Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold54
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: 3629595
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 8670 characters in sequence are not A, C, G, or T
File 17 of 20
Found at i:2910994 original size:17 final size:16
Alignment explanation
Indices: 2910971--2911011 Score: 55
Period size: 17 Copynumber: 2.5 Consensus size: 16
2910961 TTTATATTTT
* *
2910971 ATTATTTTAATATTAA
1 ATTATTTAAAAATTAA
2910987 ATTTATTTAAAAATTAA
1 A-TTATTTAAAAATTAA
2911004 ATTATTTA
1 ATTATTTA
2911012 TTTAAATATG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
16 8 0.36
17 14 0.64
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (16 bp):
ATTATTTAAAAATTAA
Found at i:2911646 original size:17 final size:17
Alignment explanation
Indices: 2911605--2911651 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
2911595 TTTTATTATT
* *
2911605 TTAAATTTTATTTTAATA
1 TTAAA-TTTATTTAAAAA
*
2911623 TTTAATTTATTTAAAAA
1 TTAAATTTATTTAAAAA
2911640 TTAAA-TTATTTA
1 TTAAATTTATTTA
2911652 TTTAAATGTA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
16 7 0.28
17 14 0.56
18 4 0.16
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
TTAAATTTATTTAAAAA
Found at i:2911652 original size:20 final size:20
Alignment explanation
Indices: 2911627--2911685 Score: 75
Period size: 20 Copynumber: 3.0 Consensus size: 20
2911617 TTAATATTTA
2911627 ATTTATTTAAAAATTAAATT
1 ATTTATTTAAAAATTAAATT
** *
2911647 ATTTATTTAAATGTAAAAATT
1 ATTTATTTAAAAAT-TAAATT
2911668 ATTT-TTTAAAAATTAAAT
1 ATTTATTTAAAAATTAAAT
2911686 AAAAATATTA
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
19 4 0.12
20 19 0.59
21 9 0.28
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (20 bp):
ATTTATTTAAAAATTAAATT
Found at i:2911683 original size:27 final size:26
Alignment explanation
Indices: 2911653--2911717 Score: 73
Period size: 26 Copynumber: 2.5 Consensus size: 26
2911643 AATTATTTAT
2911653 TTAAATGTAAAAATTATTTTTTAAAAA
1 TTAAAT-TAAAAATTATTTTTTAAAAA
2911680 TTAAA-TAAAAA-TATTATATTTAAAAA
1 TTAAATTAAAAATTATT-T-TTTAAAAA
*
2911706 AT-AATTAAAAAT
1 TTAAATTAAAAAT
2911718 AAATAATATT
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
24 4 0.12
25 9 0.27
26 15 0.45
27 5 0.15
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (26 bp):
TTAAATTAAAAATTATTTTTTAAAAA
Found at i:2911684 original size:21 final size:22
Alignment explanation
Indices: 2911627--2911684 Score: 72
Period size: 21 Copynumber: 2.8 Consensus size: 22
2911617 TTAATATTTA
2911627 ATTTATTTAAAAATT--AAATT
1 ATTTATTTAAAAATTAAAAATT
2911647 ATTTATTT--AAATGTAAAAATT
1 ATTTATTTAAAAAT-TAAAAATT
2911668 ATTT-TTTAAAAATTAAA
1 ATTTATTTAAAAATTAAA
2911685 TAAAAATATT
Statistics
Matches: 33, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
18 4 0.12
19 1 0.03
20 11 0.33
21 13 0.39
22 4 0.12
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (22 bp):
ATTTATTTAAAAATTAAAAATT
Found at i:2911690 original size:26 final size:26
Alignment explanation
Indices: 2911660--2911718 Score: 77
Period size: 26 Copynumber: 2.3 Consensus size: 26
2911650 TATTTAAATG
*
2911660 TAAAAATTATT-T-TTTAAAAATTAAA
1 TAAAAA-TATTATATTTAAAAAATAAA
*
2911685 TAAAAATATTATATTTAAAAAATAAT
1 TAAAAATATTATATTTAAAAAATAAA
2911711 TAAAAATA
1 TAAAAATA
2911719 AATAATATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
24 4 0.13
25 7 0.23
26 19 0.63
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (26 bp):
TAAAAATATTATATTTAAAAAATAAA
Found at i:2911714 original size:30 final size:30
Alignment explanation
Indices: 2911678--2911737 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
2911668 ATTTTTTAAA
*
2911678 AATTAAATAA-AAATATTATATTTAAAAAAT
1 AATTAAA-AATAAATAATATATTTAAAAAAT
* *
2911708 AATTAAAAATAAATAATATTTTTTAAAAAT
1 AATTAAAAATAAATAATATATTTAAAAAAT
2911738 TTAATTTAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 2 0.08
30 24 0.92
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (30 bp):
AATTAAAAATAAATAATATATTTAAAAAAT
Found at i:2911801 original size:15 final size:14
Alignment explanation
Indices: 2911772--2911812 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
2911762 TATAATTTTT
2911772 TATAAA-ATT-AAA
1 TATAAATATTAAAA
*
2911784 TATATATTATTAAAA
1 TATA-AATATTAAAA
2911799 TATAAATATTAAAA
1 TATAAATATTAAAA
2911813 AAATTATATT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
12 4 0.17
13 1 0.04
14 12 0.50
15 7 0.29
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (14 bp):
TATAAATATTAAAA
Found at i:2922473 original size:28 final size:27
Alignment explanation
Indices: 2922404--2922497 Score: 93
Period size: 29 Copynumber: 3.4 Consensus size: 27
2922394 TTACAATTTT
* *
2922404 TAAAATATTAAAATTTATTTTAATATAAA
1 TAAAAT-TAAAAATTTATTTAAATAT-AA
* *
2922433 TTGAAATTTAAAATTTATTTAAATATAA
1 -TAAAATTAAAAATTTATTTAAATATAA
*
2922461 TAAAATATAAAAATTTATCTAAA-ATAA
1 TAAAAT-TAAAAATTTATTTAAATATAA
2922488 -AAAATTAAAA
1 TAAAATTAAAA
2922498 TTTTTATTAT
Statistics
Matches: 58, Mismatches: 5, Indels: 7
0.83 0.07 0.10
Matches are distributed among these distances:
25 5 0.09
26 5 0.09
27 9 0.16
28 16 0.28
29 18 0.31
30 5 0.09
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.39
Consensus pattern (27 bp):
TAAAATTAAAAATTTATTTAAATATAA
Found at i:2928601 original size:29 final size:28
Alignment explanation
Indices: 2928568--2928635 Score: 84
Period size: 29 Copynumber: 2.4 Consensus size: 28
2928558 GTTAGCAATT
2928568 TATATTTATATATAT-TTAAATAATAAAA
1 TATATTTATATATATGTTAAA-AATAAAA
* * *
2928596 TAATATTTTTAAATATGTTAAAAATTAAA
1 T-ATATTTATATATATGTTAAAAATAAAA
2928625 TATATTTATAT
1 TATATTTATAT
2928636 TAAAAAATTT
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
28 9 0.27
29 19 0.58
30 5 0.15
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (28 bp):
TATATTTATATATATGTTAAAAATAAAA
Found at i:2941757 original size:19 final size:20
Alignment explanation
Indices: 2941733--2941773 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
2941723 CAATTTTACT
2941733 ATAATTAC-AGTAA-AAAAAA
1 ATAATTACTA-TAACAAAAAA
2941752 ATAATTACTATAACAAAAAA
1 ATAATTACTATAACAAAAAA
2941772 AT
1 AT
2941774 TGTTTGTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 11 0.55
20 9 0.45
ACGTcount: A:0.66, C:0.07, G:0.02, T:0.24
Consensus pattern (20 bp):
ATAATTACTATAACAAAAAA
Found at i:2948076 original size:15 final size:14
Alignment explanation
Indices: 2948049--2948095 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
2948039 AATAATTATA
2948049 TAATTTTTTAAATT
1 TAATTTTTTAAATT
*
2948063 TAATTTTTTAAAAT
1 TAATTTTTTAAATT
*
2948077 T--TTATTTAAATTT
1 TAATTTTTTAAA-TT
2948090 TAATTT
1 TAATTT
2948096 ATTTTATAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 5
0.74 0.11 0.14
Matches are distributed among these distances:
12 8 0.31
13 2 0.08
14 14 0.54
15 2 0.08
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (14 bp):
TAATTTTTTAAATT
Found at i:2948128 original size:22 final size:22
Alignment explanation
Indices: 2948085--2948128 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
2948075 ATTTTATTTA
* *
2948085 AATTTTAATTTATTTTATAAAT
1 AATTTTAAATTATATTATAAAT
2948107 AATTTTAAAATTATATTA-AAAT
1 AATTTT-AAATTATATTATAAAT
2948129 TTTATAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (22 bp):
AATTTTAAATTATATTATAAAT
Found at i:2948422 original size:16 final size:17
Alignment explanation
Indices: 2948401--2948434 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
2948391 AATATTAGAA
2948401 TTTTTTTA-TTTTAAAT
1 TTTTTTTACTTTTAAAT
*
2948417 TTTTTTTACTTTTTAAT
1 TTTTTTTACTTTTAAAT
2948434 T
1 T
2948435 AAAAATTTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.76
Consensus pattern (17 bp):
TTTTTTTACTTTTAAAT
Found at i:2949017 original size:27 final size:25
Alignment explanation
Indices: 2948971--2949020 Score: 64
Period size: 27 Copynumber: 1.9 Consensus size: 25
2948961 TTTAACTTAA
2948971 ATTATTATTTAATAACAAAAATATT
1 ATTATTATTTAATAACAAAAATATT
* *
2948996 ATTATTAATTTTAATTATAAAAATA
1 ATTATT-A-TTTAATAACAAAAATA
2949021 CTTAAAAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 6 0.29
26 1 0.05
27 14 0.67
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (25 bp):
