Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr11 ID=Chr11-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 62681010
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1052928 characters in sequence are not A, C, G, or T
File 181 of 210
Found at i:53797850 original size:29 final size:29
Alignment explanation
Indices: 53797815--53797891 Score: 120
Period size: 29 Copynumber: 2.7 Consensus size: 29
53797805 AAAAATAAAA
* *
53797815 ATTTACCAAAATACTA-CAAGTTTTTTTTT
1 ATTTACCAAAATA-TATAAACTTTTTTTTT
53797844 ATTTACCAAAATATATAAACTTTTTTTTT
1 ATTTACCAAAATATATAAACTTTTTTTTT
53797873 ATTTACCAAAATATATAAA
1 ATTTACCAAAATATATAAA
53797892 AAAAAACCAA
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
28 2 0.04
29 43 0.96
ACGTcount: A:0.42, C:0.12, G:0.01, T:0.45
Consensus pattern (29 bp):
ATTTACCAAAATATATAAACTTTTTTTTT
Found at i:53797902 original size:20 final size:18
Alignment explanation
Indices: 53797877--53797913 Score: 56
Period size: 20 Copynumber: 1.9 Consensus size: 18
53797867 TTTTTTATTT
53797877 ACCAAAATATATAAAAAAAA
1 ACCAAAATA-A-AAAAAAAA
53797897 ACCAAAATAAAAAAAAA
1 ACCAAAATAAAAAAAAA
53797914 CCTGACAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
19 1 0.06
20 9 0.53
ACGTcount: A:0.78, C:0.11, G:0.00, T:0.11
Consensus pattern (18 bp):
ACCAAAATAAAAAAAAAA
Found at i:53798058 original size:4 final size:4
Alignment explanation
Indices: 53798049--53798157 Score: 71
Period size: 4 Copynumber: 26.0 Consensus size: 4
53798039 GCAGAAGGAG
* * *
53798049 AGAA AGAA AGAA AGAA AGGAGA GGAA AGAA AAAA AGAA AGAA AGGGGA
1 AGAA AGAA AGAA AGAA A-GA-A AGAA AGAA AGAA AGAA AGAA A--GAA
* *
53798097 GGAA AGAA AGAAA AGGAA AG-G AGAA GAGAA A-AA AGAA AGAA AG-A AGAA
1 AGAA AGAA AG-AA A-GAA AGAA AGAA -AGAA AGAA AGAA AGAA AGAA AGAA
*
53798145 GAAAA AGAA AGAA
1 -AGAA AGAA AGAA
53798158 GGAAGGGAAA
Statistics
Matches: 82, Mismatches: 12, Indels: 22
0.71 0.10 0.19
Matches are distributed among these distances:
3 8 0.10
4 53 0.65
5 17 0.21
6 4 0.05
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (4 bp):
AGAA
Found at i:53798084 original size:26 final size:26
Alignment explanation
Indices: 53798044--53798148 Score: 105
Period size: 26 Copynumber: 4.2 Consensus size: 26
53798034 TGGGGGCAGA
* *
53798044 AGGAGAGAAAGAAAGAAAGAAAGGAG
1 AGGAAAGAAAAAAAGAAAGAAAGGAG
*
53798070 AGGAAAGAAAAAAAGAAAGAAAGGGG
1 AGGAAAGAAAAAAAGAAAGAAAGGAG
53798096 AGGAAAGAAAGAAAAG---GAAAGGAG
1 AGGAAAGAAA-AAAAGAAAGAAAGGAG
* *
53798120 A--AGAG-AAAAAAGAAAGAAAGAAG
1 AGGAAAGAAAAAAAGAAAGAAAGGAG
*
53798143 AAGAAA
1 AGGAAA
53798149 AAGAAAGAAG
Statistics
Matches: 66, Mismatches: 7, Indels: 13
0.77 0.08 0.15
Matches are distributed among these distances:
20 5 0.08
21 2 0.03
22 3 0.05
23 8 0.12
24 8 0.12
25 2 0.03
26 33 0.50
27 5 0.08
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (26 bp):
AGGAAAGAAAAAAAGAAAGAAAGGAG
Found at i:53798130 original size:20 final size:20
Alignment explanation
Indices: 53798107--53798207 Score: 73
Period size: 21 Copynumber: 4.9 Consensus size: 20
53798097 GGAAAGAAAG
53798107 AAAAGGAAAGGAGAAGAGAA
1 AAAAGGAAAGGAGAAGAGAA
53798127 AAAA-GAAA-GA-AAGAAGAA
1 AAAAGGAAAGGAGAAG-AGAA
* * *
53798145 GAAAAAGAAAGAAGGAAGGGAA
1 -AAAAGGAAAGGA-GAAGAGAA
*
53798167 AGACAGGGAAAGGAGAAGAGAA
1 A-A-AAGGAAAGGAGAAGAGAA
* *
53798189 AAAAGAAGAAGAAGAAGAG
1 AAAAGGA-AAGGAGAAGAG
53798208 GGAAGAAAGG
Statistics
Matches: 63, Mismatches: 9, Indels: 17
0.71 0.10 0.19
Matches are distributed among these distances:
17 3 0.05
18 6 0.10
19 8 0.13
20 11 0.17
21 13 0.21
22 12 0.19
23 10 0.16
ACGTcount: A:0.65, C:0.01, G:0.34, T:0.00
Consensus pattern (20 bp):
AAAAGGAAAGGAGAAGAGAA
Found at i:53798137 original size:16 final size:19
Alignment explanation
Indices: 53798104--53798206 Score: 70
Period size: 20 Copynumber: 5.2 Consensus size: 19
53798094 GGAGGAAAGA
* *
53798104 AAGAAAAGGAAAGGAGAAG
1 AAGAAAAAGAAAGAAGAAG
53798123 -AGAAAAAAGAAAGAAAGAAG
1 AAG-AAAAAGAAAG-AAGAAG
53798143 AAGAAAAAGAAAGAAGGAAG
1 AAGAAAAAGAAAGAA-GAAG
* *
53798163 -GGAAAGACAGGGAAAGGAGAAG
1 AAGAAA-A-A--GAAAGAAGAAG
53798185 -AGAAAAA-AGAAGAAGAAG
1 AAGAAAAAGA-AAGAAGAAG
53798203 AAGA
1 AAGA
53798207 GGGAAGAAAG
Statistics
Matches: 68, Mismatches: 6, Indels: 20
0.72 0.06 0.21
Matches are distributed among these distances:
17 1 0.01
18 10 0.15
19 18 0.26
20 21 0.31
21 4 0.06
22 8 0.12
23 6 0.09
ACGTcount: A:0.66, C:0.01, G:0.33, T:0.00
Consensus pattern (19 bp):
AAGAAAAAGAAAGAAGAAG
Found at i:53798140 original size:33 final size:33
Alignment explanation
Indices: 53798098--53798195 Score: 98
Period size: 33 Copynumber: 3.1 Consensus size: 33
53798088 GAAAGGGGAG
53798098 GAAAGAAAGAAAAGGAAAGGAGAAGAGAAAAAA
1 GAAAGAAAGAAAAGGAAAGGAGAAGAGAAAAAA
* **
53798131 GAAAGAAAGAAGAA-GAAA-AAGAA-AGAAGGAA
1 GAAAGAAAGAA-AAGGAAAGGAGAAGAGAAAAAA
* * *
53798162 G--GGAAAGACAGGGAAAGGAGAAGAGAAAAAA
1 GAAAGAAAGAAAAGGAAAGGAGAAGAGAAAAAA
53798193 GAA
1 GAA
53798196 GAAGAAGAAG
Statistics
Matches: 50, Mismatches: 9, Indels: 12
0.70 0.13 0.17
Matches are distributed among these distances:
28 1 0.02
29 10 0.20
30 4 0.08
31 14 0.28
32 4 0.08
33 15 0.30
34 2 0.04
ACGTcount: A:0.66, C:0.01, G:0.33, T:0.00
Consensus pattern (33 bp):
GAAAGAAAGAAAAGGAAAGGAGAAGAGAAAAAA
Found at i:53798560 original size:13 final size:13
Alignment explanation
Indices: 53798542--53798566 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
53798532 GAAAATAAAT
53798542 AAATGCGAAAAAG
1 AAATGCGAAAAAG
53798555 AAATGCGAAAAA
1 AAATGCGAAAAA
53798567 TGTACATGAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.08, G:0.20, T:0.08
Consensus pattern (13 bp):
AAATGCGAAAAAG
Found at i:53800423 original size:22 final size:22
Alignment explanation
Indices: 53800395--53800443 Score: 98
Period size: 22 Copynumber: 2.2 Consensus size: 22
53800385 TTTTTGGCAC
53800395 GCGTTAGTCACCGACCGAAGAA
1 GCGTTAGTCACCGACCGAAGAA
53800417 GCGTTAGTCACCGACCGAAGAA
1 GCGTTAGTCACCGACCGAAGAA
53800439 GCGTT
1 GCGTT
53800444 TTTGGCACTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.29, C:0.27, G:0.29, T:0.16
Consensus pattern (22 bp):
GCGTTAGTCACCGACCGAAGAA
Found at i:53801358 original size:36 final size:36
Alignment explanation
Indices: 53801314--53801419 Score: 101
Period size: 26 Copynumber: 3.3 Consensus size: 36
53801304 AAATAATAAA
53801314 CAAAATAATACACACTAAAATTATTAATTTTATACT
1 CAAAATAATACACACTAAAATTATTAATTTTATACT
**
53801350 ---ACGAAT--A-A-T---ATTATTAATTTTATACT
1 CAAAATAATACACACTAAAATTATTAATTTTATACT
53801376 CAAAATAATACACACTAAAATTATTAA-TTT-TACT
1 CAAAATAATACACACTAAAATTATTAATTTTATACT
*
53801410 AAAAATAATA
1 CAAAATAATA
53801420 ACTAACTATA
Statistics
Matches: 55, Mismatches: 5, Indels: 22
0.67 0.06 0.27
Matches are distributed among these distances:
26 17 0.31
29 5 0.09
30 1 0.02
31 2 0.04
32 1 0.02
33 5 0.09
34 13 0.24
35 3 0.05
36 8 0.15
ACGTcount: A:0.51, C:0.11, G:0.01, T:0.37
Consensus pattern (36 bp):
CAAAATAATACACACTAAAATTATTAATTTTATACT
Found at i:53801575 original size:3 final size:3
Alignment explanation
Indices: 53801567--53801597 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
53801557 TCTTCATACT
53801567 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC A
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC A
53801598 NNNNNNNNNN
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.32, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:53801905 original size:27 final size:27
Alignment explanation
Indices: 53801867--53801942 Score: 116
Period size: 27 Copynumber: 2.8 Consensus size: 27
53801857 ATAATACGAG
53801867 TGGTGCCGCCAATGGCATTGGCACCAT
1 TGGTGCCGCCAATGGCATTGGCACCAT
* *
53801894 TGGTGCCGCCAATGGCATTGACACCTT
1 TGGTGCCGCCAATGGCATTGGCACCAT
**
53801921 TGGTGCCGCCAATACCATTGGC
1 TGGTGCCGCCAATGGCATTGGC
53801943 GTGACCAGTG
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 44 1.00
ACGTcount: A:0.18, C:0.30, G:0.28, T:0.24
Consensus pattern (27 bp):
TGGTGCCGCCAATGGCATTGGCACCAT
Found at i:53802021 original size:20 final size:19
Alignment explanation
Indices: 53801984--53802025 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
53801974 TTTTTTGTTA
**
53801984 GGTTTTTTTTTTTAATTTT
1 GGTTTTTTTTAATAATTTT
53802003 GGTTTTTTTTAATATATTTT
1 GGTTTTTTTTAATA-ATTTT
53802023 GGT
1 GGT
53802026 AAATAAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 12 0.60
20 8 0.40
ACGTcount: A:0.14, C:0.00, G:0.14, T:0.71
Consensus pattern (19 bp):
GGTTTTTTTTAATAATTTT
Found at i:53802046 original size:28 final size:28
Alignment explanation
Indices: 53802014--53802086 Score: 110
Period size: 28 Copynumber: 2.6 Consensus size: 28
53802004 GTTTTTTTTA
**
53802014 ATATATTTTGGTAAATAAAAAAAAGTTT
1 ATATATTTTGGTAAATAAAAAAAAACTT
53802042 ATATATTTTGGTAAATAAAAAAAAACTT
1 ATATATTTTGGTAAATAAAAAAAAACTT
*
53802070 GTACTATTTTGGTAAAT
1 ATA-TATTTTGGTAAAT
53802087 TTTTATTTTT
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
28 28 0.68
29 13 0.32
ACGTcount: A:0.47, C:0.03, G:0.11, T:0.40
Consensus pattern (28 bp):
ATATATTTTGGTAAATAAAAAAAAACTT
Found at i:53802066 original size:29 final size:29
Alignment explanation
Indices: 53802014--53802086 Score: 105
Period size: 29 Copynumber: 2.6 Consensus size: 29
53802004 GTTTTTTTTA
*
53802014 ATATATTTTGGTAAATAAAAAAAAGTT-T
1 ATATATTTTGGTAAATAAAAAAAACTTGT
53802042 ATATATTTTGGTAAATAAAAAAAAACTTGT
1 ATATATTTTGGTAAAT-AAAAAAAACTTGT
*
53802072 A-CTATTTTGGTAAAT
1 ATATATTTTGGTAAAT
53802087 TTTTATTTTT
Statistics
Matches: 41, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
28 16 0.39
29 23 0.56
30 2 0.05
ACGTcount: A:0.47, C:0.03, G:0.11, T:0.40
Consensus pattern (29 bp):
ATATATTTTGGTAAATAAAAAAAACTTGT
Found at i:53807012 original size:20 final size:19
Alignment explanation
Indices: 53806987--53807039 Score: 63
Period size: 19 Copynumber: 2.7 Consensus size: 19
53806977 TTAGCAGAAA
*
53806987 AAAATTATTTAGAAAAATTT
1 AAAATTATTTA-AAAAATAT
53807007 AAAATTTATTT-AAAAATAT
1 AAAA-TTATTTAAAAAATAT
53807026 AAGAATTATTTAAA
1 AA-AATTATTTAAA
53807040 GACATTAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
