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 96 of 210
Found at i:28039000 original size:27 final size:27
Alignment explanation
Indices: 28038957--28039094 Score: 168
Period size: 27 Copynumber: 5.1 Consensus size: 27
28038947 AAGACGTTAA
* *
28038957 GAAAGAAAAGCTTTTGTGGCGAACTTT
1 GAAAGAAAAGCCTTTGTGGCGAACTCT
* ** *
28038984 GAAAGAAAAGCCATTGTGGAAAACCCT
1 GAAAGAAAAGCCTTTGTGGCGAACTCT
* * *
28039011 GAAAGAAAAGCCTTTATGGTGAGCTCT
1 GAAAGAAAAGCCTTTGTGGCGAACTCT
* *
28039038 GAAAGAAAAGCCTTTGTGGTGAGCTCT
1 GAAAGAAAAGCCTTTGTGGCGAACTCT
*
28039065 GAAAGAAAATCCTTTGTGGCGAACTCT
1 GAAAGAAAAGCCTTTGTGGCGAACTCT
28039092 GAA
1 GAA
28039095 TAAACTTTCC
Statistics
Matches: 95, Mismatches: 16, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 95 1.00
ACGTcount: A:0.36, C:0.15, G:0.25, T:0.24
Consensus pattern (27 bp):
GAAAGAAAAGCCTTTGTGGCGAACTCT
Found at i:28040168 original size:18 final size:18
Alignment explanation
Indices: 28040131--28040174 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
28040121 AGTGAAATTT
28040131 ATATAAAAATCCCTGAAGG
1 ATAT-AAAATCCCTGAAGG
*
28040150 ATTTAAAATCCCT-AGAGG
1 ATATAAAATCCCTGA-AGG
28040168 ATATAAA
1 ATATAAA
28040175 GTTTTCCGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 1 0.05
18 18 0.82
19 3 0.14
ACGTcount: A:0.48, C:0.14, G:0.14, T:0.25
Consensus pattern (18 bp):
ATATAAAATCCCTGAAGG
Found at i:28043492 original size:44 final size:44
Alignment explanation
Indices: 28043422--28043596 Score: 289
Period size: 44 Copynumber: 4.0 Consensus size: 44
28043412 AGGGTGATTA
* *
28043422 GGTGATTACATCAAAGGCATTGCCAACCACAACGTTTGAAAGAG
1 GGTGGTTACATCAAAGGCATTACCAACCACAACGTTTGAAAGAG
*
28043466 GGTGGTTACATCAAAGGCATTACCAACCACAACGTTTGAAAAAG
1 GGTGGTTACATCAAAGGCATTACCAACCACAACGTTTGAAAGAG
*
28043510 GGTGGTTACATCAAAGGCATTACTAACCACAACGTTTGAAAGAG
1 GGTGGTTACATCAAAGGCATTACCAACCACAACGTTTGAAAGAG
*
28043554 GGTGGTTACATCAAAGGCATTGA-CAACCACAATGTTTGAAAGA
1 GGTGGTTACATCAAAGGCATT-ACCAACCACAACGTTTGAAAGA
28043597 CTAGTATACA
Statistics
Matches: 123, Mismatches: 7, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
44 122 0.99
45 1 0.01
ACGTcount: A:0.37, C:0.19, G:0.22, T:0.22
Consensus pattern (44 bp):
GGTGGTTACATCAAAGGCATTACCAACCACAACGTTTGAAAGAG
Found at i:28043965 original size:46 final size:44
Alignment explanation
Indices: 28043869--28043965 Score: 108
Period size: 46 Copynumber: 2.1 Consensus size: 44
28043859 AATCCATTGA
*
28043869 TAAATAGATGTCCATAACCCCTCAAATTTATAGTATTGTAACCC
1 TAAATAGATGTCCATAACCCATCAAATTTATAGTATTGTAACCC
* *
28043913 TAAAATATGAATGTCCATAACTCAT-AAATTTATTA-TCTTGTAACCCC
1 T-AAATA-G-ATGTCCATAACCCATCAAATTTA-TAGTATTGTAA-CCC
28043960 TAAATA
1 TAAATA
28043966 ATTTATAAGG
Statistics
Matches: 45, Mismatches: 3, Indels: 8
0.80 0.05 0.14
Matches are distributed among these distances:
44 1 0.02
45 5 0.11
46 20 0.44
47 19 0.42
ACGTcount: A:0.39, C:0.20, G:0.07, T:0.34
Consensus pattern (44 bp):
TAAATAGATGTCCATAACCCATCAAATTTATAGTATTGTAACCC
Found at i:28047290 original size:16 final size:16
Alignment explanation
Indices: 28047268--28047305 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
28047258 ATTTTGATAT
28047268 CATAATTAAAACCAAAA
1 CATAATT-AAACCAAAA
*
28047285 -ATAATTTAACCAAAA
1 CATAATTAAACCAAAA
28047300 CATAAT
1 CATAAT
28047306 ATCACAAGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
15 8 0.42
16 11 0.58
ACGTcount: A:0.61, C:0.16, G:0.00, T:0.24
Consensus pattern (16 bp):
CATAATTAAACCAAAA
Found at i:28048644 original size:50 final size:51
Alignment explanation
Indices: 28048548--28048649 Score: 188
Period size: 50 Copynumber: 2.0 Consensus size: 51
28048538 TTGTTATAGA
*
28048548 GTTAGAGTGTTTTGTTGTCCATTTTTTTTTCTTAAGGATGATTTGAGAAAG
1 GTTAGAGTGTTTTGTTGTCCATTTTTTTTTCTTAAGGACGATTTGAGAAAG
28048599 GTTAGAGTGTTTTGTTGTCC-TTTTTTTTTCTTAAGGACGATTTGAGAAAG
1 GTTAGAGTGTTTTGTTGTCCATTTTTTTTTCTTAAGGACGATTTGAGAAAG
28048649 G
1 G
28048650 GGGTGTAGGA
Statistics
Matches: 50, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
50 30 0.60
51 20 0.40
ACGTcount: A:0.21, C:0.07, G:0.25, T:0.48
Consensus pattern (51 bp):
GTTAGAGTGTTTTGTTGTCCATTTTTTTTTCTTAAGGACGATTTGAGAAAG
Found at i:28049685 original size:24 final size:25
Alignment explanation
Indices: 28049658--28049706 Score: 75
Period size: 24 Copynumber: 2.0 Consensus size: 25
28049648 GAACTGGTCA
28049658 TAGAGAGAA-TTGAGGAG-GAATATT
1 TAGAGA-AATTTGAGGAGAGAATATT
28049682 TAGAGAAATTTGAGGAGAGAATATT
1 TAGAGAAATTTGAGGAGAGAATATT
28049707 GAGATTTGGG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 2 0.09
24 14 0.61
25 7 0.30
ACGTcount: A:0.43, C:0.00, G:0.31, T:0.27
Consensus pattern (25 bp):
TAGAGAAATTTGAGGAGAGAATATT
Found at i:28049708 original size:14 final size:14
Alignment explanation
Indices: 28049666--28049709 Score: 51
Period size: 12 Copynumber: 3.4 Consensus size: 14
28049656 CATAGAGAGA
28049666 ATTGAGGAG-GAAT
1 ATTGAGGAGAGAAT
*
28049679 ATTTA-GAGA-AAT
1 ATTGAGGAGAGAAT
28049691 -TTGAGGAGAGAAT
1 ATTGAGGAGAGAAT
28049704 ATTGAG
1 ATTGAG
28049710 ATTTGGGGAG
Statistics
Matches: 25, Mismatches: 2, Indels: 7
0.74 0.06 0.21
Matches are distributed among these distances:
11 3 0.12
12 10 0.40
13 7 0.28
14 5 0.20
ACGTcount: A:0.41, C:0.00, G:0.32, T:0.27
Consensus pattern (14 bp):
ATTGAGGAGAGAAT
Found at i:28049821 original size:119 final size:119
Alignment explanation
Indices: 28049686--28050042 Score: 660
Period size: 119 Copynumber: 3.0 Consensus size: 119
28049676 AATATTTAGA
*
28049686 GAAATTTGAGGAGAGAATATTGAGATTTGGGGAGGTTGTTGTTGTGGAGAGATAATAGTAGAAAA
1 GAAATTTGAGGAGAGAATATTGGGATTTGGGGAGGTTGTTGTTGTGGAGAGATAATAGTAGAAAA
*
28049751 TTAAGGGATAGGAAGTGGATGGAGAGTGTGTAGCCGAATTGGAGGATGGATTTT
66 TTAAGGGATAGGAAGTGGATGGAGAGTGTGTAGCCGAATTGGAGGACGGATTTT
*
28049805 GAAATTTGAGGTGAGAATATTGGGATTTGGGGAGGTTGTTGTTGTGGAGAGATAATAGTAGAAAA
1 GAAATTTGAGGAGAGAATATTGGGATTTGGGGAGGTTGTTGTTGTGGAGAGATAATAGTAGAAAA
28049870 TTAAGGGATAGGAAGTGGATGGAGAGTGTGTAGCCGAATTGGAGGACGGATTTT
66 TTAAGGGATAGGAAGTGGATGGAGAGTGTGTAGCCGAATTGGAGGACGGATTTT
*
28049924 GAAATTTGAGGAGAGAATATTGGGATTTGGGGAGGTTGTTGTTATGGAGAGATAATAGTAGAAAA
1 GAAATTTGAGGAGAGAATATTGGGATTTGGGGAGGTTGTTGTTGTGGAGAGATAATAGTAGAAAA
* *
28049989 TTAAGGGATAGGAAGTGGATGGAGCGTGTGTAGCCGAATTGGAGGAGGGATTTT
66 TTAAGGGATAGGAAGTGGATGGAGAGTGTGTAGCCGAATTGGAGGACGGATTTT
28050043 TGGGATTTGG
Statistics
Matches: 231, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
119 231 1.00
ACGTcount: A:0.31, C:0.02, G:0.38, T:0.28
Consensus pattern (119 bp):
GAAATTTGAGGAGAGAATATTGGGATTTGGGGAGGTTGTTGTTGTGGAGAGATAATAGTAGAAAA
TTAAGGGATAGGAAGTGGATGGAGAGTGTGTAGCCGAATTGGAGGACGGATTTT
Found at i:28051028 original size:27 final size:27
Alignment explanation
