Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A05
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: 102776486
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2328156 characters in sequence are not A, C, G, or T
File 46 of 325
Found at i:16963720 original size:13 final size:12
Alignment explanation
Indices: 16963666--16963720 Score: 53
Period size: 13 Copynumber: 4.6 Consensus size: 12
16963656 TTTAGTATTT
*
16963666 AATTAATTTTTAA
1 AATTAATTTAT-A
16963679 AATTAATTTCATA
1 AATTAATTT-ATA
16963692 AA--AATTTAT-
1 AATTAATTTATA
16963701 AATTAATTTATA
1 AATTAATTTATA
16963713 ATATTAAT
1 A-ATTAAT
16963721 AATAATCAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
9 2 0.06
10 2 0.06
11 12 0.33
12 1 0.03
13 18 0.50
14 1 0.03
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (12 bp):
AATTAATTTATA
Found at i:16964167 original size:13 final size:13
Alignment explanation
Indices: 16964149--16964178 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
16964139 TAAAATGATG
16964149 TTATATCAATAAT
1 TTATATCAATAAT
*
16964162 TTATATTAATAAT
1 TTATATCAATAAT
16964175 TTAT
1 TTAT
16964179 GAGAATTGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.53
Consensus pattern (13 bp):
TTATATCAATAAT
Found at i:16964265 original size:31 final size:29
Alignment explanation
Indices: 16964197--16964271 Score: 80
Period size: 31 Copynumber: 2.5 Consensus size: 29
16964187 AATCAAATAA
16964197 AAATTTTATATATAAAATTATACAAAATC
1 AAATTTTATATATAAAATTATACAAAATC
* * **
16964226 AAAATTTATATATACAATTGCATATTAAA-C
1 AAATTTTATATATAAAATT--ATACAAAATC
16964256 TAAATTTTATATATAA
1 -AAATTTTATATATAA
16964272 TTTTGAGATT
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
29 17 0.46
30 1 0.03
31 19 0.51
ACGTcount: A:0.52, C:0.07, G:0.01, T:0.40
Consensus pattern (29 bp):
AAATTTTATATATAAAATTATACAAAATC
Found at i:16967630 original size:16 final size:16
Alignment explanation
Indices: 16967606--16967643 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
16967596 TTTGGTTCGC
* *
16967606 TGTATTGGATTAGAGG
1 TGTAATGGAATAGAGG
16967622 TGTAATGGAATAGAGG
1 TGTAATGGAATAGAGG
16967638 TGTAAT
1 TGTAAT
16967644 AGCAAATCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.32, C:0.00, G:0.34, T:0.34
Consensus pattern (16 bp):
TGTAATGGAATAGAGG
Found at i:16967688 original size:45 final size:44
Alignment explanation
Indices: 16967622--16967716 Score: 136
Period size: 45 Copynumber: 2.1 Consensus size: 44
16967612 GGATTAGAGG
* *
16967622 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCAAAAC-ACTGTTTGGTTGAA
* **
16967667 TGTAATGGAATAGAGGCGTAATAGTAAAACTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCAAAACACTGTTTGGTTGAA
16967711 TGTAAT
1 TGTAAT
16967717 AGAGGTGTAA
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
44 18 0.40
45 27 0.60
ACGTcount: A:0.35, C:0.05, G:0.27, T:0.33
Consensus pattern (44 bp):
TGTAATGGAATAGAGGCGTAATAGCAAAACACTGTTTGGTTGAA
Found at i:16967894 original size:24 final size:24
Alignment explanation
Indices: 16967854--16967907 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
16967844 TAATTTAATC
*
16967854 ATATTTAAACATAATTATTATTAA
1 ATATTTAAACATAATTATAATTAA
*
16967878 ATATATTAAATAT-ATTATAATTAA
1 ATAT-TTAAACATAATTATAATTAA
16967902 A-ATTTA
1 ATATTTA
16967908 TAATTTAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
22 3 0.11
23 2 0.07
24 15 0.56
25 7 0.26
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (24 bp):
ATATTTAAACATAATTATAATTAA
Found at i:16969919 original size:21 final size:21
Alignment explanation
Indices: 16969895--16969967 Score: 67
Period size: 21 Copynumber: 3.3 Consensus size: 21
16969885 TTTCACATCC
16969895 TCTTCAACTGTCATTACAATT
1 TCTTCAACTGTCATTACAATT
* * * *
16969916 TCTTCAAACAAGAC-TTTCACATCC
1 TCTTC-AAC-TGTCATTACA-AT-T
16969940 TCTTCAACTGTCATTACAATT
1 TCTTCAACTGTCATTACAATT
16969961 TCTTCAA
1 TCTTCAA
16969968 ACAAGATGTT
Statistics
Matches: 39, Mismatches: 8, Indels: 10
0.68 0.14 0.18
Matches are distributed among these distances:
21 12 0.31
22 11 0.28
23 11 0.28
24 5 0.13
ACGTcount: A:0.30, C:0.27, G:0.04, T:0.38
Consensus pattern (21 bp):
TCTTCAACTGTCATTACAATT
Found at i:16969948 original size:45 final size:45
Alignment explanation
Indices: 16969884--16969973 Score: 180
Period size: 45 Copynumber: 2.0 Consensus size: 45
16969874 TCAATGTCTC
16969884 CTTTCACATCCTCTTCAACTGTCATTACAATTTCTTCAAACAAGA
1 CTTTCACATCCTCTTCAACTGTCATTACAATTTCTTCAAACAAGA
16969929 CTTTCACATCCTCTTCAACTGTCATTACAATTTCTTCAAACAAGA
1 CTTTCACATCCTCTTCAACTGTCATTACAATTTCTTCAAACAAGA
16969974 TGTTCCAGAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.31, C:0.29, G:0.04, T:0.36
Consensus pattern (45 bp):
CTTTCACATCCTCTTCAACTGTCATTACAATTTCTTCAAACAAGA
Found at i:16985988 original size:41 final size:41
Alignment explanation
Indices: 16985943--16986029 Score: 147
Period size: 41 Copynumber: 2.1 Consensus size: 41
16985933 AAAGTTAAGG
* *
16985943 TTAAGGTTTTGTTAAAATAATTTAGGTTTAGGGTTTAGGGT
1 TTAAGGTTTTGTTAAAATAATTTAGGTGTAGGGTGTAGGGT
*
16985984 TTAAGTTTTTGTTAAAATAATTTAGGTGTAGGGTGTAGGGT
1 TTAAGGTTTTGTTAAAATAATTTAGGTGTAGGGTGTAGGGT
16986025 TTAAG
1 TTAAG
16986030 AATTTTAAAA
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 43 1.00
ACGTcount: A:0.28, C:0.00, G:0.28, T:0.45
Consensus pattern (41 bp):
TTAAGGTTTTGTTAAAATAATTTAGGTGTAGGGTGTAGGGT
Found at i:16986042 original size:41 final size:41
Alignment explanation
Indices: 16985956--16986044 Score: 117
Period size: 41 Copynumber: 2.2 Consensus size: 41
16985946 AGGTTTTGTT
* * * **
16985956 AAAATAATTTAGGTTTAGGGTTTAGGGTTTAAGTTTTTGTT
1 AAAATAATTTAGGTGTAGGGTGTAGGGTTTAAGATTTTGAA
16985997 AAAATAATTTAGGTGTAGGGTGTAGGGTTTAAGAATTTT-AA
1 AAAATAATTTAGGTGTAGGGTGTAGGGTTTAAG-ATTTTGAA
16986038 AAAATAA
1 AAAATAA
16986045 ATCAAGGTTT
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
41 38 0.90
42 4 0.10
ACGTcount: A:0.36, C:0.00, G:0.24, T:0.40
Consensus pattern (41 bp):
AAAATAATTTAGGTGTAGGGTGTAGGGTTTAAGATTTTGAA
Found at i:16986088 original size:34 final size:33
Alignment explanation
Indices: 16986050--16986176 Score: 150
Period size: 34 Copynumber: 3.8 Consensus size: 33
16986040 AATAAATCAA
*
16986050 GGTTTAGAGTTTTTTCTAAAAATTAATTAAATTAG
1 GGTTTAGAG-TTTTT-AAAAAATTAATTAAATTAG
* * * *
16986085 GTTTTAGGGCTTTTAAATAAATTAATTAAACTAG
1 GGTTTAGAGTTTTTAAA-AAATTAATTAAATTAG
16986119 GGTTTAGAGTTTTTAAGAAAATTAATTAAATTAG
1 GGTTTAGAGTTTTTAA-AAAATTAATTAAATTAG
*
16986153 GGTTTAG-TTTTTTAAAAAA-TAATT
1 GGTTTAGAGTTTTTAAAAAATTAATT
16986177 TTGTGTTTAG
Statistics
Matches: 80, Mismatches: 10, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
31 5 0.06
32 4 0.05
33 9 0.11
34 54 0.68
35 8 0.10
ACGTcount: A:0.39, C:0.02, G:0.15, T:0.44
Consensus pattern (33 bp):
GGTTTAGAGTTTTTAAAAAATTAATTAAATTAG
Found at i:16986391 original size:125 final size:124
Alignment explanation
Indices: 16986227--16986623 Score: 503
Period size: 125 Copynumber: 3.2 Consensus size: 124
16986217 ATAAGGATTT
* * * *
16986227 TTTTTCCTACAGTAGTTTC-AGAAAAATTAATTTTAAGAAGACAATTCTGAA-AAGATAATGTCA
1 TTTTT-CTACAGTAGTTCCTA-AAAAA-TAATTTTGAGAAGACGATTCTGAACAA-ATAGTGTCA
* * * * * *
16986290 AAAATGCTTCAAGTAGAATGCACTATTAGCAAAATTACTGAAAAAAGCTCCTACGTGGACACTC
62 AAAACGCTTCAAGCAGGATGCACTGTCAGCAAAATTACTGAAAAAAGCTCC-ACGTGGACGCTC
* ** *
16986354 TTTTTCTACAATAGTTCCTAAAAAATAATTTTGAGAAGGTGGTTCTGAACAAATAGTGTCAAAAA
1 TTTTTCTACAGTAGTTCCTAAAAAATAATTTTGAGAAGACGATTCTGAACAAATAGTGTCAAAAA
*
16986419 CGCTTCAAGCAGGATGCACTGTCAGCAAAATTACTGAAAAAAACTCCCACGTGGACGCTC
66 CGCTTCAAGCAGGATGCACTGTCAGCAAAATTACTGAAAAAAGCT-CCACGTGGACGCTC
* * * *
16986479 TTTTTCTACAGCAGTTCTTAAAAAATAATTTTGAAAAGACGATTCTGAACAAATGGTGTCAAAAA
1 TTTTTCTACAGTAGTTCCTAAAAAATAATTTTGAGAAGACGATTCTGAACAAATAGTGTCAAAAA
*
16986544 CGATTCAAGCAGGATGCACTGTCAGCAAAATTGA-TGAAAAAAGCTTCCACGTGGACGCTC
66 CGCTTCAAGCAGGATGCACTGTCAGCAAAATT-ACTGAAAAAAGC-TCCACGTGGACGCTC
* *
16986604 TTTTTATTCAGTAGTTCCTA
1 TTTTTCTACAGTAGTTCCTA
16986624 TTTGGCCTTA
Statistics
Matches: 236, Mismatches: 29, Indels: 12
0.85 0.10 0.04
Matches are distributed among these distances:
125 208 0.88
126 22 0.09
127 6 0.03
ACGTcount: A:0.38, C:0.17, G:0.16, T:0.29
Consensus pattern (124 bp):
TTTTTCTACAGTAGTTCCTAAAAAATAATTTTGAGAAGACGATTCTGAACAAATAGTGTCAAAAA
CGCTTCAAGCAGGATGCACTGTCAGCAAAATTACTGAAAAAAGCTCCACGTGGACGCTC
Found at i:16989252 original size:31 final size:30
Alignment explanation
Indices: 16989217--16989277 Score: 70
Period size: 30 Copynumber: 2.0 Consensus size: 30
16989207 GAAACAGAAT
*
16989217 GAAAGCAAACGAAAC-AGAGAAGAACAGGGGA
1 GAAAG-AAACGAAACAAGA-AAGAAAAGGGGA
* *
16989248 GAAAGAAAGGAAAGAAGAAAGAAAAGGGGA
1 GAAAGAAACGAAACAAGAAAGAAAAGGGGA
16989278 AATAAGGTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
30 18 0.69
31 8 0.31
ACGTcount: A:0.59, C:0.07, G:0.34, T:0.00
Consensus pattern (30 bp):
GAAAGAAACGAAACAAGAAAGAAAAGGGGA
Found at i:16990853 original size:39 final size:39
Alignment explanation
Indices: 16990746--16990880 Score: 123
Period size: 39 Copynumber: 3.4 Consensus size: 39
16990736 GACCTCGAGT
* * *
16990746 CGATGAGACACTGGGTGTC-ACTATATTTCTTCGGATAGATT
1 CGATGAGACACTGGGTGTCAAC--TATTACTTCGGCTAG-TC
** ** *
16990787 CGATGAGGTACTGGGTACCAACT-TTACTTCGGCTAGGC
1 CGATGAGACACTGGGTGTCAACTATTACTTCGGCTAGTC
*
16990825 CGATGAGACACTGGGTGTCAACTATTACTTCGAACTA-TC
1 CGATGAGACACTGGGTGTCAACTATTACTTCG-GCTAGTC
*
16990864 CGATGAGGCACTGGGTG
1 CGATGAGACACTGGGTG
16990881 CCATATTGGT
Statistics
Matches: 76, Mismatches: 15, Indels: 8
0.77 0.15 0.08
Matches are distributed among these distances:
38 19 0.25
39 36 0.47
40 4 0.05
41 15 0.20
42 2 0.03
ACGTcount: A:0.24, C:0.21, G:0.27, T:0.28
Consensus pattern (39 bp):
CGATGAGACACTGGGTGTCAACTATTACTTCGGCTAGTC
Found at i:16992713 original size:24 final size:25
Alignment explanation
Indices: 16992656--16992716 Score: 74
Period size: 24 Copynumber: 2.5 Consensus size: 25
16992646 AAAAAACTTC
16992656 TATTTTATTAAAAATATAAAAATAA
1 TATTTTATTAAAAATATAAAAATAA
*
16992681 T-TTACTATT-AAAATATTAAAAA-AA
1 TATT-TTATTAAAAATA-TAAAAATAA
16992705 TATTTTATTAAA
1 TATTTTATTAAA
16992717 TGAAACAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