19 15 0.52
20 8 0.28
21 6 0.21
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.40
Consensus pattern (19 bp):
AAAATTATTTAAAAAATAT
Found at i:53809794 original size:14 final size:15
Alignment explanation
Indices: 53809775--53809804 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
53809765 TAACAGGCTG
53809775 TATTATAA-TTTAAA
1 TATTATAATTTTAAA
53809789 TATTATAATTTTAAA
1 TATTATAATTTTAAA
53809804 T
1 T
53809805 TATCTTTATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.53
15 7 0.47
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
TATTATAATTTTAAA
Found at i:53813737 original size:10 final size:9
Alignment explanation
Indices: 53813723--53813832 Score: 58
Period size: 9 Copynumber: 11.4 Consensus size: 9
53813713 TTTTTACGAA
53813723 TTTTATATT
1 TTTTATATT
53813732 TATTTATATT
1 T-TTTATATT
53813742 TTTTATAATT
1 TTTTAT-ATT
53813752 TTCTTATGACTT
1 TT-TTAT-A-TT
* *
53813764 TATTAAATT
1 TTTTATATT
*
53813773 TGTTATATT
1 TTTTATATT
*
53813782 TCTATATATT
1 T-TTTATATT
* *
53813792 TTATAATTTT
1 TT-TTATATT
* *
53813802 TTTTACAAT
1 TTTTATATT
* *
53813811 ATTTATAAT
1 TTTTATATT
*
53813820 TTTTCTATT
1 TTTTATATT
53813829 TTTT
1 TTTT
53813833 CCCAATTTTT
Statistics
Matches: 76, Mismatches: 19, Indels: 12
0.71 0.18 0.11
Matches are distributed among these distances:
9 37 0.49
10 28 0.37
11 8 0.11
12 3 0.04
ACGTcount: A:0.27, C:0.05, G:0.02, T:0.66
Consensus pattern (9 bp):
TTTTATATT
Found at i:53814411 original size:17 final size:19
Alignment explanation
Indices: 53814377--53814413 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 19
53814367 TGTATCAATA
*
53814377 TTAAATTACACTTGTTATT
1 TTAAATTACACTTATTATT
53814396 TTAAATTA-A-TTATTATT
1 TTAAATTACACTTATTATT
53814413 T
1 T
53814414 AATTGTTGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
17 8 0.47
18 1 0.06
19 8 0.47
ACGTcount: A:0.35, C:0.05, G:0.03, T:0.57
Consensus pattern (19 bp):
TTAAATTACACTTATTATT
Found at i:53814766 original size:37 final size:37
Alignment explanation
Indices: 53814720--53814791 Score: 101
Period size: 37 Copynumber: 1.9 Consensus size: 37
53814710 GAGACTTTTC
* * *
53814720 TTTTGTTTAAGTTTGATAAATT-AAATTGATCTTTTAT
1 TTTTATTTAAATTTGATAAATTGAAA-TGATATTTTAT
53814757 TTTTATTTAAATTTGATAAATTGAAATGATATTTT
1 TTTTATTTAAATTTGATAAATTGAAATGATATTTT
53814792 TTTACTTTAT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
37 28 0.90
38 3 0.10
ACGTcount: A:0.33, C:0.01, G:0.10, T:0.56
Consensus pattern (37 bp):
TTTTATTTAAATTTGATAAATTGAAATGATATTTTAT
Found at i:53817887 original size:3 final size:3
Alignment explanation
Indices: 53817879--53817928 Score: 52
Period size: 3 Copynumber: 17.0 Consensus size: 3
53817869 TTTATCCTTG
53817879 TTA TTA TTA TTA TT- TTA TTTA TTA TTA TT- TTA TTA TT- TATA TTA
1 TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA T-TA TTA
*
53817923 GTA TTA
1 TTA TTA
53817929 GGGTAGTAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
2 5 0.12
3 31 0.77
4 4 0.10
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:53817900 original size:15 final size:15
Alignment explanation
Indices: 53817882--53817912 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
53817872 ATCCTTGTTA
53817882 TTATTATTATTTTAT
1 TTATTATTATTTTAT
53817897 TTATTATTATTTTAT
1 TTATTATTATTTTAT
53817912 T
1 T
53817913 ATTTATATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (15 bp):
TTATTATTATTTTAT
Found at i:53817900 original size:18 final size:19
Alignment explanation
Indices: 53817879--53817928 Score: 70
Period size: 18 Copynumber: 2.8 Consensus size: 19
53817869 TTTATCCTTG
53817879 TTATTATTATTATT-TTAT
1 TTATTATTATTATTATTAT
53817897 TTATTATTATT-TTATTAT
1 TTATTATTATTATTATTAT
*
53817915 TTA-TATTAGTATTA
1 TTATTATTATTATTA
53817929 GGGTAGTAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
17 8 0.28
18 21 0.72
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (19 bp):
TTATTATTATTATTATTAT
Found at i:53823106 original size:14 final size:14
Alignment explanation
Indices: 53823070--53823109 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
53823060 ATGCGAGACA
*
53823070 GAAGAAGAAGGAATT
1 GAAGAAGAA-GAAAT
*
53823085 GAAAAAGAAGAAAT
1 GAAGAAGAAGAAAT
53823099 GAAGAAGAAGA
1 GAAGAAGAAGA
53823110 GCACAACTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
14 14 0.64
15 8 0.36
ACGTcount: A:0.62, C:0.00, G:0.30, T:0.07
Consensus pattern (14 bp):
GAAGAAGAAGAAAT
Found at i:53826688 original size:17 final size:17
Alignment explanation
Indices: 53826658--53826690 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
53826648 AACACTCATG
53826658 ATAATGCAATTGATAAT
1 ATAATGCAATTGATAAT
53826675 ATAATAGCAA-TGATAA
1 ATAAT-GCAATTGATAA
53826691 CAATGACAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.52, C:0.06, G:0.12, T:0.30
Consensus pattern (17 bp):
ATAATGCAATTGATAAT
Found at i:53826954 original size:3 final size:3
Alignment explanation
Indices: 53826946--53826989 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
53826936 AACCTAAAAT
53826946 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
53826990 GGAGAGCTCC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:53833999 original size:27 final size:27
Alignment explanation
Indices: 53833969--53834026 Score: 116
Period size: 27 Copynumber: 2.1 Consensus size: 27
53833959 AAAATCTTAC
53833969 TCTAAAATAAAATAAAAGAAGTGTAGT
1 TCTAAAATAAAATAAAAGAAGTGTAGT
53833996 TCTAAAATAAAATAAAAGAAGTGTAGT
1 TCTAAAATAAAATAAAAGAAGTGTAGT
53834023 TCTA
1 TCTA
53834027 TATAAGTGGC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.53, C:0.05, G:0.14, T:0.28
Consensus pattern (27 bp):
TCTAAAATAAAATAAAAGAAGTGTAGT
Found at i:53836284 original size:2 final size:2
Alignment explanation
Indices: 53836277--53836314 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
53836267 AGTTTTATGC
53836277 TA TA TA TA TA TA TA TA TA 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 TA TA
53836315 GAAATGCAGT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:53838920 original size:3 final size:3
Alignment explanation
Indices: 53838912--53838956 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
53838902 AGGTAGCAAG
53838912 CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC
1 CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC
53838957 TCATTTTTGG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.33, C:0.67, G:0.00, T:0.00
Consensus pattern (3 bp):
CAC
Found at i:53840771 original size:61 final size:61
Alignment explanation
Indices: 53840706--53840844 Score: 183
Period size: 60 Copynumber: 2.3 Consensus size: 61
53840696 ACCAAAAATT
* ** *
53840706 AATTTATTGAATTTTTTAGAATT-AGAACTAAATTGACAAACTTTGTAAATGTTGAAGGTTA
1 AATTTATTGAATTTTTTAGAATTCA-AACTAAAATGACAAACTTTGTAAACATTGAAGGCTA
* *
53840767 AATTTATTG-ATTTTTTAGAATTCAAACTAAAATGACAAATTTTGTAAACATTGATGGCTA
1 AATTTATTGAATTTTTTAGAATTCAAACTAAAATGACAAACTTTGTAAACATTGAAGGCTA
* *
53840827 AATTTGTTGAATATTTTA
1 AATTTATTGAATTTTTTA
53840845 TATTTAGGAT
Statistics
Matches: 68, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
60 51 0.75
61 17 0.25
ACGTcount: A:0.39, C:0.06, G:0.13, T:0.42
Consensus pattern (61 bp):
AATTTATTGAATTTTTTAGAATTCAAACTAAAATGACAAACTTTGTAAACATTGAAGGCTA
Found at i:53841049 original size:14 final size:14
Alignment explanation
Indices: 53841030--53841089 Score: 50
Period size: 14 Copynumber: 4.0 Consensus size: 14
53841020 TTAGTAGCCA
*
53841030 TTTTTATAGTTTTT
1 TTTTTATAATTTTT
53841044 TTTTTATAATTTTAAGT
1 TTTTTATAATTTT---T
*
53841061 CATTTT-TAATTATTT
1 -TTTTTATAATT-TTT
53841076 TTTTTATAATTTTT
1 TTTTTATAATTTTT
53841090 AAATTTGTTT
Statistics
Matches: 37, Mismatches: 3, Indels: 12
0.71 0.06 0.23
Matches are distributed among these distances:
14 19 0.51
15 6 0.16
17 6 0.16
18 6 0.16
ACGTcount: A:0.23, C:0.02, G:0.03, T:0.72
Consensus pattern (14 bp):
TTTTTATAATTTTT
Found at i:53841087 original size:22 final size:23
Alignment explanation
Indices: 53841062--53841104 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
53841052 ATTTTAAGTC
53841062 ATTTTT-AATTAT-TTTTTTTATA
1 ATTTTTAAATT-TGTTTTTTTATA
53841084 ATTTTTAAATTTGTTTTTTTA
1 ATTTTTAAATTTGTTTTTTTA
53841105 GCTTTGTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (23 bp):
ATTTTTAAATTTGTTTTTTTATA
Found at i:53854470 original size:17 final size:18
Alignment explanation
Indices: 53854433--53854471 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
53854423 CTACATGTGC
* *
53854433 GAGCTCATTTGAAGTTTT
1 GAGCTCATATGAAGTTGT
53854451 GAGCTCATAT-AAGTTGT
1 GAGCTCATATGAAGTTGT
53854468 GAGC
1 GAGC
53854472 CCACCCAAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 10 0.53
18 9 0.47
ACGTcount: A:0.26, C:0.13, G:0.26, T:0.36
Consensus pattern (18 bp):
GAGCTCATATGAAGTTGT
Found at i:53861418 original size:44 final size:44
Alignment explanation
Indices: 53861355--53861509 Score: 247
Period size: 44 Copynumber: 3.5 Consensus size: 44
53861345 TGAGTACTTT
* * *
53861355 TGATCAGTAACAAGTGATAAGTGGTAGCTTTAGCTACACCTATC
1 TGATCAGTGACAAGTGATAAGTGGTAGCTTTAGTTACACTTATC
53861399 TGATCAGTGACAAGTGATAAGTGGTAGCTTTAGTTACACTTATC
1 TGATCAGTGACAAGTGATAAGTGGTAGCTTTAGTTACACTTATC
*
53861443 TGATCAGTGACAAGTGATAAGTGGTAACTTTAGTTACACTTATC
1 TGATCAGTGACAAGTGATAAGTGGTAGCTTTAGTTACACTTATC
* * *
53861487 TTATCAGTGACAAATGACAAGTG
1 TGATCAGTGACAAGTGATAAGTG
53861510 ATGTGATATG
Statistics
Matches: 104, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
44 104 1.00
ACGTcount: A:0.32, C:0.15, G:0.21, T:0.32
Consensus pattern (44 bp):
TGATCAGTGACAAGTGATAAGTGGTAGCTTTAGTTACACTTATC
Found at i:53861584 original size:47 final size:48
Alignment explanation
Indices: 53861511--53861609 Score: 130
Period size: 47 Copynumber: 2.1 Consensus size: 48
53861501 TGACAAGTGA
** *
53861511 TGTGATATGTGATTTTCGTGTAAGACCATATCTAGGATATGGCATT-GG
1 TGTGATATGTGATTCCCGTGTAAGACCATAGCTAGGATATGGC-TTCGG
* *
53861559 TGTGATATGTG-TTCCCGTGTAAGACCATAGCTGGGCTATGGCTTCGG
1 TGTGATATGTGATTCCCGTGTAAGACCATAGCTAGGATATGGCTTCGG
53861606 TGTG
1 TGTG
53861610 TGATATAAGA
