:25694606 original size:34 final size:34
Alignment explanation
Indices: 25694563--25694630 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
25694553 ATGGTGACAT
25694563 TACTTATTTGGTGAGAAGTGCCATGTATTTTCGG
1 TACTTATTTGGTGAGAAGTGCCATGTATTTTCGG
25694597 TACTTATTTGGTGAGAAGTGCCATGTATTTTCGG
1 TACTTATTTGGTGAGAAGTGCCATGTATTTTCGG
25694631 ATCACAAAAG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.21, C:0.12, G:0.26, T:0.41
Consensus pattern (34 bp):
TACTTATTTGGTGAGAAGTGCCATGTATTTTCGG
Found at i:25698077 original size:40 final size:40
Alignment explanation
Indices: 25698018--25698230 Score: 333
Period size: 40 Copynumber: 5.4 Consensus size: 40
25698008 TGATAACCGA
25698018 GCTAAGTCCC-AAGGCATTTGTGCGAGTTACTATATCCGG
1 GCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGG
25698057 GCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGG
1 GCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGG
* *
25698097 GCTAAGTCCCGAAGGCATTTGTGCGAGCTACTATATCCAG
1 GCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGG
* *
25698137 GTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAACCGG
1 GCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGG
* *
25698177 GCTAAGTCCCAAAGGCATTTGAGCGAG-TAGCTATATCC-G
1 GCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATATCCGG
*
25698216 GCTAAATCCCGAAGG
1 GCTAAGTCCCGAAGG
25698231 TACTTGGTTT
Statistics
Matches: 160, Mismatches: 12, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
39 26 0.16
40 134 0.84
ACGTcount: A:0.25, C:0.23, G:0.26, T:0.25
Consensus pattern (40 bp):
GCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGG
Found at i:25701016 original size:22 final size:23
Alignment explanation
Indices: 25700986--25701029 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
25700976 TATTGATCAA
*
25700986 ATCACAACATATAGCATACATTT
1 ATCACAACATAAAGCATACATTT
*
25701009 ATCA-AACATAAAGCATTCATT
1 ATCACAACATAAAGCATACATT
25701030 CTCATAAATC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.45, C:0.20, G:0.05, T:0.30
Consensus pattern (23 bp):
ATCACAACATAAAGCATACATTT
Found at i:25702391 original size:48 final size:48
Alignment explanation
Indices: 25702336--25702468 Score: 146
Period size: 48 Copynumber: 2.8 Consensus size: 48
25702326 CTCAATCGAT
* *
25702336 AAGTACCTATACCATGGCCCGAAACCAAATCAAGGT-GACTTATCCT-CG
1 AAGTACCTATACCATGGCCCGAAACCAAATCAAGGTAG-CTCA-CCTCCA
* * * *
25702384 AAGTACCTATAACATGGCTCGTAGCCAAATCAAGGTAGCTCACCTCCA
1 AAGTACCTATACCATGGCCCGAAACCAAATCAAGGTAGCTCACCTCCA
* *
25702432 AAATACCTATACCGTGGCCC-AAAGCCAAATCAAGGTA
1 AAGTACCTATACCATGGCCCGAAA-CCAAATCAAGGTA
25702469 TAATTCACAC
Statistics
Matches: 70, Mismatches: 12, Indels: 6
0.80 0.14 0.07
Matches are distributed among these distances:
47 4 0.06
48 65 0.93
49 1 0.01
ACGTcount: A:0.35, C:0.29, G:0.17, T:0.20
Consensus pattern (48 bp):
AAGTACCTATACCATGGCCCGAAACCAAATCAAGGTAGCTCACCTCCA
Found at i:25705894 original size:27 final size:27
Alignment explanation
Indices: 25705864--25706041 Score: 180
Period size: 27 Copynumber: 6.6 Consensus size: 27
25705854 ATATCGAGTC
* *
25705864 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
*
25705891 CGCACACTTAGTGCTACATAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
* *
25705918 CGCACACTTAGTGCCACATAGTCAAACT
1 CGCACACTTAGTGCTACATAATC-AACT
** ** *
25705946 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
* **
25705973 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAATCAACT
* *
25706000 CGCACACTTAGTGCAACATAGTCGAA-T
1 CGCACACTTAGTGCTACATAATC-AACT
25706027 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
25706042 GTACAATTTA
Statistics
Matches: 131, Mismatches: 16, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
27 105 0.80
28 26 0.20
ACGTcount: A:0.30, C:0.29, G:0.15, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:25706003 original size:82 final size:81
Alignment explanation
Indices: 25705885--25706040 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
25705875 TGCTATATAA
*
25705885 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCCACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
25705950 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * ** *