24 15 0.50
25 15 0.50
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.43
Consensus pattern (25 bp):
TATTTTATTAAAAATATAAAAATAA
Found at i:16994694 original size:25 final size:24
Alignment explanation
Indices: 16994645--16994696 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 24
16994635 ACTGTTATAA
* *
16994645 AAAATTATAAAATAAAAATTAATT
1 AAAATTACAAAATAAAAAGTAATT
16994669 AAAATTACACAAATAAAAAAGT-ATT
1 AAAATTACA-AAAT-AAAAAGTAATT
16994694 AAA
1 AAA
16994697 TAATATTCAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 8 0.33
25 10 0.42
26 6 0.25
ACGTcount: A:0.67, C:0.04, G:0.02, T:0.27
Consensus pattern (24 bp):
AAAATTACAAAATAAAAAGTAATT
Found at i:16995336 original size:29 final size:30
Alignment explanation
Indices: 16995295--16995363 Score: 81
Period size: 29 Copynumber: 2.4 Consensus size: 30
16995285 TAATTTTATT
* *
16995295 ATTTTAATAATTTTTAAAAAATT-AAAT-TA
1 ATTTTTATTATTTTT-AAAAATTAAAATATA
*
16995324 ATTTTTATTATTTTTAAAGATTAAAATATA
1 ATTTTTATTATTTTTAAAAATTAAAATATA
16995354 A-TTTTATTAT
1 ATTTTTATTAT
16995364 CACTAATTAA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
28 6 0.17
29 26 0.74
30 3 0.09
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (30 bp):
ATTTTTATTATTTTTAAAAATTAAAATATA
Found at i:17005321 original size:21 final size:21
Alignment explanation
Indices: 17005297--17005342 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
17005287 ACATTTTTCT
17005297 AAATTTCTCAAAAAATCTCTC
1 AAATTTCTCAAAAAATCTCTC
***
17005318 AAATTTCTCCCTAAATCTCTC
1 AAATTTCTCAAAAAATCTCTC
17005339 AAAT
1 AAAT
17005343 CTCTTTTTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.39, C:0.26, G:0.00, T:0.35
Consensus pattern (21 bp):
AAATTTCTCAAAAAATCTCTC
Found at i:17005543 original size:25 final size:22
Alignment explanation
Indices: 17005492--17005574 Score: 68
Period size: 20 Copynumber: 3.8 Consensus size: 22
17005482 ATGGTAAGTG
* *
17005492 TTAATTTT-A-ATTTTTTAATA
1 TTAATTTTAATATTTTTTATTT
17005512 TT-A-TTTAATATTTTTTCATTT
1 TTAATTTTAATATTTTTT-ATTT
17005533 ATGTAATTTTAATTATTTTTTATTT
1 -T-TAATTTTAA-TATTTTTTATTT
17005558 TTAATTTGTAAT-TTTTT
1 TTAATTT-TAATATTTTT
17005575 ATAACAATCT
Statistics
Matches: 52, Mismatches: 2, Indels: 16
0.74 0.03 0.23
Matches are distributed among these distances:
18 3 0.06
19 2 0.04
20 9 0.17
21 2 0.04
22 6 0.12
23 8 0.15
24 5 0.10
25 9 0.17
26 8 0.15
ACGTcount: A:0.28, C:0.01, G:0.02, T:0.69
Consensus pattern (22 bp):
TTAATTTTAATATTTTTTATTT
Found at i:17011107 original size:126 final size:126
Alignment explanation
Indices: 17010878--17011243 Score: 520
Period size: 126 Copynumber: 2.9 Consensus size: 126
17010868 AAACAGGAAT
* * * *
17010878 TACTGTAGAAAAAGAGCATCTACGTGGGAGCTTTTTTCAATAATTTTGCTGACATTGCATCCCGC
1 TACTGTAGAAAAAGAGCGTCTACGTGGGAGCTTTTTTCAGTAATTTTGCTGACAGTGCATCCTGC
* * *
17010943 TTGAAACGTTTTTGACACTATTTTTTCAA-AATAGTCTTCTCAAAATTATTTTTTCAAG-AAC
66 TTGAAGCGTTTTTGACACTATTTTTT-AAGAATTGTCTTCTCAAAATTATTTTTGC-AGTAAC
*
17011004 TACTGTAGAAAAAGAGCGTCTACGTGGGAGCTTTTTTCAGTAATTTTGCTGACAGTGCATCCTAC
1 TACTGTAGAAAAAGAGCGTCTACGTGGGAGCTTTTTTCAGTAATTTTGCTGACAGTGCATCCTGC
* * *
17011069 TTGAAGCGTTTTTAAAACTATTTTTTAAGAATTTTCTTCTCAAAATTATTTTTGCAGTAAC
66 TTGAAGCGTTTTTGACACTATTTTTTAAGAATTGTCTTCTCAAAATTATTTTTGCAGTAAC
* * * * *
17011130 TACTATAGAAAAAGAGCGTCCACGTGGAAGCTTTTTTCAGTAATTTTGTTGACAGTACATCCTGC
1 TACTGTAGAAAAAGAGCGTCTACGTGGGAGCTTTTTTCAGTAATTTTGCTGACAGTGCATCCTGC
* * * *
17011195 TTGAAGCATTTTTGACATTATCTTTTCAGAATTGTCTTCTCAAAATTAT
66 TTGAAGCGTTTTTGACACTATTTTTTAAGAATTGTCTTCTCAAAATTAT
17011244 AGGAATAGGC
Statistics
Matches: 214, Mismatches: 24, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
125 4 0.02
126 210 0.98
ACGTcount: A:0.29, C:0.16, G:0.16, T:0.39
Consensus pattern (126 bp):
TACTGTAGAAAAAGAGCGTCTACGTGGGAGCTTTTTTCAGTAATTTTGCTGACAGTGCATCCTGC
TTGAAGCGTTTTTGACACTATTTTTTAAGAATTGTCTTCTCAAAATTATTTTTGCAGTAAC
Found at i:17035040 original size:18 final size:18
Alignment explanation
Indices: 17035019--17035211 Score: 64
Period size: 18 Copynumber: 10.3 Consensus size: 18
17035009 GAACAATTAT
17035019 TTATTCAGTAACAGTCAG
1 TTATTCAGTAACAGTCAG
* * * *
17035037 TTATTCGGTAACAATAAA
1 TTATTCAGTAACAGTCAG
* * **
17035055 TTATTCAATAATAACCAG
1 TTATTCAGTAACAGTCAG
*
17035073 TTATTCAGTATCGATCAATTGATCGG
1 TTATTCAGTA---A-C-A--G-TCAG
* *
17035099 TTATCCAGTAACAGTCAA
1 TTATTCAGTAACAGTCAG
* *
17035117 TTATTTAGTAA-AATCAG
1 TTATTCAGTAACAGTCAG
* * * *
17035134 ATATTCAGTAGCAATTAAG
1 TTATTCAGTAAC-AGTCAG
* *
17035153 TTATTCAGTGACAGTCAA
1 TTATTCAGTAACAGTCAG
** * *
17035171 TTATTTGGTAACGGTCAA
1 TTATTCAGTAACAGTCAG
* * *
17035189 TTATTCAGAAATAATCAG
1 TTATTCAGTAACAGTCAG
17035207 TTATT
1 TTATT
17035212 TTATACCTTT
Statistics
Matches: 121, Mismatches: 44, Indels: 20
0.65 0.24 0.11
Matches are distributed among these distances:
17 12 0.10
18 79 0.65
19 14 0.12
21 2 0.02
22 1 0.01
23 2 0.02
26 11 0.09
ACGTcount: A:0.37, C:0.13, G:0.14, T:0.36
Consensus pattern (18 bp):
TTATTCAGTAACAGTCAG
Found at i:17035386 original size:6 final size:6
Alignment explanation
Indices: 17035375--17035399 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
17035365 ACAAATTCGG
17035375 AACAGT AACAGT AACAGT AACAGT A
1 AACAGT AACAGT AACAGT AACAGT A
17035400 TTCAACATAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.52, C:0.16, G:0.16, T:0.16
Consensus pattern (6 bp):
AACAGT
Found at i:17035429 original size:39 final size:39
Alignment explanation
Indices: 17035383--17035477 Score: 156
Period size: 39 Copynumber: 2.4 Consensus size: 39
17035373 GGAACAGTAA
* *
17035383 CAGTAACAGTAACAGTATTCAACATACAAAGTGCTGAAT
1 CAGTAACAGTAACAGTATTCAACACACAAAGTGCCGAAT
17035422 C-GATAACAGTAACAGTATTCAACACACAAAGTGCCGAAT
1 CAG-TAACAGTAACAGTATTCAACACACAAAGTGCCGAAT
17035461 CAGTAACAGTAACAGTA
1 CAGTAACAGTAACAGTA
17035478 ACAGTAGTCG
Statistics
Matches: 52, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
38 1 0.02
39 50 0.96
40 1 0.02
ACGTcount: A:0.44, C:0.20, G:0.16, T:0.20
Consensus pattern (39 bp):
CAGTAACAGTAACAGTATTCAACACACAAAGTGCCGAAT
Found at i:17039227 original size:13 final size:14
Alignment explanation
Indices: 17039209--17039237 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
17039199 AAACCCTAAA
17039209 TTTTCTTT-TTTCT
1 TTTTCTTTCTTTCT
17039222 TTTTCTTTCTTTCT
1 TTTTCTTTCTTTCT
17039236 TT
1 TT
17039238 CTCCCCTGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (14 bp):
TTTTCTTTCTTTCT
Found at i:17039307 original size:5 final size:5
Alignment explanation
Indices: 17039297--17039328 Score: 64
Period size: 5 Copynumber: 6.4 Consensus size: 5
17039287 TTTCTTTACT
17039297 TATAA TATAA TATAA TATAA TATAA TATAA TA
1 TATAA TATAA TATAA TATAA TATAA TATAA TA
17039329 ACAATTTCTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (5 bp):
TATAA
Found at i:17039460 original size:21 final size:22
Alignment explanation
Indices: 17039421--17039461 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
17039411 CATACAATTG
*
17039421 TTAAAATAATATTATAATATCA
1 TTAAAATAATATTACAATATCA
*
17039443 TTAATATAA-ATTACAATAT
1 TTAAAATAATATTACAATAT
17039462 AACAAAATAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (22 bp):
TTAAAATAATATTACAATATCA
Found at i:17050763 original size:21 final size:21
Alignment explanation
Indices: 17050736--17050781 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
17050726 AACATGTTTA
*
17050736 AATTTTATTTTATTTATAATTT
1 AATTTAATTTT-TTTATAATTT
* *
17050758 AATTTAATTTTTTTTTATTTT
1 AATTTAATTTTTTTATAATTT
17050779 AAT
1 AAT
17050782 ATCGTACATA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 11 0.52
22 10 0.48
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (21 bp):
AATTTAATTTTTTTATAATTT
Found at i:17064454 original size:36 final size:30
Alignment explanation
Indices: 17064381--17064443 Score: 126
Period size: 30 Copynumber: 2.1 Consensus size: 30
17064371 GCTCCTATAA
17064381 TTGGTGAATACAATATCAATATTCTAAATT
1 TTGGTGAATACAATATCAATATTCTAAATT
17064411 TTGGTGAATACAATATCAATATTCTAAATT
1 TTGGTGAATACAATATCAATATTCTAAATT
17064441 TTG
1 TTG
17064444 TAGCAGGTGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.38, C:0.10, G:0.11, T:0.41
Consensus pattern (30 bp):
TTGGTGAATACAATATCAATATTCTAAATT
Found at i:17065107 original size:26 final size:27
Alignment explanation
Indices: 17065078--17065137 Score: 70
Period size: 29 Copynumber: 2.2 Consensus size: 27
17065068 TATATATTTA
*
17065078 AATATT-TTTAATAAAA-ATAAAAAAAT
1 AATATTATTTAA-AAAACAAAAAAAAAT
17065104 AATATTTTATTTAAAAAACAAAAAAAAAT
1 AATA--TTATTTAAAAAACAAAAAAAAAT
17065133 AATAT
1 AATAT
17065138 AAAATAATCA
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
26 4 0.14
27 1 0.03
28 6 0.21
29 18 0.62
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (27 bp):
AATATTATTTAAAAAACAAAAAAAAAT
Found at i:17068589 original size:15 final size:15
Alignment explanation
Indices: 17068562--17068603 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
17068552 ATCATTTATT
17068562 ATATATTATTTTTAA
1 ATATATTATTTTTAA
17068577 ATAT-TTATATTTTAA
1 ATATATTAT-TTTTAA
* *
17068592 ATTTGTTATTTT
1 ATATATTATTTT
17068604 CTTGTTCGTA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
14 4 0.17
15 16 0.67
16 4 0.17
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (15 bp):
ATATATTATTTTTAA
Found at i:17075692 original size:30 final size:30
Alignment explanation
Indices: 17075656--17075717 Score: 115
Period size: 30 Copynumber: 2.1 Consensus size: 30
17075646 AATATTTAGT
17075656 TGTATGATCTTCATCAAGCAATGATGAATC
1 TGTATGATCTTCATCAAGCAATGATGAATC
*
17075686 TGTATGATCTTCATCAGGCAATGATGAATC
1 TGTATGATCTTCATCAAGCAATGATGAATC
17075716 TG
1 TG
17075718 CTTTGAAGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.34
Consensus pattern (30 bp):
TGTATGATCTTCATCAAGCAATGATGAATC
Found at i:17078753 original size:54 final size:54
Alignment explanation
Indices: 17078688--17078796 Score: 209
Period size: 54 Copynumber: 2.0 Consensus size: 54
17078678 CAATTGGAGT
17078688 AAGCTTCTAAACCTGGTTGGTTTTTACCTCCAATAATTAATAGGAAGACCAATA
1 AAGCTTCTAAACCTGGTTGGTTTTTACCTCCAATAATTAATAGGAAGACCAATA