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
46 2 0.04
47 32 0.71
48 11 0.24
ACGTcount: A:0.20, C:0.14, G:0.30, T:0.35
Consensus pattern (48 bp):
TGTGATATGTGATTCCCGTGTAAGACCATAGCTAGGATATGGCTTCGG
Found at i:53869535 original size:25 final size:23
Alignment explanation
Indices: 53869507--53869553 Score: 58
Period size: 25 Copynumber: 2.0 Consensus size: 23
53869497 AAATAATATT
53869507 ATTTCAAAAAAATATAATATTTATA
1 ATTTCAAAAAAAT-TAAT-TTTATA
* *
53869532 ATTTTAAAATAATTAATTTTAT
1 ATTTCAAAAAAATTAATTTTAT
53869554 TATTAATTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 5 0.25
24 4 0.20
25 11 0.55
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (23 bp):
ATTTCAAAAAAATTAATTTTATA
Found at i:53871072 original size:22 final size:22
Alignment explanation
Indices: 53871032--53871089 Score: 91
Period size: 22 Copynumber: 2.7 Consensus size: 22
53871022 GATCAAAAAT
53871032 AAAATTAAGTCA-TTTTTTTAA
1 AAAATTAAGTCATTTTTTTTAA
**
53871053 AAAATTAAGTCATTTTTTTTCT
1 AAAATTAAGTCATTTTTTTTAA
53871075 AAAATTAAGTCATTT
1 AAAATTAAGTCATTT
53871090 CTCTAAGAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
21 12 0.35
22 22 0.65
ACGTcount: A:0.40, C:0.07, G:0.05, T:0.48
Consensus pattern (22 bp):
AAAATTAAGTCATTTTTTTTAA
Found at i:53872572 original size:58 final size:60
Alignment explanation
Indices: 53872438--53872550 Score: 158
Period size: 61 Copynumber: 1.9 Consensus size: 60
53872428 AATAATTTTC
* **
53872438 ATATTAAAATTAATTTAATATTTATCTTGTATATAAGTATTCTAGTAATTTAATAGATATA
1 ATATTAAATTTAATCAAATATTTATCTTG-ATATAAGTATTCTAGTAATTTAATAGATATA
* *
53872499 ATATTAAATTTAATCAAATATTTATCTTG-T-TAAGTATTTTATTAATTTAATA
1 ATATTAAATTTAATCAAATATTTATCTTGATATAAGTATTCTAGTAATTTAATA
53872551 TTAAAGTGGT
Statistics
Matches: 47, Mismatches: 5, Indels: 3
0.85 0.09 0.05
Matches are distributed among these distances:
58 20 0.43
59 1 0.02
61 26 0.55
ACGTcount: A:0.42, C:0.04, G:0.05, T:0.50
Consensus pattern (60 bp):
ATATTAAATTTAATCAAATATTTATCTTGATATAAGTATTCTAGTAATTTAATAGATATA
Found at i:53876480 original size:20 final size:20
Alignment explanation
Indices: 53876444--53876481 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
53876434 ATCCTTCTAT
*
53876444 TTTATAATTACTGAATTTAA
1 TTTATAATTACTCAATTTAA
53876464 TTTATAATATA-TCAATTT
1 TTTATAAT-TACTCAATTT
53876482 TTTATAGTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 14 0.88
21 2 0.12
ACGTcount: A:0.39, C:0.05, G:0.03, T:0.53
Consensus pattern (20 bp):
TTTATAATTACTCAATTTAA
Found at i:53876978 original size:21 final size:21
Alignment explanation
Indices: 53876954--53877004 Score: 63
Period size: 20 Copynumber: 2.5 Consensus size: 21
53876944 AGTAAGTTAA
53876954 AAATATTTTAATTAT-TATTTG
1 AAAT-TTTTAATTATATATTTG
53876975 AAATTTTT-ATTATAATATTTG
1 AAATTTTTAATTAT-ATATTTG
53876996 -AATTTTTAA
1 AAATTTTTAA
53877005 AAAGTTAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
19 5 0.19
20 11 0.41
21 11 0.41
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (21 bp):
AAATTTTTAATTATATATTTG
Found at i:53876986 original size:19 final size:19
Alignment explanation
Indices: 53876958--53877003 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
53876948 AGTTAAAAAT
*
53876958 ATTTTAATTAT-TATTTGAA
1 ATTTTTATTATATATTTG-A
53876977 ATTTTTATTATAATATTTGA
1 ATTTTTATTAT-ATATTTGA
53876997 ATTTTTA
1 ATTTTTA
53877004 AAAAGTTAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
19 10 0.42
20 8 0.33
21 6 0.25
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.61
Consensus pattern (19 bp):
ATTTTTATTATATATTTGA
Found at i:53879614 original size:20 final size:20
Alignment explanation
Indices: 53879589--53879629 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
53879579 TGAGACTATG
53879589 TTATCTTGATTCTTACATTA
1 TTATCTTGATTCTTACATTA
53879609 TTATCTTGATTCTTACATTA
1 TTATCTTGATTCTTACATTA
53879629 T
1 T
53879630 GTACCATTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.24, C:0.15, G:0.05, T:0.56
Consensus pattern (20 bp):
TTATCTTGATTCTTACATTA
Found at i:53884608 original size:17 final size:17
Alignment explanation
Indices: 53884586--53884626 Score: 73
Period size: 17 Copynumber: 2.4 Consensus size: 17
53884576 ATTGAGATCT
53884586 AAATTGGAAAAATTATG
1 AAATTGGAAAAATTATG
53884603 AAATTGGAAAAATTATG
1 AAATTGGAAAAATTATG
*
53884620 ACATTGG
1 AAATTGG
53884627 GAGTCTAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.49, C:0.02, G:0.20, T:0.29
Consensus pattern (17 bp):
AAATTGGAAAAATTATG
Found at i:53889440 original size:40 final size:39
Alignment explanation
Indices: 53889385--53889466 Score: 155
Period size: 40 Copynumber: 2.1 Consensus size: 39
53889375 TGATTAAACT
53889385 TAATCACTTTAATATTAAATTAATAAAATATTTATCAAGA
1 TAATCACTTTAATATTAAATTAATAAAATA-TTATCAAGA
53889425 TAATCACTTTAATATTAAATTAATAAAATATTATCAAGA
1 TAATCACTTTAATATTAAATTAATAAAATATTATCAAGA
53889464 TAA
1 TAA
53889467 GTATTAAATT
Statistics
Matches: 42, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
39 12 0.29
40 30 0.71
ACGTcount: A:0.51, C:0.07, G:0.02, T:0.39
Consensus pattern (39 bp):
TAATCACTTTAATATTAAATTAATAAAATATTATCAAGA
Found at i:53896828 original size:20 final size:20
Alignment explanation
Indices: 53896805--53896848 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
53896795 GTATGGTTAA
*
53896805 AAGTGGGCTTGTATCGATAG
1 AAGTGGACTTGTATCGATAG
* *
53896825 AAGTGGACTTGTATTGGTAG
1 AAGTGGACTTGTATCGATAG
53896845 AAGT
1 AAGT
53896849 CCCCCTGAGT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.27, C:0.07, G:0.34, T:0.32
Consensus pattern (20 bp):
AAGTGGACTTGTATCGATAG
Found at i:53904959 original size:32 final size:32
Alignment explanation
Indices: 53904918--53904981 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
53904908 AACCAGAAGG
53904918 GGTGTGGTCTTAAACTTTATGCCCCTCCTTGA
1 GGTGTGGTCTTAAACTTTATGCCCCTCCTTGA
53904950 GGTGTGGTCTTAAACTTTATGCCCCTCCTTGA
1 GGTGTGGTCTTAAACTTTATGCCCCTCCTTGA
53904982 AGCTGTTCTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.16, C:0.25, G:0.22, T:0.38
Consensus pattern (32 bp):
GGTGTGGTCTTAAACTTTATGCCCCTCCTTGA
Found at i:53913504 original size:109 final size:109
Alignment explanation
Indices: 53913313--53913528 Score: 423
Period size: 109 Copynumber: 2.0 Consensus size: 109
53913303 TAGAGAACAT
*
53913313 AAATGATCAATATTGGACATTACGTGCAGAGGAGGTAAGGCTCTTTGTCCTCCAAACGTGTCCCA
1 AAATGATCAATATTGGACATTACGTGCAGAGGAGGTAAGGCTCTTTGTCCTCCAAACATGTCCCA
53913378 ATTTGTATTTATACAGTATACCAATCTTAATTCTTGTAAATTAC
66 ATTTGTATTTATACAGTATACCAATCTTAATTCTTGTAAATTAC
53913422 AAATGATCAATATTGGACATTACGTGCAGAGGAGGTAAGGCTCTTTGTCCTCCAAACATGTCCCA
1 AAATGATCAATATTGGACATTACGTGCAGAGGAGGTAAGGCTCTTTGTCCTCCAAACATGTCCCA
53913487 ATTTGTATTTATACAGTATACCAATCTTAATTCTTGTAAATT
66 ATTTGTATTTATACAGTATACCAATCTTAATTCTTGTAAATT
53913529 TTACATTCTA
Statistics
Matches: 106, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
109 106 1.00
ACGTcount: A:0.31, C:0.18, G:0.16, T:0.34
Consensus pattern (109 bp):
AAATGATCAATATTGGACATTACGTGCAGAGGAGGTAAGGCTCTTTGTCCTCCAAACATGTCCCA
ATTTGTATTTATACAGTATACCAATCTTAATTCTTGTAAATTAC
Found at i:53917443 original size:86 final size:86
Alignment explanation
Indices: 53917343--53917505 Score: 317
Period size: 86 Copynumber: 1.9 Consensus size: 86
53917333 TTAATAAATT
53917343 ATAATCAGTAGGTTTGCTTGTATGAAATAATTATAGTTTTACTTAAAATTTTAGGCAATATACAC
1 ATAATCAGTAGGTTTGCTTGTATGAAATAATTATAGTTTTACTTAAAATTTTAGGCAATATACAC
*
53917408 TATTATATAAAATTTTAGGCA
66 TATTATAGAAAATTTTAGGCA
53917429 ATAATCAGTAGGTTTGCTTGTATGAAATAATTATAGTTTTACTTAAAATTTTAGGCAATATACAC
1 ATAATCAGTAGGTTTGCTTGTATGAAATAATTATAGTTTTACTTAAAATTTTAGGCAATATACAC
53917494 TATTATAGAAAA
66 TATTATAGAAAA
53917506 CTAATTTAAT
Statistics
Matches: 76, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
86 76 1.00
ACGTcount: A:0.39, C:0.08, G:0.13, T:0.40
Consensus pattern (86 bp):
ATAATCAGTAGGTTTGCTTGTATGAAATAATTATAGTTTTACTTAAAATTTTAGGCAATATACAC
TATTATAGAAAATTTTAGGCA
Found at i:53917830 original size:23 final size:24
Alignment explanation
Indices: 53917804--53917850 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
53917794 TATAATAGTT
* *
53917804 TAGGTATTTAAGTGAG-GAAAAAA
1 TAGGTACTGAAGTGAGTGAAAAAA
*
53917827 TAGGTACTGCAGTGAGTGAAAAAA
1 TAGGTACTGAAGTGAGTGAAAAAA
53917851 CCTATATTGA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 13 0.65
24 7 0.35
ACGTcount: A:0.45, C:0.04, G:0.28, T:0.23
Consensus pattern (24 bp):
TAGGTACTGAAGTGAGTGAAAAAA
Found at i:53924347 original size:28 final size:28
Alignment explanation
Indices: 53924304--53924358 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 28
53924294 ATGATGTTCA
*
53924304 TATTTGTACATTTTTCGCTCATTATTTT
1 TATTTGTACATCTTTCGCTCATTATTTT
* *
53924332 TATTTGTTCATCTTTCGCTCGTTATTT
1 TATTTGTACATCTTTCGCTCATTATTT
53924359 ATACATATTC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.15, C:0.16, G:0.09, T:0.60
Consensus pattern (28 bp):
TATTTGTACATCTTTCGCTCATTATTTT
Found at i:53926072 original size:14 final size:14
Alignment explanation
Indices: 53926053--53926086 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
53926043 CAAGGTTTTT
*
53926053 GTTTGGGGTTACGA
1 GTTTGGGGTTACAA
53926067 GTTTGGGGTTACAA
1 GTTTGGGGTTACAA
53926081 GTTTGG
1 GTTTGG
53926087 ATTCAAAGGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.15, C:0.06, G:0.41, T:0.38
Consensus pattern (14 bp):
GTTTGGGGTTACAA
Found at i:53928098 original size:22 final size:22
Alignment explanation
Indices: 53928070--53928200 Score: 154
Period size: 22 Copynumber: 6.0 Consensus size: 22
53928060 TTTATTGTTC
*
53928070 AAACATGAGAGCTTAGTACGTG
1 AAACATGAGAGCTTAGTACGTT
53928092 AAACATGAGAGCTTAGTACGTT
1 AAACATGAGAGCTTAGTACGTT
**
53928114 AGCCATGAGAGCTTAGTACGTT
1 AAACATGAGAGCTTAGTACGTT
** * * *
53928136 AGCCATGAGGGTTTAGTTCGTT
1 AAACATGAGAGCTTAGTACGTT
* ** *
53928158 AAACATTAGATTTTAATACGTT
1 AAACATGAGAGCTTAGTACGTT
53928180 AAACATGAGAGCTTAGTACGT
1 AAACATGAGAGCTTAGTACGT
53928201 NNNNNNNNNN
Statistics
Matches: 92, Mismatches: 17, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 92 1.00