25705967 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCGAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
25706031 CACTTAGTGC
65 CACTTAGTGC
25706041 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.29, G:0.15, T:0.26
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:25714067 original size:27 final size:26
Alignment explanation
Indices: 25714037--25714211 Score: 181
Period size: 27 Copynumber: 6.5 Consensus size: 26
25714027 ATATCGAGTC
* *
25714037 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGC-ACATAATCAACT
*
25714064 CGCACACTTAGTGCACATAATCAAAT
1 CGCACACTTAGTGCACATAATCAACT
*
25714090 CGCACACTTAGTGCACATAGTCAGACT
1 CGCACACTTAGTGCACATAATCA-ACT
* ** *
25714117 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTG-CACATAATCAACT
* **
25714144 CGCACACTTAGTGCATCATATTCATTT
1 CGCACACTTAGTGCA-CATAATCAACT
*
25714171 CGCACACTTAGTGCAACATAGTCGAA-T
1 CGCACACTTAGTGC-ACATAATC-AACT
25714198 CGCACACTTAGTGC
1 CGCACACTTAGTGC
25714212 TGTACAATTT
Statistics
Matches: 129, Mismatches: 14, Indels: 10
0.84 0.09 0.07
Matches are distributed among these distances:
26 33 0.26
27 86 0.67
28 10 0.08
ACGTcount: A:0.30, C:0.29, G:0.16, T:0.26
Consensus pattern (26 bp):
CGCACACTTAGTGCACATAATCAACT
Found at i:25714174 original size:54 final size:53
Alignment explanation
Indices: 25714037--25714211 Score: 203
Period size: 54 Copynumber: 3.3 Consensus size: 53
25714027 ATATCGAGTC
* *
25714037 CGCACACTCAGTGCTAT-ATAATCAACTCGCACACTTAGTG-CACATAATCAAAT
1 CGCACACTTAGTGC-ATCATAATCAACTCGCACACTTAGTGCCACATAGTC-AAT
* * *
25714090 CGCACACTTAGTGCA-CATAGTCAGACTCGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCATCATAATCA-ACTCGCACACTTAGTGCCACATAGTCAA-T
* ** *
25714144 CGCACACTTAGTGCATCATATTCATTTCGCACACTTAGTGCAACATAGTCGAAT
1 CGCACACTTAGTGCATCATAATCAACTCGCACACTTAGTGCCACATAGTC-AAT
25714198 CGCACACTTAGTGC
1 CGCACACTTAGTGC
25714212 TGTACAATTT
Statistics
Matches: 105, Mismatches: 11, Indels: 11
0.83 0.09 0.09
Matches are distributed among these distances:
52 7 0.07
53 31 0.30
54 58 0.55
55 9 0.09
ACGTcount: A:0.30, C:0.29, G:0.16, T:0.26
Consensus pattern (53 bp):
CGCACACTTAGTGCATCATAATCAACTCGCACACTTAGTGCCACATAGTCAAT
Found at i:25714204 original size:81 final size:80
Alignment explanation
Indices: 25714058--25714211 Score: 238
Period size: 81 Copynumber: 1.9 Consensus size: 80
25714048 TGCTATATAA
*
25714058 TCAACTCGCACACTTAGTGCACATAATCAAATCGCACACTTAGTGCACATAGTCAGACTCGCACA
1 TCAACTCGCACACTTAGTGCACATAATCAAATCGCACACTTAGTGCACATAGTCAGAATCGCACA
25714123 CTTAGTGCCGCATGG
66 CTTAGTGCCGCATGG
* * **
25714138 TCAATTCGCACACTTAGTGCATCATATTCATTTCGCACACTTAGTGCAACATAGTC-GAATCGCA
1 TCAACTCGCACACTTAGTGCA-CATAATCAAATCGCACACTTAGTGC-ACATAGTCAGAATCGCA
25714202 CACTTAGTGC
64 CACTTAGTGC
25714212 TGTACAATTT
Statistics
Matches: 67, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
80 20 0.30
81 39 0.58
82 8 0.12
ACGTcount: A:0.29, C:0.29, G:0.16, T:0.26
Consensus pattern (80 bp):
TCAACTCGCACACTTAGTGCACATAATCAAATCGCACACTTAGTGCACATAGTCAGAATCGCACA
CTTAGTGCCGCATGG
Found at i:25718905 original size:40 final size:39
Alignment explanation
Indices: 25718817--25718911 Score: 102
Period size: 40 Copynumber: 2.4 Consensus size: 39
25718807 TAAATCAGTA
*
25718817 TCGCACACTTAGTGCCTTCTATAGCCGAAGCTATTCCAAC
1 TCGCACACTTAGTG-CTTCTATAGCCGAAGCTATTCAAAC
* * * * *
25718857 TCGTACACTTAGTGCTATTTATAGCTGATGCTATATTAAAC
1 TCGCACACTTAGTGCT-TCTATAGCCGAAGCTAT-TCAAAC
25718898 -CGCACACTTAGTGC
1 TCGCACACTTAGTGC
25718912 CAATCATAGT
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
39 2 0.04
40 40 0.87
41 4 0.09
ACGTcount: A:0.26, C:0.26, G:0.16, T:0.32
Consensus pattern (39 bp):
TCGCACACTTAGTGCTTCTATAGCCGAAGCTATTCAAAC
Found at i:25722969 original size:26 final size:26
Alignment explanation
Indices: 25722940--25723000 Score: 77
Period size: 26 Copynumber: 2.3 Consensus size: 26
25722930 ATTTACTAAA
* *
25722940 ATACCCCTAAGTATAAAATTACCATT
1 ATACCCCTAAGTACAAAATGACCATT
* * *
25722966 ATACCCCTAGGTGCAAAGTGACCATT
1 ATACCCCTAAGTACAAAATGACCATT
25722992 ATACCCCTA
1 ATACCCCTA
25723001 GGGTTAATTT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.36, C:0.28, G:0.10, T:0.26
Consensus pattern (26 bp):
ATACCCCTAAGTACAAAATGACCATT
Found at i:25723150 original size:28 final size:28