Indices: 28050983--28051534 Score: 588
Period size: 27 Copynumber: 20.6 Consensus size: 27
28050973 AGACCCCAAA
* * **
28050983 ATAGGGT-AAATAACTGAAATACCCTT
1 ATAGGGTAAAATGACCGAAATACCCCC
*
28051009 ATAGGATAAAATGACCGAAATA-CCCC
1 ATAGGGTAAAATGACCGAAATACCCCC
* *
28051035 ATAGGGTAAAATGATCAAAATACCCCC
1 ATAGGGTAAAATGACCGAAATACCCCC
* *
28051062 ATAGGGTAAAA-AACCAAAATACCCCC
1 ATAGGGTAAAATGACCGAAATACCCCC
*
28051088 ATAGGGTAAAATGACAGAAATACCCCC
1 ATAGGGTAAAATGACCGAAATACCCCC
* * * *
28051115 ATTGGATAGAATGATCGAAATACCCCC
1 ATAGGGTAAAATGACCGAAATACCCCC
* * *
28051142 ATAGGGTAGAATGATCGAAATACCCTC
1 ATAGGGTAAAATGACCGAAATACCCCC
* *
28051169 ATAGGGTAAAACGACCGAAATACCCCT
1 ATAGGGTAAAATGACCGAAATACCCCC
* * * *
28051196 ATAGGGTAGAATAAACGAAATACCCTC
1 ATAGGGTAAAATGACCGAAATACCCCC
* * *
28051223 ATAAGATAAAATGACCAAAATACCCCC
1 ATAGGGTAAAATGACCGAAATACCCCC
* ** * * *
28051250 ATAGGTTAGTATGATCTAAATACTCCC
1 ATAGGGTAAAATGACCGAAATACCCCC
* *
28051277 ATAGGGTAGAATGACCGGAATACCCCC
1 ATAGGGTAAAATGACCGAAATACCCCC
* *
28051304 ATAGGGTAGAATGACTGAAATACCCCC
1 ATAGGGTAAAATGACCGAAATACCCCC
* * * * *
28051331 AGAGGGCAAAATTACCAAAATACCCCT
1 ATAGGGTAAAATGACCGAAATACCCCC
* * *
28051358 AGAGGGTAAAATAAACGAAATACCCCC
1 ATAGGGTAAAATGACCGAAATACCCCC
*
28051385 ATAGGGTAAAATGATCGAAATACCCCC
1 ATAGGGTAAAATGACCGAAATACCCCC
* *
28051412 ACAGGGTAAAATGACTGAAATACCCCC
1 ATAGGGTAAAATGACCGAAATACCCCC
* *
28051439 ACAGGGTAAAATGACTGAAATACCCCC
1 ATAGGGTAAAATGACCGAAATACCCCC
*
28051466 ATAGGGTAAAATGATCGAAATACCCCC
1 ATAGGGTAAAATGACCGAAATACCCCC
* * * *
28051493 ATAGAGTAATATGACCGAAATATCGCC
1 ATAGGGTAAAATGACCGAAATACCCCC
*
28051520 ATAAGGTAAAATGAC
1 ATAGGGTAAAATGAC
28051535 TGTTATGGCC
Statistics
Matches: 440, Mismatches: 83, Indels: 5
0.83 0.16 0.01
Matches are distributed among these distances:
26 51 0.12
27 389 0.88
ACGTcount: A:0.42, C:0.22, G:0.18, T:0.18
Consensus pattern (27 bp):
ATAGGGTAAAATGACCGAAATACCCCC
Found at i:28053444 original size:13 final size:13
Alignment explanation
Indices: 28053426--28053452 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
28053416 TGTATGGATT
28053426 ATCGAGATAAAAG
1 ATCGAGATAAAAG
28053439 ATCGAGATAAAAG
1 ATCGAGATAAAAG
28053452 A
1 A
28053453 CTAAAATGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.56, C:0.07, G:0.22, T:0.15
Consensus pattern (13 bp):
ATCGAGATAAAAG
Found at i:28053646 original size:70 final size:70
Alignment explanation
Indices: 28053571--28053703 Score: 248
Period size: 70 Copynumber: 1.9 Consensus size: 70
28053561 AAAATGGGGT
28053571 TGTGATTGTGAAATTGATTGAGAAATGATATATGTACTAAATTGCAAGATAGCTATTATGCAAAC
1 TGTGATTGTGAAATTGATTGAGAAATGATATATGTACTAAATTGCAAGATAGCTATTATGCAAAC
28053636 TGGGC
66 TGGGC
* *
28053641 TGTGATTGTGAAATTGATTGAGAAATGATATATGTACTAAATTGCAAGATAGTTGTTATGCAA
1 TGTGATTGTGAAATTGATTGAGAAATGATATATGTACTAAATTGCAAGATAGCTATTATGCAA
28053704 TAGAATAATG
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
70 61 1.00
ACGTcount: A:0.36, C:0.07, G:0.23, T:0.35
Consensus pattern (70 bp):
TGTGATTGTGAAATTGATTGAGAAATGATATATGTACTAAATTGCAAGATAGCTATTATGCAAAC
TGGGC
Found at i:28069545 original size:22 final size:21
Alignment explanation
Indices: 28069452--28069566 Score: 74
Period size: 22 Copynumber: 5.3 Consensus size: 21
28069442 TAGTATACTT
28069452 TTATTTTAAA-TTATCATAAATA
1 TTATTTTAAACTTATCAT--ATA
28069474 TTA-TTTAAACTTATCATATA
1 TTATTTTAAACTTATCATATA
* * * * *
28069494 TCCTAATTAAAATTTATCATGTGC
1 T--TATTTTAAACTTATCATAT-A
*
28069518 TAATTTTAAACTTATCATATTA
1 TTATTTTAAACTTATCATA-TA
* * *
28069540 TTA-TTTAGATTTATTATATA
1 TTATTTTAAACTTATCATATA
28069560 TTATTTT
1 TTATTTT
28069567 TATATAAGCT
Statistics
Matches: 72, Mismatches: 14, Indels: 15
0.71 0.14 0.15
Matches are distributed among these distances:
20 9 0.12
21 21 0.29
22 27 0.38
23 14 0.19
24 1 0.01
ACGTcount: A:0.37, C:0.08, G:0.03, T:0.52
Consensus pattern (21 bp):
TTATTTTAAACTTATCATATA
Found at i:28071782 original size:5 final size:6
Alignment explanation
Indices: 28071755--28071779 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
28071745 TCTACTTTTG
28071755 TTATTT TTATTT TTATTT TTATTT T
1 TTATTT TTATTT TTATTT TTATTT T
28071780 ATTGTTTGTT
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:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TTATTT
Found at i:28074277 original size:15 final size:15
Alignment explanation
Indices: 28074253--28074285 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
28074243 TGTATACTTG
28074253 TATATCTGTGTTAGA
1 TATATCTGTGTTAGA
*
28074268 TATATGTGTGTTAGA
1 TATATCTGTGTTAGA
28074283 TAT
1 TAT
28074286 GTTTGCAACT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.27, C:0.03, G:0.21, T:0.48
Consensus pattern (15 bp):
TATATCTGTGTTAGA
Found at i:28077834 original size:20 final size:20
Alignment explanation
Indices: 28077809--28077848 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
28077799 TTCATCTCAT
28077809 GCATCGCATCATATGCATTA
1 GCATCGCATCATATGCATTA
**
28077829 GCATCGCATTTTATGCATTA
1 GCATCGCATCATATGCATTA
28077849 TAGACCTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.23, G:0.15, T:0.35
Consensus pattern (20 bp):
GCATCGCATCATATGCATTA
Found at i:28086372 original size:222 final size:222
Alignment explanation
Indices: 28085914--28086448 Score: 743
Period size: 222 Copynumber: 2.4 Consensus size: 222
28085904 GAGCAGGTTG
* *
28085914 AGAGATAGCAGATCTTGTCTTCATGTACT-AGCATGAAGTAGATCAAAGATAACAGATCTTGTCT
1 AGAGAAAGCAGATCTTGTCTTCATGTACTGA-CGTGAAGTAGATCAAAGATAACAGATCTTGTCT
* *
28085978 TCCCATACTAGTGGCGAAGTAGATCGAAGAAAACAGATCTTGTCTTCATGTACTGGCGTGAAGTA
65 TCCCATACTGGTGGCGAAGCAGATCGAAGAAAACAGATCTTGTCTTCATGTACTGGCGTGAAGTA
* ** * * **
28086043 GATCAAAGATAACAAATCTTGTCTTCCCATACTGGTGGCGTAGTAGTTTGAAGAAAACAGATCTT
130 GATCAAAGATAACAAATCTTGTCTTCACATACTGGTCACGAAGTAGATCAAAGAAAACAGATCTT
* * **
28086108 GTCTTCCCATACTGGCGTGAAGTTGATC
195 GCCTTCCCATACTGGCGCGAAGCAGATC
* *
28086136 AGAGATACCAGATCTTGTCTTCATGTACTGACGTGAAGTAGATCAAAGATAACAGATCTTGTCTT
1 AGAGAAAGCAGATCTTGTCTTCATGTACTGACGTGAAGTAGATCAAAGATAACAGATCTTGTCTT
**
28086201 CCCATACTGGTGGCGAAGCAGATCGAAGAAAGTAGATCTTGTCTTCATGTACTGGCGTGAAGTAG
66 CCCATACTGGTGGCGAAGCAGATCGAAGAAAACAGATCTTGTCTTCATGTACTGGCGTGAAGTAG
* * * ** * *
28086266 ATCAGAGATACCAGATCTTGTCTTCATGTACTGG-CATGAAGTAGATCAAAGATAACAGATCTTG
131 ATCAAAGATAACAAATCTTGTCTTCACATACTGGTCACGAAGTAGATCAAAGAAAACAGATCTTG
* *
28086330 CCTTCTCATACTGGTGGCGAAGCAGATC
196 CCTTCCCATACTGG-CGCGAAGCAGATC
* * *
28086358 -GAAGAAAGCAGATCTTGTCTTCACGTACTGGCGTGAAGTAGATCAAAGATACCAGATCTTGTCT
1 AG-AGAAAGCAGATCTTGTCTTCATGTACTGACGTGAAGTAGATCAAAGATAACAGATCTTGTCT
28086422 TCCCATACTGGTGGCGAAGCAGATCGA
65 TCCCATACTGGTGGCGAAGCAGATCGA
28086449 GGATGGCAGA
Statistics