ACGTcount: A:0.33, C:0.14, G:0.24, T:0.30
Consensus pattern (22 bp):
AAACATGAGAGCTTAGTACGTT
Found at i:53930410 original size:3 final size:3
Alignment explanation
Indices: 53930404--53930450 Score: 78
Period size: 3 Copynumber: 15.7 Consensus size: 3
53930394 AAAATAAAAC
53930404 AAT AAT AAT AA- AAT AAT AAT AAT AAT AAT AAAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT
53930449 AA
1 AA
53930451 AACGTAAATA
Statistics
Matches: 42, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
2 2 0.05
3 37 0.88
4 3 0.07
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:53930416 original size:20 final size:21
Alignment explanation
Indices: 53930387--53930450 Score: 78
Period size: 20 Copynumber: 3.1 Consensus size: 21
53930377 ATTCTAAAAG
*
53930387 AATAAAAAAAATAA-AACAAT
1 AATAATAAAAATAATAACAAT
*
53930407 AATAAT-AAAATAATAATAAT
1 AATAATAAAAATAATAACAAT
*
53930427 AATAATAAATAATAATAATAAT
1 AATAATAAA-AATAATAACAAT
53930449 AA
1 AA
53930451 AACGTAAATA
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
19 7 0.18
20 16 0.41
21 2 0.05
22 14 0.36
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.25
Consensus pattern (21 bp):
AATAATAAAAATAATAACAAT
Found at i:53930439 original size:16 final size:16
Alignment explanation
Indices: 53930404--53930451 Score: 82
Period size: 16 Copynumber: 3.1 Consensus size: 16
53930394 AAAATAAAAC
53930404 AATAATAATAA-AAT-
1 AATAATAATAATAATA
53930418 AATAATAATAATAATA
1 AATAATAATAATAATA
53930434 AATAATAATAATAATA
1 AATAATAATAATAATA
53930450 AA
1 AA
53930452 ACGTAAATAA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.34
15 3 0.09
16 18 0.56
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (16 bp):
AATAATAATAATAATA
Found at i:53930644 original size:3 final size:3
Alignment explanation
Indices: 53930638--53930684 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
53930628 GAAATAATAA
53930638 TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TA
1 TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TA
53930685 ATAATAATAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.34, C:0.32, G:0.00, T:0.34
Consensus pattern (3 bp):
TAC
Found at i:53930689 original size:3 final size:3
Alignment explanation
Indices: 53930683--53930744 Score: 81
Period size: 3 Copynumber: 20.0 Consensus size: 3
53930673 CTACTACTAC
53930683 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA GGTAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA --TAA TAA
*
53930730 TTAA TTA -AA TAA TAA
1 -TAA TAA TAA TAA TAA
53930745 AATTGCTAAA
Statistics
Matches: 53, Mismatches: 2, Indels: 8
0.84 0.03 0.13
Matches are distributed among these distances:
2 1 0.02
3 46 0.87
4 3 0.06
5 3 0.06
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:53931457 original size:15 final size:16
Alignment explanation
Indices: 53931419--53931458 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
53931409 TATTGTTTCG
53931419 AAATAAAAAAAATCAA
1 AAATAAAAAAAATCAA
* *
53931435 GAAGAAAAAAAA-CAA
1 AAATAAAAAAAATCAA
53931450 AAATAAAAA
1 AAATAAAAA
53931459 TAAGAAAGCA
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
15 10 0.50
16 10 0.50
ACGTcount: A:0.82, C:0.05, G:0.05, T:0.07
Consensus pattern (16 bp):
AAATAAAAAAAATCAA
Found at i:53932175 original size:88 final size:91
Alignment explanation
Indices: 53932108--53932280 Score: 226
Period size: 91 Copynumber: 1.9 Consensus size: 91
53932098 CTTCTTTGTA
* * *
53932108 GCAACTTCAGGGGGACGAGATTCG-TG-G-TTTTAGTCTACTCCACTGCAACGTTAGTGAGATAA
1 GCAACTTCAGGGGGACAAGATTCGATGTGATTTTAGTCTACTCCACTGCAACGTCAGGGAGATAA
* *
53932170 GACTTGTAACTTCAACCTGCCCCACT
66 GACTTGTAGCTTCAATCTGCCCCACT
* * * *
53932196 GCGACTTCAGGGGGATAAGATTGGATGTGATTTTAGTTTACTCCACTGCAACGTCAGGGAGATAA
1 GCAACTTCAGGGGGACAAGATTCGATGTGATTTTAGTCTACTCCACTGCAACGTCAGGGAGATAA
* *
53932261 GACTTGTGGCTTAAATCTGC
66 GACTTGTAGCTTCAATCTGC
53932281 TTCCTACTAT
Statistics
Matches: 71, Mismatches: 11, Indels: 3
0.84 0.13 0.04
Matches are distributed among these distances:
88 20 0.28
89 2 0.03
90 1 0.01
91 48 0.68
ACGTcount: A:0.25, C:0.21, G:0.25, T:0.28
Consensus pattern (91 bp):
GCAACTTCAGGGGGACAAGATTCGATGTGATTTTAGTCTACTCCACTGCAACGTCAGGGAGATAA
GACTTGTAGCTTCAATCTGCCCCACT
Found at i:53932493 original size:87 final size:87
Alignment explanation
Indices: 53932434--53934183 Score: 2368
Period size: 87 Copynumber: 20.1 Consensus size: 87
53932424 TACAGAAAGA
* *
53932434 CAAGATCTGCTATCTTTAACCAACTCCACTGCAACCGATGGAGGCAA-GCTTTGTTTTCGATCTG
1 CAAGATCTGCTATCTTTAACCAGCTCCACTACAACCGATGGAGGCAAGGCTTTGTTTTCGATCTG
*
53932498 CTTCGCTGTTAATGCATGAAGG
66 CTTCGCTGTTAATGCAGGAAGG
* *
53932520 CAAGATCTGTTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTTCGATCTG
1 CAAGATCTGCTATCTTTAACCAGCTCCACTACAACCGATGGAGGCAAGGCTTTGTTTTCGATCTG
*
53932585 CTTCGCTGTTAACGCAGGAAGG
66 CTTCGCTGTTAATGCAGGAAGG
*
53932607 CAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGC-TTG-TTTCGATCTG
1 CAAGATCTGCTATCTTTAACCAGCTCCACTACAACCGATGGAGGCAAGGCTTTGTTTTCGATCTG
* * *
53932670 CTTTGATGCTAATGCAGGAAGG
66 CTTCGCTGTTAATGCAGGAAGG
* * *
53932692 CAAGATCTGCGATATTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTTCGATCTG
1 CAAGATCTGCTATCTTTAACCAGCTCCACTACAACCGATGGAGGCAAGGCTTTGTTTTCGATCTG
* **
53932757 CTTCACTGTTAATGCATAAAGG
66 CTTCGCTGTTAATGCAGGAAGG
* *
53932779 CAAGATCTGTTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTTCGATCTG
1 CAAGATCTGCTATCTTTAACCAGCTCCACTACAACCGATGGAGGCAAGGCTTTGTTTTCGATCTG
*
53932844 CTTCGCTGTTAACGCAGGAAGG
66 CTTCGCTGTTAATGCAGGAAGG
*
53932866 CAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTTCGATCTG
1 CAAGATCTGCTATCTTTAACCAGCTCCACTACAACCGATGGAGGCAAGGCTTTGTTTTCGATCTG
* *
53932931 CTTTGCTGTTAACGCAGGAAGG
66 CTTCGCTGTTAATGCAGGAAGG
* *
53932953 CAAGATCTGCGATATTTAACCAGCTCCACTACAACCGATGGAGGCAAGGCTTTGTTTTCGATCTG
1 CAAGATCTGCTATCTTTAACCAGCTCCACTACAACCGATGGAGGCAAGGCTTTGTTTTCGATCTG
*
53933018 CTTCGCTGTTAATGCATGAAGG
66 CTTCGCTGTTAATGCAGGAAGG
*
53933040 CAAGATCTGCTTTCTTTAACCAGCTCCACTACAACCGATGGAGGCAAGGCTTTGTTTTCGATCTG
1 CAAGATCTGCTATCTTTAACCAGCTCCACTACAACCGATGGAGGCAAGGCTTTGTTTTCGATCTG
*
53933105 CTTCGCTGTTAATGCATGAAGG
66 CTTCGCTGTTAATGCAGGAAGG
* *
53933127 CAAGATCTGCTTTCTTTAACCAGCTCCACTACAACCAATGGAGGCAAGGCTTTGTTTTCGATCTG
1 CAAGATCTGCTATCTTTAACCAGCTCCACTACAACCGATGGAGGCAAGGCTTTGTTTTCGATCTG
*
53933192 CTTCGTTGTTAATGCAGGAAGG
66 CTTCGCTGTTAATGCAGGAAGG
* * * *
53933214 CAAGATTTGCTTTCTTTAACCAGCTCCACTGCAACCGATGAAGGCAAGGCTTTGTTTTCGATCTG
1 CAAGATCTGCTATCTTTAACCAGCTCCACTACAACCGATGGAGGCAAGGCTTTGTTTTCGATCTG
*
53933279 CTTGGCTGTTAATGCAGGAAGG
66 CTTCGCTGTTAATGCAGGAAGG
* *
53933301 CAAGACCTGCT-TCTTTAACCAGCTACACTACAACCGATGGAGGCAAGGCTTTGTTTTCGATCTG
1 CAAGATCTGCTATCTTTAACCAGCTCCACTACAACCGATGGAGGCAAGGCTTTGTTTTCGATCTG
*
53933365 CTTCGCT-TTCAATGCATGAAGG
66 CTTCGCTGTT-AATGCAGGAAGG
* * *
53933387 CAAGATCTGCTTTCTTTAACCAGCTCCACTACAACCGATAGAGGCAAGGCTTTGCTTTCGATCTG
1 CAAGATCTGCTATCTTTAACCAGCTCCACTACAACCGATGGAGGCAAGGCTTTGTTTTCGATCTG
53933452 CTTCGCTGTTAATGCAGGAAGG
66 CTTCGCTGTTAATGCAGGAAGG
* * *
53933474 CAAGATCTGCTTTCTTTAACCAGCTCCACTACAACCTATGGAGGCAAGCCTTTGTTTTCGATCTG
1 CAAGATCTGCTATCTTTAACCAGCTCCACTACAACCGATGGAGGCAAGGCTTTGTTTTCGATCTG
*
53933539 CTTCGCTGTTAATGCAGGAATG
66 CTTCGCTGTTAATGCAGGAAGG
* *
53933561 CAAGATATGCT-TCTTTAACCAGCTCCACTACAACCGATGGAGGCGAGGCTTTGTTTTCGATCTG
1 CAAGATCTGCTATCTTTAACCAGCTCCACTACAACCGATGGAGGCAAGGCTTTGTTTTCGATCTG
* *
53933625 CTTCGCTGTTAATACATGAAGG
66 CTTCGCTGTTAATGCAGGAAGG
* * * *
53933647 CAAGATCTGCTTTCTTTAACCAGCTCCACCACAACCGAGGGAGGCAAGG-TTTGTGTCTTCAATC
1 CAAGATCTGCTATCTTTAACCAGCTCCACTACAACCGATGGAGGCAAGGCTTTGT-T-TTCGATC
* *
53933711 TGCTTCACTGTCAATGCAGGAAGG
64 TGCTTCGCTGTTAATGCAGGAAGG
* * * * * * *
53933735 CAAGATCTGTTGTCTTCAACCAGCTCCATTACAACTGA-GAGAGGCAAGG-TTTGTGTCTCCGAC
1 CAAGATCTGCTATCTTTAACCAGCTCCACTACAACCGATG-GAGGCAAGGCTTTGT-T-TTCGAT
*
53933798 CTGCTTCGCTGTCAATGCAGGAAGG
63 CTGCTTCGCTGTTAATGCAGGAAGG
** * * *
53933823 CAAGATCTTTTGTCTTCAACCAGCTTCA-TCACAACCGA-GAGAGGCAAGG-TTTGTGTCTTCGA
1 CAAGATCTGCTATCTTTAACCAGCTCCACT-ACAACCGATG-GAGGCAAGGCTTTGT-T-TTCGA
*
53933885 TCTGCTTCGCTGTCAATGCAGGAAGG
62 TCTGCTTCGCTGTTAATGCAGGAAGG
* * * *
53933911 CAAGATCTGTTGTCTTCAACCAGCTCCA-TCACAACCGA-GAGAGGTAAGG-TTTGTGTCTTCGA
1 CAAGATCTGCTATCTTTAACCAGCTCCACT-ACAACCGATG-GAGGCAAGGCTTTGT-T-TTCGA
* *
53933973 CCTGCTTCGCTGTCAATGCAGGAAGG
62 TCTGCTTCGCTGTTAATGCAGGAAGG
* * * * * *
53933999 CAAGATCTGTTGTCTTCAACCAGCTCCACCACAGCCGAGGGAGGCAAGG-TTTGTGTCTTCGATC
1 CAAGATCTGCTATCTTTAACCAGCTCCACTACAACCGATGGAGGCAAGGCTTTGT-T-TTCGATC
* **
53934063 TGCTTCGCTGTCAATGCAGGAATA
64 TGCTTCGCTGTTAATGCAGGAAGG
* * *
53934087 CAAGATCTGTTGTCTTCAACCAGCTCCA-TCACAACCGA-GAGAGGCAAGG-TTTGTGTCTTCGA
1 CAAGATCTGCTATCTTTAACCAGCTCCACT-ACAACCGATG-GAGGCAAGGCTTTGT-T-TTCGA
* * * *
53934149 ACTGCTTCGCTGTCAAGGCAGGAATG
62 TCTGCTTCGCTGTTAATGCAGGAAGG
53934175 CAAGATCTG
1 CAAGATCTG
53934184 TTATATTCAC
Statistics
Matches: 1542, Mismatches: 107, Indels: 28
0.92 0.06 0.02
Matches are distributed among these distances:
85 78 0.05
86 212 0.14
87 814 0.53
88 437 0.28
89 1 0.00
ACGTcount: A:0.24, C:0.24, G:0.23, T:0.29
Consensus pattern (87 bp):
CAAGATCTGCTATCTTTAACCAGCTCCACTACAACCGATGGAGGCAAGGCTTTGTTTTCGATCTG
CTTCGCTGTTAATGCAGGAAGG
Found at i:53933087 original size:44 final size:44
Alignment explanation
Indices: 53933037--53933174 Score: 106
Period size: 44 Copynumber: 3.2 Consensus size: 44
53933027 TAATGCATGA
53933037 AGGCAAGATCTGCTTTCTTTAACCAGCTCCACTACAACCGATGG
1 AGGCAAGATCTGCTTTCTTTAACCAGCTCCACTACAACCGATGG
* * * * * * ** * *
53933081 AGGCAAG----GCTTTGTTTTCGATCTGCTTCGCTGTTAA-TGCATGA
1 AGGCAAGATCTGCTTT-CTTT-AACCAGCTCCACT-ACAACCG-ATGG
*
53933124 AGGCAAGATCTGCTTTCTTTAACCAGCTCCACTACAACCAATGG
1 AGGCAAGATCTGCTTTCTTTAACCAGCTCCACTACAACCGATGG
53933168 AGGCAAG
1 AGGCAAG
53933175 GCTTTGTTTT
Statistics
Matches: 64, Mismatches: 21, Indels: 18
0.62 0.20 0.17
Matches are distributed among these distances:
40 5 0.08
41 3 0.05
42 9 0.14
43 12 0.19
44 19 0.30
45 8 0.12
46 3 0.05
47 5 0.08
ACGTcount: A:0.26, C:0.25, G:0.21, T:0.28
Consensus pattern (44 bp):