Alignment explanation
Indices: 25723105--25723194 Score: 105
Period size: 28 Copynumber: 3.3 Consensus size: 28
25723095 GGAAGAAGCG
**
25723105 TTCTGGTGGCTATGCCACAAATATCTGT
1 TTCTGGTGGCTACACCACAAATATCTGT
*
25723133 TTCTGGAGGCTACACCACAAATATCTG-
1 TTCTGGTGGCTACACCACAAATATCTGT
*
25723160 TTCTGGTGGCT-CTACCA-TAATATCTGT
1 TTCTGGTGGCTAC-ACCACAAATATCTGT
*
25723187 GTCTGGTG
1 TTCTGGTG
25723195 ACTCTGTCAC
Statistics
Matches: 54, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
26 9 0.17
27 21 0.39
28 24 0.44
ACGTcount: A:0.21, C:0.22, G:0.22, T:0.34
Consensus pattern (28 bp):
TTCTGGTGGCTACACCACAAATATCTGT
Found at i:25723176 original size:27 final size:27
Alignment explanation
Indices: 25723104--25723219 Score: 121
Period size: 27 Copynumber: 4.3 Consensus size: 27
25723094 TGGAAGAAGC
* *
25723104 GTTCTGGTGGCTATGCCACAAATATCT
1 GTTCTGGTGGCTCTACCACAAATATCT
*
25723131 GTTTCTGGAGGCTAC-ACCACAAATATCT
1 G-TTCTGGTGGCT-CTACCACAAATATCT
*
25723159 GTTCTGGTGGCTCTACCA-TAATATCT
1 GTTCTGGTGGCTCTACCACAAATATCT
* **
25723185 GTGTCTGGTGACTCTGTCAC-AATATCT
1 GT-TCTGGTGGCTCTACCACAAATATCT
25723212 GTTCTGGT
1 GTTCTGGT
25723220 AGCCATGCTA
Statistics
Matches: 76, Mismatches: 8, Indels: 11
0.80 0.08 0.12
Matches are distributed among these distances:
26 16 0.21
27 37 0.49
28 23 0.30
ACGTcount: A:0.21, C:0.22, G:0.22, T:0.35
Consensus pattern (27 bp):
GTTCTGGTGGCTCTACCACAAATATCT
Found at i:25727062 original size:28 final size:28
Alignment explanation
Indices: 25727017--25727106 Score: 105
Period size: 28 Copynumber: 3.3 Consensus size: 28
25727007 GGAGGAAGCG
**
25727017 TTCTGGTGGCTATGCCACAAATATCTGT
1 TTCTGGTGGCTACACCACAAATATCTGT
*
25727045 TTCTGGAGGCTACACCACAAATATCTG-
1 TTCTGGTGGCTACACCACAAATATCTGT
*
25727072 TTCTGGTGGCT-CTACCA-TAATATCTGT
1 TTCTGGTGGCTAC-ACCACAAATATCTGT
*
25727099 GTCTGGTG
1 TTCTGGTG
25727107 ACTCTGTCAC
Statistics
Matches: 54, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
26 9 0.17
27 21 0.39
28 24 0.44
ACGTcount: A:0.21, C:0.22, G:0.22, T:0.34
Consensus pattern (28 bp):
TTCTGGTGGCTACACCACAAATATCTGT
Found at i:25727088 original size:27 final size:27
Alignment explanation
Indices: 25727016--25727131 Score: 121
Period size: 27 Copynumber: 4.3 Consensus size: 27
25727006 TGGAGGAAGC
* *
25727016 GTTCTGGTGGCTATGCCACAAATATCT
1 GTTCTGGTGGCTCTACCACAAATATCT
*
25727043 GTTTCTGGAGGCTAC-ACCACAAATATCT
1 G-TTCTGGTGGCT-CTACCACAAATATCT
*
25727071 GTTCTGGTGGCTCTACCA-TAATATCT
1 GTTCTGGTGGCTCTACCACAAATATCT
* **
25727097 GTGTCTGGTGACTCTGTCAC-AATATCT
1 GT-TCTGGTGGCTCTACCACAAATATCT
25727124 GTTCTGGT
1 GTTCTGGT
25727132 AGCCATGCTA
Statistics
Matches: 76, Mismatches: 8, Indels: 11
0.80 0.08 0.12
Matches are distributed among these distances:
26 16 0.21
27 37 0.49
28 23 0.30
ACGTcount: A:0.21, C:0.22, G:0.22, T:0.35
Consensus pattern (27 bp):
GTTCTGGTGGCTCTACCACAAATATCT
Found at i:25733367 original size:40 final size:39
Alignment explanation
Indices: 25733278--25733373 Score: 120
Period size: 40 Copynumber: 2.4 Consensus size: 39
25733268 ATAAATCGGT
25733278 ATCGCACACTTAGTGCCTTCTATAGCCGAAGCTATACCAA
1 ATCGCACACTTAGTG-CTTCTATAGCCGAAGCTATACCAA
* * * ***
25733318 CTCGTACACTTAGTGCTATTTATAGCCGAAGCTATTTTAA
1 ATCGCACACTTAGTGCT-TCTATAGCCGAAGCTATACCAA
25733358 ATCGCACACTTAGTGC
1 ATCGCACACTTAGTGC
25733374 CAGTCATAGT
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
39 2 0.04
40 45 0.96
ACGTcount: A:0.28, C:0.26, G:0.16, T:0.30
Consensus pattern (39 bp):
ATCGCACACTTAGTGCTTCTATAGCCGAAGCTATACCAA
Found at i:25736128 original size:20 final size:20
Alignment explanation
Indices: 25736105--25736339 Score: 115
Period size: 20 Copynumber: 11.8 Consensus size: 20
25736095 TACTTCAGTA
25736105 CCCCTGATTGCACTTACATG
1 CCCCTGATTGCACTTACATG
* * * *
25736125 CCCCTGTTTGTA-TTTCAGTA
1 CCCCTGATTGCACTTACA-TG
* *
25736145 CCCCTAATTACACTTACATG
1 CCCCTGATTGCACTTACATG
* * *
25736165 CCCCTGTTTGTACTTTA-ATA
1 CCCCTGATTGCAC-TTACATG
* *
25736185 CCCCAGATTGCACTTACGTG
1 CCCCTGATTGCACTTACATG
* * * *
25736205 CCCCAG-TTGGTACTT-CGGTA
1 CCCCTGATT-GCACTTAC-ATG
* *
25736225 CTCCTGATTGCACTTACGTG
1 CCCCTGATTGCACTTACATG
* * *
25736245 CCCCTGTTTGTACTTA-AGTA
1 CCCCTGATTGCACTTACA-TG
**
25736265 CCTTTGATTGCACTTACATG
1 CCCCTGATTGCACTTACATG
* * *