*
17078742 AAGCTTCTAAACCTGGTTGGTTTTTTCCTCCAATAATTAATAGGAAGACCAATA
1 AAGCTTCTAAACCTGGTTGGTTTTTACCTCCAATAATTAATAGGAAGACCAATA
17078796 A
1 A
17078797 TTGTGTCTGC
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 54 1.00
ACGTcount: A:0.35, C:0.18, G:0.15, T:0.32
Consensus pattern (54 bp):
AAGCTTCTAAACCTGGTTGGTTTTTACCTCCAATAATTAATAGGAAGACCAATA
Found at i:17080321 original size:77 final size:77
Alignment explanation
Indices: 17080189--17080333 Score: 263
Period size: 77 Copynumber: 1.9 Consensus size: 77
17080179 GCAAAAGTTA
* *
17080189 CACCTGTTGAAAAGTTAATTAAGGGGGTGTTGAAAAGTCAAAAATAGAAGGTGCAATTGGCACCG
1 CACCTGTTGAAAAGTCAATTAAGGGGGTGTTGAAAAGTCAAAAATAGAAGATGCAATTGGCACCG
17080254 AAATGGAAGGTG
66 AAATGGAAGGTG
*
17080266 CACCTGTTGAAAAGTCAATTAAGGGGGTGTTGAAAAGTCAAAAATGGAAGATGCAATTGGCACCG
1 CACCTGTTGAAAAGTCAATTAAGGGGGTGTTGAAAAGTCAAAAATAGAAGATGCAATTGGCACCG
17080331 AAA
66 AAA
17080334 GAAAAAGTGA
Statistics
Matches: 65, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
77 65 1.00
ACGTcount: A:0.39, C:0.12, G:0.28, T:0.21
Consensus pattern (77 bp):
CACCTGTTGAAAAGTCAATTAAGGGGGTGTTGAAAAGTCAAAAATAGAAGATGCAATTGGCACCG
AAATGGAAGGTG
Found at i:17081391 original size:25 final size:26
Alignment explanation
Indices: 17081351--17081414 Score: 67
Period size: 26 Copynumber: 2.4 Consensus size: 26
17081341 ATAGTGATAA
* *
17081351 ATTTTTTTAATATAATCAACATTTTAC-
1 ATTTTTTTAGTA-ATTCAA-ATTTTACT
* *
17081378 ATTTTTTTAGTAATTTAATTTTTACT
1 ATTTTTTTAGTAATTCAAATTTTACT
17081404 ATTTTTTTAGT
1 ATTTTTTTAGT
17081415 TAAATTTAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
25 6 0.19
26 15 0.47
27 11 0.34
ACGTcount: A:0.30, C:0.06, G:0.03, T:0.61
Consensus pattern (26 bp):
ATTTTTTTAGTAATTCAAATTTTACT
Found at i:17081407 original size:26 final size:27
Alignment explanation
Indices: 17081372--17081424 Score: 83
Period size: 26 Copynumber: 2.0 Consensus size: 27
17081362 ATAATCAACA
17081372 TTTTACATTTTTTTAG-T-AATTTAAT
1 TTTTACATTTTTTTAGTTAAATTTAAT
17081397 TTTTACTATTTTTTTAGTTAAATTTAAT
1 TTTTAC-ATTTTTTTAGTTAAATTTAAT
17081425 CATTAATCTT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
25 6 0.24
26 10 0.40
27 1 0.04
28 8 0.32
ACGTcount: A:0.28, C:0.04, G:0.04, T:0.64
Consensus pattern (27 bp):
TTTTACATTTTTTTAGTTAAATTTAAT
Found at i:17082278 original size:14 final size:14
Alignment explanation
Indices: 17082261--17082302 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
17082251 TAAATACAAT
*
17082261 ACTCTAAACCCTAA
1 ACTCTAAACCTTAA
17082275 ACTCT-AACCTTAA
1 ACTCTAAACCTTAA
17082288 A-TACTAAACCTTAA
1 ACT-CTAAACCTTAA
17082302 A
1 A
17082303 TTCTTAAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
12 1 0.04
13 10 0.40
14 14 0.56
ACGTcount: A:0.45, C:0.29, G:0.00, T:0.26
Consensus pattern (14 bp):
ACTCTAAACCTTAA
Found at i:17090223 original size:19 final size:18
Alignment explanation
Indices: 17090184--17090225 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
17090174 TATATTTTTT
*
17090184 AAAATATTAATTATTATA
1 AAAATATTAATTATGATA
*
17090202 AAAATTATTAA-TATGATG
1 AAAA-TATTAATTATGATA
17090220 AAAATA
1 AAAATA
17090226 ATTTTTAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
17 2 0.10
18 13 0.62
19 6 0.29
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.38
Consensus pattern (18 bp):
AAAATATTAATTATGATA
Found at i:17090888 original size:16 final size:16
Alignment explanation
Indices: 17090864--17090897 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
17090854 ATTAAGTAAA
17090864 AATAAATAAATTTTAT
1 AATAAATAAATTTTAT
* *
17090880 AATATATAACTTTTAT
1 AATAAATAAATTTTAT
17090896 AA
1 AA
17090898 ATAAGCTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (16 bp):
AATAAATAAATTTTAT
Found at i:17090908 original size:14 final size:13
Alignment explanation
Indices: 17090865--17090913 Score: 53
Period size: 14 Copynumber: 3.5 Consensus size: 13
17090855 TTAAGTAAAA
*
17090865 ATAAATAAATTTT
1 ATAAATAACTTTT
17090878 ATAATATATAACTTTT
1 AT-A-A-ATAACTTTT
17090894 ATAAATAAGCTTTT
1 ATAAATAA-CTTTT
17090908 ATAAAT
1 ATAAAT
17090914 TGTCCAATAA
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
13 6 0.19
14 13 0.42
15 2 0.06
16 10 0.32
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.45
Consensus pattern (13 bp):
ATAAATAACTTTT
Found at i:17090955 original size:11 final size:12
Alignment explanation
Indices: 17090939--17090986 Score: 53
Period size: 12 Copynumber: 3.8 Consensus size: 12
17090929 ATAACATTTC
17090939 TTATAAAT-ATT
1 TTATAAATAATT
17090950 TTATAAATAATT
1 TTATAAATAATT
*
17090962 TTAAAAAGTTATATT
1 TTATAAA--TA-ATT
17090977 TTATAAATAA
1 TTATAAATAA
17090987 ATTATGATAA
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
11 8 0.26
12 10 0.32
13 2 0.06
14 2 0.06
15 9 0.29
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (12 bp):
TTATAAATAATT
Found at i:17093563 original size:148 final size:148
Alignment explanation
Indices: 17093295--17093590 Score: 565
Period size: 148 Copynumber: 2.0 Consensus size: 148
17093285 CCATCAATCT
* *
17093295 CAACAACAACCATGAATTAACAAAGTGCTGACTTCATTCCAAGTTAATTATAAACCTAGAGTCAA
1 CAACAACAACCATGAATTAACAAAGTGCTGACTTCATTCAAAATTAATTATAAACCTAGAGTCAA
17093360 TAACACCAAACTGCCGATAGCTGTAAATATCCTTCCATCCATTCCACATAGTTAATCTTTATTCC
66 TAACACCAAACTGCCGATAGCTGTAAATATCCTTCCATCCATTCCACATAGTTAATCTTTATTCC
17093425 CAGCAACTAAAATTTGTG
131 CAGCAACTAAAATTTGTG
17093443 CAACAACAACCATGAATTAACAAAGTGCTGACTTCATTCAAAATTAATTATAAACCTAGAGTCAA
1 CAACAACAACCATGAATTAACAAAGTGCTGACTTCATTCAAAATTAATTATAAACCTAGAGTCAA
*
17093508 TAACATCAAACTGCCGATAGCTGTAAATATCCTTCCATCCATTCCACATAGTTAATCTTTATTCC
66 TAACACCAAACTGCCGATAGCTGTAAATATCCTTCCATCCATTCCACATAGTTAATCTTTATTCC
17093573 CAGCAACTAAAATTTGTG
131 CAGCAACTAAAATTTGTG
17093591 AAAGATATAA
Statistics
Matches: 145, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
148 145 1.00
ACGTcount: A:0.38, C:0.24, G:0.10, T:0.29
Consensus pattern (148 bp):
CAACAACAACCATGAATTAACAAAGTGCTGACTTCATTCAAAATTAATTATAAACCTAGAGTCAA
TAACACCAAACTGCCGATAGCTGTAAATATCCTTCCATCCATTCCACATAGTTAATCTTTATTCC
CAGCAACTAAAATTTGTG
Found at i:17098017 original size:27 final size:26
Alignment explanation
Indices: 17097986--17098037 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
17097976 GTAATTTTTA
17097986 AAATTTAAAATATTTATAAAAAATATT
1 AAATTTAAAAT-TTTATAAAAAATATT
** *
17098013 AAATTTTGAATTTTTTAAAAAATAT
1 AAATTTAAAATTTTATAAAAAATAT
17098038 AAAAATTCCT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 13 0.59
27 9 0.41
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (26 bp):
AAATTTAAAATTTTATAAAAAATATT
Found at i:17098317 original size:44 final size:39
Alignment explanation
Indices: 17098236--17098314 Score: 158
Period size: 39 Copynumber: 2.0 Consensus size: 39
17098226 ATTCTATTTC
17098236 ACTTGATTTGAAAAAAATCAAATTGAATTATAATAATAT
1 ACTTGATTTGAAAAAAATCAAATTGAATTATAATAATAT
17098275 ACTTGATTTGAAAAAAATCAAATTGAATTATAATAATAT
1 ACTTGATTTGAAAAAAATCAAATTGAATTATAATAATAT
17098314 A
1 A
17098315 ATAGGAGTCG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.52, C:0.05, G:0.08, T:0.35
Consensus pattern (39 bp):
ACTTGATTTGAAAAAAATCAAATTGAATTATAATAATAT
Found at i:17103121 original size:90 final size:90
Alignment explanation
Indices: 17102958--17103318 Score: 706
Period size: 90 Copynumber: 4.0 Consensus size: 90
17102948 ATTATATAAC
17102958 TTCTATTACTCTGTTTCCAGATCCATATTCAATTATTTCTTTCCTCTCTTGCTTATTTTGTGTGT
1 TTCTATTACTCTGTTTCCAGATCCATATTCAATTATTTCTTTCCTCTCTTGCTTA-TTTGTGTGT
17103023 CATG-TTTTTGAGAATGTGAATAAGT
65 CATGTTTTTTGAGAATGTGAATAAGT
17103048 TTCTATTACTCTGTTTCCAGATCCATATTCAATTATTTCTTTCCTCTCTTGCTTATTTGTGTGTC
1 TTCTATTACTCTGTTTCCAGATCCATATTCAATTATTTCTTTCCTCTCTTGCTTATTTGTGTGTC
17103113 ATGTTTTTTGAGAATGTGAATAAGT
66 ATGTTTTTTGAGAATGTGAATAAGT
17103138 TTCTATTACTCTGTTTCCAGATCCATATTCAATTATTTCTTTCCTCTCTTGCTTATTTGTGTGTC
1 TTCTATTACTCTGTTTCCAGATCCATATTCAATTATTTCTTTCCTCTCTTGCTTATTTGTGTGTC
17103203 ATGTTTTTTGAGAATGTGAATAAGT
66 ATGTTTTTTGAGAATGTGAATAAGT
17103228 TTCTATTACTCTGTTTCCAGATCCATATTCAATTATTTCTTTCCTCTCTTGCTTATTTGTGTGTC
1 TTCTATTACTCTGTTTCCAGATCCATATTCAATTATTTCTTTCCTCTCTTGCTTATTTGTGTGTC
17103293 ATGTTTTTTGAGAATGTGAATAAGT
66 ATGTTTTTTGAGAATGTGAATAAGT
17103318 T
1 T
17103319 ATCAACTTAT
Statistics
Matches: 270, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
89 13 0.05
90 257 0.95
ACGTcount: A:0.20, C:0.17, G:0.13, T:0.50
Consensus pattern (90 bp):
TTCTATTACTCTGTTTCCAGATCCATATTCAATTATTTCTTTCCTCTCTTGCTTATTTGTGTGTC
ATGTTTTTTGAGAATGTGAATAAGT
Found at i:17118567 original size:3 final size:3
Alignment explanation
Indices: 17118502--17118548 Score: 78
Period size: 3 Copynumber: 16.0 Consensus size: 3
17118492 TTACTTTATG
*
17118502 TTA TTA TTA -TG TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
17118549 CTAGTATATG
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
2 1 0.02
3 40 0.98
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:17121591 original size:75 final size:75
Alignment explanation
Indices: 17121354--17121672 Score: 385
Period size: 75 Copynumber: 4.1 Consensus size: 75
17121344 CAAATTCTAC
* * * *
17121354 TTTCAATTACTGTTTGTC--AAAAATCAACTCATATTGCGGGAGGTGAGTTGAGCATCGGGGCAC
1 TTTCAATTATTGTTTGTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACAC
17121417 GCTGAGGTAT
66 GCTGAGGTAT
* * *
17121427 TTTCAATTATTGTTTGTAAAAAAAATCAACTCATATTGCGGGAGGTGAGTTGAGCCTCGGGGCAC
1 TTTCAATTATTGTTTGTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACAC
17121492 GCTGAGGTAT
66 GCTGAGGTAT
*
17121502 TTTCAATTATTGTTTGTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACAC
1 TTTCAATTATTGTTTGTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACAC
17121567 GCTGAGGTAT
66 GCTGAGGTAT
* *
17121577 TTTCAATTGA-TGTTTTTTCAATTTACGCTTTTCAAAAATCAACTCATATTACGAGAGGTGAGTT
1 TTTCAATT-ATTG-TTTGTC-A---A--------AAAAATCAACTCATATTGCGAGAGGTGAGTT
17121641 GAGCCTCGGGGA-ACGCTGAGGTAT
52 GAGCCTC-GGGACACGCTGAGGTAT
17121665 TTTCAATT
1 TTTCAATT
17121673 TTCATTTTTT
Statistics
Matches: 219, Mismatches: 10, Indels: 19
0.88 0.04 0.08
Matches are distributed among these distances:
73 16 0.07
75 135 0.62
76 6 0.03
77 1 0.00