AGGCAAGATCTGCTTTCTTTAACCAGCTCCACTACAACCGATGG
Found at i:53935452 original size:24 final size:24
Alignment explanation
Indices: 53935412--53935457 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
53935402 ATTTTTACTC
*
53935412 TTTCATTTTTTCATTTTTTTTTCA
1 TTTCATTTTTTCATTTTGTTTTCA
**
53935436 TTTCATTTTTTTGTTTTGTTTT
1 TTTCATTTTTTCATTTTGTTTT
53935458 GTTTTTTTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.09, C:0.09, G:0.04, T:0.78
Consensus pattern (24 bp):
TTTCATTTTTTCATTTTGTTTTCA
Found at i:53936300 original size:6 final size:7
Alignment explanation
Indices: 53936283--53936309 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
53936273 TTTTTTGGAT
53936283 TTTTTTA
1 TTTTTTA
53936290 TTTTTTA
1 TTTTTTA
53936297 TTTTTTA
1 TTTTTTA
53936304 TTTTTT
1 TTTTTT
53936310 TTGAGTTTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.11, C:0.00, G:0.00, T:0.89
Consensus pattern (7 bp):
TTTTTTA
Found at i:53937591 original size:15 final size:15
Alignment explanation
Indices: 53937571--53937600 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
53937561 AATATTCTCT
*
53937571 AATGCATGTAATGCG
1 AATGCATGAAATGCG
53937586 AATGCATGAAATGCG
1 AATGCATGAAATGCG
53937601 TGCCTACAGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.37, C:0.13, G:0.27, T:0.23
Consensus pattern (15 bp):
AATGCATGAAATGCG
Found at i:53939519 original size:3 final size:3
Alignment explanation
Indices: 53939511--53939566 Score: 112
Period size: 3 Copynumber: 18.7 Consensus size: 3
53939501 TAAATAAAAC
53939511 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
53939559 AAT AAT AA
1 AAT AAT AA
53939567 AACGTAAATA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:53940484 original size:15 final size:15
Alignment explanation
Indices: 53940447--53940485 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
53940437 TATTGTTTTG
*
53940447 AAATAAAAAAATCAA
1 AAATAAAAAAAACAA
* *
53940462 GAAGAAAAAAAACAA
1 AAATAAAAAAAACAA
53940477 AAATAAAAA
1 AAATAAAAA
53940486 TAAGAAAGCA
Statistics
Matches: 19, Mismatches: 5, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.82, C:0.05, G:0.05, T:0.08
Consensus pattern (15 bp):
AAATAAAAAAAACAA
Found at i:53942214 original size:6 final size:6
Alignment explanation
Indices: 53942205--53942241 Score: 56
Period size: 6 Copynumber: 5.8 Consensus size: 6
53942195 TCTATTTCTA
53942205 AAAAAT AAAAAAT AAAAAGT AAAAAT AAAAAT AAAAA
1 AAAAAT -AAAAAT AAAAA-T AAAAAT AAAAAT AAAAA
53942242 ATATTTTCAA
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
6 17 0.59
7 12 0.41
ACGTcount: A:0.84, C:0.00, G:0.03, T:0.14
Consensus pattern (6 bp):
AAAAAT
Found at i:53942215 original size:7 final size:7
Alignment explanation
Indices: 53942203--53942244 Score: 61
Period size: 7 Copynumber: 6.3 Consensus size: 7
53942193 TTTCTATTTC
53942203 TAAAAAA
1 TAAAAAA
53942210 TAAAAAA
1 TAAAAAA
*
53942217 TAAAAAG
1 TAAAAAA
53942224 T-AAAAA
1 TAAAAAA
53942230 T-AAAAA
1 TAAAAAA
53942236 TAAAAAA
1 TAAAAAA
53942243 TA
1 TA
53942245 TTTTCAAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
6 11 0.34
7 21 0.66
ACGTcount: A:0.81, C:0.00, G:0.02, T:0.17
Consensus pattern (7 bp):
TAAAAAA
Found at i:53942242 original size:13 final size:13
Alignment explanation
Indices: 53942205--53942244 Score: 64
Period size: 13 Copynumber: 3.1 Consensus size: 13
53942195 TCTATTTCTA
53942205 AAAAATAAAAAAT
1 AAAAATAAAAAAT
53942218 AAAAAGT-AAAAAT
1 AAAAA-TAAAAAAT
53942231 AAAAATAAAAAAT
1 AAAAATAAAAAAT
53942244 A
1 A
53942245 TTTTCAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
12 1 0.04
13 23 0.92
14 1 0.04
ACGTcount: A:0.82, C:0.00, G:0.03, T:0.15
Consensus pattern (13 bp):
AAAAATAAAAAAT
Found at i:53946804 original size:27 final size:28
Alignment explanation
Indices: 53946774--53946832 Score: 66
Period size: 27 Copynumber: 2.1 Consensus size: 28
53946764 TTTTTGTCAA
*
53946774 AATTCACACTTTAATTA-TAAAATAATT
1 AATTCACACTTAAATTATTAAAATAATT
** * *
53946801 AATTTGCACTTAAATTATTAACATATTT
1 AATTCACACTTAAATTATTAAAATAATT
53946829 AATT
1 AATT
53946833 TTAATTATTT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
27 14 0.54
28 12 0.46
ACGTcount: A:0.44, C:0.10, G:0.02, T:0.44
Consensus pattern (28 bp):
AATTCACACTTAAATTATTAAAATAATT
Found at i:53949002 original size:13 final size:13
Alignment explanation
Indices: 53948984--53949008 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
53948974 GAGATGATGA
53948984 TTTTTTCTAAATT
1 TTTTTTCTAAATT
53948997 TTTTTTCTAAAT
1 TTTTTTCTAAAT
53949009 AAGGCAATAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.08, G:0.00, T:0.68
Consensus pattern (13 bp):
TTTTTTCTAAATT
Found at i:53950842 original size:19 final size:19
Alignment explanation
Indices: 53950818--53950864 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
53950808 AATGTCTCTT
*
53950818 TTTGCATT-CATTTCATGCA
1 TTTGCATTACATTGCAT-CA
53950837 TTTGCATTACATTGCATCA
1 TTTGCATTACATTGCATCA
*
53950856 TATGCATTA
1 TTTGCATTA
53950865 GATTTTCACA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 18 0.72
20 7 0.28
ACGTcount: A:0.26, C:0.19, G:0.11, T:0.45
Consensus pattern (19 bp):
TTTGCATTACATTGCATCA
Found at i:53953726 original size:6 final size:6
Alignment explanation
Indices: 53953715--53953803 Score: 67
Period size: 6 Copynumber: 14.7 Consensus size: 6
53953705 AAAAGAGAGA
* * *
53953715 AAAAAG AAAAAG AAGGAAA- TAGAAG AAAAAAG AAAGAAG AAGAAG -AAAAG
1 AAAAAG AAAAAG AA--AAAG AAAAAG A-AAAAG AAA-AAG AAAAAG AAAAAG
* * *
53953765 AAAAAG -AAAAG GAAAAG AAAAAG TAAAAG TAAAAG AAAA
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAA
53953804 TGAGAGGCCA
Statistics
Matches: 67, Mismatches: 9, Indels: 14
0.74 0.10 0.16
Matches are distributed among these distances:
5 11 0.16
6 42 0.63
7 11 0.16
8 3 0.04
ACGTcount: A:0.75, C:0.00, G:0.21, T:0.03
Consensus pattern (6 bp):
AAAAAG
Found at i:53953744 original size:20 final size:20
Alignment explanation
Indices: 53953703--53953772 Score: 69
Period size: 20 Copynumber: 3.6 Consensus size: 20
53953693 AATGTTAAGA
*
53953703 AAAAAAGAGAGAA-AA-AAG
1 AAAAAAGAAAGAAGAAGAAG
*
53953721 -AAAAAGAAGGAA-ATAGAAG
1 AAAAAAGAAAGAAGA-AGAAG
53953740 AAAAAAGAAAGAAGAAGAAG
1 AAAAAAGAAAGAAGAAGAAG
53953760 AAAAGAA-AAAGAA
1 AAAA-AAGAAAGAA
53953773 AAGGAAAAGA
Statistics
Matches: 44, Mismatches: 3, Indels: 8
0.80 0.05 0.15
Matches are distributed among these distances:
17 11 0.25
18 1 0.02
19 3 0.07
20 26 0.59
21 3 0.07
ACGTcount: A:0.76, C:0.00, G:0.23, T:0.01
Consensus pattern (20 bp):
AAAAAAGAAAGAAGAAGAAG
Found at i:53953765 original size:11 final size:11
Alignment explanation
Indices: 53953699--53953785 Score: 58
Period size: 11 Copynumber: 7.9 Consensus size: 11
53953689 AAAAAATGTT
*
53953699 AAGAAAAAAAG
1 AAGAAGAAAAG
53953710 AGAGAA-AAAAG
1 A-AGAAGAAAAG
*
53953721 AAAAAGAAGGAA-
1 AAGAAGAA--AAG
53953733 ATAGAAGAAAA-
1 A-AGAAGAAAAG
*
53953744 AAGAA-AGAAG
1 AAGAAGAAAAG
53953754 AAGAAGAAAAG
1 AAGAAGAAAAG
*
53953765 AAAAAGAAAAGG
1 AAGAAGAAAA-G
53953777 AA-AAGAAAA
1 AAGAAGAAAA
53953786 AGTAAAAGTA
Statistics
Matches: 63, Mismatches: 5, Indels: 16
0.75 0.06 0.19
Matches are distributed among these distances:
9 3 0.05
10 12 0.19
11 32 0.51
12 8 0.13
13 8 0.13
ACGTcount: A:0.76, C:0.00, G:0.23, T:0.01
Consensus pattern (11 bp):
AAGAAGAAAAG
Found at i:53953803 original size:11 final size:11
Alignment explanation
Indices: 53953716--53953803 Score: 72
Period size: 11 Copynumber: 7.8 Consensus size: 11
53953706 AAAGAGAGAA
53953716 AAAAGAAAAAG
1 AAAAGAAAAAG
* *
53953727 -AAGGAAATAG
1 AAAAGAAAAAG
*
53953737 AAGA-AAAAAG
1 AAAAGAAAAAG
*
53953747 AAAGAAGAAGAAG
1 -AA-AAGAAAAAG
53953760 AAAAGAAAAAG
1 AAAAGAAAAAG
*
53953771 AAAAGGAAAAG
1 AAAAGAAAAAG
*
53953782 AAAAAGTAAAAG
1 -AAAAGAAAAAG
53953794 TAAAAGAAAA
1 -AAAAGAAAA
53953804 TGAGAGGCCA
Statistics
Matches: 60, Mismatches: 12, Indels: 9
0.74 0.15 0.11
Matches are distributed among these distances:
10 13 0.22
11 21 0.35
12 21 0.35
13 5 0.08
ACGTcount: A:0.75, C:0.00, G:0.22, T:0.03
Consensus pattern (11 bp):
AAAAGAAAAAG
Found at i:53953803 original size:18 final size:16
Alignment explanation
Indices: 53953715--53953803 Score: 83
Period size: 17 Copynumber: 5.2 Consensus size: 16
53953705 AAAAGAGAGA
*
53953715 AAAAAGAAAA-AGAAGG
1 AAAAAGAAAAGA-AAAG
*
53953731 AAATAGAAGAA-AAAAG
1 AAAAAGAA-AAGAAAAG
53953747 AAAGAAGAAGAAGAAAAG
1 AAA-AAGAA-AAGAAAAG
53953765 AAAAAGAAAAGGAAAAG
1 AAAAAGAAAA-GAAAAG
53953782 AAAAAGTAAAAGTAAAAG
1 AAAAAG-AAAAG-AAAAG
53953800 AAAA
1 AAAA
53953804 TGAGAGGCCA
Statistics
Matches: 64, Mismatches: 3, Indels: 10
0.83 0.04 0.13
Matches are distributed among these distances:
16 15 0.23
17 28 0.44
18 21 0.33
ACGTcount: A:0.75, C:0.00, G:0.21, T:0.03
Consensus pattern (16 bp):
AAAAAGAAAAGAAAAG
Found at i:53955268 original size:89 final size:89
Alignment explanation
Indices: 53955129--53955681 Score: 822
Period size: 89 Copynumber: 6.2 Consensus size: 89
53955119 CTAAAAACAA
* *
53955129 CAGATCTTGCCTTCCTGTACTGACGGCAAAGCAGAAT-GAAGACA-TCAGCCTTGCCTTCGTGTA
1 CAGATCTTGCCTTCCTGTACTGACGGCGAAGCAG-ATCGAAGACACT-AGCCTTGCCTTCCTGTA
53955192 CTGACAGCGGAGCAGACTGAAGATAG
64 CTGACAGCGGAGCAGACTGAAGATAG
* *
53955218 CAGATATTGCCTTCCTGTACTGACGGTGAAGCAGATCGAAGACACTAGCCTTGCCTTCCTGTACT
1 CAGATCTTGCCTTCCTGTACTGACGGCGAAGCAGATCGAAGACACTAGCCTTGCCTTCCTGTACT
*
53955283 GACAGCGGAGTAGACTGAAGATAG
66 GACAGCGGAGCAGACTGAAGATAG
*
53955307 CAGATCTTGCCTTCCTGTACTGACGGTGAAGCAGATCGAAGACACTAGCCTTGCCTTCCTGTACT
1 CAGATCTTGCCTTCCTGTACTGACGGCGAAGCAGATCGAAGACACTAGCCTTGCCTTCCTGTACT
*
53955372 GACAGCGGAGTAGACTGAAGATAG
66 GACAGCGGAGCAGACTGAAGATAG
* * *
53955396 CAGATCTTGCCTTCCTGTACTGATGGCGAAGCAGATTGAAGACACTAGCCTTGCCTTCCTATACT
1 CAGATCTTGCCTTCCTGTACTGACGGCGAAGCAGATCGAAGACACTAGCCTTGCCTTCCTGTACT
53955461 GACAGCGGAGCAGACTGAAGATAG
66 GACAGCGGAGCAGACTGAAGATAG
* * ** * *
53955485 CAGATCTTGCCTTCATGTACTAATAGAGAAGCAGATCGAAGACACCAGCCTTGCCTTCCTGTACT
1 CAGATCTTGCCTTCCTGTACTGACGGCGAAGCAGATCGAAGACACTAGCCTTGCCTTCCTGTACT
* *
53955550 GACAGCGAAGCAGACTGAAGATAA