25736285 CCCCTGTTTGTACTT-CAGTA
1 CCCCTGATTGCACTTACA-TG
*
25736305 CCCCTGATTGCACAT-CGATG
1 CCCCTGATTGCACTTAC-ATG
*
25736325 CCCCTGTTTGCACTT
1 CCCCTGATTGCACTT
25736340 TGGTGCCCCT
Statistics
Matches: 156, Mismatches: 47, Indels: 24
0.69 0.21 0.11
Matches are distributed among these distances:
19 12 0.08
20 132 0.85
21 12 0.08
ACGTcount: A:0.18, C:0.31, G:0.16, T:0.35
Consensus pattern (20 bp):
CCCCTGATTGCACTTACATG
Found at i:25736145 original size:40 final size:40
Alignment explanation
Indices: 25736091--25736339 Score: 329
Period size: 40 Copynumber: 6.2 Consensus size: 40
25736081 ATGTTCCCCA
25736091 TTTGTACTTCAGTACCCCTGATTGCACTTACATGCCCCTG
1 TTTGTACTTCAGTACCCCTGATTGCACTTACATGCCCCTG
* * *
25736131 TTTGTATTTCAGTACCCCTAATTACACTTACATGCCCCTG
1 TTTGTACTTCAGTACCCCTGATTGCACTTACATGCCCCTG
* * * * *
25736171 TTTGTACTTTAATACCCCAGATTGCACTTACGTGCCCCAG
1 TTTGTACTTCAGTACCCCTGATTGCACTTACATGCCCCTG
* * * *
25736211 TTGGTACTTCGGTACTCCTGATTGCACTTACGTGCCCCTG
1 TTTGTACTTCAGTACCCCTGATTGCACTTACATGCCCCTG
* **
25736251 TTTGTACTTAAGTACCTTTGATTGCACTTACATGCCCCTG
1 TTTGTACTTCAGTACCCCTGATTGCACTTACATGCCCCTG
*
25736291 TTTGTACTTCAGTACCCCTGATTGCACAT-CGATGCCCCTG
1 TTTGTACTTCAGTACCCCTGATTGCACTTAC-ATGCCCCTG
*
25736331 TTTGCACTT
1 TTTGTACTT
25736340 TGGTGCCCCT
Statistics
Matches: 178, Mismatches: 30, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
39 1 0.01
40 177 0.99
ACGTcount: A:0.18, C:0.30, G:0.16, T:0.36
Consensus pattern (40 bp):
TTTGTACTTCAGTACCCCTGATTGCACTTACATGCCCCTG
Found at i:25736346 original size:20 final size:20
Alignment explanation
Indices: 25736192--25736357 Score: 86
Period size: 20 Copynumber: 8.2 Consensus size: 20
25736182 ATACCCCAGA
*
25736192 TTGCACTTAC-GTGCCCCAGT
1 TTGCACTT-CGGTGCCCCTGT
* * * * *
25736212 TGGTACTTCGGTACTCCTGA
1 TTGCACTTCGGTGCCCCTGT
25736232 TTGCACTTAC-GTGCCCCTGT
1 TTGCACTT-CGGTGCCCCTGT
* ** * ** *
25736252 TTGTACTTAAGTACCTTTGA
1 TTGCACTTCGGTGCCCCTGT
*
25736272 TTGCACTTAC-ATGCCCCTGT
1 TTGCACTT-CGGTGCCCCTGT
* * * *
25736292 TTGTACTTCAGTACCCCTGA
1 TTGCACTTCGGTGCCCCTGT
* *
25736312 TTGCACATCGATGCCCCTGT
1 TTGCACTTCGGTGCCCCTGT
*
25736332 TTGCACTTTGGTGCCCCTGT
1 TTGCACTTCGGTGCCCCTGT
25736352 TGTGCA
1 T-TGCA
25736358 TCTATGATGC
Statistics
Matches: 103, Mismatches: 37, Indels: 11
0.68 0.25 0.07
Matches are distributed among these distances:
19 2 0.02
20 96 0.93
21 5 0.05
ACGTcount: A:0.15, C:0.30, G:0.20, T:0.36
Consensus pattern (20 bp):
TTGCACTTCGGTGCCCCTGT
Found at i:25741390 original size:21 final size:20
Alignment explanation
Indices: 25741366--25741404 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
25741356 GAGTACTTCG
25741366 ATGTTTAATGATAGATTATGA
1 ATGTTTAATGATAG-TTATGA
*
25741387 ATGTTTGATGATAGTTAT
1 ATGTTTAATGATAGTTAT
25741405 ACAAGTTTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.46
Consensus pattern (20 bp):
ATGTTTAATGATAGTTATGA
Found at i:25748714 original size:93 final size:93
Alignment explanation
Indices: 25748601--25748772 Score: 299
Period size: 93 Copynumber: 1.8 Consensus size: 93
25748591 CGCCCATAAG
* * *
25748601 CGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCAGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCACATCCATAAGTGAACTCAGACTCAACTCA
25748666 ACGAGTTCGGATGCCTAGTTACATCTCA
66 ACGAGTTCGGATGCCTAGTTACATCTCA
* *
25748694 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCACATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCACATCCATAAGTGAACTCAGACTCAACTCA
25748759 ACGAGTTCGGATGC
66 ACGAGTTCGGATGC
25748773 TCAATCATCC
Statistics
Matches: 74, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 74 1.00
ACGTcount: A:0.29, C:0.30, G:0.20, T:0.21
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGACATTCACATCCATAAGTGAACTCAGACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATCTCA
Found at i:25748769 original size:46 final size:46
Alignment explanation
Indices: 25748594--25748769 Score: 207
Period size: 46 Copynumber: 3.8 Consensus size: 46
25748584 TGTAACCCGC
* * * *
25748594 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCACAT
* *
25748640 CCATAAGTGAACTCAGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCACAT
*
25748690 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCACAT
*