80 1 0.00
88 57 0.26
89 3 0.01
ACGTcount: A:0.28, C:0.16, G:0.24, T:0.33
Consensus pattern (75 bp):
TTTCAATTATTGTTTGTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACAC
GCTGAGGTAT
Found at i:17121657 original size:88 final size:88
Alignment explanation
Indices: 17121522--17121700 Score: 281
Period size: 88 Copynumber: 2.0 Consensus size: 88
17121512 TGTTTGTCAA
*
17121522 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTGA
1 AAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATT-A
*
17121587 T-GTTTTTTCAATTTACGCTTTTC
65 TCATTTTTTCAATTTACGCTTTTC
* *
17121610 AAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCGGGGA-ACGCTGAGGTATTTTCAATTT
1 AAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTC-AGGACACGCTGAGGTATTTTCAATTA
*
17121674 TCATTTTTTCAATTTATGCTTTTC
65 TCATTTTTTCAATTTACGCTTTTC
17121698 AAA
1 AAA
17121701 TTCTGCTTTC
Statistics
Matches: 84, Mismatches: 5, Indels: 4
0.90 0.05 0.04
Matches are distributed among these distances:
87 1 0.01
88 80 0.95
89 3 0.04
ACGTcount: A:0.28, C:0.16, G:0.20, T:0.36
Consensus pattern (88 bp):
AAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTAT
CATTTTTTCAATTTACGCTTTTC
Found at i:17121860 original size:89 final size:90
Alignment explanation
Indices: 17121690--17121860 Score: 238
Period size: 89 Copynumber: 1.9 Consensus size: 90
17121680 TTTCAATTTA
** * * * *
17121690 TGCTTTTCAAATTCTGCTTTCCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGT
1 TGCTTTTCAAATTAAGCTTTCAAAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAGCT
*
17121755 CACATGTCGAGGTATTTTCAAAATC
66 CACATGTCGAGCTATTTTCAAAATC
*
17121780 TGCTTTTCAAATTAAG-TTTCAAAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTTAGCT
1 TGCTTTTCAAATTAAGCTTTCAAAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAGCT
*
17121844 CACGTG-CTGAGCTATTT
66 CACATGTC-GAGCTATTT
17121861 CTGTTATAAT
Statistics
Matches: 71, Mismatches: 9, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
88 1 0.01
89 56 0.79
90 14 0.20
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.33
Consensus pattern (90 bp):
TGCTTTTCAAATTAAGCTTTCAAAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAGCT
CACATGTCGAGCTATTTTCAAAATC
Found at i:17123497 original size:11 final size:11
Alignment explanation
Indices: 17123481--17123518 Score: 58
Period size: 11 Copynumber: 3.4 Consensus size: 11
17123471 TTTCATTACT
17123481 TTATGTTATTA
1 TTATGTTATTA
17123492 TTATGTTATTA
1 TTATGTTATTA
*
17123503 TTATTATTATTA
1 TTA-TGTTATTA
17123515 TTAT
1 TTAT
17123519 TATTACTAGT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
11 15 0.60
12 10 0.40
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.66
Consensus pattern (11 bp):
TTATGTTATTA
Found at i:17123542 original size:3 final size:3
Alignment explanation
Indices: 17123486--17123523 Score: 60
Period size: 3 Copynumber: 13.0 Consensus size: 3
17123476 TTACTTTATG
*
17123486 TTA TTA TTA -TG TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
17123524 CTAGTATATG
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
2 1 0.03
3 31 0.97
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:17124401 original size:17 final size:17
Alignment explanation
Indices: 17124370--17124415 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 17
17124360 TATGTATGCC
*
17124370 ATGTATATATATATGTAT
1 ATGTATAT-TTTATGTAT
17124388 ATGTATATTTTATGTAT
1 ATGTATATTTTATGTAT
17124405 ATTGT-TATTTT
1 A-TGTATATTTT
17124416 CTATCGTCAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
17 15 0.58
18 11 0.42
ACGTcount: A:0.30, C:0.00, G:0.11, T:0.59
Consensus pattern (17 bp):
ATGTATATTTTATGTAT
Found at i:17128724 original size:75 final size:75
Alignment explanation
Indices: 17128487--17128805 Score: 385
Period size: 75 Copynumber: 4.1 Consensus size: 75
17128477 CAAATTCTAC
* * * *
17128487 TTTCAATTACTGTTTGTC--AAAAATCAACTCATATTGCGGGAGGTGAGTTGAGCATCGGGGCAC
1 TTTCAATTATTGTTTGTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACAC
17128550 GCTGAGGTAT
66 GCTGAGGTAT
* * *
17128560 TTTCAATTATTGTTTGTAAAAAAAATCAACTCATATTGCGGGAGGTGAGTTGAGCCTCGGGGCAC
1 TTTCAATTATTGTTTGTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACAC
17128625 GCTGAGGTAT
66 GCTGAGGTAT
*
17128635 TTTCAATTATTGTTTGTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACAC
1 TTTCAATTATTGTTTGTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACAC
17128700 GCTGAGGTAT
66 GCTGAGGTAT
* *
17128710 TTTCAATTGA-TGTTTTTTCAATTTACGCTTTTCAAAAATCAACTCATATTACGAGAGGTGAGTT
1 TTTCAATT-ATTG-TTTGTC-A---A--------AAAAATCAACTCATATTGCGAGAGGTGAGTT
17128774 GAGCCTCGGGGA-ACGCTGAGGTAT
52 GAGCCTC-GGGACACGCTGAGGTAT
17128798 TTTCAATT
1 TTTCAATT
17128806 TTCATTTTTT
Statistics
Matches: 219, Mismatches: 10, Indels: 19
0.88 0.04 0.08
Matches are distributed among these distances:
73 16 0.07
75 135 0.62
76 6 0.03
77 1 0.00
80 1 0.00
88 57 0.26
89 3 0.01
ACGTcount: A:0.28, C:0.16, G:0.24, T:0.33
Consensus pattern (75 bp):
TTTCAATTATTGTTTGTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACAC
GCTGAGGTAT
Found at i:17128790 original size:88 final size:88
Alignment explanation
Indices: 17128655--17128833 Score: 281
Period size: 88 Copynumber: 2.0 Consensus size: 88
17128645 TGTTTGTCAA
*
17128655 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTGA
1 AAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATT-A
*
17128720 T-GTTTTTTCAATTTACGCTTTTC
65 TCATTTTTTCAATTTACGCTTTTC
* *
17128743 AAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCGGGGA-ACGCTGAGGTATTTTCAATTT
1 AAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTC-AGGACACGCTGAGGTATTTTCAATTA
*
17128807 TCATTTTTTCAATTTATGCTTTTC
65 TCATTTTTTCAATTTACGCTTTTC
17128831 AAA
1 AAA
17128834 TTCTGCTTTC
Statistics
Matches: 84, Mismatches: 5, Indels: 4
0.90 0.05 0.04
Matches are distributed among these distances:
87 1 0.01
88 80 0.95
89 3 0.04
ACGTcount: A:0.28, C:0.16, G:0.20, T:0.36
Consensus pattern (88 bp):
AAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTAT
CATTTTTTCAATTTACGCTTTTC
Found at i:17128993 original size:89 final size:90
Alignment explanation
Indices: 17128823--17128993 Score: 238
Period size: 89 Copynumber: 1.9 Consensus size: 90
17128813 TTTCAATTTA
** * * * *
17128823 TGCTTTTCAAATTCTGCTTTCCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGT
1 TGCTTTTCAAATTAAGCTTTCAAAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAGCT
*
17128888 CACATGTCGAGGTATTTTCAAAATC
66 CACATGTCGAGCTATTTTCAAAATC
*
17128913 TGCTTTTCAAATTAAG-TTTCAAAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTTAGCT
1 TGCTTTTCAAATTAAGCTTTCAAAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAGCT
*
17128977 CACGTG-CTGAGCTATTT
66 CACATGTC-GAGCTATTT
17128994 CTGTTATAAT
Statistics
Matches: 71, Mismatches: 9, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
88 1 0.01
89 56 0.79
90 14 0.20
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.33
Consensus pattern (90 bp):
TGCTTTTCAAATTAAGCTTTCAAAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAGCT
CACATGTCGAGCTATTTTCAAAATC
Found at i:17130627 original size:11 final size:11
Alignment explanation
Indices: 17130611--17130648 Score: 58
Period size: 11 Copynumber: 3.4 Consensus size: 11
17130601 TTTCATTACT
17130611 TTATGTTATTA
1 TTATGTTATTA
17130622 TTATGTTATTA
1 TTATGTTATTA
*
17130633 TTATTATTATTA
1 TTA-TGTTATTA
17130645 TTAT
1 TTAT
17130649 TACTAGTATA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
11 15 0.60
12 10 0.40
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.66
Consensus pattern (11 bp):
TTATGTTATTA
Found at i:17130669 original size:3 final size:3
Alignment explanation
Indices: 17130616--17130650 Score: 54
Period size: 3 Copynumber: 12.0 Consensus size: 3
17130606 TTACTTTATG
*
17130616 TTA TTA TTA -TG TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
17130651 CTAGTATATG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 1 0.03
3 28 0.97
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:17131526 original size:17 final size:17
Alignment explanation
Indices: 17131495--17131540 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 17
17131485 TATGTATGCC
*
17131495 ATGTATATATATATGTAT
1 ATGTATAT-TTTATGTAT
17131513 ATGTATATTTTATGTAT
1 ATGTATATTTTATGTAT
17131530 ATTGT-TATTTT
1 A-TGTATATTTT
17131541 CTATCGTCAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
17 15 0.58
18 11 0.42
ACGTcount: A:0.30, C:0.00, G:0.11, T:0.59
Consensus pattern (17 bp):
ATGTATATTTTATGTAT
Found at i:17135756 original size:18 final size:18
Alignment explanation
Indices: 17135733--17135771 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
17135723 ATTTTATAAT
* * *
17135733 ATTTTTACTTATTTTTTA
1 ATTTTTAATAATTTTTCA
17135751 ATTTTTAATAATTTTTCA
1 ATTTTTAATAATTTTTCA
17135769 ATT
1 ATT
17135772 GAATTGGTTG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.28, C:0.05, G:0.00, T:0.67
Consensus pattern (18 bp):
ATTTTTAATAATTTTTCA
Found at i:17136758 original size:9 final size:9
Alignment explanation
Indices: 17136744--17136776 Score: 59
Period size: 9 Copynumber: 3.8 Consensus size: 9
17136734 TTCTTATATT
17136744 TTTTTTTAC
1 TTTTTTTAC
17136753 TTTTTTTAC
1 TTTTTTTAC
17136762 -TTTTTTAC
1 TTTTTTTAC
17136770 TTTTTTT
1 TTTTTTT
17136777 TTATATTTGG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 8 0.35
9 15 0.65
ACGTcount: A:0.09, C:0.09, G:0.00, T:0.82
Consensus pattern (9 bp):
TTTTTTTAC
Found at i:17136765 original size:7 final size:8
Alignment explanation
Indices: 17136745--17136775 Score: 53
Period size: 8 Copynumber: 3.8 Consensus size: 8
17136735 TCTTATATTT
17136745 TTTTTTAC
1 TTTTTTAC
17136753 TTTTTTTAC
1 -TTTTTTAC
17136762 TTTTTTAC
1 TTTTTTAC
17136770 TTTTTT
1 TTTTTT
17136776 TTTATATTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 14 0.64
9 8 0.36
ACGTcount: A:0.10, C:0.10, G:0.00, T:0.81
Consensus pattern (8 bp):
TTTTTTAC
Found at i:17136863 original size:36 final size:37
Alignment explanation
Indices: 17136791--17136864 Score: 100
Period size: 37 Copynumber: 2.0 Consensus size: 37
17136781 ATTTGGTCTC
*