ATTATTATTTAATAACAAAAATATT
Found at i:2949375 original size:2 final size:2
Alignment explanation
Indices: 2949357--2949390 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
2949347 ACTAAGAAGG
* *
2949357 TA TA CA TA TA TA CA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2949391 GAGAGAGAGA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (2 bp):
TA
Found at i:2949859 original size:16 final size:17
Alignment explanation
Indices: 2949824--2949856 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
2949814 TATATTATAT
2949824 ATAAAAATAATAATAAA
1 ATAAAAATAATAATAAA
2949841 ATAAAAA-AAT-ATAAA
1 ATAAAAATAATAATAAA
2949856 A
1 A
2949857 ATATTCATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.38
16 3 0.19
17 7 0.44
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (17 bp):
ATAAAAATAATAATAAA
Found at i:2950517 original size:12 final size:12
Alignment explanation
Indices: 2950500--2950526 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
2950490 AGCCTTAACC
2950500 TTTGGTCAAAGA
1 TTTGGTCAAAGA
2950512 TTTGGTCAAAGA
1 TTTGGTCAAAGA
2950524 TTT
1 TTT
2950527 TTAAGTGACC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.30, C:0.07, G:0.22, T:0.41
Consensus pattern (12 bp):
TTTGGTCAAAGA
Found at i:2956242 original size:12 final size:12
Alignment explanation
Indices: 2956225--2956251 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
2956215 AGCCTTAACC
2956225 TTTGGTCAAAGA
1 TTTGGTCAAAGA
2956237 TTTGGTCAAAGA
1 TTTGGTCAAAGA
2956249 TTT
1 TTT
2956252 TTAAGTGACC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.30, C:0.07, G:0.22, T:0.41
Consensus pattern (12 bp):
TTTGGTCAAAGA
Found at i:2960726 original size:26 final size:26
Alignment explanation
Indices: 2960697--2960754 Score: 98
Period size: 26 Copynumber: 2.2 Consensus size: 26
2960687 ACTAACATAA
* *
2960697 AATTAAACTTGTTATAATGAAGTAAT
1 AATTAAACTTGTTATAATAAAGCAAT
2960723 AATTAAACTTGTTATAATAAAGCAAT
1 AATTAAACTTGTTATAATAAAGCAAT
2960749 AATTAA
1 AATTAA
2960755 TAAACCCTAG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.50, C:0.05, G:0.09, T:0.36
Consensus pattern (26 bp):
AATTAAACTTGTTATAATAAAGCAAT
Found at i:2962435 original size:2 final size:2
Alignment explanation
Indices: 2962430--2962459 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2962420 AACTGGACAA
2962430 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
2962460 TTTTGTATTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
GT
Found at i:2967203 original size:32 final size:32
Alignment explanation
Indices: 2967162--2967223 Score: 115
Period size: 32 Copynumber: 1.9 Consensus size: 32
2967152 AAGTAGGTAT
*
2967162 TTGTGGACCTGTTTTGTTTTGTCATGGTTCTG
1 TTGTGGACCTGTTTTGTTTTATCATGGTTCTG
2967194 TTGTGGACCTGTTTTGTTTTATCATGGTTC
1 TTGTGGACCTGTTTTGTTTTATCATGGTTC
2967224 AGCTAATTTG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.08, C:0.13, G:0.26, T:0.53
Consensus pattern (32 bp):
TTGTGGACCTGTTTTGTTTTATCATGGTTCTG
Found at i:2972532 original size:92 final size:92
Alignment explanation
Indices: 2972412--2972589 Score: 275
Period size: 92 Copynumber: 1.9 Consensus size: 92
2972402 TGTTAGTATA
* *
2972412 TTTTGGTTAAAATAGTATATTGGCATCTTATCTTATTCCATTTCCTGTAAAATAATGACTAGTGT
1 TTTTGGTTAAAATAGTATATCGGCATCTTAGCTTATTCCATTTCCTGTAAAATAATGACTAGTGT
** *
2972477 CTTGAATATGTTTGGTTGCAGGATATT
66 CTCAAATATGTCTGGTTGCAGGATATT
* * * *
2972504 TTTTGGTTAAAATAGTCTATCGGTATCTTAGCTTATTCTATTTCCTGTAAGATAATGACTAGTGT
1 TTTTGGTTAAAATAGTATATCGGCATCTTAGCTTATTCCATTTCCTGTAAAATAATGACTAGTGT
2972569 CTCAAATATGTCTGGTTGCAG
66 CTCAAATATGTCTGGTTGCAG
2972590 CGTATTCATC
Statistics
Matches: 77, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
92 77 1.00
ACGTcount: A:0.26, C:0.12, G:0.18, T:0.43
Consensus pattern (92 bp):
TTTTGGTTAAAATAGTATATCGGCATCTTAGCTTATTCCATTTCCTGTAAAATAATGACTAGTGT
CTCAAATATGTCTGGTTGCAGGATATT
Found at i:2977847 original size:240 final size:240
Alignment explanation
Indices: 2977424--2977858 Score: 701
Period size: 240 Copynumber: 1.8 Consensus size: 240
2977414 AGGCACGGAG
* * *
2977424 AACCAGTTCTAGAAATGAAACTGGTGAAAGAGGTGTTTTGAATGATATGTCCATTTCCAAGCTGT
1 AACCAGTTCTAGAAAGGAAACTGGTGAAAGAGGTGTTTTGAATGATATATCCATTTCCAAGCTAT
* * *
2977489 TCTTTTATGAACCCAATTGATTTAGGGTAACTAGGCAAGGTGATGGATTTGGCCTTGGTGTTCTG
66 TCTTTTATGAACCCAATTGATTTAGAGTAACTAAGCAAGGTGATGGATTTGGCCTTGGTGTTCCG
* *
2977554 AATTTCTTTTTTATTTTAATTTTAAAAGGTTTCTTTTTTATAATGTATTCTGCTTGCCTTCTTGT
131 AATTTCCTTTTTATTTTAATTTTAAAAGGTTTCTTTTGTATAATGTATTCTGCTTGCCTTCTTGT
2977619 CTTCCTGTAGTTTGGTACATAGGCCGGGTGGAAGACAATGAAGCA
196 CTTCCTGTAGTTTGGTACATAGGCCGGGTGGAAGACAATGAAGCA
* * * * *
2977664 AACCAGTTCTAGAAAGGATACTGGTGAAAGAGTTTTTTTGAATGATTTATCCATTTCCGAGCTAT
1 AACCAGTTCTAGAAAGGAAACTGGTGAAAGAGGTGTTTTGAATGATATATCCATTTCCAAGCTAT
* *
2977729 TCGTTTTATGAACCCAATTGATTTAGAGTAATTAAGCAAGGTGCTGGA-TTGGCCTTGGTGTTCC
66 TC-TTTTATGAACCCAATTGATTTAGAGTAACTAAGCAAGGTGATGGATTTGGCCTTGGTGTTCC
* *
2977793 GGATTTCCTTTTTATTTTAGTTTTAAAAGGTTTCTTTTGTATAATGTATTCTGCTTGCCTTCTTG
130 GAATTTCCTTTTTATTTTAATTTTAAAAGGTTTCTTTTGTATAATGTATTCTGCTTGCCTTCTTG
2977858 T
195 T
2977859 AGTTTGTTAG
Statistics
Matches: 177, Mismatches: 17, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
240 136 0.77
241 41 0.23
ACGTcount: A:0.24, C:0.14, G:0.21, T:0.41
Consensus pattern (240 bp):
AACCAGTTCTAGAAAGGAAACTGGTGAAAGAGGTGTTTTGAATGATATATCCATTTCCAAGCTAT
TCTTTTATGAACCCAATTGATTTAGAGTAACTAAGCAAGGTGATGGATTTGGCCTTGGTGTTCCG
AATTTCCTTTTTATTTTAATTTTAAAAGGTTTCTTTTGTATAATGTATTCTGCTTGCCTTCTTGT
CTTCCTGTAGTTTGGTACATAGGCCGGGTGGAAGACAATGAAGCA
Found at i:2983306 original size:18 final size:19
Alignment explanation
Indices: 2983285--2983320 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
2983275 GGTCAATTTG
2983285 ATTA-TTTTTAATTTTTTA
1 ATTACTTTTTAATTTTTTA
*
2983303 ATTACTTTTTTATTTTTT
1 ATTACTTTTTAATTTTTT
2983321 TTTTCAATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.22, C:0.03, G:0.00, T:0.75
Consensus pattern (19 bp):
ATTACTTTTTAATTTTTTA
Found at i:2983355 original size:22 final size:20
Alignment explanation
Indices: 2983308--2983348 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 20
2983298 TTTTAATTAC
*
2983308 TTTTTTATTTTTTTTTTCAA
1 TTTTTCATTTTTTTTTTCAA
2983328 TTTTTCATTTATTTGTTTTCA
1 TTTTTCATTT-TTT-TTTTCA
2983349 TCTTTTCTGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 9 0.50
21 3 0.17
22 6 0.33
ACGTcount: A:0.15, C:0.07, G:0.02, T:0.76
Consensus pattern (20 bp):
TTTTTCATTTTTTTTTTCAA
Found at i:2986393 original size:26 final size:26
Alignment explanation
Indices: 2986348--2986401 Score: 67
Period size: 25 Copynumber: 2.1 Consensus size: 26
2986338 TAAAAGGTTA
*
2986348 TATTTTTTTTTAATTTTTAA-AAATT
1 TATTTTTTTTTAATTATTAAGAAATT
2986373 TATTTTATTTTT-ATTAATTAAGAAATT
1 TATTTT-TTTTTAATT-ATTAAGAAATT
2986400 TA
1 TA
2986402 CATATTAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
25 9 0.36
26 9 0.36
27 7 0.28
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (26 bp):
TATTTTTTTTTAATTATTAAGAAATT
Found at i:2986477 original size:30 final size:30
Alignment explanation
Indices: 2986441--2986520 Score: 88
Period size: 31 Copynumber: 2.6 Consensus size: 30
2986431 AATAAGATAA
* *
2986441 AAATAAATTTTTAATTTTATTATTTTATCT
1 AAATAAATTTTTAATTTTATAATTGTATCT
* * *
2986471 AAATAAAATTTTATATTTTGTAATTGTATTT
1 AAATAAATTTTTA-ATTTTATAATTGTATCT
**
2986502 AAATAAATTAATAATTTTA
1 AAATAAATTTTTAATTTTA
2986521 ATTAAAACTA
Statistics
Matches: 40, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
30 17 0.43
31 23 0.57
ACGTcount: A:0.42, C:0.01, G:0.03, T:0.54
Consensus pattern (30 bp):
AAATAAATTTTTAATTTTATAATTGTATCT
Found at i:2986639 original size:18 final size:18
Alignment explanation
Indices: 2986584--2986646 Score: 58
Period size: 18 Copynumber: 3.5 Consensus size: 18
2986574 TCTTTTTATT
**
2986584 TATATTTAAAT-AAATTT
1 TATATTTAAATAAAATAA
*
2986601 TTTATTTAAATATAAA-AA
1 TATATTTAAATA-AAATAA
*
2986619 TATATTTAAATAAAATGA
1 TATATTTAAATAAAATAA
2986637 TATAATTTAA
1 TAT-ATTTAA
2986647 TATTTTAAAC
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
17 13 0.35
18 15 0.41
19 9 0.24
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (18 bp):