Matches: 279, Mismatches: 31, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
221 35 0.13
222 243 0.87
223 1 0.00
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.27
Consensus pattern (222 bp):
AGAGAAAGCAGATCTTGTCTTCATGTACTGACGTGAAGTAGATCAAAGATAACAGATCTTGTCTT
CCCATACTGGTGGCGAAGCAGATCGAAGAAAACAGATCTTGTCTTCATGTACTGGCGTGAAGTAG
ATCAAAGATAACAAATCTTGTCTTCACATACTGGTCACGAAGTAGATCAAAGAAAACAGATCTTG
CCTTCCCATACTGGCGCGAAGCAGATC
Found at i:28086432 original size:133 final size:133
Alignment explanation
Indices: 28085948--28086423 Score: 686
Period size: 133 Copynumber: 3.6 Consensus size: 133
28085938 GTACTAGCAT
* * * * * * *
28085948 GAAGTAGATCAAAGATAA-CAGATCTTGTCTTCCCATACTAGTG-GCGAAGTAGATCGAAGAAAA
1 GAAGCAGATCGAAGA-AAGCAGATCTTGTCTTCACATACT-G-GCGTGAAGTAGATCAAAGATAC
*
28086011 CAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAACAAATCTTGTCTTCCCATACT
63 CAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAACAGATCTTGTCTTCCCATACT
28086076 GGTGGC
128 GGTGGC
* * * * * * * *
28086082 GTAGTAGTTTGAAGAAAACAGATCTTGTCTTCCCATACTGGCGTGAAGTTGATCAGAGATACCAG
1 GAAGCAGATCGAAGAAAGCAGATCTTGTCTTCACATACTGGCGTGAAGTAGATCAAAGATACCAG
*
28086147 ATCTTGTCTTCATGTACTGACGTGAAGTAGATCAAAGATAACAGATCTTGTCTTCCCATACTGGT
66 ATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAACAGATCTTGTCTTCCCATACTGGT
28086212 GGC
131 GGC
* ** *
28086215 GAAGCAGATCGAAGAAAGTAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAGAGATACCAG
1 GAAGCAGATCGAAGAAAGCAGATCTTGTCTTCACATACTGGCGTGAAGTAGATCAAAGATACCAG
* * *
28086280 ATCTTGTCTTCATGTACTGGCATGAAGTAGATCAAAGATAACAGATCTTGCCTTCTCATACTGGT
66 ATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAACAGATCTTGTCTTCCCATACTGGT
28086345 GGC
131 GGC
*
28086348 GAAGCAGATCGAAGAAAGCAGATCTTGTCTTCACGTACTGGCGTGAAGTAGATCAAAGATACCAG
1 GAAGCAGATCGAAGAAAGCAGATCTTGTCTTCACATACTGGCGTGAAGTAGATCAAAGATACCAG
28086413 ATCTTGTCTTC
66 ATCTTGTCTTC
28086424 CCATACTGGT
Statistics
Matches: 311, Mismatches: 29, Indels: 5
0.90 0.08 0.01
Matches are distributed among these distances:
132 1 0.00
133 278 0.89
134 32 0.10
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.28
Consensus pattern (133 bp):
GAAGCAGATCGAAGAAAGCAGATCTTGTCTTCACATACTGGCGTGAAGTAGATCAAAGATACCAG
ATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAACAGATCTTGTCTTCCCATACTGGT
GGC
Found at i:28086459 original size:89 final size:89
Alignment explanation
Indices: 28085922--28086448 Score: 603
Period size: 89 Copynumber: 5.9 Consensus size: 89
28085912 TGAGAGATAG
* * *
28085922 CAGATCTTGTCTTCATGTACTAGCATGAAGTAGATCAAAGATAACAGATCTTGTCTTCCCATACT
1 CAGATCTTGTCTTCACGTACTGGCGTGAAGTAGATCAAAGATAACAGATCTTGTCTTCCCATACT
*
28085987 AGTGGCGAAGTAGATCGAAGAAAA
66 GGTGGCGAAGTAGATCGAAGAAAA
* *
28086011 CAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAACAAATCTTGTCTTCCCATACT
1 CAGATCTTGTCTTCACGTACTGGCGTGAAGTAGATCAAAGATAACAGATCTTGTCTTCCCATACT
* * *
28086076 GGTGGCGTAGTAGTTTGAAGAAAA
66 GGTGGCGAAGTAGATCGAAGAAAA
* * * * * ***
28086100 CAGATCTTGTCTTCCCATACTGGCGTGAAGTTGATCAGAGATACCAGATCTTGTCTTCATGTACT
1 CAGATCTTGTCTTCACGTACTGGCGTGAAGTAGATCAAAGATAACAGATCTTGTCTTCCCATACT
** * * *
28086165 -GACGTGAAGTAGATCAAAGATAA
66 GGTGGCGAAGTAGATCGAAGAAAA
* * * * * * * ***
28086188 CAGATCTTGTCTTCCCATACTGGTGGCGAAGCAGATCGAAGA-AAGTAGATCTTGTCTTCATGTA
1 CAGATCTTGTCTTCACGTACTGG-CGTGAAGTAGATCAAAGATAA-CAGATCTTGTCTTCCCATA
* * * *
28086252 CTGG-CGTGAAGTAGATC-AGAGATAC
64 CTGGTGGCGAAGTAGATCGA-AGAAAA
* * * *
28086277 CAGATCTTGTCTTCATGTACTGGCATGAAGTAGATCAAAGATAACAGATCTTGCCTTCTCATACT
1 CAGATCTTGTCTTCACGTACTGGCGTGAAGTAGATCAAAGATAACAGATCTTGTCTTCCCATACT
* *
28086342 GGTGGCGAAGCAGATCGAAGAAAG
66 GGTGGCGAAGTAGATCGAAGAAAA
*
28086366 CAGATCTTGTCTTCACGTACTGGCGTGAAGTAGATCAAAGATACCAGATCTTGTCTTCCCATACT
1 CAGATCTTGTCTTCACGTACTGGCGTGAAGTAGATCAAAGATAACAGATCTTGTCTTCCCATACT
*
28086431 GGTGGCGAAGCAGATCGA
66 GGTGGCGAAGTAGATCGA
28086449 GGATGGCAGA
Statistics
Matches: 374, Mismatches: 57, Indels: 14
0.84 0.13 0.03
Matches are distributed among these distances:
88 71 0.19
89 301 0.80
90 2 0.01
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.28
Consensus pattern (89 bp):
CAGATCTTGTCTTCACGTACTGGCGTGAAGTAGATCAAAGATAACAGATCTTGTCTTCCCATACT
GGTGGCGAAGTAGATCGAAGAAAA
Found at i:28091167 original size:16 final size:16
Alignment explanation
Indices: 28091146--28091204 Score: 55
Period size: 18 Copynumber: 3.4 Consensus size: 16
28091136 ACATTTTAAA
28091146 TAATTTTAAGTTTTTT
1 TAATTTTAAGTTTTTT
*
28091162 TAATTTTAGAATTTTTTT
1 TAATTTT--AAGTTTTTT
* *
28091180 TATTTTTATGATTTTTT
1 TAATTTTAAG-TTTTTT
28091197 ATAATTTT
1 -TAATTTT
28091205 TCAGGAATTT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
16 8 0.24
17 6 0.18
18 20 0.59
ACGTcount: A:0.25, C:0.00, G:0.05, T:0.69
Consensus pattern (16 bp):
TAATTTTAAGTTTTTT
Found at i:28091177 original size:18 final size:18
Alignment explanation
Indices: 28091156--28091204 Score: 64
Period size: 18 Copynumber: 2.7 Consensus size: 18
28091146 TAATTTTAAG
28091156 TTTTTTTAATTTTA-GAAT
1 TTTTTTTAATTTTATG-AT
*
28091174 TTTTTTTATTTTTATGAT
1 TTTTTTTAATTTTATGAT
*
28091192 TTTTTATAATTTT
1 TTTTTTTAATTTT
28091205 TCAGGAATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
18 26 0.96
19 1 0.04
ACGTcount: A:0.22, C:0.00, G:0.04, T:0.73
Consensus pattern (18 bp):
TTTTTTTAATTTTATGAT
Found at i:28091203 original size:19 final size:18
Alignment explanation
Indices: 28091156--28091215 Score: 61
Period size: 18 Copynumber: 3.2 Consensus size: 18
28091146 TAATTTTAAG
28091156 TTTTTTTAA-TTTTAGAA
1 TTTTTTTAATTTTTAGAA
*
28091173 TTTTTTTTATTTTTATG-A
1 TTTTTTTAATTTTTA-GAA
28091191 TTTTTTATAATTTTTCAGGAA
1 TTTTTT-TAATTTTT-A-GAA
28091212 TTTT
1 TTTT
28091216 GAGCTTTTAA
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
17 8 0.23
18 12 0.34
19 8 0.23
20 2 0.06
21 5 0.14
ACGTcount: A:0.23, C:0.02, G:0.07, T:0.68
Consensus pattern (18 bp):
TTTTTTTAATTTTTAGAA
Found at i:28094318 original size:43 final size:42
Alignment explanation
Indices: 28094173--28094412 Score: 368
Period size: 43 Copynumber: 5.8 Consensus size: 42
28094163 GTTTACAAAC
*
28094173 AAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGTTTAGAA
1 AAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGAA
*
28094215 AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAG--
1 AAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGAA
*
28094255 --AAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAGAAA
1 AAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAG-AA
*
28094296 AAAAACGCCTCTAAAGACCATGTTCTTTAGCGGCGCTTAGAAA
1 AAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAG-AA
28094339 AAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGAA
1 AAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGAA
*
28094381 AAAAA---CGCTAAAGATCATGTTCTTTAGCGGCG
1 AAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCG
28094413 TTTATTCTTA
Statistics
Matches: 187, Mismatches: 6, Indels: 13
0.91 0.03 0.06
Matches are distributed among these distances:
38 38 0.20
39 26 0.14
42 45 0.24
43 78 0.42
ACGTcount: A:0.34, C:0.22, G:0.21, T:0.23
Consensus pattern (42 bp):
AAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGAA
Found at i:28094455 original size:42 final size:42
Alignment explanation
Indices: 28094404--28094483 Score: 108
Period size: 42 Copynumber: 1.9 Consensus size: 42
28094394 ATCATGTTCT
* *
28094404 TTAGCGGCGTTTATTCTT-AAGCGCCGCTAAAGAACATGAAAA
1 TTAGCGGCGTTT-TTCTTAAAACCCCGCTAAAGAACATGAAAA
* *
28094446 TTAGTGGCGTTTTTTTTAAAACCCCGCTAAAGAACATG
1 TTAGCGGCGTTTTTCTTAAAACCCCGCTAAAGAACATG
28094484 TTCTTTAGCG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
41 4 0.12
42 29 0.88
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.30
Consensus pattern (42 bp):
TTAGCGGCGTTTTTCTTAAAACCCCGCTAAAGAACATGAAAA
Found at i:28094478 original size:166 final size:164
Alignment explanation
Indices: 28094173--28094499 Score: 415
Period size: 166 Copynumber: 2.0 Consensus size: 164
28094163 GTTTACAAAC
*
28094173 AAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGTTTAGAAAAAAACGCCGCTAAAGAACATGT
1 AAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGAAAAAAA--CCGCTAAAGAACATGT
**** *
28094238 TCTTTAGCGGCGCTTAGAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAGAAAAAAAACG
64 TCTTTAGCGGCGCTTAGAAACGCCGCTAAAGAACATGAAAATTAGCGGCGCTTAGAAAAAAAACC
* *
28094303 CCTCTAAAGACCATGTTCTTTAGCGGCGCTTAGAAA
129 CCGCTAAAGAACATGTTCTTTAGCGGCGCTTAGAAA
*
28094339 AAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGAAAAAAA-CGCTAAAGATCATGTTC
1 AAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGAAAAAAACCGCTAAAGAACATGTTC
* * * * ******
28094403 TTTAGCGGCGTTTATTCTTAAGCGCCGCTAAAGAACATGAAAATTAGTGGCG-TTTTTTTTAAAA
66 TTTAGCGGCGCTTA----GAAACGCCGCTAAAGAACATGAAAATTAGCGGCGCTTAGAAAAAAAA
28094467 CCCCGCTAAAGAACATGTTCTTTAGCGGCGCTT
127 CCCCGCTAAAGAACATGTTCTTTAGCGGCGCTT
28094500 TTATACAAAA
Statistics
Matches: 138, Mismatches: 19, Indels: 8
0.84 0.12 0.05
Matches are distributed among these distances:
163 29 0.21
166 82 0.59
167 27 0.20
ACGTcount: A:0.32, C:0.21, G:0.20, T:0.26
Consensus pattern (164 bp):
AAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGAAAAAAACCGCTAAAGAACATGTTC
TTTAGCGGCGCTTAGAAACGCCGCTAAAGAACATGAAAATTAGCGGCGCTTAGAAAAAAAACCCC
GCTAAAGAACATGTTCTTTAGCGGCGCTTAGAAA
Found at i:28094865 original size:21 final size:21
Alignment explanation
Indices: 28094817--28094866 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
28094807 TTTTGGCCTG
*
28094817 CTCTGCTTCTCTCGCTGCAGC
1 CTCTGCTTCCCTCGCTGCAGC
* * *
28094838 TTTTGCTTCCCTCGCTGCCGC
1 CTCTGCTTCCCTCGCTGCAGC
28094859 CTCTGCTT
1 CTCTGCTT
28094867 TAAGTTGTAG
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.02, C:0.42, G:0.18, T:0.38
Consensus pattern (21 bp):
CTCTGCTTCCCTCGCTGCAGC
Found at i:28100485 original size:9 final size:9
Alignment explanation
Indices: 28100471--28100811 Score: 136
Period size: 9 Copynumber: 37.8 Consensus size: 9
28100461 ATAAAGAAAA
28100471 TTATGTAAG
1 TTATGTAAG
*
28100480 TTATGTACG
1 TTATGTAAG
28100489 TGTATGT-A-
1 T-TATGTAAG
28100497 TTATGTAAG
1 TTATGTAAG
28100506 TTATGT-A-
1 TTATGTAAG
**
28100513 TTAAATAAG
1 TTATGTAAG
*
28100522 CTATGTAAG
1 TTATGTAAG
*
28100531 TTGTGTATTATG
1 TTATGTA--A-G
*
28100543 TCAT-TAAG
1 TTATGTAAG
28100551 TTATGTAAG
1 TTATGTAAG
28100560 TTCAGTGGTAAG
1 TT-A-T-GTAAG
** *
28100572 TATAAATGAG
1 T-TATGTAAG
28100582 TTATGTAAG
1 TTATGTAAG
* *
28100591 TATATCATATG
1 T-TAT-GTAAG
* * *
28100602 ATATAT-AT
1 TTATGTAAG
28100610 TTATGT-A-
1 TTATGTAAG
* * * *
28100617 TAAAGAAAA
1 TTATGTAAG
28100626 TTATGTAAG
1 TTATGTAAG
*
28100635 TTATGTACG
1 TTATGTAAG
28100644 TGTATGT-A-
1 T-TATGTAAG
28100652 TTATGTAAG
1 TTATGTAAG
*
28100661 TTTTGT-A-
1 TTATGTAAG
**
28100668 TTAAATAAG
1 TTATGTAAG
*
28100677 CTATGTAAG
1 TTATGTAAG
*
28100686 TTGTGTATTATG
1 TTATGTA--A-G
*
28100698 TCAT-TAAG
1 TTATGTAAG
28100706 TTATGTAAG
1 TTATGTAAG
**
28100715 TTATCAAAG
1 TTATGTAAG
* * *
28100724 TAATGCATG
1 TTATGTAAG
28100733 TTATGTAAG
1 TTATGTAAG
28100742 TTATGTAAG
1 TTATGTAAG
28100751 TTATGTAAG
1 TTATGTAAG
*
28100760 TTA--AAAG
1 TTATGTAAG
*
28100767 TATTATGTAGG
1 --TTATGTAAG
28100778 TTATGTAAG
1 TTATGTAAG
*
28100787 TTGTGTAAG
1 TTATGTAAG
28100796 TTATGTAAG
1 TTATGTAAG
28100805 TTATGTA
1 TTATGTA
28100812 TGCTAAGTAT
Statistics
Matches: 241, Mismatches: 61, Indels: 60
0.67 0.17 0.17
Matches are distributed among these distances:
7 23 0.10
8 22 0.09
9 149 0.62
10 21 0.09
11 12 0.05
12 13 0.05
13 1 0.00
ACGTcount: A:0.34, C:0.03, G:0.20, T:0.43
Consensus pattern (9 bp):
TTATGTAAG
Found at i:28100512 original size:16 final size:17
Alignment explanation
Indices: 28100480--28100515 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
28100470 ATTATGTAAG
*
28100480 TTATGTACGTGTATGTA
1 TTATGTAAGTGTATGTA
28100497 TTATGTAAGT-TATGTA
1 TTATGTAAGTGTATGTA
28100513 TTA
1 TTA
28100516 AATAAGCTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 9 0.50
17 9 0.50
ACGTcount: A:0.28, C:0.03, G:0.19, T:0.50
Consensus pattern (17 bp):
TTATGTAAGTGTATGTA
Found at i:28100527 original size:51 final size:51
Alignment explanation
Indices: 28100472--28100692 Score: 152
Period size: 51 Copynumber: 4.3 Consensus size: 51
28100462 TAAAGAAAAT
28100472 TATGTAAGTTATGTACGTGTATGTATTATGTAAGTTATGTATTAAATAAGC
1 TATGTAAGTTATGTACGTGTATGTATTATGTAAGTTATGTATTAAATAAGC
* ** **
28100523 TATGTAAGTTGTGTATTATGTCAT-TAAGTTATGTAAGTTCA-GTGGTAAGTATAA--
1 TATGTAAGTTATGTA-CGTGT-ATGT-A-TTATGTAAGTT-ATGTATTAA--ATAAGC
* * * * * * * **
28100577 -ATG--AGTTATGTAAGTATATCATATGATATATATTTATGTA-TAAAGAAAAT
1 TATGTAAGTTATGTACGTGTAT-GTATTATGTA-AGTTATGTATTAAA-TAAGC
*
28100627 TATGTAAGTTATGTACGTGTATGTATTATGTAAGTTTTGTATTAAATAAGC
1 TATGTAAGTTATGTACGTGTATGTATTATGTAAGTTATGTATTAAATAAGC
*
28100678 TATGTAAGTTGTGTA
1 TATGTAAGTTATGTA
28100693 TTATGTCATT
Statistics
Matches: 127, Mismatches: 25, Indels: 36
0.68 0.13 0.19
Matches are distributed among these distances:
47 1 0.01
48 2 0.02
49 11 0.09
50 8 0.06
51 49 0.39
52 15 0.12
53 20 0.16
54 16 0.13
55 1 0.01
56 4 0.03
ACGTcount: A:0.34, C:0.03, G:0.19, T:0.43
Consensus pattern (51 bp):
TATGTAAGTTATGTACGTGTATGTATTATGTAAGTTATGTATTAAATAAGC
Found at i:28100686 original size:155 final size:155
Alignment explanation
Indices: 28100404--28100716 Score: 617
Period size: 155 Copynumber: 2.0 Consensus size: 155
28100394 AGGGTAAGTT
28100404 GTTCAGTGGTAAGTATAAATGAGTTATGTAAGTATATCATATGATATATATTTATGTATAAAGAA