17136791 TTTCTTAGATTTTTTTCTTTTTTAAGTTTCATATTAT
1 TTTCTTAGATTTTTTTCTTATTTAAGTTTCATATTAT
17136828 TTTCTTA-ATTTATTTTGCTTATTTAA-TTT-ATATTAT
1 TTTCTTAGATTT-TTTT-CTTATTTAAGTTTCATATTAT
17136864 T
1 T
17136865 AATTTTAAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
36 12 0.35
37 14 0.41
38 8 0.24
ACGTcount: A:0.22, C:0.07, G:0.04, T:0.68
Consensus pattern (37 bp):
TTTCTTAGATTTTTTTCTTATTTAAGTTTCATATTAT
Found at i:17136878 original size:23 final size:22
Alignment explanation
Indices: 17136852--17136942 Score: 64
Period size: 23 Copynumber: 4.1 Consensus size: 22
17136842 TTGCTTATTT
*
17136852 AATTTATATTATTAATTTTAAAA
1 AATTTATAATATT-ATTTTAAAA
*
17136875 AATTTGTAATA-TATATTTAAAA
1 AATTTATAATATTAT-TTTAAAA
**
17136897 TGTTTTATAATATT-TTTT-AAA
1 -AATTTATAATATTATTTTAAAA
* *
17136918 AATTT-TAATTATCATTTTTAAA
1 AATTTATAA-TATTATTTTAAAA
17136940 AAT
1 AAT
17136943 ATTTTTTAAC
Statistics
Matches: 54, Mismatches: 8, Indels: 13
0.72 0.11 0.17
Matches are distributed among these distances:
19 3 0.06
20 6 0.11
21 9 0.17
22 17 0.31
23 18 0.33
24 1 0.02
ACGTcount: A:0.44, C:0.01, G:0.02, T:0.53
Consensus pattern (22 bp):
AATTTATAATATTATTTTAAAA
Found at i:17137228 original size:18 final size:18
Alignment explanation
Indices: 17137205--17137251 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 18
17137195 GTGATTATTA
17137205 ATAAATTTAAATATAAAT
1 ATAAATTTAAATATAAAT
*
17137223 ATAAATTTTAA-A-AAAT
1 ATAAATTTAAATATAAAT
*
17137239 ATATA-TTAAATAT
1 ATAAATTTAAATAT
17137252 TATTTTATAA
Statistics
Matches: 24, Mismatches: 3, Indels: 5
0.75 0.09 0.16
Matches are distributed among these distances:
15 4 0.17
16 9 0.38
17 1 0.04
18 10 0.42
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
ATAAATTTAAATATAAAT
Found at i:17137411 original size:26 final size:27
Alignment explanation
Indices: 17137380--17137444 Score: 71
Period size: 26 Copynumber: 2.4 Consensus size: 27
17137370 ATTTTAAATA
* * *
17137380 AATTTTTAAATTCATTTAA-AAATTAT
1 AATTTTTAAATTAATATAAGAAATCAT
*
17137406 AATTTTTTAA-TAATATAAGAAATCAT
1 AATTTTTAAATTAATATAAGAAATCAT
17137432 AATATTTTAAATT
1 AAT-TTTTAAATT
17137445 TTTTTTAAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
25 6 0.19
26 18 0.58
27 6 0.19
28 1 0.03
ACGTcount: A:0.48, C:0.03, G:0.02, T:0.48
Consensus pattern (27 bp):
AATTTTTAAATTAATATAAGAAATCAT
Found at i:17137608 original size:21 final size:21
Alignment explanation
Indices: 17137569--17137612 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
17137559 ATTTAAAATG
17137569 TTTTATAATATATTTTTTACAA
1 TTTTATAATATATTTTTTA-AA
17137591 TTTTA-AATAT-TATTTTTAAA
1 TTTTATAATATAT-TTTTTAAA
17137611 TT
1 TT
17137613 CTTTTTTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
20 5 0.24
21 11 0.52
22 5 0.24
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.61
Consensus pattern (21 bp):
TTTTATAATATATTTTTTAAA
Found at i:17137737 original size:18 final size:19
Alignment explanation
Indices: 17137714--17137756 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
17137704 GTGACTATTA
17137714 ATAAATTT-AAATATAAAT
1 ATAAATTTAAAATATAAAT
17137732 ATAAATTTAAAAATATAAAT
1 ATAAATTT-AAAATATAAAT
17137752 -TAAAT
1 ATAAAT
17137757 ATATTTTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.35
19 5 0.22
20 10 0.43
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (19 bp):
ATAAATTTAAAATATAAAT
Found at i:17140771 original size:30 final size:30
Alignment explanation
Indices: 17140735--17140857 Score: 183
Period size: 30 Copynumber: 4.1 Consensus size: 30
17140725 GTCCCAGAGC
*
17140735 AGTTCATATAACCCGGACATAGGTGGTTCG
1 AGTTCATATCACCCGGACATAGGTGGTTCG
* *
17140765 AGTTCATATCACTCGGACATGGGTGGTTCG
1 AGTTCATATCACCCGGACATAGGTGGTTCG
* *
17140795 AGTTCTTATCACCCGGACATGGGTGGTTCG
1 AGTTCATATCACCCGGACATAGGTGGTTCG
* *
17140825 AGTTCATATCACCCGGATATAGGCGGTTCG
1 AGTTCATATCACCCGGACATAGGTGGTTCG
17140855 AGT
1 AGT
17140858 CCATTTGACC
Statistics
Matches: 84, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 84 1.00
ACGTcount: A:0.22, C:0.21, G:0.28, T:0.28
Consensus pattern (30 bp):
AGTTCATATCACCCGGACATAGGTGGTTCG
Found at i:17144278 original size:25 final size:26
Alignment explanation
Indices: 17144224--17144278 Score: 60
Period size: 26 Copynumber: 2.2 Consensus size: 26
17144214 TGTTTTAGCC
* * *
17144224 TTTTTTTTTTTTAAGTTTTGACTTTC
1 TTTTTCTTTTTTAAGTCTTGACTTTA
17144250 TTTTTCTTTTTTAAGTCCTT-A-TTTA
1 TTTTTCTTTTTTAAGT-CTTGACTTTA
17144275 TTTT
1 TTTT
17144279 ATTTATTTCG
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
25 7 0.28
26 16 0.64
27 2 0.08
ACGTcount: A:0.13, C:0.09, G:0.05, T:0.73
Consensus pattern (26 bp):
TTTTTCTTTTTTAAGTCTTGACTTTA
Found at i:17144352 original size:25 final size:26
Alignment explanation
Indices: 17144305--17144358 Score: 74
Period size: 25 Copynumber: 2.1 Consensus size: 26
17144295 TTGAAATGTA
*
17144305 TTTTTTAAAAATATTTTATAATATATT
1 TTTTTTAAAAATA-TTTAAAATATATT
*
17144332 TTTTTTATAAATA-TTAAAATATATT
1 TTTTTTAAAAATATTTAAAATATATT
17144357 TT
1 TT
17144359 CAAATTATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 13 0.52
27 12 0.48
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (26 bp):
TTTTTTAAAAATATTTAAAATATATT
Found at i:17144380 original size:32 final size:33
Alignment explanation
Indices: 17144327--17144398 Score: 103
Period size: 31 Copynumber: 2.2 Consensus size: 33
17144317 ATTTTATAAT
*
17144327 ATATTTTTTTTATAAATATTAAAATATATTTTCA
1 ATATTATTTTTATAAATATT-AAATATATTTTCA
*
17144361 A-ATTATTTTT-TAAATATTAAATATATTTTTA
1 ATATTATTTTTATAAATATTAAATATATTTTCA
17144392 ATATTAT
1 ATATTAT
17144399 AAAACATTTA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
31 13 0.37
32 13 0.37
33 8 0.23
34 1 0.03
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (33 bp):
ATATTATTTTTATAAATATTAAATATATTTTCA
Found at i:17144446 original size:29 final size:28
Alignment explanation
Indices: 17144414--17144474 Score: 86
Period size: 29 Copynumber: 2.1 Consensus size: 28
17144404 ATTTAAAACG
*
17144414 ATTTAAAATGATTTAAAATATTTTTTAA
1 ATTTAAAATCATTTAAAATATTTTTTAA
* *
17144442 TATTTTAAATCATTTTAAATATTTTTTAA
1 -ATTTAAAATCATTTAAAATATTTTTTAA
17144471 ATTT
1 ATTT
17144475 TACATAGAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
28 4 0.14
29 25 0.86
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.56
Consensus pattern (28 bp):
ATTTAAAATCATTTAAAATATTTTTTAA
Found at i:17144447 original size:9 final size:9
Alignment explanation
Indices: 17144368--17144466 Score: 56
Period size: 10 Copynumber: 10.4 Consensus size: 9
17144358 TCAAATTATT
17144368 TTTTAAATA
1 TTTTAAATA
*
17144377 -TTAAATATA
1 TTTTAA-ATA
*
17144386 TTTTTAATA
1 TTTTAAATA
* *
17144395 TTATAAAACA
1 TT-TTAAATA
* *
17144405 TTTAAAACGA
1 TTTTAAA-TA
*
17144415 TTTAAAATGA
1 TTTTAAAT-A
*
17144425 TTTAAAATA
1 TTTTAAATA
*
17144434 TTTTTTAATA
1 -TTTTAAATA
17144444 TTTTAAATCA
1 TTTTAAAT-A
17144454 TTTTAAATA
1 TTTTAAATA
17144463 TTTT
1 TTTT
17144467 TTAAATTTTA
Statistics
Matches: 72, Mismatches: 11, Indels: 14
0.74 0.11 0.14
Matches are distributed among these distances:
8 4 0.06
9 26 0.36
10 42 0.58
ACGTcount: A:0.44, C:0.03, G:0.02, T:0.51
Consensus pattern (9 bp):
TTTTAAATA
Found at i:17144714 original size:22 final size:22
Alignment explanation
Indices: 17144677--17144719 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
17144667 AAAATATGGT
17144677 TAATATTTAAAAAATTATATTTA
1 TAATATTTAAAAAATTA-ATTTA
*
17144700 TAAT-TTTCAAAAATTAATTT
1 TAATATTTAAAAAATTAATTT
17144720 GAGAAATATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 4 0.21
22 11 0.58
23 4 0.21
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (22 bp):
TAATATTTAAAAAATTAATTTA
Found at i:17145265 original size:22 final size:24
Alignment explanation
Indices: 17145230--17145323 Score: 85
Period size: 22 Copynumber: 4.1 Consensus size: 24
17145220 ATAAAGTTAA
17145230 AAAATATTTTTAAAAATAATAAT-T
1 AAAATA-TTTTAAAAATAATAATAT
*
17145254 AAAA-ATTTT-AAAA-AATATTAT
1 AAAATATTTTAAAAATAATAATAT
*
17145275 AAAATATTTTAAATAT-AT-AT-T
1 AAAATATTTTAAAAATAATAATAT
* *
17145296 ACAAATTTTTTAAAATTAATAATAT
1 A-AAATATTTTAAAAATAATAATAT
17145321 AAA
1 AAA
17145324 TTAAATAAGT
Statistics
Matches: 56, Mismatches: 6, Indels: 16
0.72 0.08 0.21
Matches are distributed among these distances:
20 5 0.09
21 11 0.20
22 22 0.39
23 8 0.14
24 8 0.14
25 2 0.04
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.41
Consensus pattern (24 bp):
AAAATATTTTAAAAATAATAATAT
Found at i:17145324 original size:23 final size:22
Alignment explanation
Indices: 17145235--17145325 Score: 71
Period size: 23 Copynumber: 4.1 Consensus size: 22
17145225 GTTAAAAAAT
*
17145235 ATTTTTAAAAATAATAAT-TAA
1 ATTTTTTAAAATAATAATATAA
** *
17145256 AAATTTTAAAA-AATATTATAAA
1 ATTTTTTAAAATAATAATAT-AA
* * *
17145278 ATATTTT-AAATATATATTACAA
1 ATTTTTTAAAATA-ATAATATAA
17145300 ATTTTTTAAAATTAATAATATAA
1 ATTTTTTAAAA-TAATAATATAA
17145323 ATT
1 ATT
17145326 AAATAAGTAA
Statistics
Matches: 55, Mismatches: 9, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
20 5 0.09
21 12 0.22
22 17 0.31
23 19 0.35
24 2 0.04
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (22 bp):
ATTTTTTAAAATAATAATATAA
Found at i:17145353 original size:36 final size:37
Alignment explanation
Indices: 17145313--17145386 Score: 100
Period size: 37 Copynumber: 2.0 Consensus size: 37
17145303 TTTTAAAATT
*
17145313 AATAATAT-AAA-TTAAATAAGTAAAATAAAT-TAAGAA
1 AATAATATAAAACTTAAAAAAG-AAAA-AAATCTAAGAA
17145349 AATAATATAAAACTTAAAAAAGAAAAAAATCTAAGAA
1 AATAATATAAAACTTAAAAAAGAAAAAAATCTAAGAA
17145386 A
1 A
17145387 GAGACAAAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
36 12 0.35
37 14 0.41
38 8 0.24
ACGTcount: A:0.69, C:0.03, G:0.05, T:0.23
Consensus pattern (37 bp):
AATAATATAAAACTTAAAAAAGAAAAAAATCTAAGAA
Found at i:17145358 original size:18 final size:18
Alignment explanation
Indices: 17145308--17145359 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 18
17145298 AAATTTTTTA
*
17145308 AAATTAATAATATAAATT
1 AAATAAATAATATAAATT
* *
17145326 AAATAAGTAAAATAAATT
1 AAATAAATAATATAAATT
17145344 AAGA-AAATAATATAAA
1 AA-ATAAATAATATAAA