25748733 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA
25748770 TGCTCAATCA
Statistics
Matches: 110, Mismatches: 11, Indels: 18
0.79 0.08 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
44 2 0.02
45 2 0.02
46 62 0.56
47 28 0.25
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.30, C:0.30, G:0.20, T:0.20
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCACAT
Found at i:25751082 original size:27 final size:26
Alignment explanation
Indices: 25751052--25751184 Score: 115
Period size: 27 Copynumber: 4.9 Consensus size: 26
25751042 TACCCCTGGG
*
25751052 TTGTAAAGTTATCGAAATACCCTTGAT
1 TTGTAAA-TTACCGAAATACCCTTGAT
* **
25751079 TTGTGAAATTACCCAAATACCCTCAAT
1 TTGT-AAATTACCGAAATACCCTTGAT
* ** *
25751106 TTTTGAAATTACCGAAATACCCCAGAC
1 TTGT-AAATTACCGAAATACCCTTGAT
* *
25751133 TTGTAAAATTACTGAAATACCCCT-AGT
1 TTGT-AAATTACCGAAATACCCTTGA-T
25751160 TTGTATAATTACCGAAATACCCTTG
1 TTGTA-AATTACCGAAATACCCTTG
25751185 TAGTGTAAAA
Statistics
Matches: 85, Mismatches: 17, Indels: 7
0.78 0.16 0.06
Matches are distributed among these distances:
26 2 0.02
27 80 0.94
28 3 0.04
ACGTcount: A:0.35, C:0.21, G:0.11, T:0.32
Consensus pattern (26 bp):
TTGTAAATTACCGAAATACCCTTGAT
Found at i:25751204 original size:27 final size:26
Alignment explanation
Indices: 25751134--25751222 Score: 79
Period size: 27 Copynumber: 3.3 Consensus size: 26
25751124 ACCCCAGACT
* * *
25751134 TGTAAAATTACTGAAATACCCCTAGTT
1 TGTAAAATTACAGAAATA-CCCTTGTA
* *
25751161 TGTATAATTACCGAAATACCCTTGTA
1 TGTAAAATTACAGAAATACCCTTGTA
* **
25751187 GTGTAAAATTACAAAAATATTCTTGTA
1 -TGTAAAATTACAGAAATACCCTTGTA
25751214 TGGTAAAAT
1 T-GTAAAAT
25751223 GACTATTTTA
Statistics
Matches: 51, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
26 7 0.14
27 44 0.86
ACGTcount: A:0.39, C:0.13, G:0.12, T:0.35
Consensus pattern (26 bp):
TGTAAAATTACAGAAATACCCTTGTA
Found at i:25751205 original size:54 final size:53
Alignment explanation
Indices: 25751022--25751205 Score: 156
Period size: 54 Copynumber: 3.4 Consensus size: 53
25751012 TAGGACCCCC
* * * * * *
25751022 GACTTGTAAAGTTCCTAAAATACCCCTGGGTTGTAAAGTTATCGAAATACCCTT
1 GACTTGTAAAATTACAAAAATACCCCTAGTTTGTAAA-TTACCGAAATACCCTT
* * ** * * **
25751076 GATTTGTGAAATTACCCAAATA-CCCTCAATTTTTGAAATTACCGAAATACCCCA
1 GACTTGTAAAATTACAAAAATACCCCT-AGTTTGT-AAATTACCGAAATACCCTT
**
25751130 GACTTGTAAAATTACTGAAATACCCCTAGTTTGTATAATTACCGAAATACCCTT
1 GACTTGTAAAATTACAAAAATACCCCTAGTTTGTA-AATTACCGAAATACCCTT
*
25751184 GTA-GTGTAAAATTACAAAAATA
1 G-ACTTGTAAAATTACAAAAATA
25751206 TTCTTGTATG
Statistics
Matches: 101, Mismatches: 24, Indels: 10
0.75 0.18 0.07
Matches are distributed among these distances:
53 5 0.05
54 88 0.87
55 8 0.08
ACGTcount: A:0.37, C:0.20, G:0.12, T:0.31
Consensus pattern (53 bp):
GACTTGTAAAATTACAAAAATACCCCTAGTTTGTAAATTACCGAAATACCCTT
Found at i:25752718 original size:50 final size:50
Alignment explanation
Indices: 25752660--25752759 Score: 191
Period size: 50 Copynumber: 2.0 Consensus size: 50
25752650 GTTTTCGAAA
*
25752660 AACACTTCAATGTGACATGTCAGATCGGGTTTGGGGTGTTACAAACTAAC
1 AACACTTCAATGTGACATGTCAGATCAGGTTTGGGGTGTTACAAACTAAC
25752710 AACACTTCAATGTGACATGTCAGATCAGGTTTGGGGTGTTACAAACTAAC
1 AACACTTCAATGTGACATGTCAGATCAGGTTTGGGGTGTTACAAACTAAC
25752760 TAATGCTCCT
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 49 1.00
ACGTcount: A:0.31, C:0.18, G:0.23, T:0.28
Consensus pattern (50 bp):
AACACTTCAATGTGACATGTCAGATCAGGTTTGGGGTGTTACAAACTAAC
Found at i:25755401 original size:25 final size:25
Alignment explanation
Indices: 25755373--25755420 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
25755363 TTATATTATG
* * *
25755373 AAAATGACTGTTTTGCCCCTAGGTA
1 AAAATGACCGTTATACCCCTAGGTA
25755398 AAAATGACCGTTATACCCCTAGG
1 AAAATGACCGTTATACCCCTAGG
25755421 GTTTACTTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.31, C:0.23, G:0.19, T:0.27
Consensus pattern (25 bp):
AAAATGACCGTTATACCCCTAGGTA
Found at i:25755562 original size:27 final size:26
Alignment explanation
Indices: 25755532--25755653 Score: 185
Period size: 26 Copynumber: 4.7 Consensus size: 26
25755522 GAGGAAGTGC
25755532 AAAAGGGCTTATGCCCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTATTG
*
25755558 AAAAAGGGGTTATGCCCCAGTTTATTG
1 -AAAAGGGCTTATGCCCCAGTTTATTG
*
25755585 AAAAGGGCTGATGCCCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTATTG
**
25755611 AAAAGGGCTT-TGCCCCAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTATTG
25755636 AAAAGGGCTT-TGCCCCAG
1 AAAAGGGCTTATGCCCCAG
25755654 GTATTAAAGA
Statistics
Matches: 89, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
25 31 0.35
26 33 0.37
27 25 0.28
ACGTcount: A:0.27, C:0.21, G:0.25, T:0.26
Consensus pattern (26 bp):
AAAAGGGCTTATGCCCCAGTTTATTG
Found at i:25756739 original size:17 final size:17
Alignment explanation
Indices: 25756717--25756749 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
25756707 AGTGAAAACG
25756717 AGTAAAACA-ACATAATC
1 AGTAAAA-ATACATAATC
25756734 AGTAAAAATACATAAT
1 AGTAAAAATACATAAT
25756750 GTTCATAAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 1 0.07
17 14 0.93
ACGTcount: A:0.61, C:0.12, G:0.06, T:0.21
Consensus pattern (17 bp):
AGTAAAAATACATAATC
Found at i:25757694 original size:47 final size:47
Alignment explanation
Indices: 25757625--25757790 Score: 271
Period size: 47 Copynumber: 3.5 Consensus size: 47
25757615 AGACACATAG
25757625 GACAAGGATACCATGTAAGACCATGTTTGGAACATGGAATTTGGTAA
1 GACAAGGATACCATGTAAGACCATGTTTGGAACATGGAATTTGGTAA
* *
25757672 GACAAGGATACCATGTAAGACCATGTTTGGAACATGGCATTTGGCAA
1 GACAAGGATACCATGTAAGACCATGTTTGGAACATGGAATTTGGTAA
*
25757719 GACAAGGATACCATGTAAGACCATGTTTGGAACA-CGACATTTGGTAA
1 GACAAGGATACCATGTAAGACCATGTTTGGAACATGGA-ATTTGGTAA
* *
25757766 GATAAGGATATCATGTAAGACCATG
1 GACAAGGATACCATGTAAGACCATG
25757791 CCAAGGCATG
Statistics
Matches: 111, Mismatches: 7, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
46 1 0.01
47 110 0.99
ACGTcount: A:0.36, C:0.15, G:0.25, T:0.24
Consensus pattern (47 bp):
GACAAGGATACCATGTAAGACCATGTTTGGAACATGGAATTTGGTAA
Found at i:25788391 original size:50 final size:49
Alignment explanation
Indices: 25788201--25788390 Score: 168
Period size: 50 Copynumber: 3.8 Consensus size: 49
25788191 ATTGTGAATA
* * *
25788201 CACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCATACT-GTTAAGT
1 CACGTGTGTAGTACTAAGTGCAGGCTACTACGCGTATCAT--TGGTTAGGT
* * * * * * *
25788251 CGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACTCAATGACTTCGAT
1 CACGTGTGTAGTACTAAGTGCAGGCTACTACGCGTA-TCATTG-GTTAGGT
* * ** *
25788302 CACGTCTGTAGTAC-AACATGCAGGCTACTACATGTATCAGTTGGTGAGGT
1 CACGTGTGTAGTACTAA-GTGCAGGCTACTACGCGTATCA-TTGGTTAGGT
*
25788352 CACGTGTGTAGTACTAAGTGCAGGCTACTATGCGTATCA
1 CACGTGTGTAGTACTAAGTGCAGGCTACTACGCGTATCA
25788391 GATAGCTTCG
Statistics
Matches: 107, Mismatches: 27, Indels: 12
0.73 0.18 0.08
Matches are distributed among these distances:
49 1 0.01
50 71 0.66
51 35 0.33
ACGTcount: A:0.26, C:0.21, G:0.25, T:0.29
Consensus pattern (49 bp):
CACGTGTGTAGTACTAAGTGCAGGCTACTACGCGTATCATTGGTTAGGT
Found at i:25794574 original size:30 final size:30
Alignment explanation
Indices: 25794540--25794600 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 30
25794530 CCCCTAGTAC
25794540 AAACTTTGGCAAAATTAC-CATTTTGCCCCT
1 AAACTTTGGCAAAATTACAC-TTTTGCCCCT
* * *
25794570 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTGGCAAAATTACACTTTTGCCCCT
25794600 A
1 A
25794601 GGCTCGAGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
30 26 0.96
31 1 0.04
ACGTcount: A:0.28, C:0.26, G:0.08, T:0.38
Consensus pattern (30 bp):
AAACTTTGGCAAAATTACACTTTTGCCCCT
Found at i:25804201 original size:27 final size:26
Alignment explanation
Indices: 25804163--25804250 Score: 113
Period size: 27 Copynumber: 3.3 Consensus size: 26
25804153 TGGAGGAAGC
*
25804163 GTTCTGGTGGCTATGCCACAAATATCT
1 GTTCTGGTGGCTCTGCCAC-AATATCT
*
25804190 GTTCTGGTGGCTCTGCCACAATATTT
1 GTTCTGGTGGCTCTGCCACAATATCT
** *
25804216 GTATCTGGTGATTCTGTCACAATATCT
1 GT-TCTGGTGGCTCTGCCACAATATCT
25804243 GTTCTGGT
1 GTTCTGGT
25804251 AGCCATGCTG
Statistics
Matches: 54, Mismatches: 6, Indels: 3
0.86 0.10 0.05
Matches are distributed among these distances:
26 14 0.26
27 40 0.74
ACGTcount: A:0.18, C:0.20, G:0.23, T:0.39
Consensus pattern (26 bp):
GTTCTGGTGGCTCTGCCACAATATCT
Found at i:25805406 original size:21 final size:20
Alignment explanation
Indices: 25805371--25805419 Score: 62
Period size: 21 Copynumber: 2.4 Consensus size: 20
25805361 ACCAGCTCAC
*
25805371 TTGAGCTCGTTTTAGCTTGT