TATATTTAAATAAAATAA
Found at i:2995850 original size:4 final size:4
Alignment explanation
Indices: 2995841--2995868 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
2995831 CACGGAAGAG
2995841 TCTT TCTT TCTT TCTT TCTT TCTT TCTT
1 TCTT TCTT TCTT TCTT TCTT TCTT TCTT
2995869 GCCATCCCTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (4 bp):
TCTT
Found at i:2999222 original size:11 final size:12
Alignment explanation
Indices: 2999206--2999234 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
2999196 AATTAATAGT
2999206 TAATAAATT-AA
1 TAATAAATTAAA
2999217 TAATAAATTAAA
1 TAATAAATTAAA
2999229 TAATAA
1 TAATAA
2999235 GTTCTATATG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 9 0.53
12 8 0.47
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (12 bp):
TAATAAATTAAA
Found at i:3001149 original size:14 final size:14
Alignment explanation
Indices: 3001130--3001158 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
3001120 TTTTTGACAT
3001130 TGGTTTCAAATCAG
1 TGGTTTCAAATCAG
3001144 TGGTTTCAAATCAG
1 TGGTTTCAAATCAG
3001158 T
1 T
3001159 AATCAGCATC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.28, C:0.14, G:0.21, T:0.38
Consensus pattern (14 bp):
TGGTTTCAAATCAG
Found at i:3002864 original size:19 final size:19
Alignment explanation
Indices: 3002842--3002878 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
3002832 GGGCTTGCAA
3002842 ATTCATATTTGTTTTCCAT
1 ATTCATATTTGTTTTCCAT
*
3002861 ATTCATATTTTTTTTCCA
1 ATTCATATTTGTTTTCCA
3002879 GCATGTCAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.22, C:0.16, G:0.03, T:0.59
Consensus pattern (19 bp):
ATTCATATTTGTTTTCCAT
Found at i:3003055 original size:2 final size:2
Alignment explanation
Indices: 3003048--3003076 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3003038 ATTGGCTTAT
3003048 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3003077 GTGTGTGAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3005875 original size:12 final size:13
Alignment explanation
Indices: 3005847--3005876 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
3005837 ACCTCTACAG
3005847 ATCAGGAAATAAA
1 ATCAGGAAATAAA
3005860 ATCAGGAAAT-AA
1 ATCAGGAAATAAA
3005872 ATCAG
1 ATCAG
3005877 TAATTGACTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 7 0.41
13 10 0.59
ACGTcount: A:0.57, C:0.10, G:0.17, T:0.17
Consensus pattern (13 bp):
ATCAGGAAATAAA
Found at i:3007451 original size:102 final size:102
Alignment explanation
Indices: 3007306--3007499 Score: 289
Period size: 102 Copynumber: 1.9 Consensus size: 102
3007296 TGTTAGTATA
* * *
3007306 TTTTGGTTAAAATAGTATATTGGCATCTTATCTTATTCCATTTCCTGTAAAATAATGACTAGTGT
1 TTTTGGTTAAAATAGTATATCGGCATCTTAGCTTATTCCATTTCCTATAAAATAATGACTAGTGT
* *
3007371 CTCAAATATGTTTAGTTGCAGGATATTTTTTCAGATT
66 CTCAAATATGTCTAGTTGCAGCATATTTTTTCAGATT
* * * * *
3007408 TTTTGGTTAAAATAGTCTATCGGTATCTTAGCTTGTTCTATTTCCTATAAGATAATGACTAGTGT
1 TTTTGGTTAAAATAGTATATCGGCATCTTAGCTTATTCCATTTCCTATAAAATAATGACTAGTGT
*
3007473 CTCAAATATGTCTGGTTGCAGCATATT
66 CTCAAATATGTCTAGTTGCAGCATATT
3007500 CATCTTCCTC
Statistics
Matches: 81, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
102 81 1.00
ACGTcount: A:0.27, C:0.13, G:0.16, T:0.44
Consensus pattern (102 bp):
TTTTGGTTAAAATAGTATATCGGCATCTTAGCTTATTCCATTTCCTATAAAATAATGACTAGTGT
CTCAAATATGTCTAGTTGCAGCATATTTTTTCAGATT
Found at i:3009185 original size:22 final size:23
Alignment explanation
Indices: 3009160--3009202 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
3009150 GGTGAGAGGG
3009160 TAATGAA-AATCTT-TAAAATACT
1 TAATGAATAAT-TTATAAAATACT
*
3009182 TAATTAATAATTTATAAAATA
1 TAATGAATAATTTATAAAATA
3009203 TATATTTATG
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 8 0.44
23 10 0.56
ACGTcount: A:0.53, C:0.05, G:0.02, T:0.40
Consensus pattern (23 bp):
TAATGAATAATTTATAAAATACT
Found at i:3009751 original size:24 final size:22
Alignment explanation
Indices: 3009711--3009754 Score: 70
Period size: 24 Copynumber: 1.9 Consensus size: 22
3009701 AAAAATAATT
3009711 ATAAAAAAATATTAAAATTAAA
1 ATAAAAAAATATTAAAATTAAA
3009733 ATAAAAATATATATTAAAATTA
1 ATAAAAA-A-ATATTAAAATTA
3009755 TGTAATATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 7 0.35
23 1 0.05
24 12 0.60
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (22 bp):
ATAAAAAAATATTAAAATTAAA
Found at i:3009775 original size:15 final size:16
Alignment explanation
Indices: 3009747--3009782 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
3009737 AAATATATAT
3009747 TAAA-ATTATGTAATA
1 TAAATATTATGTAATA
3009762 TAAATATTAT-TAATA
1 TAAATATTATGTAATA
3009777 -AAATAT
1 TAAATAT
3009783 ATAAAAAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 6 0.30
15 9 0.45
16 5 0.25
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.42
Consensus pattern (16 bp):
TAAATATTATGTAATA
Found at i:3009813 original size:26 final size:24
Alignment explanation
Indices: 3009757--3009805 Score: 75
Period size: 23 Copynumber: 2.1 Consensus size: 24
3009747 TAAAATTATG
*
3009757 TAATAT-AAATATTATTAATAAAA
1 TAATATAAAAAATTATTAATAAAA
3009780 T-ATATAAAAAATTATTAATAAAA
1 TAATATAAAAAATTATTAATAAAA
3009803 TAA
1 TAA
3009806 AATATAAATC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
22 4 0.17
23 18 0.78
24 1 0.04
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (24 bp):
TAATATAAAAAATTATTAATAAAA
Found at i:3009814 original size:23 final size:25
Alignment explanation
Indices: 3009747--3009814 Score: 72
Period size: 23 Copynumber: 2.8 Consensus size: 25
3009737 AAATATATAT
*
3009747 TAAAATTATGTAATATAAATATTATTAA
1 TAAAA-TATATAATAT-AA-ATTATTAA
3009775 TAAAATATATAA-A-AAATTATTAA
1 TAAAATATATAATATAAATTATTAA
3009798 TAAAATA-A-AATATAAAT
1 TAAAATATATAATATAAAT
3009815 CATAGTTAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
21 2 0.05
22 2 0.05
23 19 0.51
24 2 0.05
26 1 0.03
27 6 0.16
28 5 0.14
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.37
Consensus pattern (25 bp):
TAAAATATATAATATAAATTATTAA
Found at i:3010100 original size:7 final size:7
Alignment explanation
Indices: 3010056--3010122 Score: 55
Period size: 7 Copynumber: 9.3 Consensus size: 7
3010046 ATAAAATAAA
3010056 ATATTTT
1 ATATTTT
3010063 -TATTTT
1 ATATTTT
3010069 ATCATTTT
1 AT-ATTTT
*
3010077 ATATAATTA
1 ATAT--TTT
*
3010086 AAATTTT
1 ATATTTT
3010093 ATATTTT
1 ATATTTT
* *
3010100 ATAATTA
1 ATATTTT
*
3010107 AGATTTT
1 ATATTTT
3010114 ATATTTT
1 ATATTTT
3010121 AT
1 AT
3010123 GCTTGTATTT
Statistics
Matches: 46, Mismatches: 10, Indels: 8
0.72 0.16 0.12
Matches are distributed among these distances:
6 6 0.13
7 28 0.61
8 7 0.15
9 5 0.11
ACGTcount: A:0.36, C:0.01, G:0.01, T:0.61
Consensus pattern (7 bp):
ATATTTT
Found at i:3010104 original size:21 final size:21
Alignment explanation
Indices: 3010064--3010122 Score: 82
Period size: 21 Copynumber: 2.7 Consensus size: 21
3010054 AAATATTTTT
3010064 ATTTTATCATTTTATATAATTAAA
1 ATTTTAT-A-TTT-TATAATTAAA
*
3010088 ATTTTATATTTTATAATTAAG
1 ATTTTATATTTTATAATTAAA
3010109 ATTTTATATTTTAT
1 ATTTTATATTTTAT
3010123 GCTTGTATTT
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
21 23 0.68
22 3 0.09
23 1 0.03
24 7 0.21
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (21 bp):
ATTTTATATTTTATAATTAAA
Found at i:3010178 original size:23 final size:22
Alignment explanation
Indices: 3010129--3010181 Score: 72
Period size: 22 Copynumber: 2.4 Consensus size: 22
3010119 TTATGCTTGT
*
3010129 ATTTAAATAAATCAATAATTTA
1 ATTTAAATAAATAAATAATTTA
3010151 ATTTAAACTAAATAAAT-ATTTA
1 ATTTAAA-TAAATAAATAATTTA
3010173 ATTTTAAAT
1 A-TTTAAAT
3010182 TTATATTAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
22 14 0.50
23 14 0.50
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (22 bp):
ATTTAAATAAATAAATAATTTA
Found at i:3016830 original size:21 final size:21
Alignment explanation
Indices: 3016804--3016846 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
3016794 GCAAAGTCCC
3016804 CTTCCTCATCATGATCAACCT
1 CTTCCTCATCATGATCAACCT
*
3016825 CTTCCTCGTCATGATCAACCT
1 CTTCCTCATCATGATCAACCT
3016846 C
1 C
3016847 AAGCGTGGAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.21, C:0.40, G:0.07, T:0.33
Consensus pattern (21 bp):