66 GACAGCGGAGCAGACTGAAGATAG
* * * * * *
53955574 CAGATCTTGCCTTCCTATACTGACAGCGAAGCAGATCGAAGACACCAGTCTTGCATTCCAGTACT
1 CAGATCTTGCCTTCCTGTACTGACGGCGAAGCAGATCGAAGACACTAGCCTTGCCTTCCTGTACT
* *
53955639 GACAGCGGAGTAGGCTGAAGATAG
66 GACAGCGGAGCAGACTGAAGATAG
* *
53955663 AAGATCTTGCCTTCTTGTA
1 CAGATCTTGCCTTCCTGTA
53955682 AGACAATGTT
Statistics
Matches: 427, Mismatches: 35, Indels: 4
0.92 0.08 0.01
Matches are distributed among these distances:
88 2 0.00
89 424 0.99
90 1 0.00
ACGTcount: A:0.28, C:0.24, G:0.24, T:0.23
Consensus pattern (89 bp):
CAGATCTTGCCTTCCTGTACTGACGGCGAAGCAGATCGAAGACACTAGCCTTGCCTTCCTGTACT
GACAGCGGAGCAGACTGAAGATAG
Found at i:53958764 original size:14 final size:14
Alignment explanation
Indices: 53958747--53958776 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
53958737 ACTTGAGCCA
*
53958747 CAAGCCTTGTGGGC
1 CAAGCCGTGTGGGC
53958761 CAAGCCGTGTGGGC
1 CAAGCCGTGTGGGC
53958775 CA
1 CA
53958777 CACGGGTCAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.17, C:0.30, G:0.37, T:0.17
Consensus pattern (14 bp):
CAAGCCGTGTGGGC
Found at i:53961574 original size:29 final size:30
Alignment explanation
Indices: 53961540--53961601 Score: 81
Period size: 31 Copynumber: 2.1 Consensus size: 30
53961530 GTTTCACGTG
53961540 TATAATT-ATACCAAATTAAAATTCATATA
1 TATAATTAATACCAAATTAAAATTCATATA
** *
53961569 TATAATTACATATTAAATTAAAGTTCATATA
1 TATAATTA-ATACCAAATTAAAATTCATATA
53961600 TA
1 TA
53961602 ATTTTAAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 7 0.25
31 21 0.75
ACGTcount: A:0.50, C:0.08, G:0.02, T:0.40
Consensus pattern (30 bp):
TATAATTAATACCAAATTAAAATTCATATA
Found at i:53969594 original size:17 final size:16
Alignment explanation
Indices: 53969569--53969627 Score: 64
Period size: 17 Copynumber: 3.6 Consensus size: 16
53969559 GCAACCCAAT
*
53969569 TTTTATTTTTTATTTT
1 TTTTATTTTTTATTTA
*
53969585 TTTTATTTTTTTCTTTA
1 TTTTA-TTTTTTATTTA
* *
53969602 CTTTATTTATTACTTTA
1 TTTTATTTTTTA-TTTA
53969619 TTTTATTTT
1 TTTTATTTT
53969628 ATTTTACTTA
Statistics
Matches: 34, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
16 10 0.29
17 24 0.71
ACGTcount: A:0.15, C:0.05, G:0.00, T:0.80
Consensus pattern (16 bp):
TTTTATTTTTTATTTA
Found at i:53977394 original size:21 final size:22
Alignment explanation
Indices: 53977349--53977395 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
53977339 TAACATGTTG
53977349 AATTTTAATTAATTTTATAATA
1 AATTTTAATTAATTTTATAATA
* * *
53977371 AATTTTGATTTATTTT-TGATA
1 AATTTTAATTAATTTTATAATA
53977392 AATT
1 AATT
53977396 CACACAAAGG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 8 0.36
22 14 0.64
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.57
Consensus pattern (22 bp):
AATTTTAATTAATTTTATAATA
Found at i:53979946 original size:27 final size:27
Alignment explanation
Indices: 53979916--53979967 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
53979906 AAATGTTTAT
*
53979916 TTTAAGTCATTTTATGTTAGAGTCTGG
1 TTTAAGTCAATTTATGTTAGAGTCTGG
*
53979943 TTTAAGTCAATTTATGTTAGTGTCT
1 TTTAAGTCAATTTATGTTAGAGTCT
53979968 CGAAACATCA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.23, C:0.08, G:0.19, T:0.50
Consensus pattern (27 bp):
TTTAAGTCAATTTATGTTAGAGTCTGG
Found at i:53983688 original size:15 final size:14
Alignment explanation
Indices: 53983661--53983687 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
53983651 AGGGTTAGTA
53983661 AAATATTAAAAAAT
1 AAATATTAAAAAAT
53983675 AAATATTAAAAAA
1 AAATATTAAAAAA
53983688 ACACAAGACA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (14 bp):
AAATATTAAAAAAT
Found at i:53984621 original size:29 final size:29
Alignment explanation
Indices: 53984558--53984627 Score: 72
Period size: 29 Copynumber: 2.4 Consensus size: 29
53984548 GTTAATGATT
53984558 TGTA-AAAATTGAATAAAATAAAAAATTCA
1 TGTATAAAATT-AATAAAATAAAAAATTCA
* * *
53984587 TATATAAAATTACATAAAAT-CAAAATTTA
1 TGTATAAAATTA-ATAAAATAAAAAATTCA
*
53984616 TGTATAACATTA
1 TGTATAAAATTA
53984628 TACATTTAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
29 21 0.62
30 13 0.38
ACGTcount: A:0.57, C:0.06, G:0.04, T:0.33
Consensus pattern (29 bp):
TGTATAAAATTAATAAAATAAAAAATTCA
Found at i:53985574 original size:72 final size:71
Alignment explanation
Indices: 53985394--53985591 Score: 208
Period size: 72 Copynumber: 2.8 Consensus size: 71
53985384 AGTTAGATCA
* * *
53985394 TTAGCGGCGTTTTACTG-AAAGCGCCGC--AAAAACCAAAGACAAACGATGCCGTTTCTGAGTTT
1 TTAGCGGCGTTTT--TGAAAAGCGCCGCTAAAAAACCTAAGACAAACGGTGCCGTTTCGGAGTTT
53985456 TTGGGGAT
64 TTGGGGAT
* * ****
53985464 TTAGCGACGTTTTT-AATCAAGCGCCACTAATTTTCCTAAGACAAACGGTGCCGTTTCGGTAGTT
1 TTAGCGGCGTTTTTGAA--AAGCGCCGCTAAAAAACCTAAGACAAACGGTGCCGTTTCGG-AGTT
53985528 TTT-GGGAT
63 TTTGGGGAT
* *
53985536 TTAGCGGCGTTTTTGGAAAAGCGCCGCTAAAAAACCTAAGCCAAACGGTGTCGTTT
1 TTAGCGGCGTTTTT-GAAAAGCGCCGCTAAAAAACCTAAGACAAACGGTGCCGTTT
53985592 TCCAAGCTTT
Statistics
Matches: 103, Mismatches: 17, Indels: 14
0.77 0.13 0.10
Matches are distributed among these distances:
68 2 0.02
70 20 0.19
72 72 0.70
73 7 0.07
74 2 0.02
ACGTcount: A:0.27, C:0.20, G:0.24, T:0.29
Consensus pattern (71 bp):
TTAGCGGCGTTTTTGAAAAGCGCCGCTAAAAAACCTAAGACAAACGGTGCCGTTTCGGAGTTTTT
GGGGAT
Found at i:53986436 original size:13 final size:13
Alignment explanation
Indices: 53986414--53986455 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 13
53986404 TGAGTTTGGG
* *
53986414 GTTTAAGGTTTGA
1 GTTTAGGGTTTTA
53986427 GTTTAGGGTTTTA
1 GTTTAGGGTTTTA
*
53986440 G-CTAGGGTTTTA
1 GTTTAGGGTTTTA
53986452 GTTT
1 GTTT
53986456 GGAAATTGAA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
12 11 0.46
13 13 0.54
ACGTcount: A:0.17, C:0.02, G:0.31, T:0.50
Consensus pattern (13 bp):
GTTTAGGGTTTTA
Found at i:53986612 original size:14 final size:14
Alignment explanation
Indices: 53986584--53986672 Score: 58
Period size: 14 Copynumber: 6.4 Consensus size: 14
53986574 TTCCCAAAAA
53986584 TATGGTTTA-GGTT
1 TATGGTTTAGGGTT
53986597 TATGGTTTAGGGTT
1 TATGGTTTAGGGTT
** *
53986611 TACAGTTTAGAGTT
1 TATGGTTTAGGGTT
53986625 TA-GAGTTTTA-GGTT
1 TATG-G-TTTAGGGTT
** *
53986639 TGGGGTTTAGGATT
1 TATGGTTTAGGGTT
* * *
53986653 TAAGATTTAAGGTT
1 TATGGTTTAGGGTT
53986667 TATGGT
1 TATGGT
53986673 ATATATATTG
Statistics
Matches: 57, Mismatches: 14, Indels: 9
0.71 0.17 0.11
Matches are distributed among these distances:
13 13 0.23
14 39 0.68
15 5 0.09
ACGTcount: A:0.21, C:0.01, G:0.30, T:0.47
Consensus pattern (14 bp):
TATGGTTTAGGGTT
Found at i:53986639 original size:21 final size:19
Alignment explanation
Indices: 53986587--53986668 Score: 56
Period size: 21 Copynumber: 3.9 Consensus size: 19
53986577 CCAAAAATAT
53986587 GGTTTAGGTTTATGGTTTAG
1 GGTTTAGGTTTA-GGTTTAG
*
53986607 GGTTTACAGTTTAGAGTTTAG
1 GGTTTA-GGTTTAG-GTTTAG
* *
53986628 AGTTTTAGGTTTGGGGTTTAG
1 -GGTTTAGGTTT-AGGTTTAG
* *
53986649 GATTTAAGATTTAAGGTTTA
1 GGTTT-AGGTTT-AGGTTTA
53986669 TGGTATATAT
Statistics
Matches: 49, Mismatches: 8, Indels: 9
0.74 0.12 0.14
Matches are distributed among these distances:
20 11 0.22
21 32 0.65
22 6 0.12
ACGTcount: A:0.22, C:0.01, G:0.30, T:0.46
Consensus pattern (19 bp):
GGTTTAGGTTTAGGTTTAG
Found at i:53987238 original size:115 final size:114
Alignment explanation
Indices: 53987109--53987348 Score: 372
Period size: 115 Copynumber: 2.1 Consensus size: 114
53987099 GGCGCTTCAG
* * ** ** *
53987109 AAAAAATGCCGCTAAAGGTCATATATTACCGGCGTTTTTTGAAGAAACGCCGTAAATTTCCTTTA
1 AAAAAACGCCGCTAAAAGTCATATATTACCGGCGTTTTACGAAGAAACGCCACAAATTGCCTTTA
53987174 ACTGTAACAAAGACGGTGCCGTTTTGTTGTTTTCTTTTAGTGGCGCATTT
66 ACTGTAACAAAGACGGTGCCGTTTTGTTGTTTTCTTTTAGTGGCGCA-TT
* *
53987224 AAAAAACGCCGCTAAAAGTGATATGTTACCGGCGTTTTACGAAGAAACGCCACAAATTGCCTTTA
1 AAAAAACGCCGCTAAAAGTCATATATTACCGGCGTTTTACGAAGAAACGCCACAAATTGCCTTTA
*
53987289 ACTGTGACAAAGACGGTGCCGTTTTGTTGTTTTCTTTTAGTGGCGCATT
66 ACTGTAACAAAGACGGTGCCGTTTTGTTGTTTTCTTTTAGTGGCGCATT
53987338 ATAAAAACGCC
1 A-AAAAACGCC
53987349 ACAAATATTT
Statistics
Matches: 114, Mismatches: 10, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
114 3 0.03
115 111 0.97
ACGTcount: A:0.29, C:0.19, G:0.20, T:0.32
Consensus pattern (114 bp):
AAAAAACGCCGCTAAAAGTCATATATTACCGGCGTTTTACGAAGAAACGCCACAAATTGCCTTTA
ACTGTAACAAAGACGGTGCCGTTTTGTTGTTTTCTTTTAGTGGCGCATT
Found at i:53988264 original size:34 final size:34
Alignment explanation
Indices: 53988214--53988325 Score: 197
Period size: 34 Copynumber: 3.3 Consensus size: 34
53988204 CGTAAAAAAT
* *
53988214 GATTTTCCATCTGTAAAAATTGATTTTGCATTTA
1 GATTTTGCATCCGTAAAAATTGATTTTGCATTTA
53988248 GATTTTGCATCCGTAAAAATTGATTTTGCATTTA
1 GATTTTGCATCCGTAAAAATTGATTTTGCATTTA
*
53988282 GATTTTGCATCCGTAAAAAATGATTTTGCATTTA
1 GATTTTGCATCCGTAAAAATTGATTTTGCATTTA
53988316 GATTTTGCAT
1 GATTTTGCAT
53988326 GCTGGAAGAA
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
34 75 1.00
ACGTcount: A:0.29, C:0.12, G:0.14, T:0.45
Consensus pattern (34 bp):
GATTTTGCATCCGTAAAAATTGATTTTGCATTTA
Found at i:53989801 original size:24 final size:25
Alignment explanation
Indices: 53989768--53989826 Score: 86
Period size: 23 Copynumber: 2.4 Consensus size: 25
53989758 TAATATTCCG
*
53989768 ATATTAATTTTATTTACCTTGAATT
1 ATATTAATTTTATTTACCTTAAATT
53989793 ATA-TAA-TTTATTTACCTTAAATT
1 ATATTAATTTTATTTACCTTAAATT
*
53989816 TTATTAATTTT
1 ATATTAATTTT
53989827 TTAAATTTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
23 18 0.60
24 6 0.20
25 6 0.20
ACGTcount: A:0.34, C:0.07, G:0.02, T:0.58
Consensus pattern (25 bp):
ATATTAATTTTATTTACCTTAAATT
Found at i:53990046 original size:9 final size:9
Alignment explanation
Indices: 53990032--53990157 Score: 162
Period size: 9 Copynumber: 14.0 Consensus size: 9
53990022 AATTAAATAT
53990032 CTTACATAA
1 CTTACATAA
53990041 CTTACATAA
1 CTTACATAA
* * *
53990050 ATTAAATAT
1 CTTACATAA
53990059 CTTACATAA
1 CTTACATAA
53990068 CTTACATAA
1 CTTACATAA
* *
53990077 ATTAAATAA
1 CTTACATAA
53990086 CTTACATAA
1 CTTACATAA
53990095 CTTACATAA
1 CTTACATAA
* *
53990104 CTTAAATAT
1 CTTACATAA
53990113 CTTACATAA
1 CTTACATAA
53990122 CTTACATAA
1 CTTACATAA
* * *
53990131 ATTAAATAT