1 GTTCAGTGGTAAGTATAAATGAGTTATGTAAGTATATCATATGATATATATTTATGTATAAAGAA
28100469 AATTATGTAAGTTATGTACGTGTATGTATTATGTAAGTTATGTATTAAATAAGCTATGTAAGTTG
66 AATTATGTAAGTTATGTACGTGTATGTATTATGTAAGTTATGTATTAAATAAGCTATGTAAGTTG
28100534 TGTATTATGTCATTAAGTTATGTAA
131 TGTATTATGTCATTAAGTTATGTAA
28100559 GTTCAGTGGTAAGTATAAATGAGTTATGTAAGTATATCATATGATATATATTTATGTATAAAGAA
1 GTTCAGTGGTAAGTATAAATGAGTTATGTAAGTATATCATATGATATATATTTATGTATAAAGAA
*
28100624 AATTATGTAAGTTATGTACGTGTATGTATTATGTAAGTTTTGTATTAAATAAGCTATGTAAGTTG
66 AATTATGTAAGTTATGTACGTGTATGTATTATGTAAGTTATGTATTAAATAAGCTATGTAAGTTG
28100689 TGTATTATGTCATTAAGTTATGTAA
131 TGTATTATGTCATTAAGTTATGTAA
28100714 GTT
1 GTT
28100717 ATCAAAGTAA
Statistics
Matches: 157, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
155 157 1.00
ACGTcount: A:0.35, C:0.03, G:0.19, T:0.42
Consensus pattern (155 bp):
GTTCAGTGGTAAGTATAAATGAGTTATGTAAGTATATCATATGATATATATTTATGTATAAAGAA
AATTATGTAAGTTATGTACGTGTATGTATTATGTAAGTTATGTATTAAATAAGCTATGTAAGTTG
TGTATTATGTCATTAAGTTATGTAA
Found at i:28100849 original size:54 final size:53
Alignment explanation
Indices: 28100732--28100860 Score: 136
Period size: 54 Copynumber: 2.4 Consensus size: 53
28100722 AGTAATGCAT
* *
28100732 GTTATGTAAGTTATGTAAGTTATGTAAGTTAAAAGTATTATGTAGGTTATGTAA
1 GTTACGTAAGTTATGTAAGTTATGTAAGCT-AAAGTATTATGTAGGTTATGTAA
** * *
28100786 GTTGTGTAAGTTATGTAAGTTATGTATGCT-AAGTATTATGTAAGTCGTTATGTTA
1 GTTACGTAAGTTATGTAAGTTATGTAAGCTAAAGTATTATGT-AG--GTTATGTAA
* *
28100841 -TTACGTAAGTTCTTTAAGTT
1 GTTACGTAAGTTATGTAAGTT
28100861 TATATATAAG
Statistics
Matches: 64, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
52 11 0.17
53 2 0.03
54 43 0.67
55 8 0.12
ACGTcount: A:0.30, C:0.03, G:0.22, T:0.45
Consensus pattern (53 bp):
GTTACGTAAGTTATGTAAGTTATGTAAGCTAAAGTATTATGTAGGTTATGTAA
Found at i:28100951 original size:37 final size:38
Alignment explanation
Indices: 28100900--28100996 Score: 169
Period size: 37 Copynumber: 2.6 Consensus size: 38
28100890 AGTTAATATG
*
28100900 TAAGTAATGTATTATGTAAGTTTATATAAAAAAA-TTA
1 TAAGTTATGTATTATGTAAGTTTATATAAAAAAATTTA
*
28100937 TAAGTTATGAATTATGTAAGTTTATATAAAAAAATTTA
1 TAAGTTATGTATTATGTAAGTTTATATAAAAAAATTTA
28100975 TAAGTTATGTATTATGTAAGTT
1 TAAGTTATGTATTATGTAAGTT
28100997 AAAAGTAATG
Statistics
Matches: 56, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
37 32 0.57
38 24 0.43
ACGTcount: A:0.44, C:0.00, G:0.12, T:0.43
Consensus pattern (38 bp):
TAAGTTATGTATTATGTAAGTTTATATAAAAAAATTTA
Found at i:28101002 original size:23 final size:23
Alignment explanation
Indices: 28100976--28101019 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
28100966 AAAAATTTAT
*
28100976 AAGTTATGTATTATGTAAGTTAA
1 AAGTAATGTATTATGTAAGTTAA
28100999 AAGTAATGTATTATGTAAGTT
1 AAGTAATGTATTATGTAAGTT
28101020 TACATATAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.39, C:0.00, G:0.18, T:0.43
Consensus pattern (23 bp):
AAGTAATGTATTATGTAAGTTAA
Found at i:28101085 original size:63 final size:63
Alignment explanation
Indices: 28101018--28101136 Score: 238
Period size: 63 Copynumber: 1.9 Consensus size: 63
28101008 ATTATGTAAG
28101018 TTTACATATAAGTAAACTTACTTAAATTTTAGTAAGTAATGTATTTAAGTAACATACTTGAAT
1 TTTACATATAAGTAAACTTACTTAAATTTTAGTAAGTAATGTATTTAAGTAACATACTTGAAT
28101081 TTTACATATAAGTAAACTTACTTAAATTTTAGTAAGTAATGTATTTAAGTAACATA
1 TTTACATATAAGTAAACTTACTTAAATTTTAGTAAGTAATGTATTTAAGTAACATA
28101137 TTCAAGTAAT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
63 56 1.00
ACGTcount: A:0.42, C:0.08, G:0.09, T:0.41
Consensus pattern (63 bp):
TTTACATATAAGTAAACTTACTTAAATTTTAGTAAGTAATGTATTTAAGTAACATACTTGAAT
Found at i:28101131 original size:13 final size:13
Alignment explanation
Indices: 28101113--28101164 Score: 52
Period size: 13 Copynumber: 4.0 Consensus size: 13
28101103 TAAATTTTAG
*
28101113 TAAGTAATGTATT
1 TAAGTAATATATT
*
28101126 TAAGTAACATATT
1 TAAGTAATATATT
* *
28101139 CAAGTAATAAATT
1 TAAGTAATATATT
28101152 TAA-TATATATATT
1 TAAGTA-ATATATT
28101165 AGTAATAAGT
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
12 2 0.06
13 29 0.94
ACGTcount: A:0.46, C:0.04, G:0.08, T:0.42
Consensus pattern (13 bp):
TAAGTAATATATT
Found at i:28102564 original size:18 final size:18
Alignment explanation
Indices: 28102543--28102580 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
28102533 TTTCTTCAAA
* *
28102543 AATATTAACATTGCAGGT
1 AATATTAACACTGCAAGT
28102561 AATATTAACACTGCAAGT
1 AATATTAACACTGCAAGT
28102579 AA
1 AA
28102581 CTAACAAACA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.45, C:0.13, G:0.13, T:0.29
Consensus pattern (18 bp):
AATATTAACACTGCAAGT
Found at i:28103626 original size:365 final size:364
Alignment explanation
Indices: 28102950--28103663 Score: 936
Period size: 365 Copynumber: 2.0 Consensus size: 364
28102940 TAAGTCAGAC
*
28102950 TTGCGGCGTTTTAATTAAAAACACCACTAAAATTTCAAGTACAGAAAGAAACGGCGCCGTTTTAT
1 TTGCGGCGTTTTAATTAAAAACACCACTAAAATTTCAAGTACAGAAAGAAACGGCGCCATTTTAT
* * * * * *
28103015 AAAAATACAAGAAAACCTGGTGTTTTCTCAAACACGCCACAATCAATATATTATCGAACTGGCGT
66 AAAAATACAAGAAAACCTGGCGTTTTCCCAAAAACGCCACAATCAATATATTATCGAACCGACGC
** * *
28103080 CGTTTTCAGTAAATTTTATACATCTTTGCGGTGTTTTTAATAAAACGCCACTAAAAGATTCCATC
131 CGTTTTCAGTAAATTTTATACATCCCTGCGGCGTTTGTAATAAAACGCCACTAAAAGATTCCATC
* * *
28103145 CTTCAACTAAAACAGCGTCGTTTTCGCAGAGTTCAAATATTATTTACGGCGCTTTAAGGAAAAAC
196 CTTCAACTAAAACAGCGCCGTTTTCGCAAAGTTCAAATATTATTTACAGCGCTTTAAGGAAAAAC
* * * *
28103210 GCCACAAGATAAAGTTATCCCCTCAGTCGAAACGCCGACGTATAGGTAAATGCAA-TAAATATTT
261 GCCACAAGATAAACTTATCCCCTCAATCGAAACGACGACGTATAGGTAAATGCAACCAAATATTT
*
28103274 GTGGAGCTTTTTATAAAAACGCCGGTAATGTCAAACTTT
326 GTGGAGCTTTTTAGAAAAACGCCGGTAATGTCAAACTTT
** *
28103313 TTGCGGCG-TTTAATTGGAAACGCCACTAAAATTTCAAGTACAGAAAGAAACGGCGCCATTTTAT
1 TTGCGGCGTTTTAATTAAAAACACCACTAAAATTTCAAGTACAGAAAGAAACGGCGCCATTTTAT
* * *
28103377 AAAAATATAAGGAAACGTTCTGGCGTTTTCCCAAAAACGCCACAATTAATATATTATCGAACCGA
66 AAAAATACAAGAAAAC---CTGGCGTTTTCCCAAAAACGCCACAATCAATATATTATCGAACCGA
* *
28103442 CGCCGTTTTCAGTAAATTTTATACATCCCTGCGGCGTTTGTAATAAAACGCCACTCAAATATTCC
128 CGCCGTTTTCAGTAAATTTTATACATCCCTGCGGCGTTTGTAATAAAACGCCACTAAAAGATTCC
* * * * * **
28103507 ATCCTTCAACTTAAACGGTGCCGTTTTGGCAAAGTTTAAA-AGTTATTTACAGCGCTTTTCGGTA
193 ATCCTTCAACTAAAACAGCGCCGTTTTCGCAAAGTTCAAATA-TTATTTACAGCGCTTTAAGG-A
* * * * *
28103571 AAAA-GCCACAA-CTAAAACTTATTCCCT-AATCCGAAATGACGCCGTATCGGTAAATGCAACCA
256 AAAACGCCACAAGAT-AAACTTATCCCCTCAAT-CGAAACGACGACGTATAGGTAAATGCAACCA
* * * *
28103633 AATTTTTGTGGCGTTTTTTAGCAAAACGCCG
319 AATATTTGTGGAGCTTTTTAGAAAAACGCCG
28103664 CTAAATCTTA
Statistics
Matches: 300, Mismatches: 43, Indels: 13
0.84 0.12 0.04
Matches are distributed among these distances:
362 66 0.22