CTTCCTCATCATGATCAACCT
Found at i:3026824 original size:26 final size:26
Alignment explanation
Indices: 3026788--3026840 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
3026778 GTATTTTCTG
3026788 AACTTGTTATAATAAAGTAATAATTA
1 AACTTGTTATAATAAAGTAATAATTA
3026814 AACTTGTTATAATAAAGTAATAATTA
1 AACTTGTTATAATAAAGTAATAATTA
3026840 A
1 A
3026841 TGAACCCTAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.51, C:0.04, G:0.08, T:0.38
Consensus pattern (26 bp):
AACTTGTTATAATAAAGTAATAATTA
Found at i:3030326 original size:33 final size:33
Alignment explanation
Indices: 3030279--3030342 Score: 110
Period size: 33 Copynumber: 1.9 Consensus size: 33
3030269 TAGTTGAAAC
*
3030279 CAGTTTTCCCCTACTAATGAAAGTGGTTCCTGT
1 CAGTTTTCCACTACTAATGAAAGTGGTTCCTGT
*
3030312 CAGTTTTCCACTACTACTGAAAGTGGTTCCT
1 CAGTTTTCCACTACTAATGAAAGTGGTTCCT
3030343 ATTCTTCTGC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.22, C:0.25, G:0.17, T:0.36
Consensus pattern (33 bp):
CAGTTTTCCACTACTAATGAAAGTGGTTCCTGT
Found at i:3032335 original size:31 final size:31
Alignment explanation
Indices: 3032297--3032358 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
3032287 CCTGCAATGG
3032297 CCTTTGTGATTCGGGAGCAACTTTATGAAGT
1 CCTTTGTGATTCGGGAGCAACTTTATGAAGT
3032328 CCTTTGTGATTCGGGAGCAACTTTATGAAGT
1 CCTTTGTGATTCGGGAGCAACTTTATGAAGT
3032359 AGCTATAATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.23, C:0.16, G:0.26, T:0.35
Consensus pattern (31 bp):
CCTTTGTGATTCGGGAGCAACTTTATGAAGT
Found at i:3037247 original size:21 final size:21
Alignment explanation
Indices: 3037221--3037265 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
3037211 AGTTAGGCTT
3037221 TGAAGAGTTGGGTTCAAGAGG
1 TGAAGAGTTGGGTTCAAGAGG
*
3037242 TGAAGAGTTGGGTTTAAGAGG
1 TGAAGAGTTGGGTTCAAGAGG
3037263 TGA
1 TGA
3037266 GGGGCTTTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.29, C:0.02, G:0.42, T:0.27
Consensus pattern (21 bp):
TGAAGAGTTGGGTTCAAGAGG
Found at i:3037319 original size:31 final size:31
Alignment explanation
Indices: 3037284--3037342 Score: 73
Period size: 31 Copynumber: 1.9 Consensus size: 31
3037274 TAGAGTTGGG
* *
3037284 TTTTTAAAAATAATATTAATAAATAATTTTA
1 TTTTTAAAAATAACAATAATAAATAATTTTA
* * *
3037315 TTTTTTAGAATAACAATAATTAATAATT
1 TTTTTAAAAATAACAATAATAAATAATT
3037343 AGGCAGTAAG
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 23 1.00
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (31 bp):
TTTTTAAAAATAACAATAATAAATAATTTTA
Found at i:3040311 original size:43 final size:43
Alignment explanation
Indices: 3040250--3040380 Score: 226
Period size: 43 Copynumber: 3.0 Consensus size: 43
3040240 GACAGATGGT
*
3040250 TTGAAATTGAAGAAAAAAAGAGAAACGTATGTGAAAAGTTTTC
1 TTGAAATTGAAGAAAAAAAGAGAAACGTATGTGAAAAATTTTC
* *
3040293 TTGAAATTGAAGAAAAAAAGAGAAACGTGTGTGAAAATTTTTC
1 TTGAAATTGAAGAAAAAAAGAGAAACGTATGTGAAAAATTTTC
*
3040336 TTGAAATTGAAGAAAAAAGGAGAAACGTATGTGAAAAATTTTC
1 TTGAAATTGAAGAAAAAAAGAGAAACGTATGTGAAAAATTTTC
3040379 TT
1 TT
3040381 TCTTTTTAGT
Statistics
Matches: 83, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
43 83 1.00
ACGTcount: A:0.47, C:0.05, G:0.21, T:0.27
Consensus pattern (43 bp):
TTGAAATTGAAGAAAAAAAGAGAAACGTATGTGAAAAATTTTC
Found at i:3040943 original size:18 final size:19
Alignment explanation
Indices: 3040909--3040944 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
3040899 GGGCTTGCAA
3040909 ATTCATATTTGTTTTCCAT
1 ATTCATATTTGTTTTCCAT
3040928 ATTCATATTT-TTTTCCA
1 ATTCATATTTGTTTTCCA
3040945 GCATGTGAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.22, C:0.17, G:0.03, T:0.58
Consensus pattern (19 bp):
ATTCATATTTGTTTTCCAT
Found at i:3041127 original size:2 final size:2
Alignment explanation
Indices: 3041122--3041163 Score: 59
Period size: 2 Copynumber: 21.5 Consensus size: 2
3041112 TATACATACT
* *
3041122 TA TA TA TA T- TA TA TA TA TA TA TA TA TA TA TG TA TA TG TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3041163 T
1 T
3041164 GTGTGCATCT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3042884 original size:39 final size:39
Alignment explanation
Indices: 3042825--3042902 Score: 147
Period size: 39 Copynumber: 2.0 Consensus size: 39
3042815 GAACTTCTAT
*
3042825 TATGGCTTTGTTCTCAATTTGCTGGTTCATGATTTAGGG
1 TATGCCTTTGTTCTCAATTTGCTGGTTCATGATTTAGGG
3042864 TATGCCTTTGTTCTCAATTTGCTGGTTCATGATTTAGGG
1 TATGCCTTTGTTCTCAATTTGCTGGTTCATGATTTAGGG
3042903 GTAGACGTGC
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.15, C:0.14, G:0.24, T:0.46
Consensus pattern (39 bp):
TATGCCTTTGTTCTCAATTTGCTGGTTCATGATTTAGGG
Found at i:3044163 original size:2 final size:2
Alignment explanation
Indices: 3044156--3044196 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
3044146 CCTTCTCCCT
3044156 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
3044197 TAACGTTTAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:3044880 original size:15 final size:15
Alignment explanation
Indices: 3044842--3044881 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
3044832 TTAATATTTA
*
3044842 AAAATTTA-GATATT
1 AAAATTTATAATATT
3044856 AAATATTTATAATATT
1 AAA-ATTTATAATATT
3044872 AAAATTTATA
1 AAAATTTATA
3044882 CTTATATAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
14 3 0.13
15 12 0.52
16 8 0.35
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (15 bp):
AAAATTTATAATATT
Found at i:3044933 original size:16 final size:16
Alignment explanation
Indices: 3044907--3044969 Score: 61
Period size: 15 Copynumber: 4.4 Consensus size: 16
3044897 GTAACAATAT
*
3044907 TAAAT-TTTAATATTA
1 TAAATATTTAATATCA
3044922 TAAATATTTAATATCA
1 TAAATATTTAATATCA
3044938 -AAATATTT--TAT--
1 TAAATATTTAATATCA
3044949 T-AATATTTAATATC-
1 TAAATATTTAATATCA
3044963 TAAATAT
1 TAAATAT
3044970 AAGTATAAAT
Statistics
Matches: 41, Mismatches: 1, Indels: 12
0.76 0.02 0.22
Matches are distributed among these distances:
11 7 0.17
13 6 0.15
14 1 0.02
15 18 0.44
16 9 0.22
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.49
Consensus pattern (16 bp):
TAAATATTTAATATCA
Found at i:3044955 original size:26 final size:26
Alignment explanation
Indices: 3044919--3044969 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
3044909 AATTTTAATA
3044919 TTATAAATATTTAATATCAAAATATT
1 TTATAAATATTTAATATCAAAATATT
* *
3044945 TTATTAATATTTAATATCTAAATAT
1 TTATAAATATTTAATATCAAAATAT
3044970 AAGTATAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (26 bp):
TTATAAATATTTAATATCAAAATATT
Found at i:3045088 original size:39 final size:39
Alignment explanation
Indices: 3044990--3045089 Score: 107
Period size: 40 Copynumber: 2.6 Consensus size: 39
3044980 AATAAGTTAT
*
3044990 TTATATTTT-TT-AAATTTTTAATAAAATTTTTACATAG
1 TTATATTTTATTAAAATTTTTAATAAAATTTTTACATAC
* * * *
3045027 TTTTATATAAGTATAAATTTTTAATAAAA-TTTTACAATAC
1 TTATATTTTATTA-AAATTTTTAATAAAATTTTTAC-ATAC
*
3045067 TTATATTTTATTAAAAATTTTAA
1 TTATATTTTATTAAAATTTTTAA
3045090 AAATATAAAT
Statistics
Matches: 49, Mismatches: 10, Indels: 6
0.75 0.15 0.09
Matches are distributed among these distances:
37 6 0.12
38 1 0.02
39 15 0.31
40 27 0.55
ACGTcount: A:0.42, C:0.03, G:0.02, T:0.53
Consensus pattern (39 bp):
TTATATTTTATTAAAATTTTTAATAAAATTTTTACATAC
Found at i:3049256 original size:2 final size:2
Alignment explanation
Indices: 3049249--3049295 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
3049239 GCTCTCCCAA
*
3049249 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TT
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
3049291 TG TG T
1 TG TG T
3049296 TTTTAATTTG
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.00, C:0.00, G:0.47, T:0.53
Consensus pattern (2 bp):
TG
Found at i:3051195 original size:2 final size:2
Alignment explanation
Indices: 3051190--3051214 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3051180 CACACACGTC
3051190 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
3051215 TACTATTCTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3054858 original size:12 final size:13
Alignment explanation
Indices: 3054831--3054863 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
3054821 CGGATCTAAC
3054831 AAAAAAAAGATTAA
1 AAAAAAAAGA-TAA
3054845 AAAAAAAAGA-AA