1 CTTACATAA
53990140 CTTACATAA
1 CTTACATAA
53990149 CTTACATAA
1 CTTACATAA
53990158 ATTAAGTAAA
Statistics
Matches: 97, Mismatches: 20, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
9 97 1.00
ACGTcount: A:0.48, C:0.17, G:0.00, T:0.36
Consensus pattern (9 bp):
CTTACATAA
Found at i:53990178 original size:27 final size:27
Alignment explanation
Indices: 53990020--53990162 Score: 268
Period size: 27 Copynumber: 5.3 Consensus size: 27
53990010 TTATGACATT
53990020 TAAATTAAATATCTTACATAACTTACA
1 TAAATTAAATATCTTACATAACTTACA
53990047 TAAATTAAATATCTTACATAACTTACA
1 TAAATTAAATATCTTACATAACTTACA
*
53990074 TAAATTAAATAACTTACATAACTTACA
1 TAAATTAAATATCTTACATAACTTACA
*
53990101 TAACTTAAATATCTTACATAACTTACA
1 TAAATTAAATATCTTACATAACTTACA
53990128 TAAATTAAATATCTTACATAACTTACA
1 TAAATTAAATATCTTACATAACTTACA
53990155 TAAATTAA
1 TAAATTAA
53990163 GTAAATTAAA
Statistics
Matches: 112, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 112 1.00
ACGTcount: A:0.49, C:0.15, G:0.00, T:0.36
Consensus pattern (27 bp):
TAAATTAAATATCTTACATAACTTACA
Found at i:53995743 original size:29 final size:29
Alignment explanation
Indices: 53995709--53995767 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
53995699 CGAGAGAAGC
53995709 AGAGGCCGCAGCGAAAGAAGCAGCGAGAG
1 AGAGGCCGCAGCGAAAGAAGCAGCGAGAG
*
53995738 AGAGGCCGCAGCGAGAGAAGCAGCGAGAG
1 AGAGGCCGCAGCGAAAGAAGCAGCGAGAG
53995767 A
1 A
53995768 AGTAGAGGCC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.37, C:0.20, G:0.42, T:0.00
Consensus pattern (29 bp):
AGAGGCCGCAGCGAAAGAAGCAGCGAGAG
Found at i:53995755 original size:15 final size:15
Alignment explanation
Indices: 53995709--53995755 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 15
53995699 CGAGAGAAGC
*
53995709 AGAGGCCGCAGCGAA
1 AGAGGCCGCAGCGAG
* * *
53995724 AGAAGCAGC-GAGAG
1 AGAGGCCGCAGCGAG
53995738 AGAGGCCGCAGCGAG
1 AGAGGCCGCAGCGAG
53995753 AGA
1 AGA
53995756 AGCAGCGAGA
Statistics
Matches: 24, Mismatches: 7, Indels: 2
0.73 0.21 0.06
Matches are distributed among these distances:
14 10 0.42
15 14 0.58
ACGTcount: A:0.36, C:0.21, G:0.43, T:0.00
Consensus pattern (15 bp):
AGAGGCCGCAGCGAG
Found at i:53995762 original size:12 final size:12
Alignment explanation
Indices: 53995716--53995769 Score: 54
Period size: 12 Copynumber: 4.1 Consensus size: 12
53995706 AGCAGAGGCC
*
53995716 GCAGCGAAAGAA
1 GCAGCGAGAGAA
53995728 GCAGCGAGAGAGA
1 GCAGCGAGAGA-A
53995741 GGCCGCAGCGAGAGAA
1 ----GCAGCGAGAGAA
53995757 GCAGCGAGAGAA
1 GCAGCGAGAGAA
53995769 G
1 G
53995770 TAGAGGCCGC
Statistics
Matches: 36, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
12 23 0.64
13 1 0.03
16 1 0.03
17 11 0.31
ACGTcount: A:0.39, C:0.19, G:0.43, T:0.00
Consensus pattern (12 bp):
GCAGCGAGAGAA
Found at i:53995781 original size:21 final size:21
Alignment explanation
Indices: 53995757--53995814 Score: 89
Period size: 21 Copynumber: 2.8 Consensus size: 21
53995747 AGCGAGAGAA
53995757 GCAGCGAGAGAAGTAGAGGCC
1 GCAGCGAGAGAAGTAGAGGCC
** *
53995778 GCAGTAAGAGAAGCAGAGGCC
1 GCAGCGAGAGAAGTAGAGGCC
53995799 GCAGCGAGAGAAGTAG
1 GCAGCGAGAGAAGTAG
53995815 CAATAGAAGC
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.36, C:0.17, G:0.41, T:0.05
Consensus pattern (21 bp):
GCAGCGAGAGAAGTAGAGGCC
Found at i:53995788 original size:33 final size:32
Alignment explanation
Indices: 53995699--53995793 Score: 117
Period size: 33 Copynumber: 3.0 Consensus size: 32
53995689 GCGGCTACAA
53995699 CGAGAGAAGCAGAGGCCGCAGCGAA-AGAAGCAG
1 CGAGAGAAG-AGAGGCCGCAGC-AAGAGAAGCAG
*
53995732 C--GAG-AGAGAGGCCGCAGCGAGAGAAGCAG
1 CGAGAGAAGAGAGGCCGCAGCAAGAGAAGCAG
*
53995761 CGAGAGAAGTAGAGGCCGCAGTAAGAGAAGCAG
1 CGAGAGAAG-AGAGGCCGCAGCAAGAGAAGCAG
53995794 AGGCCGCAGC
Statistics
Matches: 54, Mismatches: 3, Indels: 10
0.81 0.04 0.15
Matches are distributed among these distances:
28 1 0.02
29 21 0.39
30 2 0.04
31 6 0.11
32 2 0.04
33 22 0.41
ACGTcount: A:0.38, C:0.19, G:0.41, T:0.02
Consensus pattern (32 bp):
CGAGAGAAGAGAGGCCGCAGCAAGAGAAGCAG
Found at i:53995795 original size:29 final size:29
Alignment explanation
Indices: 53995701--53995795 Score: 95
Period size: 29 Copynumber: 3.1 Consensus size: 29
53995691 GGCTACAACG
53995701 AGAGAAGCAGAGGCCGCAGCGAA-AGAAGC
1 AGAGAAG-AGAGGCCGCAGCGAAGAGAAGC
* *
53995730 AGCGAGAGAGAGGCCGCAGCGAGAGAAGCAGC
1 AGAGA-AGAGAGGCCGCAGCGA-AG-AGAAGC
*
53995762 GAGAGAAGTAGAGGCCGCAG-TAAGAGAAGC
1 -AGAGAAG-AGAGGCCGCAGCGAAGAGAAGC
53995792 AGAG
1 AGAG
53995796 GCCGCAGCGA
Statistics
Matches: 55, Mismatches: 5, Indels: 12
0.76 0.07 0.17
Matches are distributed among these distances:
29 22 0.40
30 8 0.15
31 2 0.04
32 8 0.15
33 15 0.27
ACGTcount: A:0.39, C:0.18, G:0.41, T:0.02
Consensus pattern (29 bp):
AGAGAAGAGAGGCCGCAGCGAAGAGAAGC
Found at i:53996294 original size:42 final size:42
Alignment explanation
Indices: 53996245--53996601 Score: 382
Period size: 42 Copynumber: 8.4 Consensus size: 42
53996235 GCGTTTGTGA
53996245 AATAAGCGCCGCTAAAGAACACT-A-CTTTTAGCGGCGTTTTTT
1 AATAAGCGCCGCTAAAGAACA-TGATC-TTTAGCGGCGTTTTTT
* * ** *
53996287 AATAAGCGCCGCTATAGAACATTA-CTTTTAGAAGCGCTTTCTTC
1 AATAAGCGCCGCTAAAGAACATGATC-TTTAGCGGCG-TTT-TTT
* * *
53996331 CA-AATCGTCGCTAAAGAACATGATCTTTAGCGGCGTTTTTT
1 AATAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTT
* *
53996372 ACAAAAGCGCCGCTAAAGAACATGATCTTTAGCGGCATTTTTT
1 A-ATAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTT
** * **
53996415 CCTAAGCGTCGCTAAAGAACATGATCTTTAGCAACGTTTTTT
1 AATAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTT
* * *
53996457 TATAAGCTCCGCTAAAGAACATGATCTTTAGGGGCGTTTCTTT
1 AATAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTT-TTT
* *
53996500 -CTAAGCGCCGCTAAAGAGCATGATCTTTAGCGGCGTTTTTT
1 AATAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTT
**
53996541 TCTAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTT
1 AATAAGCGCCGCTAAAGAACATGATCTTTAGCGGCG-TTTTTT
* *
53996584 ATGTAAGCGCCGCAAAAG
1 A-ATAAGCGCCGCTAAAG
53996602 TTAGTGACGT
Statistics
Matches: 267, Mismatches: 38, Indels: 18
0.83 0.12 0.06
Matches are distributed among these distances:
41 6 0.02
42 170 0.64
43 73 0.27
44 18 0.07
ACGTcount: A:0.28, C:0.21, G:0.20, T:0.31
Consensus pattern (42 bp):
AATAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTT
Found at i:53996704 original size:22 final size:22
Alignment explanation
Indices: 53996673--53996715 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
53996663 TAGTGGCGTT
* *
53996673 AAAAAGCGCCGCTAAAGACCTA
1 AAAAAACGCCGCTAAAAACCTA
53996695 AAAAAACGCCGCTAAAAACCT
1 AAAAAACGCCGCTAAAAACCT
53996716 GTTCTGCTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.49, C:0.28, G:0.14, T:0.09
Consensus pattern (22 bp):
AAAAAACGCCGCTAAAAACCTA
Found at i:54001124 original size:42 final size:42
Alignment explanation
Indices: 54001078--54001215 Score: 154
Period size: 42 Copynumber: 3.3 Consensus size: 42
54001068 GACTTGTCTG
**
54001078 ATGATGCACTTATGTGCTTGTATATTTGCTTCGGTTCATCCA
1 ATGATGCACTTATGTGCTAATATATTTGCTTCGGTTCATCCA
* *
54001120 ATGATGCACTTATGTG-TCAATATATTTGTTTCAGTTCATCCAA
1 ATGATGCACTTATGTGCT-AATATATTTGCTTCGGTTCATCC-A
* * * *
54001163 AT-ATGCACTATGTGTGCCAATATATTTGCTTCGGTTTATCTA
1 ATGATGCACT-TATGTGCTAATATATTTGCTTCGGTTCATCCA
*
54001205 ATAATGCACTT
1 ATGATGCACTT
54001216 CGGTGCCAAA
Statistics
Matches: 81, Mismatches: 10, Indels: 10
0.80 0.10 0.10
Matches are distributed among these distances:
41 1 0.01
42 46 0.57
43 34 0.42
ACGTcount: A:0.25, C:0.17, G:0.16, T:0.42
Consensus pattern (42 bp):
ATGATGCACTTATGTGCTAATATATTTGCTTCGGTTCATCCA
Found at i:54001212 original size:43 final size:41
Alignment explanation
Indices: 54001098--54001214 Score: 146
Period size: 43 Copynumber: 2.8 Consensus size: 41
54001088 TATGTGCTTG
*
54001098 TATATTTGCTTCGGTTCATCCAATGATGCACTTATGTGTCAA
1 TATATTTGCTTCGGTTCATCCAATAATGCAC-TATGTGTCAA
* *
54001140 TATATTTGTTTCAGTTCATCCAA-ATATGCACTATGTGTGCCAA
1 TATATTTGCTTCGGTTCATCCAATA-ATGCACTATGTGT--CAA
* *
54001183 TATATTTGCTTCGGTTTATCTAATAATGCACT
1 TATATTTGCTTCGGTTCATCCAATAATGCACT
54001215 TCGGTGCCAA
Statistics
Matches: 64, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
41 7 0.11
42 27 0.42
43 29 0.45
44 1 0.02
ACGTcount: A:0.26, C:0.18, G:0.15, T:0.42
Consensus pattern (41 bp):
TATATTTGCTTCGGTTCATCCAATAATGCACTATGTGTCAA
Found at i:54004865 original size:19 final size:19
Alignment explanation
Indices: 54004841--54004878 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
54004831 GAGAAGGATT
*
54004841 ATTATGCCGTCTACAATTC
1 ATTATGCCATCTACAATTC
54004860 ATTATGCCATCTACAATTC
1 ATTATGCCATCTACAATTC
54004879 CAATTAGGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.29, C:0.26, G:0.08, T:0.37
Consensus pattern (19 bp):
ATTATGCCATCTACAATTC
Found at i:54006160 original size:31 final size:29
Alignment explanation
Indices: 54006125--54006182 Score: 71
Period size: 31 Copynumber: 1.9 Consensus size: 29
54006115 AATATTATTT
*
54006125 TATTAATTTTATATTAAAGTGATTATCTTAA
1 TATTAAATTTA-ATTAAA-TGATTATCTTAA
* *
54006156 TATTAAATTTAATTTAATGTTTATCTT
1 TATTAAATTTAATTAAATGATTATCTT
54006183 GTAGATAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 9 0.38
30 5 0.21
31 10 0.42
ACGTcount: A:0.36, C:0.03, G:0.05, T:0.55
Consensus pattern (29 bp):
TATTAAATTTAATTAAATGATTATCTTAA
Found at i:54006246 original size:17 final size:16
Alignment explanation
Indices: 54006212--54006266 Score: 60
Period size: 17 Copynumber: 3.4 Consensus size: 16
54006202 TTTTGATAAG
54006212 ATTTAATATTTAATTTA
1 ATTTAATATTT-ATTTA
54006229 ATTTAATATTTATCTTA
1 ATTTAATATTTAT-TTA
*
54006246 A-TAAATA-TTATATTA
1 ATTTAATATTTAT-TTA
54006261 ATTTAA
1 ATTTAA
54006267 AACTAAAGTG
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
15 8 0.24
16 10 0.30
17 15 0.45
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.55
Consensus pattern (16 bp):
ATTTAATATTTATTTA
Found at i:54006771 original size:14 final size:14
Alignment explanation
Indices: 54006752--54006778 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
54006742 TGTTATATCT
54006752 ATAAGCAAAAATAG
1 ATAAGCAAAAATAG