17145360 ACTTAAAAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
18 27 0.96
19 1 0.04
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.29
Consensus pattern (18 bp):
AAATAAATAATATAAATT
Found at i:17145448 original size:8 final size:8
Alignment explanation
Indices: 17145402--17145453 Score: 50
Period size: 8 Copynumber: 6.1 Consensus size: 8
17145392 AAAATATAAG
17145402 AAAAAAATT
1 AAAAAAA-T
**
17145411 AAAAAGTT
1 AAAAAAAT
*
17145419 AAAAAAGT
1 AAAAAAAT
17145427 AAAATAAAT
1 AAAA-AAAT
17145436 AAAAAAAAT
1 -AAAAAAAT
17145445 AAAAAAAT
1 AAAAAAAT
17145453 A
1 A
17145454 TATAAGAACC
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
8 20 0.56
9 12 0.33
10 4 0.11
ACGTcount: A:0.79, C:0.00, G:0.04, T:0.17
Consensus pattern (8 bp):
AAAAAAAT
Found at i:17154747 original size:2 final size:2
Alignment explanation
Indices: 17154735--17154769 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
17154725 AACGCTACAT
17154735 TC TC T- TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
17154770 AGCAAAGAGA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:17161499 original size:41 final size:41
Alignment explanation
Indices: 17161442--17161532 Score: 164
Period size: 41 Copynumber: 2.2 Consensus size: 41
17161432 ATACGCATAG
17161442 TATAATTTTACTTTCCTAACTTTAGTTTGAGAATGTCAGGA
1 TATAATTTTACTTTCCTAACTTTAGTTTGAGAATGTCAGGA
*
17161483 TATAATTTTACTTTCCTAACTTTAGTTTGAGAATGTCAGGT
1 TATAATTTTACTTTCCTAACTTTAGTTTGAGAATGTCAGGA
17161524 TATACATTT
1 TATA-ATTT
17161533 CTAACTTTAA
Statistics
Matches: 48, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
41 44 0.92
42 4 0.08
ACGTcount: A:0.29, C:0.12, G:0.13, T:0.46
Consensus pattern (41 bp):
TATAATTTTACTTTCCTAACTTTAGTTTGAGAATGTCAGGA
Found at i:17172997 original size:16 final size:19
Alignment explanation
Indices: 17172966--17173005 Score: 59
Period size: 16 Copynumber: 2.3 Consensus size: 19
17172956 TTACGAGTAG
17172966 GTTTTTGTATGTTATTT-T
1 GTTTTTGTATGTTATTTCT
17172984 GTTTTTG-A-GTTATTTCT
1 GTTTTTGTATGTTATTTCT
17173001 GTTTT
1 GTTTT
17173006 AGAACTGAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.33
17 7 0.33
18 7 0.33
ACGTcount: A:0.10, C:0.03, G:0.17, T:0.70
Consensus pattern (19 bp):
GTTTTTGTATGTTATTTCT
Found at i:17180399 original size:3 final size:3
Alignment explanation
Indices: 17180391--17180429 Score: 71
Period size: 3 Copynumber: 13.3 Consensus size: 3
17180381 TACCCCACAA
17180391 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA- AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
17180430 GAACTGAGGG
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.06
3 33 0.94
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:17192801 original size:7 final size:7
Alignment explanation
Indices: 17192789--17192821 Score: 57
Period size: 7 Copynumber: 4.6 Consensus size: 7
17192779 TCGGTATAAA
17192789 AAAAAAG
1 AAAAAAG
17192796 AAAAAAG
1 AAAAAAG
17192803 AAAAAAG
1 AAAAAAG
17192810 AAAGAAAG
1 AAA-AAAG
17192818 AAAA
1 AAAA
17192822 GAAGCATGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
7 18 0.72
8 7 0.28
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:17193223 original size:25 final size:24
Alignment explanation
Indices: 17193186--17193417 Score: 169
Period size: 25 Copynumber: 9.5 Consensus size: 24
17193176 GACCTCAGCA
17193186 TGCTCTCTGATTATTAGCACGCTAG
1 TGCTCTCTGATTATTAGCACG-TAG
* *
17193211 TGCTCTCTAATTATTAGCACGCCAG
1 TGCTCTCTGATTATTAGCACG-TAG
* *
17193236 TGCTCTCTAATTATTAGCACGCCAG
1 TGCTCTCTGATTATTAGCACG-TAG
* * *
17193261 TGCTTTCTG---ATTAGCACATTTG
1 TGCTCTCTGATTATTAGCAC-GTAG
17193283 TGCTCTCTGA-TATTTAGCACGTCAG
1 TGCTCTCTGATTA-TTAGCACGT-AG
* *
17193308 TGATCTCTGA-TATTTAGCATGTCAG
1 TGCTCTCTGATTA-TTAGCACGT-AG
17193333 TGCTCTCTGA-TATTTAGCACGTCAG
1 TGCTCTCTGATTA-TTAGCACGT-AG
* *
17193358 TGCTCTCTG---ATTAGCACATTTG
1 TGCTCTCTGATTATTAGCAC-GTAG
17193380 TGCTCTCTGA-TATTTAGCACGTCAG
1 TGCTCTCTGATTA-TTAGCACGT-AG
*
17193405 TGCTCTCTAATTA
1 TGCTCTCTGATTA
17193418 GCACATTTGT
Statistics
Matches: 177, Mismatches: 19, Indels: 21
0.82 0.09 0.10
Matches are distributed among these distances:
22 34 0.19
23 2 0.01
24 4 0.02
25 135 0.76
26 2 0.01
ACGTcount: A:0.21, C:0.23, G:0.18, T:0.38
Consensus pattern (24 bp):
TGCTCTCTGATTATTAGCACGTAG
Found at i:17193300 original size:47 final size:47
Alignment explanation
Indices: 17193235--17193435 Score: 278
Period size: 47 Copynumber: 4.2 Consensus size: 47
17193225 TAGCACGCCA
* * *
17193235 GTGCTCTCTAAT-TATTAGCACGCCAGTGCTTTCTGATTAGCACATTT
1 GTGCTCTCTGATAT-TTAGCACGTCAGTGCTCTCTGATTAGCACATTT
* ** **
17193282 GTGCTCTCTGATATTTAGCACGTCAGTGATCTCTGATATTTAGCATGTCA
1 GTGCTCTCTGATATTTAGCACGTCAGTGCTCTCTG--A-TTAGCACATTT
17193332 GTGCTCTCTGATATTTAGCACGTCAGTGCTCTCTGATTAGCACATTT
1 GTGCTCTCTGATATTTAGCACGTCAGTGCTCTCTGATTAGCACATTT
*
17193379 GTGCTCTCTGATATTTAGCACGTCAGTGCTCTCTAATTAGCACATTT
1 GTGCTCTCTGATATTTAGCACGTCAGTGCTCTCTGATTAGCACATTT
17193426 GTGCTCTCTG
1 GTGCTCTCTG
17193436 TTCATCAGTG
Statistics
Matches: 136, Mismatches: 14, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
47 92 0.68
48 2 0.01
49 1 0.01
50 41 0.30
ACGTcount: A:0.20, C:0.23, G:0.19, T:0.38
Consensus pattern (47 bp):
GTGCTCTCTGATATTTAGCACGTCAGTGCTCTCTGATTAGCACATTT
Found at i:17193352 original size:97 final size:97
Alignment explanation
Indices: 17193186--17193417 Score: 337
Period size: 97 Copynumber: 2.4 Consensus size: 97
17193176 GACCTCAGCA
17193186 TGCTCTCTGAT-TATTAGCACG-CTAGTGCTCTCTAATTATTAGCACGCCAGTGCTCTCTAATTA
1 TGCTCTCTGATAT-TTAGCACGTC-AGTGCTCTCTAATTATTAGCACGCCAGTGCTCTCTAATTA
*
17193249 TTAGCACGCCAGTGCTTTCTGATTAGCACATTTG
64 TTAGCACGCCAGTGCTCTCTGATTAGCACATTTG
* * * * *
17193283 TGCTCTCTGATATTTAGCACGTCAGTGATCTCTGA-TATTTAGCATGTCAGTGCTCTCTGA-TAT
1 TGCTCTCTGATATTTAGCACGTCAGTGCTCTCTAATTA-TTAGCACGCCAGTGCTCTCTAATTA-
*
17193346 TTAGCACGTCAGTGCTCTCTGATTAGCACATTTG
64 TTAGCACGCCAGTGCTCTCTGATTAGCACATTTG
17193380 TGCTCTCTGATATTTAGCACGTCAGTGCTCTCTAATTA
1 TGCTCTCTGATATTTAGCACGTCAGTGCTCTCTAATTA
17193418 GCACATTTGT
Statistics
Matches: 121, Mismatches: 9, Indels: 9
0.87 0.06 0.06
Matches are distributed among these distances:
96 4 0.03
97 113 0.93
98 4 0.03
ACGTcount: A:0.21, C:0.23, G:0.18, T:0.38
Consensus pattern (97 bp):
TGCTCTCTGATATTTAGCACGTCAGTGCTCTCTAATTATTAGCACGCCAGTGCTCTCTAATTATT
AGCACGCCAGTGCTCTCTGATTAGCACATTTG
Found at i:17193429 original size:22 final size:22
Alignment explanation
Indices: 17193357--17193434 Score: 93
Period size: 22 Copynumber: 3.4 Consensus size: 22
17193347 TAGCACGTCA
*
17193357 GTGCTCTCTGATTAGCACATTT
1 GTGCTCTCTAATTAGCACATTT
* **
17193379 GTGCTCTCTGATATTTAGCACGTCA
1 GTGCTCTCT-A-A-TTAGCACATTT
17193404 GTGCTCTCTAATTAGCACATTT
1 GTGCTCTCTAATTAGCACATTT
17193426 GTGCTCTCT
1 GTGCTCTCT
17193435 GTTCATCAGT
Statistics
Matches: 46, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
22 26 0.57
23 1 0.02
24 2 0.04
25 17 0.37
ACGTcount: A:0.18, C:0.24, G:0.18, T:0.40
Consensus pattern (22 bp):
GTGCTCTCTAATTAGCACATTT
Found at i:17203628 original size:51 final size:51
Alignment explanation
Indices: 17203552--17203663 Score: 179
Period size: 51 Copynumber: 2.2 Consensus size: 51
17203542 CTCAAACTTA
* *
17203552 CTTCATACTTCATCCGGAATTATTACCTTGTTGCTCTAACTTCAACAAGAG
1 CTTCATATTTCATCCGGAATAATTACCTTGTTGCTCTAACTTCAACAAGAG
* * *
17203603 CTTCATATTTCATCCGGAATAATTACTTTGTTGCTCTAGCTTTAACAAGAG
1 CTTCATATTTCATCCGGAATAATTACCTTGTTGCTCTAACTTCAACAAGAG
17203654 CTTCATATTT
1 CTTCATATTT
17203664 TATCTGGATA
Statistics
Matches: 56, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
51 56 1.00
ACGTcount: A:0.27, C:0.22, G:0.12, T:0.39
Consensus pattern (51 bp):
CTTCATATTTCATCCGGAATAATTACCTTGTTGCTCTAACTTCAACAAGAG
Found at i:17206038 original size:30 final size:31
Alignment explanation
Indices: 17206014--17206072 Score: 84
Period size: 30 Copynumber: 1.9 Consensus size: 31
17206004 GTAAATACTC
* * *
17206014 AAAATTTGAGGGATTAA-AGTGTAAATATGA
1 AAAATTCGAAGGACTAATAGTGTAAATATGA
17206044 AAAATTCGAAGGACTAATAGTGTAAATAT
1 AAAATTCGAAGGACTAATAGTGTAAATAT
17206073 TTTAAGGGTG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 14 0.56
31 11 0.44
ACGTcount: A:0.47, C:0.03, G:0.20, T:0.29
Consensus pattern (31 bp):
AAAATTCGAAGGACTAATAGTGTAAATATGA
Found at i:17211418 original size:18 final size:20
Alignment explanation
Indices: 17211376--17211412 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
17211366 ATATTTTATG
*
17211376 ATTA-TTTAATTAGATATAT
1 ATTATTTTAATGAGATATAT
17211395 ATTATTTTAATGAGATAT
1 ATTATTTTAATGAGATAT
17211413 TTTATTATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 4 0.25
20 12 0.75
ACGTcount: A:0.41, C:0.00, G:0.08, T:0.51
Consensus pattern (20 bp):
ATTATTTTAATGAGATATAT
Found at i:17213624 original size:46 final size:46
Alignment explanation
Indices: 17213572--17213844 Score: 361
Period size: 46 Copynumber: 6.0 Consensus size: 46
17213562 AGTGTGCTCT
* *
17213572 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACGATGGCAAC
1 CTGATATGAAACGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
*
17213618 CTGATATGAAACGTGTAAGACCATGGTTGAAAGATACCATGGCAGC
1 CTGATATGAAACGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
17213664 CTGATATGAAACGTGTAAGACCATGGTTGAAAGATACCATGGC-AC
1 CTGATATGAAACGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
17213709 CTGATATGAAACGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAACGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* *** ****
17213755 ATGACGGGAAATAAATAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAACGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * * * * * *
17213801 ATGACA-GAAAATGAGTAAGACCATAGTTGAAAGACACTATGGCA
1 CTGATATG-AAACGTGTAAGACCATGGTTGAAAGATACCATGGCA
17213845 TCATGTCAAA
Statistics
Matches: 207, Mismatches: 18, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
45 45 0.22
46 162 0.78
ACGTcount: A:0.39, C:0.16, G:0.25, T:0.21
Consensus pattern (46 bp):
CTGATATGAAACGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
Found at i:17213748 original size:91 final size:92
Alignment explanation
Indices: 17213572--17213844 Score: 370
Period size: 91 Copynumber: 3.0 Consensus size: 92