1 AAAAAAAAGATAA
3054857 AAAAAAA
1 AAAAAAA
3054864 CTGTCGAAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 9 0.47
14 10 0.53
ACGTcount: A:0.88, C:0.00, G:0.06, T:0.06
Consensus pattern (13 bp):
AAAAAAAAGATAA
Found at i:3055716 original size:16 final size:16
Alignment explanation
Indices: 3055692--3055722 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3055682 GTAAAAAAAA
*
3055692 ATAATTAAAATATAAT
1 ATAAATAAAATATAAT
3055708 ATAAATAAAATATAA
1 ATAAATAAAATATAA
3055723 AAATATAATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (16 bp):
ATAAATAAAATATAAT
Found at i:3055767 original size:48 final size:48
Alignment explanation
Indices: 3055698--3055816 Score: 147
Period size: 46 Copynumber: 2.5 Consensus size: 48
3055688 AAAAATAATT
3055698 AAAATATAATATAAATAAAATATAAAAATATAATAAATTAAAT-TTTATAA-
1 AAAATATAATAT-AAT-AAA-ATAAAAATATAATAAATTAAATATTT-TAAG
*
3055748 AAAATATAATAT-TTAAAATAAAAATATAATAAATTAAATATTTTAAG
1 AAAATATAATATAATAAAATAAAAATATAATAAATTAAATATTTTAAG
* *
3055795 AAAGTATAATA-AATAATATAAA
1 AAAATATAATATAATAAAATAAA
3055817 TCAGTATATG
Statistics
Matches: 62, Mismatches: 4, Indels: 9
0.83 0.05 0.12
Matches are distributed among these distances:
46 25 0.40
47 24 0.39
48 1 0.02
50 12 0.19
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.34
Consensus pattern (48 bp):
AAAATATAATATAATAAAATAAAAATATAATAAATTAAATATTTTAAG
Found at i:3056473 original size:2 final size:2
Alignment explanation
Indices: 3056466--3056508 Score: 52
Period size: 2 Copynumber: 22.0 Consensus size: 2
3056456 ATACTGAAAT
* * *
3056466 TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA AA T- TA TA AA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3056507 TA
1 TA
3056509 ATTTTTTAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:3057874 original size:15 final size:16
Alignment explanation
Indices: 3057849--3057879 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
3057839 TAAAAGTGAA
3057849 AAAATTTAAATTATTT
1 AAAATTTAAATTATTT
3057865 AAAA-TTAAATTATTT
1 AAAATTTAAATTATTT
3057880 CTGTGTTATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.73
16 4 0.27
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
AAAATTTAAATTATTT
Found at i:3058114 original size:14 final size:15
Alignment explanation
Indices: 3058080--3058117 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
3058070 GAAAGTGAGA
3058080 AAAAATTTAAAATAT
1 AAAAATTTAAAATAT
3058095 AAAAATTTAAAA-AT
1 AAAAATTTAAAATAT
*
3058109 ATAAATTTA
1 AAAAATTTA
3058118 TGATATATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 10 0.45
15 12 0.55
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (15 bp):
AAAAATTTAAAATAT
Found at i:3059497 original size:15 final size:16
Alignment explanation
Indices: 3059477--3059507 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
3059467 GGTAATAATA
3059477 AAATAAATTT-AATTT
1 AAATAAATTTGAATTT
3059492 AAATAAATTTGAATTT
1 AAATAAATTTGAATTT
3059508 TATTATTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.67
16 5 0.33
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (16 bp):
AAATAAATTTGAATTT
Found at i:3060295 original size:21 final size:22
Alignment explanation
Indices: 3060256--3060301 Score: 60
Period size: 21 Copynumber: 2.1 Consensus size: 22
3060246 AATTATAATT
*
3060256 TAATTTAATTTAATAAAATA-A
1 TAATTTAATATAATAAAATATA
3060277 TAATTTAAATATAAT-AAATATA
1 TAATTT-AATATAATAAAATATA
3060299 TAA
1 TAA
3060302 ATAAATTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 11 0.50
22 11 0.50
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (22 bp):
TAATTTAATATAATAAAATATA
Found at i:3060296 original size:26 final size:25
Alignment explanation
Indices: 3060239--3060348 Score: 71
Period size: 26 Copynumber: 4.2 Consensus size: 25
3060229 TTTGTATTAT
* * *
3060239 ATAAAAAAATTATAATTT-AATTTA
1 ATAAATAAATAATAATTTAAATATA
*
3060263 ATTTAATAAAATAATAATTTAAATATA
1 A-TAAAT-AAATAATAATTTAAATATA
* * *
3060290 ATAAATATATAAATAAATTAAATTTTA
1 ATAAATAAAT-AATAATTTAAA-TATA
*
3060317 CATAAATATATAATAA-TTATAATATA
1 -ATAAATAAATAATAATTTA-AATATA
*
3060343 AAAAAT
1 ATAAAT
3060349 GCAACAACAG
Statistics
Matches: 69, Mismatches: 10, Indels: 13
0.75 0.11 0.14
Matches are distributed among these distances:
24 1 0.01
25 11 0.16
26 31 0.45
27 16 0.23
28 10 0.14
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (25 bp):
ATAAATAAATAATAATTTAAATATA
Found at i:3060712 original size:40 final size:37
Alignment explanation
Indices: 3060612--3060715 Score: 93
Period size: 40 Copynumber: 2.6 Consensus size: 37
3060602 AGAGGTGTAA
* *
3060612 TTTATTAATAAAATATTAA-AATATTATATTTTTAATT
1 TTTATAAATAAAATA-TAATAAAATTATATTTTTAATT
* * *
3060649 TTTATAATTTAAAAATTAAAATAAAATTATTTTTATTAATT
1 TTTATAA-AT-AAAA-TATAATAAAATTATATTT-TTAATT
3060690 TTAATATAAATAAAATATAATAAAAT
1 TT--TATAAATAAAATATAATAAAAT
3060716 AATAAATACA
Statistics
Matches: 53, Mismatches: 7, Indels: 11
0.75 0.10 0.15
Matches are distributed among these distances:
37 6 0.11
38 1 0.02
39 6 0.11
40 22 0.42
41 12 0.23
42 1 0.02
43 5 0.09
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (37 bp):
TTTATAAATAAAATATAATAAAATTATATTTTTAATT
Found at i:3063316 original size:29 final size:31
Alignment explanation
Indices: 3063254--3063311 Score: 84
Period size: 29 Copynumber: 1.9 Consensus size: 31
3063244 AAAAATATTT
* *
3063254 TATAATTTTATATTT--AATTTTTTATAATA
1 TATAAATTTATATTTAAAATTTTTAATAATA
3063283 TATAAATTTATATTTAAAATTTTTAATAA
1 TATAAATTTATATTTAAAATTTTTAATAA
3063312 AATAATATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 14 0.56
31 11 0.44
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (31 bp):
TATAAATTTATATTTAAAATTTTTAATAATA
Found at i:3063324 original size:31 final size:32
Alignment explanation
Indices: 3063257--3063331 Score: 88
Period size: 31 Copynumber: 2.5 Consensus size: 32
3063247 AATATTTTAT
*
3063257 AATTTTATATTT--AATTTTTTATAATATATA
1 AATTTTATATTTAAAATTTTTAATAATATATA
3063287 AA-TTTATATTTAAAATTTTTAATAA-A-ATA
1 AATTTTATATTTAAAATTTTTAATAATATATA
*
3063316 ATATTTTATATATAAA
1 A-ATTTTATATTTAAA
3063332 TTTAATTAAG
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
29 13 0.33
30 4 0.10
31 22 0.56
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (32 bp):
AATTTTATATTTAAAATTTTTAATAATATATA
Found at i:3063944 original size:20 final size:21
Alignment explanation
Indices: 3063915--3063970 Score: 60
Period size: 20 Copynumber: 2.7 Consensus size: 21
3063905 ATATTAAATA
*
3063915 AAAATATATTTTAAATTAATT
1 AAAATTTATTTTAAATTAATT
* * *
3063936 -AAATTTATTTTGATTTTATT
1 AAAATTTATTTTAAATTAATT
*
3063956 AAAATTAATTTTAAA
1 AAAATTTATTTTAAA
3063971 ATATAAATAC
Statistics
Matches: 27, Mismatches: 7, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
20 16 0.59
21 11 0.41
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (21 bp):
AAAATTTATTTTAAATTAATT
Found at i:3064733 original size:24 final size:25
Alignment explanation
Indices: 3064671--3064735 Score: 77
Period size: 23 Copynumber: 2.8 Consensus size: 25
3064661 TATATTTAAA
*
3064671 TTAATTTAA--ATAATATAATTATT
1 TTAATTTAATTATAAAATAATTATT
3064694 TT-ATATTAATTA-AAAATAATT-TT
1 TTAAT-TTAATTATAAAATAATTATT
3064717 TTAATTTAATTATAAAATA
1 TTAATTTAATTATAAAATA
3064736 TATAAATATT
Statistics
Matches: 36, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
22 2 0.06
23 17 0.47
24 16 0.44
25 1 0.03
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (25 bp):
TTAATTTAATTATAAAATAATTATT
Found at i:3064764 original size:28 final size:29
Alignment explanation
Indices: 3064733--3064791 Score: 66
Period size: 28 Copynumber: 2.1 Consensus size: 29
3064723 TAATTATAAA
*
3064733 ATATATAAATATTAAT-ATAAAATATTTT
1 ATATATAAATATTAATAATAAAATAATTT
* * * *
3064761 ATATTTTAATTTTAATAATAAATTAATTT
1 ATATATAAATATTAATAATAAAATAATTT
3064790 AT
1 AT
3064792 GAACTCAATC
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
28 13 0.52
29 12 0.48
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (29 bp):
ATATATAAATATTAATAATAAAATAATTT
Found at i:3065701 original size:26 final size:31
Alignment explanation
Indices: 3065669--3065736 Score: 85
Period size: 26 Copynumber: 2.4 Consensus size: 31
3065659 ACAATATAAT
*
3065669 TATATAATATAAT-TA-AAACAT-A-AAAAA