1 TTGAGCTCGTTTTAGCTCGT
*
25805391 TTGAGCTTGATTTTAGCTCGT
1 TTGAGCTCG-TTTTAGCTCGT
*
25805412 TTCAGCTC
1 TTGAGCTC
25805420 ATTTGTTTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
20 8 0.33
21 16 0.67
ACGTcount: A:0.12, C:0.18, G:0.22, T:0.47
Consensus pattern (20 bp):
TTGAGCTCGTTTTAGCTCGT
Found at i:25808007 original size:134 final size:134
Alignment explanation
Indices: 25807806--25808051 Score: 368
Period size: 134 Copynumber: 1.8 Consensus size: 134
25807796 CTACTTCAGG
* * * * *
25807806 GAGATGAGGCTGGTGGCCTAAATCTGTTCCATTGCTACTTCAAGAAGATAAGATTTGTCGTCTTT
1 GAGATAAGACTGGTGGCCTAAATCTGTTCCATTGCTACCTCAAGAAGATAAGATTTGTCATCATT
* *
25807871 GATCTGCTCCACTTCTATCTCAAAGAGATAAGATCTACAATCTTCAGCCTACTCCTTTGCTACCT
66 GATCTACTCCACTGCTATCTCAAAGAGATAAGATCTACAATCTTCAGCCTACTCCTTTGCTACCT
25807936 CAAA
131 CAAA
* * *
25807940 GAGATAAGACTGGTGGCTTAAATCTGCTTCCCTT-CTGCCTCAAGAAGATAAGATTTGTCATCAT
1 GAGATAAGACTGGTGGCCTAAATCTG-TTCCATTGCTACCTCAAGAAGATAAGATTTGTCATCAT
* *
25808004 TGATCTATTCCACTGCTATCTCAAGGAGATAAGATCTACAATCTTCAG
65 TGATCTACTCCACTGCTATCTCAAAGAGATAAGATCTACAATCTTCAG
25808052 TCTGCTTCCT
Statistics
Matches: 99, Mismatches: 12, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
134 93 0.94
135 6 0.06
ACGTcount: A:0.28, C:0.23, G:0.17, T:0.32
Consensus pattern (134 bp):
GAGATAAGACTGGTGGCCTAAATCTGTTCCATTGCTACCTCAAGAAGATAAGATTTGTCATCATT
GATCTACTCCACTGCTATCTCAAAGAGATAAGATCTACAATCTTCAGCCTACTCCTTTGCTACCT
CAAA
Found at i:25808100 original size:134 final size:134
Alignment explanation
Indices: 25807845--25808102 Score: 322
Period size: 134 Copynumber: 1.9 Consensus size: 134
25807835 CATTGCTACT
* * * *
25807845 TCAAGAAGATAAGATTTGTCGTCTTTGATCTGCTCCACTTCTATCTCAAAGAGATAAGATCTACA
1 TCAAGAAGATAAGATTTGTCATCATTGATCTACTCCACTGCTATCTCAAAGAGATAAGATCTACA
* ****
25807910 ATCTTCAGCCTACTCCTTTGCTACCTCAAAGAGATAAGACTGGTGGCTTAAATCTGCTTCCCTTC
66 ATCTTCAGCCTACTCCTTTGATACCTCAAAGAGATAAGACTACAAGCTTAAATCTGCTTCCCTTC
25807975 TGCC
131 TGCC
* *
25807979 TCAAGAAGATAAGATTTGTCATCATTGATCTATTCCACTGCTATCTCAAGGAGATAAGATCTACA
1 TCAAGAAGATAAGATTTGTCATCATTGATCTACTCCACTGCTATCTCAAAGAGATAAGATCTACA
* * ** * * *
25808044 ATCTTCAGTCTGCTTCC-TTGATACCTC-GGGAAGATAAGACTACAATCTTCAGTCTGCTT
66 ATCTTCAGCCTAC-TCCTTTGATACCTCAAAG-AGATAAGACTACAAGCTTAAATCTGCTT
25808103 ATGTCAAATG
Statistics
Matches: 104, Mismatches: 18, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
133 1 0.01
134 100 0.96
135 3 0.03
ACGTcount: A:0.28, C:0.24, G:0.16, T:0.32
Consensus pattern (134 bp):
TCAAGAAGATAAGATTTGTCATCATTGATCTACTCCACTGCTATCTCAAAGAGATAAGATCTACA
ATCTTCAGCCTACTCCTTTGATACCTCAAAGAGATAAGACTACAAGCTTAAATCTGCTTCCCTTC
TGCC
Found at i:25814503 original size:46 final size:46
Alignment explanation
Indices: 25814453--25814625 Score: 208
Period size: 46 Copynumber: 3.7 Consensus size: 46
25814443 TGGTTGAGCA
*
25814453 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* * * * *
25814499 TCCGAACTCGTTGAGTTGAGTTCGAGTTC-GTGA--GATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAA--A--CG
*
25814546 TCCGAACTCGTTGAGTTGAGTCCGAGTTCATTTATGGATGCAAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* *
25814592 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
25814626 GGGGCGGGTT
Statistics
Matches: 106, Mismatches: 14, Indels: 14
0.79 0.10 0.10
Matches are distributed among these distances:
43 6 0.06
45 3 0.03
46 60 0.57
47 28 0.26
48 3 0.03
50 6 0.06
ACGTcount: A:0.23, C:0.20, G:0.27, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
Found at i:25814609 original size:93 final size:93
Alignment explanation
Indices: 25814450--25814620 Score: 297
Period size: 93 Copynumber: 1.8 Consensus size: 93
25814440 GGATGGTTGA
* *
25814450 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAGT
*
25814515 TGAGTTCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* *
25814543 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCATTTATGGATGCAAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAGT
25814608 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
25814621 ACTTAGGGGC
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.22, C:0.20, G:0.28, T:0.29
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:25816591 original size:25 final size:25
Alignment explanation