17213562 AGTGTGCTCT
*
17213572 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACGATGGCAACCTGATATGAAACGTGTAAG
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAACGTGTAAG
*
17213637 ACCATGGTTGAAAGATACCATGGCAGC
66 ACCATGGTTGAAAGATACCATGGCAAC
*
17213664 CTGATATGAAACGTGTAAGACCATGGTTGAAAGATACCATGGC-ACCTGATATGAAACGTGTAAG
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAACGTGTAAG
17213728 ACCATGGTTGAAAGATACCATGGCAAC
66 ACCATGGTTGAAAGATACCATGGCAAC
* *** *** * * * *
17213755 ATGACGGGAAATAAATAAGACCATGGTTGAAAGATACCATGGCAACATGACA-GAAAATGAGTAA
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATG-AAACGTGTAA
* * *
17213819 GACCATAGTTGAAAGACACTATGGCA
65 GACCATGGTTGAAAGATACCATGGCA
17213845 TCATGTCAAA
Statistics
Matches: 161, Mismatches: 18, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
91 83 0.52
92 78 0.48
ACGTcount: A:0.39, C:0.16, G:0.25, T:0.21
Consensus pattern (92 bp):
CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAACGTGTAAG
ACCATGGTTGAAAGATACCATGGCAAC
Found at i:17213819 original size:137 final size:137
Alignment explanation
Indices: 17213572--17213844 Score: 368
Period size: 137 Copynumber: 2.0 Consensus size: 137
17213562 AGTGTGCTCT
* * * * * ***
17213572 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACGATGGCAACCTGATATGAAACGTGTAAG
1 CTGATATGAAACGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGACAGGAAACAAATAAG
* * * * * *
17213637 ACCATGGTTGAAAGATACCATGGCAGCCTGATATGAAACGTGTAAGACCATGGTTGAAAGATACC
66 ACCATGGTTGAAAGATACCATGGCAACATGACATGAAACGAGTAAGACCATAGTTGAAAGACACC
17213702 ATGGCAC
131 ATGGCAC
* *
17213709 CTGATATGAAACGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGACGGGAAATAAATAAG
1 CTGATATGAAACGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGACAGGAAACAAATAAG
*
17213774 ACCATGGTTGAAAGATACCATGGCAACATGACA-GAAAATGAGTAAGACCATAGTTGAAAGACAC
66 ACCATGGTTGAAAGATACCATGGCAACATGACATG-AAACGAGTAAGACCATAGTTGAAAGACAC
*
17213838 TATGGCA
130 CATGGCA
17213845 TCATGTCAAA
Statistics
Matches: 117, Mismatches: 18, Indels: 2
0.85 0.13 0.01
Matches are distributed among these distances:
136 1 0.01
137 116 0.99
ACGTcount: A:0.39, C:0.16, G:0.25, T:0.21
Consensus pattern (137 bp):
CTGATATGAAACGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGACAGGAAACAAATAAG
ACCATGGTTGAAAGATACCATGGCAACATGACATGAAACGAGTAAGACCATAGTTGAAAGACACC
ATGGCAC
Found at i:17216600 original size:132 final size:130
Alignment explanation
Indices: 17216006--17216611 Score: 415
Period size: 131 Copynumber: 4.6 Consensus size: 130
17215996 CGTGGAATCA
* * * * * * ** *
17216006 TGCCCTAACGTGTTAGGTTGCAATTTCTCGTTTGCTC-AAAGTAATCGAAGGTCCCTTTAGAATT
1 TGCCCTATCGTGCTGGGTTGCAATTTCTCATTTGCTCGAAA-CAATCAAATATCCCTTCA-AATT
* * * ** * *
17216070 TCACCCATGTCTTT-TAAAAATCCCTT-AAATGAAGGCGATGTGT-GATATTTGGCAATTCACAG
64 TCACTCATGT-TTTCTAAAAA-CCTTTAAAACGAAGGAAATGT-TCGATGTTTGGCAATTCAGAG
*
17216132 AATCG
126 AATAG
* * * * ** *
17216137 TGCCTTAACGTGCTGGGTTGCAATTTCTCGTTCGCTTAAAATAATCAAATATCCCTTCAAAATTT
1 TGCCCTATCGTGCTGGGTTGCAATTTCTCATTTGCTCGAAACAATCAAATATCCCTTC-AAATTT
* * * * ** * *
17216202 CACTCGTGTCTTCTAAAAATCCTTTAAAATGAAGGCAATACTC-AGTGTTTGACAATCCAG-GAA
65 CACTCATGTTTTCTAAAAA-CCTTTAAAACGAAGGAAATGTTCGA-TGTTTGGCAATTCAGAGAA
17216265 TCA-
128 T-AG
** * * * **
17216268 TGCCCTATCGTGCTGGGTTGTGATTTCTCGTTTGCTCGAAACAATCAAATATTCCTTTAGGTTTT
1 TGCCCTATCGTGCTGGGTTGCAATTTCTCATTTGCTCGAAACAATCAAATATCCCTTCA-AATTT
* ** *
17216333 CACTCATGTTTAT-TAAAAACCTTTCAAAACGAAGGTAATGTTCGATGTTTGGTGATT-TGAGAA
65 CACTCATGTTT-TCTAAAAACCTTT-AAAACGAAGGAAATGTTCGATGTTTGGCAATTCAGAGAA
*
17216396 TCG
128 TAG
* ** * * * * *
17216399 TGCCCTGTCGTGCTGGGTTGCGCTTTTTCATCTG-TCCTAAACAATCGAAGATCCCTTCGAAATT
1 TGCCCTATCGTGCTGGGTTGCAATTTCTCATTTGCT-CGAAACAATCAAATATCCCTTC-AAATT
* * * * *
17216463 TCACTCACGTTTTCTAAAAACCCTTTAAAACGAAAGAAATGTTCGACGTTTGGCAATTCGGGGAA
64 TCACTCATGTTTTCTAAAAA-CCTTTAAAACGAAGGAAATGTTCGATGTTTGGCAATTCAGAGAA
17216528 TAG
128 TAG
* * * * *
17216531 TGCCCTATCGTGCTGGGCTGCAATTTCCCATTTGCTC-AAGATAATCGAATATCTCTTCATAATT
1 TGCCCTATCGTGCTGGGTTGCAATTTCTCATTTGCTCGAA-ACAATCAAATATCCCTTCA-AATT
*
17216595 TCACTCGTGTTTTCTAA
64 TCACTCATGTTTTCTAA
17216612 GGCGATGCAA
Statistics
Matches: 375, Mismatches: 79, Indels: 41
0.76 0.16 0.08
Matches are distributed among these distances:
130 11 0.03
131 260 0.69
132 103 0.27
133 1 0.00
ACGTcount: A:0.27, C:0.21, G:0.18, T:0.34
Consensus pattern (130 bp):
TGCCCTATCGTGCTGGGTTGCAATTTCTCATTTGCTCGAAACAATCAAATATCCCTTCAAATTTC
ACTCATGTTTTCTAAAAACCTTTAAAACGAAGGAAATGTTCGATGTTTGGCAATTCAGAGAATAG
Found at i:17229203 original size:15 final size:16
Alignment explanation
Indices: 17229183--17229212 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
17229173 GAAAATTGCC
17229183 AAAATGGG-CTAAATA
1 AAAATGGGACTAAATA
17229198 AAAATGGGACTAAAT
1 AAAATGGGACTAAAT
17229213 TGGAATATCT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.53, C:0.07, G:0.20, T:0.20
Consensus pattern (16 bp):
AAAATGGGACTAAATA
Found at i:17236802 original size:17 final size:19
Alignment explanation
Indices: 17236768--17236805 Score: 62
Period size: 17 Copynumber: 2.1 Consensus size: 19
17236758 AAACCTTGAA
17236768 TTTTCTCTTTTCTTCTTTC
1 TTTTCTCTTTTCTTCTTTC
17236787 TTTTCTC-TTT-TTCTTTC
1 TTTTCTCTTTTCTTCTTTC
17236804 TT
1 TT
17236806 CCTTCCCCTG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 9 0.47
18 3 0.16
19 7 0.37
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (19 bp):
TTTTCTCTTTTCTTCTTTC
Found at i:17238195 original size:42 final size:41
Alignment explanation
Indices: 17238146--17238259 Score: 158
Period size: 42 Copynumber: 2.7 Consensus size: 41
17238136 TTCGTTTTCT
** * *
17238146 TGATGCCATAGTTCAACTATGGTCTTACACATCTTCGCATA-A
1 TGATGCCATAGCCCAGCTATGGTCTTACACATATT--CATATA
17238188 TGATGCCATAGCCCAGCTATGGTCTTACACATATTCATATA
1 TGATGCCATAGCCCAGCTATGGTCTTACACATATTCATATA
17238229 TCGATGCCATAGCCCAGCTATGGTCTTACAC
1 T-GATGCCATAGCCCAGCTATGGTCTTACAC
17238260 GTAATCACAC
Statistics
Matches: 66, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
40 4 0.06
41 2 0.03
42 60 0.91
ACGTcount: A:0.27, C:0.26, G:0.16, T:0.31
Consensus pattern (41 bp):
TGATGCCATAGCCCAGCTATGGTCTTACACATATTCATATA
Found at i:17238401 original size:47 final size:46
Alignment explanation
Indices: 17238231--17238398 Score: 201
Period size: 47 Copynumber: 3.6 Consensus size: 46
17238221 TTCATATATC
* * *
17238231 GATGCCATAGCCCAGCTATGGTCTTACACGTAATCACACATCACATAT
1 GATGCCATAGCCCAGATATGGTCTTACACGT-ATCACATATCACA-CT
* * *
17238279 CGATGCCATAGCCCAGTTATGGTCTTACACGAATCACATATCTCACT
1 -GATGCCATAGCCCAGATATGGTCTTACACGTATCACATATCACACT
* * * *
17238326 GATGCCATATCCCAGATATGGTCTTATACAGTAGCATATATCACACT
1 GATGCCATAGCCCAGATATGGTCTTACAC-GTATCACATATCACACT
*
17238373 GATGCCATATCCCAGATATGGTCTTA
1 GATGCCATAGCCCAGATATGGTCTTA
17238399 TACGGAAATC
Statistics
Matches: 106, Mismatches: 12, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
46 26 0.25
47 40 0.38
48 11 0.10
49 29 0.27
ACGTcount: A:0.30, C:0.27, G:0.15, T:0.28
Consensus pattern (46 bp):
GATGCCATAGCCCAGATATGGTCTTACACGTATCACATATCACACT
Found at i:17238410 original size:95 final size:95
Alignment explanation
Indices: 17238189--17238398 Score: 238
Period size: 95 Copynumber: 2.3 Consensus size: 95
17238179 TTCGCATAAT
* * * *
17238189 GATGCCATAGCCCAGCTATGGTCTTACAC-ATAT-TCATATAT--C-GATGCCATAGCCCAGCTA
1 GATGCCATAGCCCAGATATGGTCTTACACGA-ATCACATATCTCACTGATGCCATAGCCCAGATA
*
17238249 TGGTCTTACACGTAATCACACATCACATATC
65 TGGTCTTACACGTAAGCACACATCACATATC
* *
17238280 GATGCCATAGCCCAGTTATGGTCTTACACGAATCACATATCTCACTGATGCCATATCCCAGATAT
1 GATGCCATAGCCCAGATATGGTCTTACACGAATCACATATCTCACTGATGCCATAGCCCAGATAT
* * * *
17238345 GGTCTTATACAGT-AGCATATATCACA-CT-
66 GGTCTTACAC-GTAAGCACACATCACATATC
*
17238373 GATGCCATATCCCAGATATGGTCTTA
1 GATGCCATAGCCCAGATATGGTCTTA
17238399 TACGGAAATC
Statistics
Matches: 101, Mismatches: 12, Indels: 10
0.82 0.10 0.08
Matches are distributed among these distances:
91 30 0.30
92 7 0.07
93 24 0.24
94 2 0.02
95 36 0.36
96 2 0.02
ACGTcount: A:0.30, C:0.27, G:0.15, T:0.29
Consensus pattern (95 bp):
GATGCCATAGCCCAGATATGGTCTTACACGAATCACATATCTCACTGATGCCATAGCCCAGATAT
GGTCTTACACGTAAGCACACATCACATATC
Found at i:17238455 original size:31 final size:31
Alignment explanation
Indices: 17238420--17238568 Score: 244
Period size: 31 Copynumber: 4.8 Consensus size: 31
17238410 CTTGTCACTT
*
17238420 GTAGCCGGAGCTACCACTATTCACTGATCAG
1 GTAGCCGGAGCTACCACTTTTCACTGATCAG
17238451 GTAGCCGGAGCTACCACTTTTCACTGATCAG
1 GTAGCCGGAGCTACCACTTTTCACTGATCAG
17238482 GTAGCCGGAGCTACCACTTTTCACTGATCAG
1 GTAGCCGGAGCTACCACTTTTCACTGATCAG
** * *
17238513 GTAGTAGAAGCTACCACTTTTCACTGCTCAG
1 GTAGCCGGAGCTACCACTTTTCACTGATCAG
*
17238544 GTAGCCGAAGCTACCACTTTTCACT
1 GTAGCCGGAGCTACCACTTTTCACT
17238569 TGTTATTTGT
Statistics
Matches: 111, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 111 1.00
ACGTcount: A:0.24, C:0.29, G:0.21, T:0.26
Consensus pattern (31 bp):
GTAGCCGGAGCTACCACTTTTCACTGATCAG
Found at i:17238648 original size:50 final size:50
Alignment explanation
Indices: 17238544--17238720 Score: 282
Period size: 50 Copynumber: 3.5 Consensus size: 50
17238534 CACTGCTCAG
* * *
17238544 GTAGCCGAAGCTACCACTTTTCACTTGTTATTTGTCCTTGATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTT-TCATTTGTCCTTGATCAGATAAGT
* * *
17238595 GTAGTCGAAGCTATCACTTATCACTTTCACTTGTCCTTGATCAGATAAAT
1 GTAGCCGAAGCTATCACTTATCACTTTCATTTGTCCTTGATCAGATAAGT
*
17238645 GTAGCCGAAGCTATTACTTATCACTTTCATTTGTCCTTGATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTTTCATTTGTCCTTGATCAGATAAGT
17238695 GTAGCCGAAGCTATCACTTATCACTT
1 GTAGCCGAAGCTATCACTTATCACTT
17238721 GTTGCCATGG
Statistics
Matches: 115, Mismatches: 11, Indels: 1
0.91 0.09 0.01
Matches are distributed among these distances:
50 92 0.80
51 23 0.20
ACGTcount: A:0.26, C:0.22, G:0.16, T:0.36
Consensus pattern (50 bp):
GTAGCCGAAGCTATCACTTATCACTTTCATTTGTCCTTGATCAGATAAGT
Found at i:17241868 original size:11 final size:12
Alignment explanation
Indices: 17241847--17241871 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
17241837 ACCAAATGAC