1 TATATAATATAATATATAAAAATAATAAAAA
3065696 TA-ATAATA-AATATATAAAAATAATAAAAA
1 TATATAATATAATATATAAAAATAATAAAAA
3065725 TATATAATATAA
1 TATATAATATAA
3065737 ATCATTAATA
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
25 3 0.09
26 8 0.24
27 7 0.21
28 1 0.03
29 7 0.21
30 6 0.18
31 2 0.06
ACGTcount: A:0.68, C:0.01, G:0.00, T:0.31
Consensus pattern (31 bp):
TATATAATATAATATATAAAAATAATAAAAA
Found at i:3065705 original size:20 final size:21
Alignment explanation
Indices: 3065677--3065721 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
3065667 ATTATATAAT
3065677 ATAATTAAAACATA-AAAAATA
1 ATAATT-AAACATATAAAAATA
*
3065698 ATAA-TAAATATATAAAAATA
1 ATAATTAAACATATAAAAATA
3065718 ATAA
1 ATAA
3065722 AAATATATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 6 0.27
20 12 0.55
21 4 0.18
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (21 bp):
ATAATTAAACATATAAAAATA
Found at i:3065720 original size:23 final size:23
Alignment explanation
Indices: 3065690--3065737 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
3065680 ATTAAAACAT
*
3065690 AAAAAATAATAATAAAT-ATATA
1 AAAAAATAAAAATAAATAATATA
*
3065712 AAAATAATAAAAATATATAATATA
1 AAAA-AATAAAAATAAATAATATA
3065736 AA
1 AA
3065738 TCATTAATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 4 0.18
23 11 0.50
24 7 0.32
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (23 bp):
AAAAAATAAAAATAAATAATATA
Found at i:3065723 original size:9 final size:10
Alignment explanation
Indices: 3065691--3065731 Score: 59
Period size: 10 Copynumber: 4.2 Consensus size: 10
3065681 TTAAAACATA
3065691 AAAAATA-AT
1 AAAAATATAT
3065700 AATAAATATAT
1 AA-AAATATAT
3065711 AAAAATA-AT
1 AAAAATATAT
3065720 AAAAATATAT
1 AAAAATATAT
3065730 AA
1 AA
3065732 TATAAATCAT
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
9 11 0.38
10 14 0.48
11 4 0.14
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (10 bp):
AAAAATATAT
Found at i:3065774 original size:7 final size:8
Alignment explanation
Indices: 3065697--3065817 Score: 51
Period size: 8 Copynumber: 15.4 Consensus size: 8
3065687 CATAAAAAAT
3065697 AATA-ATA
1 AATATATA
3065704 AATATATA
1 AATATATA
*
3065712 AAAATAATA
1 AATAT-ATA
*
3065721 AAAATATA
1 AATATATA
*
3065729 TA-ATATA
1 AATATATA
3065736 AATCAT-TA
1 AAT-ATATA
*
3065744 ATATATTTA
1 A-ATATATA
3065753 AATTTATATA
1 AA--TATATA
3065763 AATATA-A
1 AATATATA
* *
3065770 AATATTTT
1 AATATATA
3065778 AA-ATATA
1 AATATATA
*
3065785 ATTATCATA
1 AATAT-ATA
*
3065794 TA-ATA-A
1 AATATATA
3065800 AATA-ATA
1 AATATATA
*
3065807 AAAATATA
1 AATATATA
3065815 AAT
1 AAT
3065818 TAAAAAAATC
Statistics
Matches: 86, Mismatches: 14, Indels: 27
0.68 0.11 0.21
Matches are distributed among these distances:
6 3 0.03
7 26 0.30
8 32 0.37
9 18 0.21
10 7 0.08
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (8 bp):
AATATATA
Found at i:3065774 original size:25 final size:28
Alignment explanation
Indices: 3065731--3065781 Score: 72
Period size: 26 Copynumber: 1.9 Consensus size: 28
3065721 AAAATATATA
*
3065731 ATATAAATCATTAATATA-TTTAAATTT
1 ATATAAATCATTAAAATATTTTAAATTT
3065758 ATATAAAT-A-TAAAATATTTTAAAT
1 ATATAAATCATTAAAATATTTTAAAT
3065782 ATAATTATCA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 6 0.27
26 8 0.36
27 8 0.36
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (28 bp):
ATATAAATCATTAAAATATTTTAAATTT
Found at i:3065839 original size:15 final size:16
Alignment explanation
Indices: 3065796--3065843 Score: 55
Period size: 15 Copynumber: 3.1 Consensus size: 16
3065786 TTATCATATA
*
3065796 ATAAAATAATAAAAAT
1 ATAAATTAATAAAAAT
3065812 ATAAATTAA-AAAAAT
1 ATAAATTAATAAAAAT
* *
3065827 CT-ACTTAATAAAAAT
1 ATAAATTAATAAAAAT
3065842 AT
1 AT
3065844 TTTGAAAAAG
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
14 5 0.19
15 14 0.52
16 8 0.30
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.29
Consensus pattern (16 bp):
ATAAATTAATAAAAAT
Found at i:3066708 original size:6 final size:6
Alignment explanation
Indices: 3066697--3066756 Score: 54
Period size: 6 Copynumber: 10.0 Consensus size: 6
3066687 TATATTAATT
* *
3066697 ATATAA ATATAA ATAT-A ATATAA ATTATTAA ATAT-A TTA-AA ATTTTAA
1 ATATAA ATATAA ATATAA ATATAA A-TA-TAA ATATAA ATATAA A-TATAA
3066745 ATATAA ATATAA
1 ATATAA ATATAA
3066757 TATTTATATT
Statistics
Matches: 44, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
5 9 0.20
6 24 0.55
7 7 0.16
8 4 0.09
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (6 bp):
ATATAA
Found at i:3066717 original size:17 final size:18
Alignment explanation
Indices: 3066697--3066756 Score: 70
Period size: 17 Copynumber: 3.3 Consensus size: 18
3066687 TATATTAATT
3066697 ATATAAA-TATAAATATA
1 ATATAAATTATAAATATA
3066714 ATATAAATTATTAAATATA
1 ATATAAATTA-TAAATATA
* *
3066733 TTA-AAATTTTAAATATAA
1 ATATAAATTATAAATAT-A
3066751 ATATAA
1 ATATAA
3066757 TATTTATATT
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
17 14 0.39
18 10 0.28
19 12 0.33
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
ATATAAATTATAAATATA
Found at i:3066734 original size:42 final size:40
Alignment explanation
Indices: 3066687--3066775 Score: 117
Period size: 42 Copynumber: 2.1 Consensus size: 40
3066677 TAAATTTTTT
3066687 TATATT-AATTATATAAATATAAATATAATATAAATTATTAAA
1 TATATTAAATT-T-TAAATATAAATATAATATAAA-TATTAAA
**
3066729 TATATTAAAATTTTAAATATAAATATAATATTTATATTAAA
1 TATATT-AAATTTTAAATATAAATATAATATAAATATTAAA
3066770 TATATT
1 TATATT
3066776 TTATTAATTA
Statistics
Matches: 43, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
41 13 0.30
42 25 0.58
43 1 0.02
44 4 0.09
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (40 bp):
TATATTAAATTTTAAATATAAATATAATATAAATATTAAA
Found at i:3066794 original size:14 final size:15
Alignment explanation
Indices: 3066756--3066794 Score: 55
Period size: 14 Copynumber: 2.7 Consensus size: 15
3066746 TATAAATATA
3066756 ATATTTATATTAAAT
1 ATATTTATATTAAAT
*
3066771 ATATTT-TATTAATT
1 ATATTTATATTAAAT
3066785 AT-TTTATATT
1 ATATTTATATT
3066795 TTATTATTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
13 3 0.14
14 13 0.59
15 6 0.27
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
ATATTTATATTAAAT
Found at i:3067363 original size:18 final size:16
Alignment explanation
Indices: 3067332--3067377 Score: 56
Period size: 18 Copynumber: 2.7 Consensus size: 16
3067322 AATATTAACC
3067332 AAATAATTATTTTTTA
1 AAATAATTATTTTTTA
3067348 AAATATATTAATTTTTTA
1 AAATA-ATT-ATTTTTTA
*
3067366 AATTAATATATT
1 AAATAAT-TATT
3067378 AGTTAAACGT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
16 5 0.19
17 8 0.31
18 13 0.50
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (16 bp):
AAATAATTATTTTTTA
Found at i:3067534 original size:27 final size:28
Alignment explanation
Indices: 3067488--3067546 Score: 86
Period size: 27 Copynumber: 2.1 Consensus size: 28
3067478 TGTTAAATTT
3067488 TATTAATTATTAATTAAAAAAATTAAA-A
1 TATTAATTATTAATTAAAAAAA-TAAATA
*
3067516 TATTAA-TATTAATTTAAAAAATAAATA
1 TATTAATTATTAATTAAAAAAATAAATA
3067543 TATT
1 TATT
3067547 TTATAAAATA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
26 4 0.14
27 19 0.66
28 6 0.21
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (28 bp):
TATTAATTATTAATTAAAAAAATAAATA
Found at i:3067542 original size:19 final size:18
Alignment explanation
Indices: 3067510--3067558 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
3067500 ATTAAAAAAA
* *
3067510 TTAAAATATTAATATTAAT
1 TTAAAAAATAAATA-TAAT
*
3067529 TTAAAAAATAAATATATT
1 TTAAAAAATAAATATAAT
*
3067547 TTATAAAATAAA
1 TTAAAAAATAAA
3067559 ATTTTAAATA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
18 14 0.54
19 12 0.46
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
TTAAAAAATAAATATAAT
Found at i:3069332 original size:3 final size:3
Alignment explanation
Indices: 3069324--3069351 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
3069314 TGAAGGATTT
3069324 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
3069352 GATCTGGTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:3075852 original size:18 final size:18
Alignment explanation
Indices: 3075811--3075853 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