Indices: 25816563--25816619 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 25
25816553 TTTGGCTTGA
**
25816563 CATTTACTAAGCAATATCGGATATT
1 CATTTACTAAGCAATATCAAATATT
* *
25816588 CATTTATTAGGCAATATCAAATATT
1 CATTTACTAAGCAATATCAAATATT
25816613 CAATTTA
1 C-ATTTA
25816620 TTCTTTAACA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
25 22 0.81
26 5 0.19
ACGTcount: A:0.39, C:0.14, G:0.09, T:0.39
Consensus pattern (25 bp):
CATTTACTAAGCAATATCAAATATT
Found at i:25818794 original size:2 final size:2
Alignment explanation
Indices: 25818789--25818815 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
25818779 GGGGGGGGGA
25818789 AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC A
25818816 TCATCCATCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:25822834 original size:9 final size:9
Alignment explanation
Indices: 25822816--25822888 Score: 61
Period size: 9 Copynumber: 8.6 Consensus size: 9
25822806 TTTATTTAAG
25822816 TTAA-GTGT
1 TTAATGTGT
25822824 TTAATGTGT
1 TTAATGTGT
25822833 TT--TGTGT
1 TTAATGTGT
25822840 TTAATAAGTGT
1 TTAAT--GTGT
25822851 TTAAATGTGT
1 TT-AATGTGT
*
25822861 TTAATATG-
1 TTAATGTGT
25822869 TT--TGT-T
1 TTAATGTGT
25822875 TTAATGTGT
1 TTAATGTGT
25822884 TTAAT
1 TTAAT
25822889 TGTAGGTGTC
Statistics
Matches: 53, Mismatches: 2, Indels: 19
0.72 0.03 0.26
Matches are distributed among these distances:
6 4 0.08
7 7 0.13
8 9 0.17
9 18 0.34
10 6 0.11
11 6 0.11
12 3 0.06
ACGTcount: A:0.25, C:0.00, G:0.19, T:0.56
Consensus pattern (9 bp):
TTAATGTGT
Found at i:25822861 original size:21 final size:22
Alignment explanation
Indices: 25822835--25822888 Score: 74
Period size: 23 Copynumber: 2.5 Consensus size: 22
25822825 TAATGTGTTT
25822835 TGTGTTTAATAAG-TGTTTAAA
1 TGTGTTTAATAAGTTGTTTAAA
* *
25822856 TGTGTTTAATATGTTTGTTTTAA
1 TGTGTTTAATAAG-TTGTTTAAA
25822879 TGTGTTTAAT
1 TGTGTTTAAT
25822889 TGTAGGTGTC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 12 0.41
23 17 0.59
ACGTcount: A:0.26, C:0.00, G:0.19, T:0.56
Consensus pattern (22 bp):
TGTGTTTAATAAGTTGTTTAAA
Found at i:25825723 original size:30 final size:30
Alignment explanation
Indices: 25825689--25825749 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
25825679 TCCTTAACTC
25825689 AAACTTTGGAAAAATTACAATTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
* * * * *
25825719 AAACTTTTGCACATTTACACTTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
25825749 A
1 A
25825750 GGATCGGGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.31, C:0.25, G:0.08, T:0.36
Consensus pattern (30 bp):
AAACTTTGGAAAAATTACAATTTTGCCCCT
Found at i:25830165 original size:30 final size:30
Alignment explanation
Indices: 25830131--25830191 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
25830121 TCCTTAACTC
25830131 AAACTTTAGAAAAATTACAATTTTGCCCCT
1 AAACTTTAGAAAAATTACAATTTTGCCCCT
* * * * *
25830161 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTAGAAAAATTACAATTTTGCCCCT
25830191 A
1 A
25830192 GGCTGGGAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.33, C:0.23, G:0.07, T:0.38
Consensus pattern (30 bp):
AAACTTTAGAAAAATTACAATTTTGCCCCT
Found at i:25832065 original size:28 final size:29
Alignment explanation
Indices: 25832008--25832067 Score: 79
Period size: 28 Copynumber: 2.1 Consensus size: 29
25831998 ATTTATTTAA
*
25832008 CAATTTAACCCCTCAATTTACACTTTTGT
1 CAATTTAACCCCTCAATTGACACTTTTGT
*
25832037 CAATTTAATCCCT-AATTGACA-TTGTTGT
1 CAATTTAACCCCTCAATTGACACTT-TTGT
25832065 CAA
1 CAA
25832068 AAATCACTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
27 2 0.07
28 14 0.50
29 12 0.43
ACGTcount: A:0.30, C:0.23, G:0.07, T:0.40
Consensus pattern (29 bp):
CAATTTAACCCCTCAATTGACACTTTTGT
Found at i:25836099 original size:18 final size:18
Alignment explanation
Indices: 25836078--25836127 Score: 52
Period size: 18 Copynumber: 2.8 Consensus size: 18
25836068 AAAAGAAAAA
25836078 GAGAAGGAAAAAGAGAT-C
1 GAGAAGGAAAAAGA-ATGC
*
25836096 GAG-AGTGAAAAAGAATGT
1 GAGAAG-GAAAAAGAATGC
25836114 GAGAA-GAAAAAGAA
1 GAGAAGGAAAAAGAA
25836128 AATTGAAAAC
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
17 13 0.46
18 14 0.50
19 1 0.04
ACGTcount: A:0.58, C:0.02, G:0.32, T:0.08
Consensus pattern (18 bp):
GAGAAGGAAAAAGAATGC
Done.