363 8 0.03
364 4 0.01
365 190 0.63
366 32 0.11
ACGTcount: A:0.34, C:0.21, G:0.16, T:0.29
Consensus pattern (364 bp):
TTGCGGCGTTTTAATTAAAAACACCACTAAAATTTCAAGTACAGAAAGAAACGGCGCCATTTTAT
AAAAATACAAGAAAACCTGGCGTTTTCCCAAAAACGCCACAATCAATATATTATCGAACCGACGC
CGTTTTCAGTAAATTTTATACATCCCTGCGGCGTTTGTAATAAAACGCCACTAAAAGATTCCATC
CTTCAACTAAAACAGCGCCGTTTTCGCAAAGTTCAAATATTATTTACAGCGCTTTAAGGAAAAAC
GCCACAAGATAAACTTATCCCCTCAATCGAAACGACGACGTATAGGTAAATGCAACCAAATATTT
GTGGAGCTTTTTAGAAAAACGCCGGTAATGTCAAACTTT
Found at i:28103725 original size:24 final size:24
Alignment explanation
Indices: 28103698--28103778 Score: 83
Period size: 24 Copynumber: 3.2 Consensus size: 24
28103688 TGTATCATTC
*
28103698 ATTTAAATAATTAATTTCCTATCT
1 ATTTAAATAATTAATTACCTATCT
*
28103722 ATTTAAACAATTAATTACCTA-CAAATT
1 ATTTAAATAATTAATTACCTATC----T
*
28103749 AATTTAAATAATTAATTACCTATTT
1 -ATTTAAATAATTAATTACCTATCT
28103774 ATTTA
1 ATTTA
28103779 TTTGTTTATT
Statistics
Matches: 47, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
23 1 0.02
24 24 0.51
25 1 0.02
27 1 0.02
28 20 0.43
ACGTcount: A:0.43, C:0.11, G:0.00, T:0.46
Consensus pattern (24 bp):
ATTTAAATAATTAATTACCTATCT
Found at i:28103781 original size:28 final size:26
Alignment explanation
Indices: 28103698--28103781 Score: 73
Period size: 28 Copynumber: 3.2 Consensus size: 26
28103688 TGTATCATTC
* *
28103698 ATTTAAATAATTAATTTCC--TATCT
1 ATTTAAATAATTAATTACCTATATTT
* * *
28103722 ATTTAAACAATTAATTACCTACAAATTA
1 ATTTAAATAATTAATTACCT--ATATTT
28103750 ATTTAAATAATTAATTACCTATTTATTT
1 ATTTAAATAATTAATTACCTA--TATTT
28103778 ATTT
1 ATTT
28103782 GTTTATTTAT
Statistics
Matches: 46, Mismatches: 8, Indels: 8
0.74 0.13 0.13
Matches are distributed among these distances:
24 17 0.37
26 1 0.02
28 28 0.61
ACGTcount: A:0.42, C:0.11, G:0.00, T:0.48
Consensus pattern (26 bp):
ATTTAAATAATTAATTACCTATATTT
Found at i:28104219 original size:14 final size:14
Alignment explanation
Indices: 28104200--28104233 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
28104190 GATCTTGAAT
*
28104200 CCCTAACCCTTAAC
1 CCCTAACCCATAAC
*
28104214 CCCTAATCCATAAC
1 CCCTAACCCATAAC
28104228 CCCTAA
1 CCCTAA
28104234 ACATTATTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.32, C:0.47, G:0.00, T:0.21
Consensus pattern (14 bp):
CCCTAACCCATAAC
Found at i:28104347 original size:14 final size:13
Alignment explanation
Indices: 28104330--28104373 Score: 54
Period size: 14 Copynumber: 3.3 Consensus size: 13
28104320 CCCTAACTCT
28104330 TAACATCTAACCCC
1 TAACA-CTAACCCC
28104344 TAACA-TAACCCC
1 TAACACTAACCCC
*
28104356 TAACCCCTAACCCC
1 TAA-CACTAACCCC
28104370 TAAC
1 TAAC
28104374 CCTTAACCCA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
12 10 0.37
13 2 0.07
14 15 0.56
ACGTcount: A:0.36, C:0.45, G:0.00, T:0.18
Consensus pattern (13 bp):
TAACACTAACCCC
Found at i:28104391 original size:14 final size:14
Alignment explanation
Indices: 28104337--28104393 Score: 64
Period size: 14 Copynumber: 4.2 Consensus size: 14
28104327 TCTTAACATC
*
28104337 TAACCCCTAA--CA
1 TAACCCCTAACCCT
*
28104349 TAACCCCTAACCCC
1 TAACCCCTAACCCT
28104363 TAACCCCTAACCCT
1 TAACCCCTAACCCT
* *
28104377 TAACCCATAAACCT
1 TAACCCCTAACCCT
28104391 TAA
1 TAA
28104394 ATCACATTAA
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
12 10 0.26
14 29 0.74
ACGTcount: A:0.37, C:0.44, G:0.00, T:0.19
Consensus pattern (14 bp):
TAACCCCTAACCCT
Found at i:28105241 original size:114 final size:113
Alignment explanation
Indices: 28104995--28105522 Score: 589
Period size: 113 Copynumber: 4.7 Consensus size: 113
28104985 ATTACTAAGC
* * * * ** *
28104995 ATTAGCGGCGCTTTACAAAAAACGCCACTAAAT-CCCGAAAGCTCAAAAAACGGCGTCGTTGTGC
1 ATTAGCGTCGCTTTCCGAAAAACGCCGCTAAATCCCCGAAAGCTCAGGAAACGGCGTCGTTGGGC
* ***** * * *
28105059 TTAGG-TTATTTGTGGCGCTTAATCTAAAACGTCGCTAATGCCTGGAT
66 TTAGGTTTTTTTGTGGCGCTTTGGAAAAAACGCCGCTAAAGCCTGGGT
* * * * * *
28105106 ATTAGCGGCTCTTACTTGAAAAACGCCGCTAAATCCCCGAAAGCTCAGGAAACAGCATCGTTGGG
1 ATTAGCGTCGCTTTC-CGAAAAACGCCGCTAAATCCCCGAAAGCTCAGGAAACGGCGTCGTTGGG
*
28105171 CTTAGGTTTTTTTGTGGCGCTTTGGAAAAAACGCCGCTAAAGCTATGGGT
65 CTTAGGTTTTTTTGTGGCGCTTTGGAAAAAACGCCGCTAAAGC-CTGGGT
* * *
28105221 ATTAGCGTCGCTTTCCGAAAAAAGCCGCTAAGTCACCGAAAGCTCAGGAAACGGCGTCGTTGGGC
1 ATTAGCGTCGCTTTCCGAAAAACGCCGCTAAATCCCCGAAAGCTCAGGAAACGGCGTCGTTGGGC
* *
28105286 TTAGG-TTTTTTGTGGCGCTTTGGAAAAAACGCCACTAAATCCCTGGGT
66 TTAGGTTTTTTTGTGGCGCTTTGGAAAAAACGCCGCTAAA-GCCTGGGT
*
28105334 ATTAGCGTCGC-TTCCTGAAAAACGCCGCTAAATCCCAGAAAGCTCAGGAAACGGCGTCGTTGGG
1 ATTAGCGTCGCTTTCC-GAAAAACGCCGCTAAATCCCCGAAAGCTCAGGAAACGGCGTCGTTGGG
* * * ***
28105398 CTCAGTTTTTTTTGTGGCACTTTGTTGAAAACGCCGCTAAAGCCTGGGT
65 CTTAGGTTTTTTTGTGGCGCTTTGGAAAAAACGCCGCTAAAGCCTGGGT
* ** * * *
28105447 TTTAGCGTCGC-TTCAAAAAAAACGCCGCTAATTCCCCTAAAGCTCAGAAAACGGCGTCGTTGGG
1 ATTAGCGTCGCTTTC-CGAAAAACGCCGCTAAATCCCCGAAAGCTCAGGAAACGGCGTCGTTGGG
* *
28105511 ATTAGGTATTTT
65 CTTAGGTTTTTT
28105523 GCGGCACTTT
Statistics
Matches: 353, Mismatches: 56, Indels: 14
0.83 0.13 0.03
Matches are distributed among these distances:
111 12 0.03
112 19 0.05
113 199 0.56
114 107 0.30
115 16 0.05
ACGTcount: A:0.27, C:0.23, G:0.24, T:0.26
Consensus pattern (113 bp):
ATTAGCGTCGCTTTCCGAAAAACGCCGCTAAATCCCCGAAAGCTCAGGAAACGGCGTCGTTGGGC
TTAGGTTTTTTTGTGGCGCTTTGGAAAAAACGCCGCTAAAGCCTGGGT
Found at i:28105431 original size:227 final size:225
Alignment explanation
Indices: 28104995--28105532 Score: 659
Period size: 227 Copynumber: 2.4 Consensus size: 225
28104985 ATTACTAAGC
* * * * *
28104995 ATTAGCGGCGCTTTACAAAAAACGCCACTAAATCCCGAAAGCTCAAAAAACGGCGTCGTTGTGCT
1 ATTAGCGTCGCTTTCCAAAAAACGCCGCTAAATCCCGAAAGCTCAGAAAACGGCGTCGTTGGGCT
* * *** * * * * *
28105060 TAGGTTATTTGTGGCGCTTAATCTAAAACGTCGCTAATGCCTGGATATTAGCGGCTCTTACTTGA
66 TAGGTTTTTTGTGGCGCTTTAGAAAAAACGCCACTAATCCCTGGATATTAGCGGCGCTTACCTGA
* * *
28105125 AAAACGCCGCTAAATCCCCGAAAGCTCAGGAAACAGCATCGTTGGGCTTAGGTTTTTTTGTGGCG
131 AAAACGCCGCTAAATCCCAGAAAGCTCAGGAAACAGCATCGTTGGGCTCAGGTTTTTTTGTGGCA
28105190 CTTTGGAAAAAACGCCGCTAAAGCTATGGGT
196 CTTTGGAAAAAACGCCGCTAAAGC-ATGGGT
* *
28105221 ATTAGCGTCGCTTTCCGAAAAAA-GCCGCTAAGTCACCGAAAGCTCAGGAAACGGCGTCGTTGGG
1 ATTAGCGTCGCTTTCC-AAAAAACGCCGCTAAATC-CCGAAAGCTCAGAAAACGGCGTCGTTGGG
* * *
28105285 CTTAGGTTTTTTGTGGCGCTTTGGAAAAAACGCCACTAAATCCCTGGGTATTAGCGTCGCTT-CC
64 CTTAGGTTTTTTGTGGCGCTTTAGAAAAAACGCCACT-AATCCCTGGATATTAGCGGCGCTTACC
* * *
28105349 TGAAAAACGCCGCTAAATCCCAGAAAGCTCAGGAAACGGCGTCGTTGGGCTCAGTTTTTTTTGTG
128 TGAAAAACGCCGCTAAATCCCAGAAAGCTCAGGAAACAGCATCGTTGGGCTCAGGTTTTTTTGTG
*** *
28105414 GCACTTTGTTGAAAACGCCGCTAAAGCCTGGGT
193 GCACTTTGGAAAAAACGCCGCTAAAGCATGGGT
* * * *
28105447 TTTAGCGTCGC-TTCAAAAAAAACGCCGCTAATTCCCCTAAAGCTCAGAAAACGGCGTCGTTGGG