3075801 ATTGAGTATT
*
3075811 AATTTAATTAATATAATAT
1 AATTT-ATTAATATAATAA
* *
3075830 TATTTATTAATTTAATAA
1 AATTTATTAATATAATAA
3075848 AATTTA
1 AATTTA
3075854 AAAAAATTAA
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
18 16 0.80
19 4 0.20
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
AATTTATTAATATAATAA
Found at i:3075883 original size:24 final size:24
Alignment explanation
Indices: 3075855--3075904 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 24
3075845 TAAAATTTAA
*
3075855 AAAAATTAATAAATTAA-TTAAAAAT
1 AAAAATT-AT-AAGTAACTTAAAAAT
3075880 AAAAATTATAAGTAACTTAAAAAT
1 AAAAATTATAAGTAACTTAAAAAT
3075904 A
1 A
3075905 TTAAAAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 5 0.22
24 11 0.48
25 7 0.30
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (24 bp):
AAAAATTATAAGTAACTTAAAAAT
Found at i:3076720 original size:15 final size:14
Alignment explanation
Indices: 3076688--3076747 Score: 59
Period size: 15 Copynumber: 4.1 Consensus size: 14
3076678 AAAAAATATC
* *
3076688 AAAAATTTAAATTTA
1 AAAAATATAAA-TAA
3076703 AAAAATATAAATAA
1 AAAAATATAAATAA
*
3076717 AAAAATA-AACTAA
1 AAAAATATAAATAA
3076730 AAAAATATTAAATCAA
1 AAAAATA-TAAAT-AA
3076746 AA
1 AA
3076748 GCATGTTTAA
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
13 12 0.32
14 9 0.24
15 13 0.34
16 4 0.11
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.25
Consensus pattern (14 bp):
AAAAATATAAATAA
Found at i:3076724 original size:12 final size:13
Alignment explanation
Indices: 3076701--3076736 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
3076691 AATTTAAATT
3076701 TAAAAAATATAAA-
1 TAAAAAA-ATAAAC
3076714 TAAAAAAATAAAC
1 TAAAAAAATAAAC
3076727 TAAAAAAATA
1 TAAAAAAATA
3076737 TTAAATCAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 5 0.23
13 17 0.77
ACGTcount: A:0.78, C:0.03, G:0.00, T:0.19
Consensus pattern (13 bp):
TAAAAAAATAAAC
Found at i:3076879 original size:16 final size:17
Alignment explanation
Indices: 3076860--3076898 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
3076850 AAATTTGAAC
3076860 ATAA-AAATTTAAATTT
1 ATAATAAATTTAAATTT
*
3076876 ATAATAATTTTAAATTT
1 ATAATAAATTTAAATTT
3076893 A-AATAA
1 ATAATAA
3076899 CTCAATTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 9 0.43
17 12 0.57
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
ATAATAAATTTAAATTT
Found at i:3078150 original size:36 final size:36
Alignment explanation
Indices: 3078098--3078168 Score: 133
Period size: 36 Copynumber: 2.0 Consensus size: 36
3078088 AAAAAGATAG
*
3078098 CATTTGTTAATTTTAGCATTGTCTTTTGTCTGTTTC
1 CATTTGTTAATATTAGCATTGTCTTTTGTCTGTTTC
3078134 CATTTGTTAATATTAGCATTGTCTTTTGTCTGTTT
1 CATTTGTTAATATTAGCATTGTCTTTTGTCTGTTT
3078169 TCCTTTTTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.15, C:0.13, G:0.14, T:0.58
Consensus pattern (36 bp):
CATTTGTTAATATTAGCATTGTCTTTTGTCTGTTTC
Found at i:3080352 original size:2 final size:2
Alignment explanation
Indices: 3080345--3080381 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
3080335 TAAACACGGT
3080345 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3080382 TAAGTTTTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3080913 original size:15 final size:16
Alignment explanation
Indices: 3080893--3080927 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
3080883 TTTTTTATCT
3080893 GTAAT-AATTTGTGAG
1 GTAATAAATTTGTGAG
3080908 GTAATAGAATTTGTGAG
1 GTAATA-AATTTGTGAG
3080925 GTA
1 GTA
3080928 TGGTTATCGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 5 0.28
17 13 0.72
ACGTcount: A:0.34, C:0.00, G:0.29, T:0.37
Consensus pattern (16 bp):
GTAATAAATTTGTGAG
Found at i:3087916 original size:32 final size:34
Alignment explanation
Indices: 3087866--3087934 Score: 90
Period size: 32 Copynumber: 2.1 Consensus size: 34
3087856 TATATATTTG
*
3087866 TAAATTTATTAAATAATAAAAA-TATTTAT-ATT
1 TAAAATTATTAAATAATAAAAATTATTTATAATT
*
3087898 TAAAATTATTTAAA-AATAAAAATTATTTTTAATT
1 TAAAATTA-TTAAATAATAAAAATTATTTATAATT
3087932 TAA
1 TAA
3087935 GAATAATAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
32 15 0.47
33 11 0.34
34 6 0.19
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (34 bp):
TAAAATTATTAAATAATAAAAATTATTTATAATT
Found at i:3087917 original size:16 final size:16
Alignment explanation
Indices: 3087874--3087925 Score: 50
Period size: 17 Copynumber: 3.1 Consensus size: 16
3087864 TGTAAATTTA
*
3087874 TTAAATAATAAAAATAT
1 TTAAA-AATAAAATTAT
* **
3087891 TTATATTTAAAATTAT
1 TTAAAAATAAAATTAT
3087907 TTAAAAATAAAAATTAT
1 TTAAAAAT-AAAATTAT
3087924 TT
1 TT
3087926 TTAATTTAAG
Statistics
Matches: 27, Mismatches: 7, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
16 13 0.48
17 14 0.52
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
TTAAAAATAAAATTAT
Found at i:3088169 original size:23 final size:20
Alignment explanation
Indices: 3088143--3088192 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 20
3088133 TATTAAAATT
3088143 TATATAAAACGAATTATTATTAA
1 TATATAAAA--AATTA-TATTAA
* *
3088166 TATATCAAAATTTATATTAA
1 TATATAAAAAATTATATTAA
3088186 TATATAA
1 TATATAA
3088193 TATTTTAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 12 0.50
21 4 0.17
23 8 0.33
ACGTcount: A:0.52, C:0.04, G:0.02, T:0.42
Consensus pattern (20 bp):
TATATAAAAAATTATATTAA
Found at i:3088199 original size:20 final size:20
Alignment explanation
Indices: 3088160--3088236 Score: 65
Period size: 20 Copynumber: 4.0 Consensus size: 20
3088150 AACGAATTAT
*
3088160 TATTAATATATCAA-AATTTA
1 TATTAATATAT-AATATTTTA
3088180 TATTAATATATAATATTTTA
1 TATTAATATATAATATTTTA
*
3088200 AATATAAT-TAT--TATTTTA
1 TAT-TAATATATAATATTTTA
*
3088218 TTTTAATA-ATAATAATTTT
1 TATTAATATATAAT-ATTTT
3088237 TTTAATAAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
17 6 0.13
18 8 0.17
19 3 0.06
20 26 0.55
21 4 0.09
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.53
Consensus pattern (20 bp):
TATTAATATATAATATTTTA
Found at i:3088220 original size:23 final size:23
Alignment explanation
Indices: 3088193--3088240 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
3088183 TAATATATAA
*
3088193 TATTTTAA-ATATAATTATTATTT
1 TATTTTAATA-ATAATAATTATTT
*
3088216 TATTTTAATAATAATAATTTTTT
1 TATTTTAATAATAATAATTATTT
3088239 TA
1 TA
3088241 ATAAAAAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 21 0.95
24 1 0.05
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (23 bp):
TATTTTAATAATAATAATTATTT
Found at i:3089317 original size:27 final size:27
Alignment explanation
Indices: 3089285--3089370 Score: 83
Period size: 27 Copynumber: 3.3 Consensus size: 27
3089275 TTATTATTTT
*
3089285 TATATTATAAATATATTTAATATATTA
1 TATATTATAAATATAATTAATATATTA
*
3089312 TATATTTATAAA-AAAATTAATAT-TT-
1 TATA-TTATAAATATAATTAATATATTA
* *
3089337 TA-ATTATTTATTATAATT-ATATATTA
1 TATATTA-TAAATATAATTAATATATTA
3089363 TATATTAT
1 TATATTAT
3089371 TATTTTATAT
Statistics
Matches: 48, Mismatches: 5, Indels: 13
0.73 0.08 0.20
Matches are distributed among these distances:
23 3 0.06
24 7 0.15
25 9 0.19
26 5 0.10
27 17 0.35
28 7 0.15
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (27 bp):
TATATTATAAATATAATTAATATATTA
Found at i:3089353 original size:13 final size:13
Alignment explanation
Indices: 3089332--3089371 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
3089322 AAAAAATTAA
*
3089332 TATTTTAATTATT
1 TATTATAATTATT
*
3089345 TATTATAATTATA
1 TATTATAATTATT
3089358 TATTATATATTATT
1 TATTATA-ATTATT
3089372 ATTTTATATT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
13 18 0.78
14 5 0.22
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
TATTATAATTATT
Found at i:3089368 original size:20 final size:20
Alignment explanation
Indices: 3089285--3089387 Score: 72
Period size: 20 Copynumber: 5.2 Consensus size: 20
3089275 TTATTATTTT
*
3089285 TATATTATAAATATAT-TTAA
1 TATATTATAATTATATATT-A
*
3089305 TATATTATATATT-TATA-AA
1 TATATTATA-ATTATATATTA
* * *
3089324 AAAATTA-ATATTTTA-ATTA
1 TATATTATA-ATTATATATTA
*
3089343 TTTATTATAATTATATATTA
1 TATATTATAATTATATATTA
* *
3089363 TATATTATTATTTTATATTA
1 TATATTATAATTATATATTA
3089383 TATAT
1 TATAT
3089388 ATTATCTAAA
Statistics
Matches: 65, Mismatches: 12, Indels: 12