54006766 ATAAGCAAAAATA
1 ATAAGCAAAAATA
54006779 AATTTCTCTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.67, C:0.07, G:0.11, T:0.15
Consensus pattern (14 bp):
ATAAGCAAAAATAG
Found at i:54022530 original size:24 final size:24
Alignment explanation
Indices: 54022466--54022652 Score: 125
Period size: 23 Copynumber: 8.0 Consensus size: 24
54022456 ATATATACAT
54022466 ATTTTGATGCTTAAATGCT-TCCC
1 ATTTTGATGCTTAAATGCTGTCCC
* * * * * * *
54022489 AATTTGTTACATATATGCTGTACT
1 ATTTTGATGCTTAAATGCTGTCCC
54022513 ATTTTGATGCTTAAATGCTG-CCC
1 ATTTTGATGCTTAAATGCTGTCCC
* * * * *
54022536 AATTT-ATTACATATATGCTGTCCA
1 ATTTTGA-TGCTTAAATGCTGTCCC
*
54022560 ATTTTAATGCTTAAATGCTG-CCC
1 ATTTTGATGCTTAAATGCTGTCCC
* * * * *
54022583 AATTTGTTGCATATATGCTGTCCA
1 ATTTTGATGCTTAAATGCTGTCCC
54022607 ATTTTGATGCTTAAATGCTG-CCC
1 ATTTTGATGCTTAAATGCTGTCCC
* * *
54022630 AATTTGTTG-TATATATGCTGTCC
1 ATTTTGATGCT-TAAATGCTGTCC
54022653 AGTTTTGGTG
Statistics
Matches: 119, Mismatches: 38, Indels: 13
0.70 0.22 0.08
Matches are distributed among these distances:
22 2 0.02
23 63 0.53
24 53 0.45
25 1 0.01
ACGTcount: A:0.25, C:0.18, G:0.14, T:0.42
Consensus pattern (24 bp):
ATTTTGATGCTTAAATGCTGTCCC
Found at i:54022649 original size:23 final size:23
Alignment explanation
Indices: 54022527--54022726 Score: 127
Period size: 23 Copynumber: 8.5 Consensus size: 23
54022517 TGATGCTTAA
* **
54022527 ATGCTGCCCAATTTATTACATAT
1 ATGCTGCCCAATTTGTTGTATAT
* *
54022550 ATGCTGTCCAATTT-TAATGCT-TAA
1 ATGCTGCCCAATTTGT--TG-TATAT
*
54022574 ATGCTGCCCAATTTGTTGCATAT
1 ATGCTGCCCAATTTGTTGTATAT
* * *
54022597 ATGCTGTCCAATTTTGATGCT-TAA
1 ATGCTGCCCAA-TTTGTTG-TATAT
54022621 ATGCTGCCCAATTTGTTGTATAT
1 ATGCTGCCCAATTTGTTGTATAT
* * * * *
54022644 ATGCTGTCCAGTTTTGGTGTAAAA
1 ATGCTGCCCA-ATTTGTTGTATAT
* **
54022668 ATGCTGCTCAAACTGTTGTATATAT
1 ATGCTGCCCAATTTGTTG--TATAT
* *
54022693 ATGCTGCCCAAATTGTTGTATTT
1 ATGCTGCCCAATTTGTTGTATAT
*
54022716 ATGCTGTCCAA
1 ATGCTGCCCAA
54022727 ATTTTGGTGT
Statistics
Matches: 135, Mismatches: 31, Indels: 22
0.72 0.16 0.12
Matches are distributed among these distances:
22 2 0.01
23 62 0.46
24 51 0.38
25 20 0.15
ACGTcount: A:0.26, C:0.18, G:0.17, T:0.40
Consensus pattern (23 bp):
ATGCTGCCCAATTTGTTGTATAT
Found at i:54022664 original size:24 final size:23
Alignment explanation
Indices: 54022503--54022673 Score: 82
Period size: 24 Copynumber: 7.3 Consensus size: 23
54022493 TGTTACATAT
*
54022503 ATGCTGTACTATTTTGATGCT-TAA
1 ATGCTGT-CCATTTTGATG-TATAA
* * *
54022527 ATGCTGCCCAATTT-AT-TACATAT
1 ATGCTGTCCATTTTGATGT--ATAA
*
54022550 ATGCTGTCCAATTTTAATGCT-TAA
1 ATGCTGTCC-ATTTTGATG-TATAA
* * * * *
54022574 ATGCTGCCCAATTTGTTGCATAT
1 ATGCTGTCCATTTTGATGTATAA
54022597 ATGCTGTCCAATTTTGATGCT-TAA
1 ATGCTGTCC-ATTTTGATG-TATAA
* * * *
54022621 ATGCTGCCCAATTTGTTGTATAT
1 ATGCTGTCCATTTTGATGTATAA
* *
54022644 ATGCTGTCCAGTTTTGGTGTAAAA
1 ATGCTGTCCA-TTTTGATGTATAA
54022668 ATGCTG
1 ATGCTG
54022674 CTCAAACTGT
Statistics
Matches: 108, Mismatches: 27, Indels: 24
0.68 0.17 0.15
Matches are distributed among these distances:
20 1 0.01
22 3 0.03
23 49 0.45
24 52 0.48
25 2 0.02
27 1 0.01
ACGTcount: A:0.25, C:0.17, G:0.17, T:0.41
Consensus pattern (23 bp):
ATGCTGTCCATTTTGATGTATAA
Found at i:54022674 original size:47 final size:47
Alignment explanation
Indices: 54022466--54022659 Score: 307
Period size: 47 Copynumber: 4.1 Consensus size: 47
54022456 ATATATACAT
* * * *
54022466 ATTTTGATGCTTAAATGCTTCCCAATTTGTTACATATATGCTGTACT
1 ATTTTGATGCTTAAATGCTGCCCAATTTGTTGCATATATGCTGTCCA
* *
54022513 ATTTTGATGCTTAAATGCTGCCCAATTTATTACATATATGCTGTCCA
1 ATTTTGATGCTTAAATGCTGCCCAATTTGTTGCATATATGCTGTCCA
*
54022560 ATTTTAATGCTTAAATGCTGCCCAATTTGTTGCATATATGCTGTCCA
1 ATTTTGATGCTTAAATGCTGCCCAATTTGTTGCATATATGCTGTCCA
*
54022607 ATTTTGATGCTTAAATGCTGCCCAATTTGTTGTATATATGCTGTCCA
1 ATTTTGATGCTTAAATGCTGCCCAATTTGTTGCATATATGCTGTCCA
*
54022654 GTTTTG
1 ATTTTG
54022660 GTGTAAAAAT
Statistics
Matches: 137, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
47 137 1.00
ACGTcount: A:0.25, C:0.18, G:0.15, T:0.43
Consensus pattern (47 bp):
ATTTTGATGCTTAAATGCTGCCCAATTTGTTGCATATATGCTGTCCA
Found at i:54022685 original size:47 final size:47
Alignment explanation
Indices: 54022466--54022692 Score: 294
Period size: 47 Copynumber: 4.8 Consensus size: 47
54022456 ATATATACAT
* ** * *
54022466 ATTTTGATGCTTAAATGCTTCCCAATTTGTTACATATATGCTGTACT
1 ATTTTGATGCTTAAATGCTGCCCAATTTGTTGTATATATGCTGTCCA
* **
54022513 ATTTTGATGCTTAAATGCTGCCCAATTTATTACATATATGCTGTCCA
1 ATTTTGATGCTTAAATGCTGCCCAATTTGTTGTATATATGCTGTCCA
* *
54022560 ATTTTAATGCTTAAATGCTGCCCAATTTGTTGCATATATGCTGTCCA
1 ATTTTGATGCTTAAATGCTGCCCAATTTGTTGTATATATGCTGTCCA
54022607 ATTTTGATGCTTAAATGCTGCCCAATTTGTTGTATATATGCTGTCCA
1 ATTTTGATGCTTAAATGCTGCCCAATTTGTTGTATATATGCTGTCCA
* * * * **
54022654 GTTTTGGTG-TAAAAATGCTGCTCAAACTGTTGTATATAT
1 ATTTTGATGCT-TAAATGCTGCCCAATTTGTTGTATATAT
54022693 ATGCTGCCCA
Statistics
Matches: 164, Mismatches: 15, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
46 1 0.01
47 163 0.99
ACGTcount: A:0.26, C:0.17, G:0.15, T:0.42
Consensus pattern (47 bp):
ATTTTGATGCTTAAATGCTGCCCAATTTGTTGTATATATGCTGTCCA
Found at i:54022697 original size:25 final size:23
Alignment explanation
Indices: 54022668--54022727 Score: 75
Period size: 25 Copynumber: 2.5 Consensus size: 23
54022658 TGGTGTAAAA
*
54022668 ATGCTGCTCAAACTGTTGTATATAT
1 ATGCTGCCCAAACTGTTGTAT-T-T
*
54022693 ATGCTGCCCAAATTGTTGTATTT
1 ATGCTGCCCAAACTGTTGTATTT
*
54022716 ATGCTGTCCAAA
1 ATGCTGCCCAAA
54022728 TTTTGGTGTG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
23 12 0.38
24 1 0.03
25 19 0.59
ACGTcount: A:0.27, C:0.18, G:0.17, T:0.38
Consensus pattern (23 bp):
ATGCTGCCCAAACTGTTGTATTT
Found at i:54022709 original size:72 final size:71
Alignment explanation
Indices: 54022618--54022799 Score: 215
Period size: 71 Copynumber: 2.5 Consensus size: 71
54022608 TTTTGATGCT
* * *
54022618 TAAATGCTGCCCAATTTGTTGTATATATGCTGTCC-AGTTTTGGTGTAAAAATGCTGCTCAAACT
1 TAAATGCTGCCCAAATTGTTGTATATATGCTGTCCAAATTTTGGTGTAAAAATACTG-TC-AACT
54022682 GTT-GTATA
64 -TTGGTATA
* * * *
54022690 TATATGCTGCCCAAATTGTTGTATTTATGCTGTCCAAATTTTGGTGTGAAAATACTGTCTACTTT
1 TAAATGCTGCCCAAATTGTTGTATATATGCTGTCCAAATTTTGGTGTAAAAATACTGTCAACTTT
54022755 GGTATA
66 GGTATA
* * * * *
54022761 TAAATGCTGTCCAAATTGATGTATAAAAGTTGTCCAAAT
1 TAAATGCTGCCCAAATTGTTGTATATATGCTGTCCAAAT
54022800 AGGGTAGATT
Statistics
Matches: 94, Mismatches: 14, Indels: 5
0.83 0.12 0.04
Matches are distributed among these distances:
70 2 0.02
71 40 0.43
72 34 0.36
73 18 0.19
ACGTcount: A:0.29, C:0.14, G:0.18, T:0.39
Consensus pattern (71 bp):
TAAATGCTGCCCAAATTGTTGTATATATGCTGTCCAAATTTTGGTGTAAAAATACTGTCAACTTT
GGTATA
Found at i:54022785 original size:23 final size:23
Alignment explanation
Indices: 54022571--54022799 Score: 113
Period size: 23 Copynumber: 9.7 Consensus size: 23
54022561 TTTTAATGCT
* * *
54022571 TAAATGCTGCCCAATTTGTTGCA
1 TAAATGCTGTCCAAATTGTTGTA
* * *
54022594 TATATGCTGTCCAATTTTGATGCT-
1 TAAATGCTGTCCAA-ATTGTTG-TA
* *
54022618 TAAATGCTGCCCAATTTGTTGTA
1 TAAATGCTGTCCAAATTGTTGTA
* ** *
54022641 TATATGCTGTCCAGTTTTGGTGTA
1 TAAATGCTGTCCA-AATTGTTGTA
* *
54022665 AAAATGCTG-CTCAAACTGTTGTA
1 TAAATGCTGTC-CAAATTGTTGTA
*
54022688 TATATATGCTGCCCAAATTGTTGTA
1 TA-A-ATGCTGTCCAAATTGTTGTA
** *
54022713 TTTATGCTGTCCAAATT-TTGGTG
1 TAAATGCTGTCCAAATTGTT-GTA
* * ** * *
54022736 TGAAAATACTGTCTACTTTGGTATA
1 T--AAATGCTGTCCAAATTGTTGTA
*
54022761 TAAATGCTGTCCAAATTGATGTA
1 TAAATGCTGTCCAAATTGTTGTA
* *
54022784 TAAAAGTTGTCCAAAT
1 TAAATGCTGTCCAAAT
54022800 AGGGTAGATT
Statistics
Matches: 154, Mismatches: 40, Indels: 24
0.71 0.18 0.11
Matches are distributed among these distances:
22 3 0.02
23 83 0.54
24 36 0.23
25 30 0.19
26 2 0.01
ACGTcount: A:0.28, C:0.15, G:0.18, T:0.39
Consensus pattern (23 bp):
TAAATGCTGTCCAAATTGTTGTA
Found at i:54023097 original size:2 final size:2
Alignment explanation
Indices: 54023090--54023130 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
54023080 AAGAAAATGT
54023090 TA TA 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 TA TA T
54023131 TCGAACATGT
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:54024470 original size:16 final size:16
Alignment explanation
Indices: 54024449--54024479 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
54024439 TTCACTATTA
*
54024449 TATCTTTTGTATTTTC
1 TATCTTTTATATTTTC
54024465 TATCTTTTATATTTT
1 TATCTTTTATATTTT
54024480 GCATGCATAG
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:0.16, C:0.10, G:0.03, T:0.71
Consensus pattern (16 bp):
TATCTTTTATATTTTC
Found at i:54031102 original size:11 final size:11
Alignment explanation
Indices: 54031088--54031174 Score: 51
Period size: 11 Copynumber: 8.3 Consensus size: 11
54031078 GAGAAATTTA
54031088 AGAGGAAATTG
1 AGAGGAAATTG
*
54031099 AGAGCAAATTG
1 AGAGGAAATTG
**
54031110 AGATTAAA-T-
1 AGAGGAAATTG
* *
54031119 A-TGG-ATTTG
1 AGAGGAAATTG
54031128 AGA-GAAATTTG
1 AGAGGAAA-TTG
54031139 -GAAGGAAATTG
1 AG-AGGAAATTG
* *
54031150 AGAGCAATTTG
1 AGAGGAAATTG
54031161 AGAGGAAATTG
1 AGAGGAAATTG
54031172 AGA
1 AGA
54031175 AATGATTAAT
Statistics
Matches: 55, Mismatches: 13, Indels: 16
0.65 0.15 0.19
Matches are distributed among these distances:
7 1 0.02
8 1 0.02
9 3 0.05
10 3 0.05
11 42 0.76
12 5 0.09
ACGTcount: A:0.44, C:0.02, G:0.30, T:0.24
Consensus pattern (11 bp):
AGAGGAAATTG
Found at i:54031132 original size:51 final size:51
Alignment explanation
Indices: 54031064--54031163 Score: 148
Period size: 51 Copynumber: 2.0 Consensus size: 51
54031054 TAAAAATTAA
54031064 AAATAGGGATTTAAGAGAAATTTA-AGAGGAAATTGAGAGCAAATTGAGATT
1 AAATAGGGATTTAAGAGAAATTTAGA-AGGAAATTGAGAGCAAATTGAGATT
* * * *
54031115 AAATATGGATTTGAGAGAAATTTGGAAGGAAATTGAGAGCAATTTGAGA
1 AAATAGGGATTTAAGAGAAATTTAGAAGGAAATTGAGAGCAAATTGAGA
54031164 GGAAATTGAG
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
51 43 0.98
52 1 0.02
ACGTcount: A:0.45, C:0.02, G:0.27, T:0.26
Consensus pattern (51 bp):
AAATAGGGATTTAAGAGAAATTTAGAAGGAAATTGAGAGCAAATTGAGATT
Done.