1 ATTAGCGTCGCTTTC-CAAAAAACGCCGCTAAAT-CCCGAAAGCTCAGAAAACGGCGTCGTTGGG
* * * *
28105511 ATTAGGTATTTTGCGGCACTTT
64 CTTAGGTTTTTTGTGGCGCTTT
28105533 TTTAAAACGC
Statistics
Matches: 267, Mismatches: 39, Indels: 12
0.84 0.12 0.04
Matches are distributed among these distances:
225 9 0.03
226 92 0.34
227 146 0.55
228 20 0.07
ACGTcount: A:0.27, C:0.23, G:0.24, T:0.26
Consensus pattern (225 bp):
ATTAGCGTCGCTTTCCAAAAAACGCCGCTAAATCCCGAAAGCTCAGAAAACGGCGTCGTTGGGCT
TAGGTTTTTTGTGGCGCTTTAGAAAAAACGCCACTAATCCCTGGATATTAGCGGCGCTTACCTGA
AAAACGCCGCTAAATCCCAGAAAGCTCAGGAAACAGCATCGTTGGGCTCAGGTTTTTTTGTGGCA
CTTTGGAAAAAACGCCGCTAAAGCATGGGT
Found at i:28108778 original size:24 final size:24
Alignment explanation
Indices: 28108751--28108927 Score: 149
Period size: 24 Copynumber: 7.4 Consensus size: 24
28108741 CAGTAATTGG
*
28108751 CTTTGTGGCATACTCTGTAAGTGC
1 CTTTGTGGTATACTCTGTAAGTGC
* * *
28108775 CTTTGTGGTACATTTTGTAAGTGCC
1 CTTTGTGGTATACTCTGTAAGTG-C
* *
28108800 CTTTGTGGTGTACTCTATAAGTG-
1 CTTTGTGGTATACTCTGTAAGTGC
* * * *
28108823 TTTTGTGGCATATTCTGTTAGTGC
1 CTTTGTGGTATACTCTGTAAGTGC
* * * *
28108847 CTTTGTGGCATACTTTGCAACTGC
1 CTTTGTGGTATACTCTGTAAGTGC
* * *
28108871 CTTTGTGGTATATTCTATAAGTGT
1 CTTTGTGGTATACTCTGTAAGTGC
* * * *
28108895 CTTTGTGGTGTACTATGTAAATGT
1 CTTTGTGGTATACTCTGTAAGTGC
28108919 CTTTGTGGT
1 CTTTGTGGT
28108928 GTATTCAAGG
Statistics
Matches: 118, Mismatches: 33, Indels: 4
0.76 0.21 0.03
Matches are distributed among these distances:
23 17 0.14
24 82 0.69
25 19 0.16
ACGTcount: A:0.16, C:0.15, G:0.24, T:0.45
Consensus pattern (24 bp):
CTTTGTGGTATACTCTGTAAGTGC
Found at i:28108900 original size:72 final size:73
Alignment explanation
Indices: 28108751--28108926 Score: 212
Period size: 72 Copynumber: 2.4 Consensus size: 73
28108741 CAGTAATTGG
* * * * *
28108751 CTTTGTGGCATACTCTGTAAGTGCCTTTGTGGTACATTTTGTAAGTGCCCTTTGTGGTGTACTCT
1 CTTTGTGGCATACTCTGTAAGTGCCTTTGTGGCACACTTTGCAACTGCCCTTTGTGGTATACTCT
28108816 ATAAGTGT
66 ATAAGTGT
* * * *
28108824 -TTTGTGGCATATTCTGTTAGTGCCTTTGTGGCATACTTTGCAACTG-CCTTTGTGGTATATTCT
1 CTTTGTGGCATACTCTGTAAGTGCCTTTGTGGCACACTTTGCAACTGCCCTTTGTGGTATACTCT
28108887 ATAAGTGT
66 ATAAGTGT
** * * *
28108895 CTTTGTGGTGTACTATGTAAATGTCTTTGTGG
1 CTTTGTGGCATACTCTGTAAGTGCCTTTGTGG
28108927 TGTATTCAAG
Statistics
Matches: 86, Mismatches: 16, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
71 23 0.27
72 63 0.73
ACGTcount: A:0.16, C:0.15, G:0.24, T:0.44
Consensus pattern (73 bp):
CTTTGTGGCATACTCTGTAAGTGCCTTTGTGGCACACTTTGCAACTGCCCTTTGTGGTATACTCT
ATAAGTGT
Found at i:28108923 original size:48 final size:48
Alignment explanation
Indices: 28108751--28108933 Score: 179
Period size: 48 Copynumber: 3.8 Consensus size: 48
28108741 CAGTAATTGG
* *
28108751 CTTTGTGGCATACTCTGTAAGTGCCTTTGTGGTACATTTTGTAAGTGCC
1 CTTTGTGGCATACTCTGTAAGTGCCTTTGTGGTATATTCTGTAAGTG-C
** * * * *
28108800 CTTTGTGGTGTACTCTATAAGTG-TTTTGTGGCATATTCTGTTAGTGC
1 CTTTGTGGCATACTCTGTAAGTGCCTTTGTGGTATATTCTGTAAGTGC
* * * * *
28108847 CTTTGTGGCATACTTTGCAACTGCCTTTGTGGTATATTCTATAAGTGT
1 CTTTGTGGCATACTCTGTAAGTGCCTTTGTGGTATATTCTGTAAGTGC
** * * * *
28108895 CTTTGTGGTGTACTATGTAAATGTCTTTGTGGTGTATTC
1 CTTTGTGGCATACTCTGTAAGTGCCTTTGTGGTATATTC
28108934 AAGGGTGCCT
Statistics
Matches: 107, Mismatches: 26, Indels: 3
0.79 0.19 0.02
Matches are distributed among these distances:
47 18 0.17
48 69 0.64
49 20 0.19
ACGTcount: A:0.16, C:0.15, G:0.24, T:0.45
Consensus pattern (48 bp):
CTTTGTGGCATACTCTGTAAGTGCCTTTGTGGTATATTCTGTAAGTGC
Found at i:28112582 original size:88 final size:88
Alignment explanation
Indices: 28112443--28112678 Score: 313
Period size: 87 Copynumber: 2.7 Consensus size: 88
28112433 TAAAAAGCTT
** * *
28112443 TCAAACTTTTTCAACAAAAAGCAATTAAG----AATTTTTTTTGCACTCAATTGGGTACTTGAAT
1 TCAAACTTTTTCAA-AAAAAGCAATTAAGCCCTTGTTTTTTTTACACTCAATTGGGTACTTGAAC
28112504 TTTCAAAA-TGCATCAAAAAGACCC
65 TTT-AAAAGTGCATCAAAAAGACCC
* *
28112528 TCAAACTTTTTCAAAAAAAGCAATTAAGCCCTTGTTTTTTTTACACTCAATTGGGTAGTTAAACT
1 TCAAACTTTTTCAAAAAAAGCAATTAAGCCCTTGTTTTTTTTACACTCAATTGGGTACTTGAACT
28112593 TTAAAAGTGCATCAAAAAGACCC
66 TTAAAAGTGCATCAAAAAGACCC
* * * * *
28112616 TCAAA-ATTTTCAAAAATACCAATTAAGCCCTTGCTTTTTTTACACTCAATTAGGTACTTGAAC
1 TCAAACTTTTTCAAAAAAAGCAATTAAGCCCTTGTTTTTTTTACACTCAATTGGGTACTTGAAC
28112679 CCTCCCTAAT
Statistics
Matches: 133, Mismatches: 13, Indels: 8
0.86 0.08 0.05
Matches are distributed among these distances:
84 14 0.11
85 14 0.11
87 55 0.41
88 50 0.38
ACGTcount: A:0.37, C:0.19, G:0.10, T:0.34
Consensus pattern (88 bp):
TCAAACTTTTTCAAAAAAAGCAATTAAGCCCTTGTTTTTTTTACACTCAATTGGGTACTTGAACT
TTAAAAGTGCATCAAAAAGACCC
Found at i:28112796 original size:29 final size:28
Alignment explanation
Indices: 28112764--28112838 Score: 71
Period size: 29 Copynumber: 2.6 Consensus size: 28
28112754 AATATAAATC
28112764 AATAAAAGTTATAAAAAT-TATTAAATTTT
1 AATAAAA-TTATAAAAATAT-TTAAATTTT
**
28112793 AATAAAAAAATATAAAATATTTAAATTTT
1 AATAAAATTATA-AAAATATTTAAATTTT
* *
28112822 ATTAAAAATTAGAAAAA
1 AAT-AAAATTATAAAAA
28112839 AATTAGAAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
28 3 0.08
29 27 0.73
30 7 0.19
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (28 bp):
AATAAAATTATAAAAATATTTAAATTTT
Found at i:28112810 original size:21 final size:22
Alignment explanation
Indices: 28112776--28112816 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
28112766 TAAAAGTTAT
* *
28112776 AAAAATTATTAAAT-TTTAATA
1 AAAAAATATAAAATATTTAATA
28112797 AAAAAATATAAAATATTTAA
1 AAAAAATATAAAATATTTAA
28112817 ATTTTATTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (22 bp):
AAAAAATATAAAATATTTAATA
Found at i:28112839 original size:11 final size:11
Alignment explanation
Indices: 28112825--28112849 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
28112815 AAATTTTATT
28112825 AAAAATTAGAA
1 AAAAATTAGAA
28112836 AAAAATTAGAA
1 AAAAATTAGAA
28112847 AAA
1 AAA
28112850 TCCTAAAAAA
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:0.76, C:0.00, G:0.08, T:0.16
Consensus pattern (11 bp):
AAAAATTAGAA
Found at i:28113001 original size:11 final size:11
Alignment explanation
Indices: 28112987--28113018 Score: 55
Period size: 11 Copynumber: 2.8 Consensus size: 11
28112977 ATAAGCATTT
28112987 TATAATTTTTC
1 TATAATTTTTC
28112998 TATAATTTTTC
1 TATAATTTTTC
28113009 TATAACTTTT
1 TATAA-TTTT
28113019 ATTGATTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 16 0.80
12 4 0.20
ACGTcount: A:0.28, C:0.09, G:0.00, T:0.62
Consensus pattern (11 bp):
TATAATTTTTC
Found at i:28113183 original size:22 final size:22
Alignment explanation
Indices: 28113158--28113205 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
28113148 TTCATATGCA
28113158 TTTTACAATTTTTTATAATTTCT
1 TTTTACAA-TTTTTATAATTTCT