0.73 0.13 0.13
Matches are distributed among these distances:
18 6 0.09
19 18 0.28
20 39 0.60
21 2 0.03
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
TATATTATAATTATATATTA
Found at i:3089371 original size:27 final size:27
Alignment explanation
Indices: 3089304--3089387 Score: 77
Period size: 25 Copynumber: 3.2 Consensus size: 27
3089294 AATATATTTA
* ** *
3089304 ATATATTATATATT-TATAAAAAAATT
1 ATATATTATATATTATTTATTATAATT
*
3089330 A-ATATTTTA-ATTATTTATTATAATT
1 ATATATTATATATTATTTATTATAATT
*
3089355 ATATATTATATATTA-TTATTTTATATT
1 ATATATTATATATTATTTATTATA-ATT
3089382 ATATAT
1 ATATAT
3089388 ATTATCTAAA
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
24 3 0.06
25 16 0.34
26 15 0.32
27 13 0.28
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (27 bp):
ATATATTATATATTATTTATTATAATT
Found at i:3089374 original size:13 final size:13
Alignment explanation
Indices: 3089339--3089383 Score: 56
Period size: 13 Copynumber: 3.4 Consensus size: 13
3089329 TAATATTTTA
3089339 ATTATTTATTATA-
1 ATTA-TTATTATAT
3089352 ATTATATATTATAT
1 ATTAT-TATTATAT
*
3089366 ATTATTATTTTAT
1 ATTATTATTATAT
3089379 ATTAT
1 ATTAT
3089384 ATATATTATC
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
12 1 0.03
13 23 0.79
14 5 0.17
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
ATTATTATTATAT
Found at i:3089787 original size:35 final size:32
Alignment explanation
Indices: 3089747--3089828 Score: 87
Period size: 32 Copynumber: 2.5 Consensus size: 32
3089737 CTATAATATT
3089747 AAATATAATATAATTATATAATATAAAAAAT-AATA
1 AAATATAATATAA-TAT-T-ATA-AAAAAATAAATA
*
3089782 AAATATGATATAATATTATAAAAAAATAAATA
1 AAATATAATATAATATTATAAAAAAATAAATA
*
3089814 TAATACTAATA-AATA
1 AAATA-TAATATAATA
3089829 AATATATTAA
Statistics
Matches: 42, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
31 7 0.17
32 15 0.36
33 5 0.12
34 3 0.07
35 12 0.29
ACGTcount: A:0.65, C:0.01, G:0.01, T:0.33
Consensus pattern (32 bp):
AAATATAATATAATATTATAAAAAAATAAATA
Found at i:3089792 original size:27 final size:25
Alignment explanation
Indices: 3089738--3089864 Score: 105
Period size: 28 Copynumber: 4.8 Consensus size: 25
3089728 TGTGGACTCC
* * *
3089738 TATAATATTAAATATAATATAATTA
1 TATAATATAAAAAATAATAAAATTA
3089763 TATAATATAAAAAATAATAAAATATGA
1 TATAATATAAAAAATAATAAAAT-T-A
*
3089790 TATAATATTATAAAAA-AATAAATATAA
1 TATAATA-TA-AAAAATAATAAA-ATTA
*
3089817 TACTAATA-AATAAATATATTAAAATTTA
1 TA-TAATATAA-AAA-ATAATAAAA-TTA
3089845 TATAATATAAATAAATAATA
1 TATAATATAAA-AAATAATA
3089865 TATTAAAATT
Statistics
Matches: 83, Mismatches: 7, Indels: 22
0.74 0.06 0.20
Matches are distributed among these distances:
25 21 0.25
26 5 0.06
27 24 0.29
28 26 0.31
29 7 0.08
ACGTcount: A:0.62, C:0.01, G:0.01, T:0.36
Consensus pattern (25 bp):
TATAATATAAAAAATAATAAAATTA
Found at i:3089817 original size:22 final size:23
Alignment explanation
Indices: 3089775--3089832 Score: 64
Period size: 23 Copynumber: 2.5 Consensus size: 23
3089765 TAATATAAAA
* *
3089775 AATAATAAAATATGATATAATA-T
1 AATAAAAAAATA-AATATAATACT
*
3089798 TATAAAAAAATAAATATAATACT
1 AATAAAAAAATAAATATAATACT
*
3089821 AATAAATAAATA
1 AATAAAAAAATA
3089833 TATTAAAATT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
22 8 0.28
23 21 0.72
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.31
Consensus pattern (23 bp):
AATAAAAAAATAAATATAATACT
Found at i:3089823 original size:6 final size:5
Alignment explanation
Indices: 3089738--3089922 Score: 92
Period size: 5 Copynumber: 38.6 Consensus size: 5
3089728 TGTGGACTCC
*
3089738 TATAA TATTAAA TATAA TATAA T-T-A TATAA TATAA -A-AA -ATAA TAAAA
1 TATAA TA-T-AA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA
* * *
3089785 TATGA TATAA TAT-- TATAA AAAAA TA-AA TATAA TACTAA TA-AA TA-AA
1 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TA-TAA TATAA TATAA
* * * * * *
3089831 TATAT TAAAA T-TTA TATAA TATAA -ATAA -ATAA TATAT TAAAA T-TTA
1 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA
* * * *
3089877 TATAAA TATAA AATAT TTTAAA TATAA TTATAA TATGA TATAA TAT
1 TAT-AA TATAA TATAA TAT-AA TATAA -TATAA TATAA TATAA TAT
3089923 GTACATATAA
Statistics
Matches: 136, Mismatches: 27, Indels: 34
0.69 0.14 0.17
Matches are distributed among these distances:
3 8 0.06
4 29 0.21
5 76 0.56
6 19 0.14
7 4 0.03
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.39
Consensus pattern (5 bp):
TATAA
Found at i:3089870 original size:32 final size:33
Alignment explanation
Indices: 3089811--3089888 Score: 124
Period size: 33 Copynumber: 2.4 Consensus size: 33
3089801 AAAAAAATAA
3089811 ATATAATACT-AATAAATAAATATATTAAAATTT
1 ATATAATA-TAAATAAATAAATATATTAAAATTT
3089844 ATATAATATAAATAAAT-AATATATTAAAATTT
1 ATATAATATAAATAAATAAATATATTAAAATTT
3089876 ATATAAATATAAA
1 ATAT-AATATAAA
3089889 ATATTTTAAA
Statistics
Matches: 43, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
32 20 0.47
33 23 0.53
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.38
Consensus pattern (33 bp):
ATATAATATAAATAAATAAATATATTAAAATTT
Found at i:3089888 original size:29 final size:32
Alignment explanation
Indices: 3089811--3089887 Score: 120
Period size: 32 Copynumber: 2.3 Consensus size: 32
3089801 AAAAAAATAA
3089811 ATATAATACTAATAAATAAATATATTAAAATTT
1 ATATAATA-TAATAAATAAATATATTAAAATTT
3089844 ATATAATATAAATAAAT-AATATATTAAAATTT
1 ATATAATAT-AATAAATAAATATATTAAAATTT
3089876 ATATAAATATAA
1 ATAT-AATATAA
3089888 AATATTTTAA
Statistics
Matches: 42, Mismatches: 0, Indels: 5
0.89 0.00 0.11
Matches are distributed among these distances:
32 22 0.52
33 20 0.48
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (32 bp):
ATATAATATAATAAATAAATATATTAAAATTT
Found at i:3089891 original size:27 final size:30
Alignment explanation
Indices: 3089811--3089898 Score: 101
Period size: 32 Copynumber: 2.9 Consensus size: 30
3089801 AAAAAAATAA
3089811 ATATAATACTAATAAATAAATATATTAAAATTT
1 ATATAATA-TAAT-AA-AAATATATTAAAATTT
3089844 ATATAATATAAATAAATAATATATTAAAATTT
1 ATATAATAT-AATAAA-AATATATTAAAATTT
*
3089876 ATATAA-AT-AT-AAAATATTTTAAA
1 ATATAATATAATAAAAATATATTAAA
3089899 TATAATTATA
Statistics
Matches: 52, Mismatches: 1, Indels: 10
0.83 0.02 0.16
Matches are distributed among these distances:
27 10 0.19
28 2 0.04
29 2 0.04
31 3 0.06
32 24 0.46
33 11 0.21
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (30 bp):
ATATAATATAATAAAAATATATTAAAATTT
Found at i:3090412 original size:3 final size:3
Alignment explanation
Indices: 3090406--3090438 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
3090396 TTTTTTTATA
3090406 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
3090439 TAAGTGTATG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:3090960 original size:15 final size:16
Alignment explanation
Indices: 3090940--3090969 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
3090930 ATAAAAAATA
3090940 ATTAAAATAT-TATAC
1 ATTAAAATATATATAC
3090955 ATTAAAATATATATA
1 ATTAAAATATATATA
3090970 AAATAAATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (16 bp):
ATTAAAATATATATAC
Found at i:3095880 original size:33 final size:32
Alignment explanation
Indices: 3095838--3095902 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 32
3095828 TGACACTTCT
3095838 CAGTTTTATAACTTGTAATGACACAAAGAAAAA
1 CAGTTTTATAACTTGTAATGACA-AAAGAAAAA
* * *
3095871 CAGTTTTATAACTTTTAATTACAGAAGAAAAA
1 CAGTTTTATAACTTGTAATGACAAAAGAAAAA
3095903 GGGTACAACT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 8 0.28
33 21 0.72
ACGTcount: A:0.48, C:0.11, G:0.11, T:0.31
Consensus pattern (32 bp):
CAGTTTTATAACTTGTAATGACAAAAGAAAAA
Found at i:3100401 original size:49 final size:49
Alignment explanation
Indices: 3100339--3100432 Score: 170
Period size: 49 Copynumber: 1.9 Consensus size: 49
3100329 AAGCAATTAC
*
3100339 ATTGCTCCTAATAAAACTAATAACATCAATTCACTTCTCCTTTTTAATA
1 ATTGCTCCAAATAAAACTAATAACATCAATTCACTTCTCCTTTTTAATA
*
3100388 ATTGCTCCAAATAAAACTAGTAACATCAATTCACTTCTCCTTTTT
1 ATTGCTCCAAATAAAACTAATAACATCAATTCACTTCTCCTTTTT
3100433 GTTTTCTAAT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 43 1.00
ACGTcount: A:0.35, C:0.23, G:0.03, T:0.38
Consensus pattern (49 bp):
ATTGCTCCAAATAAAACTAATAACATCAATTCACTTCTCCTTTTTAATA
Done.