17241847 TTCATTTTTTTT
1 TTCATTTTTTTT
17241859 TTCATTTTTTTT
1 TTCATTTTTTTT
17241871 T
1 T
17241872 ATAAAAATTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.08, G:0.00, T:0.84
Consensus pattern (12 bp):
TTCATTTTTTTT
Found at i:17242570 original size:39 final size:37
Alignment explanation
Indices: 17242503--17242595 Score: 98
Period size: 39 Copynumber: 2.5 Consensus size: 37
17242493 ACCAGAATGG
* *
17242503 CACCCAGTGCCTCATCGGATAGTTCGAAGCAATAGTTGA
1 CACCCAGTGCCTCATCGGAAAGTCCGAAG-AA-AGTTGA
* *
17242542 CACCCAGTGTCTCATCGGCAAAG-CCGAAGAAAGTTGG
1 CACCCAGTGCCTCATCGG-AAAGTCCGAAGAAAGTTGA
* *
17242579 TACCCAGTACCTCATCG
1 CACCCAGTGCCTCATCG
17242596 AATCTATCCG
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
37 19 0.41
38 2 0.04
39 22 0.48
40 3 0.07
ACGTcount: A:0.28, C:0.29, G:0.23, T:0.20
Consensus pattern (37 bp):
CACCCAGTGCCTCATCGGAAAGTCCGAAGAAAGTTGA
Found at i:17243731 original size:20 final size:20
Alignment explanation
Indices: 17243697--17243736 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
17243687 TTCTATTCTG
*
17243697 TTTCTTTTCTGTTTTGTTTC
1 TTTCTTTTCTGTTTTATTTC
17243717 TTTCTTTTTCT-TTTTATTTC
1 TTTC-TTTTCTGTTTTATTTC
17243737 CTTTTATTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.03, C:0.15, G:0.05, T:0.78
Consensus pattern (20 bp):
TTTCTTTTCTGTTTTATTTC
Found at i:17243903 original size:31 final size:28
Alignment explanation
Indices: 17243867--17243934 Score: 73
Period size: 31 Copynumber: 2.3 Consensus size: 28
17243857 TTGTCTTTAT
**
17243867 TTAATTTATTTCTTAATATAATATTTATAA
1 TTAATTTATTTAATAATAT-A-ATTTATAA
* *
17243897 TGTAATTAATTTAATAATATACTTTATAA
1 T-TAATTTATTTAATAATATAATTTATAA
17243926 TTAATTTAT
1 TTAATTTAT
17243935 ATATTTATAT
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
28 7 0.22
29 8 0.25
30 2 0.06
31 15 0.47
ACGTcount: A:0.41, C:0.03, G:0.01, T:0.54
Consensus pattern (28 bp):
TTAATTTATTTAATAATATAATTTATAA
Found at i:17243951 original size:21 final size:20
Alignment explanation
Indices: 17243913--17243951 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
17243903 TAATTTAATA
*
17243913 ATATACTTTATAATTAATTT
1 ATATACTTTATAAATAATTT
*
17243933 ATATATTTATATAAATAAT
1 ATATACTT-TATAAATAAT
17243952 AATATAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 7 0.44
21 9 0.56
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (20 bp):
ATATACTTTATAAATAATTT
Found at i:17248901 original size:21 final size:21
Alignment explanation
Indices: 17248859--17248901 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
17248849 TTCACTATAC
*
17248859 ATTCTTTCATCAGTATCATTT
1 ATTCTTTCATCAGCATCATTT
*
17248880 ATTCTTTCTTCAGACATC-TTT
1 ATTCTTTCATCAG-CATCATTT
17248901 A
1 A
17248902 ATCTATAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 16 0.84
22 3 0.16
ACGTcount: A:0.23, C:0.21, G:0.05, T:0.51
Consensus pattern (21 bp):
ATTCTTTCATCAGCATCATTT
Found at i:17249212 original size:11 final size:12
Alignment explanation
Indices: 17249191--17249215 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
17249181 ACCAAATGAC
17249191 TTCATTTTTTTT
1 TTCATTTTTTTT
17249203 TTCATTTTTTTT
1 TTCATTTTTTTT
17249215 T
1 T
17249216 ATAAAAATTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.08, G:0.00, T:0.84
Consensus pattern (12 bp):
TTCATTTTTTTT
Found at i:17249941 original size:39 final size:37
Alignment explanation
Indices: 17249874--17249966 Score: 98
Period size: 39 Copynumber: 2.5 Consensus size: 37
17249864 ACCAGAATGG
* *
17249874 CACCCAGTGCCTCATCGGATAGTTCGAAGCAATAGTTGA
1 CACCCAGTGCCTCATCGGAAAGTCCGAAG-AA-AGTTGA
* *
17249913 CACCCAGTGTCTCATCGGCAAAG-CCGAAGAAAGTTGG
1 CACCCAGTGCCTCATCGG-AAAGTCCGAAGAAAGTTGA
* *
17249950 TACCCAGTACCTCATCG
1 CACCCAGTGCCTCATCG
17249967 AATCTATCCG
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
37 19 0.41
38 2 0.04
39 22 0.48
40 3 0.07
ACGTcount: A:0.28, C:0.29, G:0.23, T:0.20
Consensus pattern (37 bp):
CACCCAGTGCCTCATCGGAAAGTCCGAAGAAAGTTGA
Found at i:17251074 original size:11 final size:11
Alignment explanation
Indices: 17251058--17251082 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
17251048 TCCTTTGTTC
17251058 TTTCTATTCTG
1 TTTCTATTCTG
17251069 TTTCTATTCTG
1 TTTCTATTCTG
17251080 TTT
1 TTT
17251083 TGTTTCTTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.08, C:0.16, G:0.08, T:0.68
Consensus pattern (11 bp):
TTTCTATTCTG
Found at i:17251086 original size:16 final size:14
Alignment explanation
Indices: 17251051--17251097 Score: 51
Period size: 16 Copynumber: 3.2 Consensus size: 14
17251041 CCTCTGTTCC
17251051 TTTG-TTCTTTCTAT
1 TTTGTTTCTTTCT-T
*
17251065 TCTGTTTCTATTCTGT
1 TTTGTTTCT-TTCT-T
17251081 TTTGTTTCTTTCTT
1 TTTGTTTCTTTCTT
17251095 TTT
1 TTT
17251098 CTTTTTATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
14 7 0.25
15 8 0.29
16 13 0.46
ACGTcount: A:0.04, C:0.15, G:0.09, T:0.72
Consensus pattern (14 bp):
TTTGTTTCTTTCTT
Found at i:17251275 original size:31 final size:28
Alignment explanation
Indices: 17251239--17251306 Score: 73
Period size: 31 Copynumber: 2.3 Consensus size: 28
17251229 TTGTCTTTAT
**
17251239 TTAATTTATTTCTTAATATAATATTTATAA
1 TTAATTTATTTAATAATAT-A-ATTTATAA
* *
17251269 TGTAATTAATTTAATAATATACTTTATAA
1 T-TAATTTATTTAATAATATAATTTATAA
17251298 TTAATTTAT
1 TTAATTTAT
17251307 ATATTTATAT
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
28 7 0.22
29 8 0.25
30 2 0.06
31 15 0.47
ACGTcount: A:0.41, C:0.03, G:0.01, T:0.54
Consensus pattern (28 bp):
TTAATTTATTTAATAATATAATTTATAA
Found at i:17251323 original size:21 final size:20
Alignment explanation
Indices: 17251280--17251328 Score: 55
Period size: 21 Copynumber: 2.5 Consensus size: 20
17251270 GTAATTAATT
*
17251280 TAATA-ATATACTTTATAAT
1 TAATATATATACTTTATAAA
* *
17251299 TAATTTATATATTTATATAAA
1 TAATATATATACTT-TATAAA
17251320 TAATATATA
1 TAATATATA
17251329 AAAATCTAAG
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
19 4 0.17
20 7 0.29
21 13 0.54
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (20 bp):
TAATATATATACTTTATAAA
Found at i:17252517 original size:30 final size:29
Alignment explanation
Indices: 17252481--17252541 Score: 104
Period size: 30 Copynumber: 2.1 Consensus size: 29
17252471 AAACGGAAGT
17252481 TTTGGCACTAAGTGTGCGATTTAAACTAGC
1 TTTGGCACTAAGTGTGCGATTT-AACTAGC
*
17252511 TTTGGCACTAAGTGTGTGATTTAACTAGC
1 TTTGGCACTAAGTGTGCGATTTAACTAGC
17252540 TT
1 TT
17252542 CGACTACTTG
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
29 9 0.30
30 21 0.70
ACGTcount: A:0.25, C:0.15, G:0.23, T:0.38
Consensus pattern (29 bp):
TTTGGCACTAAGTGTGCGATTTAACTAGC
Found at i:17261283 original size:19 final size:19
Alignment explanation
Indices: 17261256--17261295 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
17261246 AAGTTTTTTA
17261256 TATTATTAA-ATTATATTAT
1 TATTATTAATA-TATATTAT
*
17261275 TATTTTTAATATATATTAT
1 TATTATTAATATATATTAT
17261294 TA
1 TA
17261296 ACTCTAAGCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 18 0.95
20 1 0.05
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (19 bp):
TATTATTAATATATATTAT
Found at i:17264120 original size:14 final size:15
Alignment explanation
Indices: 17264101--17264130 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
17264091 TACGCATTTA
17264101 ATTTTTAAATATTGT
1 ATTTTTAAATATTGT
*
17264116 ATTTTTAATTATTGT
1 ATTTTTAAATATTGT
17264131 TACTTGAAAT
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:0.30, C:0.00, G:0.07, T:0.63
Consensus pattern (15 bp):
ATTTTTAAATATTGT
Found at i:17264872 original size:15 final size:13
Alignment explanation
Indices: 17264842--17264877 Score: 54
Period size: 15 Copynumber: 2.6 Consensus size: 13
17264832 TGTTTAACTA
17264842 ATAATTATAAATT
1 ATAATTATAAATT
17264855 ATAATTATAATTATT
1 ATAATTATAA--ATT
17264870 ATAATTAT
1 ATAATTAT
17264878 CACAATATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 10 0.48
15 11 0.52
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (13 bp):
ATAATTATAAATT
Found at i:17264955 original size:117 final size:116
Alignment explanation
Indices: 17264754--17264985 Score: 312
Period size: 118 Copynumber: 2.0 Consensus size: 116
17264744 TAAAATTAAT
* *
17264754 TAATTATCACAATTTATTTCTATATTTATACTTAAAGTTCTATTTAAATAATAAATCTATTTTAA
1 TAATTATCACAATTTATTTCTATATTTATACTCAAAGTTCTATTCAAATAATAAATCTATTTTAA
* *
17264819 ATTTTAGCATATTTGTTTAACTAAT-AATTATAAATTATAATTATAATTATTA
66 ATATTAGCAAATTTGTTTAACTAATAAATT-TAAATTA-AATTATAATTATTA
* * *
17264871 TAATTATCACAATATT-TTTCTATATTTTATGA-TCAATGTTCTATTCAAGTAATAAATTTATTT
1 TAATTATCACAAT-TTATTTCTATA-TTTAT-ACTCAAAGTTCTATTCAAATAATAAATCTATTT
17264934 TAAA-ATTAGCACAATTT-TTTAACTAATAAATTTAAATTAAATTATAATTATT
63 TAAATATTAGCA-AATTTGTTTAACTAATAAATTTAAATTAAATTATAATTATT
17264986 TTTAAAGTTA
Statistics
Matches: 103, Mismatches: 7, Indels: 11
0.85 0.06 0.09
Matches are distributed among these distances:
116 13 0.13
117 44 0.43
118 45 0.44
119 1 0.01
ACGTcount: A:0.41, C:0.07, G:0.03, T:0.49
Consensus pattern (116 bp):
TAATTATCACAATTTATTTCTATATTTATACTCAAAGTTCTATTCAAATAATAAATCTATTTTAA
ATATTAGCAAATTTGTTTAACTAATAAATTTAAATTAAATTATAATTATTA
Found at i:17271036 original size:13 final size:14
Alignment explanation
Indices: 17271000--17271039 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
17270990 TTAAACAAAG
*
17271000 AAAGAAAGAAAATAA
1 AAAGAAAG-AAAGAA
17271015 AAAGAAAGAAAGAA
1 AAAGAAAGAAAGAA
17271029 AAAG-AAGAAAG
1 AAAGAAAGAAAG
17271040 GAATGCACGG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
13 7 0.29
14 9 0.38
15 8 0.33
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.03
Consensus pattern (14 bp):
AAAGAAAGAAAGAA
Found at i:17301064 original size:14 final size:14
Alignment explanation
Indices: 17301024--17301066 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
17301014 TTGTGATTAT
17301024 TTTAATTTTATTGTA
1 TTTAATTTTA-TGTA
* *
17301039 TATAATTATATGTA
1 TTTAATTTTATGTA
*
17301053 TTTACTTTTATGTA
1 TTTAATTTTATGTA
17301067 GGATAAAAAC
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
14 15 0.65
15 8 0.35
ACGTcount: A:0.30, C:0.02, G:0.07, T:0.60
Consensus pattern (14 bp):
TTTAATTTTATGTA
Done.