*
28113181 TTTTACGATTTTTATAATTT-T
1 TTTTACAATTTTTATAATTTCT
28113202 TTTT
1 TTTT
28113206 CTAATTGTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 5 0.21
22 12 0.50
23 7 0.29
ACGTcount: A:0.23, C:0.06, G:0.02, T:0.69
Consensus pattern (22 bp):
TTTTACAATTTTTATAATTTCT
Found at i:28113570 original size:94 final size:94
Alignment explanation
Indices: 28113458--28113631 Score: 235
Period size: 94 Copynumber: 1.9 Consensus size: 94
28113448 GCTTAATTGC
** * * * * * *
28113458 TTTTTTTGAAAATGTTTGAGGGTCTTTTTTATGCA-TGTGAAAGTTCAAGTACTCAATTGAG-TT
1 TTTTTTTGAAAAAATTTGAGGGTCCTTTTGAGGCATTGTGAAAGTTCAAGTACCCAATTAAGCGT
28113521 CAAAAAAAAAGTAAGAGCTTAATTTATTTTA
66 -AAAAAAAAA-TAAGAGCTTAATTTATTTTA
*
28113552 TTTTTTTGAAAAAATTTGAGGGTCCTTTTGAGGCATTTTGAAAGTTCAAGTACCCAATTAAGCGT
1 TTTTTTTGAAAAAATTTGAGGGTCCTTTTGAGGCATTGTGAAAGTTCAAGTACCCAATTAAGCGT
28113617 AAAAAAAAATAAGAG
66 AAAAAAAAATAAGAG
28113632 TTCAATTACT
Statistics
Matches: 69, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
94 36 0.52
95 32 0.46
96 1 0.01
ACGTcount: A:0.36, C:0.09, G:0.18, T:0.37
Consensus pattern (94 bp):
TTTTTTTGAAAAAATTTGAGGGTCCTTTTGAGGCATTGTGAAAGTTCAAGTACCCAATTAAGCGT
AAAAAAAAATAAGAGCTTAATTTATTTTA
Found at i:28128641 original size:18 final size:18
Alignment explanation
Indices: 28128620--28128657 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
28128610 TTCCAAAACA
*
28128620 TTATTC-ATTTACAAATTG
1 TTATTCAATTT-CAAAATG
28128638 TTATTCAATTTCAAAATG
1 TTATTCAATTTCAAAATG
28128656 TT
1 TT
28128658 TTTTTTTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.34, C:0.11, G:0.05, T:0.50
Consensus pattern (18 bp):
TTATTCAATTTCAAAATG
Found at i:28135372 original size:25 final size:25
Alignment explanation
Indices: 28135344--28135406 Score: 83
Period size: 25 Copynumber: 2.5 Consensus size: 25
28135334 TTAAGTGTTT
*
28135344 TCAGTATAGT-CTATCTATAGTAGTC
1 TCAGTATA-TACTACCTATAGTAGTC
*
28135369 TCAGTATATACTACCTATAGTAGTT
1 TCAGTATATACTACCTATAGTAGTC
*
28135394 TCAGGATATACTA
1 TCAGTATATACTA
28135407 TCAAAGACAG
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
24 1 0.03
25 33 0.97
ACGTcount: A:0.32, C:0.16, G:0.14, T:0.38
Consensus pattern (25 bp):
TCAGTATATACTACCTATAGTAGTC
Found at i:28135879 original size:23 final size:24
Alignment explanation
Indices: 28135835--28135879 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
28135825 AAAATCCTAC
*
28135835 CCATCCAGCCTCTACACACCATCT
1 CCATCCAACCTCTACACACCATCT
*
28135859 CCATCCAACC-CTACACTCCAT
1 CCATCCAACCTCTACACACCAT
28135880 GTGGGGATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 10 0.53
24 9 0.47
ACGTcount: A:0.27, C:0.51, G:0.02, T:0.20
Consensus pattern (24 bp):
CCATCCAACCTCTACACACCATCT
Found at i:28138256 original size:208 final size:208
Alignment explanation
Indices: 28137895--28138307 Score: 720
Period size: 208 Copynumber: 2.0 Consensus size: 208
28137885 CTTTCCTAAT
*
28137895 TAAAATGCAGACCTTGCCTATCTCAAAATTCCAATAGAATTAGAATTCCATCATCTTTTTATATT
1 TAAAATGCAGACCTTGCCTATCTCAAAATTCCAATAGAATTAGAATTCCATCACCTTTTTATATT
* *
28137960 CTTTTCTTAATTAGACTTTCATATTGCTCCTTTTCAAATCCTAATAGAATCTGCTCTCCATCTTT
66 CTTTTCCTAATTAGACTTTCATATTGCTCCTTTTCAAATCCTAATAGAATCTGCTCTCCATCTTC
*
28138025 CTATTTATTTTATTTTCTATTTTCTTTCTCTTTTCTTTACACCATATTTTTATCCTAATTG-TTG
131 CTATTTATTTTATTTTCTATTTTCTTTATCTTTTCTTTACACCATATTTTTATCCTAATTGTTTG
28138089 ATAATTATTTTGAA
196 -TAATTATTTTGAA
*
28138103 TAAAATGCATACCTTGCCTATCTCAAAATTCCAATAGAATTAGAATTCCATCACCTTTTTATATT
1 TAAAATGCAGACCTTGCCTATCTCAAAATTCCAATAGAATTAGAATTCCATCACCTTTTTATATT
* * * *
28138168 CTTTTCCTAATTATATTTTCATATTGCTCCTTTTCAAATCCTAATATAATCTGCTCTCTATCTTC
66 CTTTTCCTAATTAGACTTTCATATTGCTCCTTTTCAAATCCTAATAGAATCTGCTCTCCATCTTC
*
28138233 CTATTTATTTTATTTTTTATTTTCTTTATCTTTTCTTTACACCATATTTTTATCCTAATTGTTTG
131 CTATTTATTTTATTTTCTATTTTCTTTATCTTTTCTTTACACCATATTTTTATCCTAATTGTTTG
28138298 TAATTATTTT
196 TAATTATTTT
28138308 TTTCGAATAA
Statistics
Matches: 194, Mismatches: 10, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
208 191 0.98
209 3 0.02
ACGTcount: A:0.26, C:0.19, G:0.05, T:0.50
Consensus pattern (208 bp):
TAAAATGCAGACCTTGCCTATCTCAAAATTCCAATAGAATTAGAATTCCATCACCTTTTTATATT
CTTTTCCTAATTAGACTTTCATATTGCTCCTTTTCAAATCCTAATAGAATCTGCTCTCCATCTTC
CTATTTATTTTATTTTCTATTTTCTTTATCTTTTCTTTACACCATATTTTTATCCTAATTGTTTG
TAATTATTTTGAA
Found at i:28140000 original size:18 final size:18
Alignment explanation
Indices: 28139979--28140043 Score: 67
Period size: 18 Copynumber: 3.4 Consensus size: 18
28139969 CTAGTGTTTT
28139979 ATCCACAACGAGTGGTAC
1 ATCCACAACGAGTGGTAC
* **
28139997 ATCCACAATGATGAGTGGTTT
1 ATCCAC-A--ACGAGTGGTAC
28140018 ATCCACAACGAGTGGTAC
1 ATCCACAACGAGTGGTAC
*
28140036 ATACACAA
1 ATCCACAA
28140044 TGATGAGTGG
Statistics
Matches: 37, Mismatches: 7, Indels: 6
0.74 0.14 0.12
Matches are distributed among these distances:
18 21 0.57
19 1 0.03
20 1 0.03
21 14 0.38
ACGTcount: A:0.35, C:0.23, G:0.20, T:0.22
Consensus pattern (18 bp):
ATCCACAACGAGTGGTAC
Found at i:28140014 original size:21 final size:21
Alignment explanation
Indices: 28139988--28140063 Score: 77
Period size: 21 Copynumber: 3.8 Consensus size: 21
28139978 TATCCACAAC
28139988 GAGTGGTACATCCACAATGAT
1 GAGTGGTACATCCACAATGAT
** *
28140009 GAGTGGTTTATCCAC-A--AC
1 GAGTGGTACATCCACAATGAT
*
28140027 GAGTGGTACATACACAATGAT
1 GAGTGGTACATCCACAATGAT
**
28140048 GAGTGGTTTATCCACA
1 GAGTGGTACATCCACA
28140064 GCGTGGTGTG
Statistics
Matches: 42, Mismatches: 10, Indels: 6
0.72 0.17 0.10
Matches are distributed among these distances:
18 13 0.31
19 1 0.02
20 1 0.02
21 27 0.64
ACGTcount: A:0.32, C:0.18, G:0.24, T:0.26
Consensus pattern (21 bp):
GAGTGGTACATCCACAATGAT
Found at i:28140030 original size:39 final size:39
Alignment explanation
Indices: 28139971--28140063 Score: 168
Period size: 39 Copynumber: 2.4 Consensus size: 39
28139961 TTTTATTACT
* *
28139971 AGTGTTTTATCCACAACGAGTGGTACATCCACAATGATG
1 AGTGGTTTATCCACAACGAGTGGTACATACACAATGATG
28140010 AGTGGTTTATCCACAACGAGTGGTACATACACAATGATG
1 AGTGGTTTATCCACAACGAGTGGTACATACACAATGATG
28140049 AGTGGTTTATCCACA
1 AGTGGTTTATCCACA
28140064 GCGTGGTGTG
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 52 1.00
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (39 bp):
AGTGGTTTATCCACAACGAGTGGTACATACACAATGATG
Found at i:28142164 original size:41 final size:41
Alignment explanation
Indices: 28142105--28142316 Score: 334
Period size: 41 Copynumber: 5.1 Consensus size: 41
28142095 TATCTTATAC
* * *
28142105 GATCTGAATCAGGCTATAAGCCTAGTAGGCTAAGTGCCGGT
1 GATCTGAATCAGGTTATAAACCTAGCAGGCTAAGTGCCGGT
*
28142146 GATCTGAATCAGGTTATAAACCTAGCAGGCTAAATGCCGGT
1 GATCTGAATCAGGTTATAAACCTAGCAGGCTAAGTGCCGGT
28142187 GATCTGAATCAGGTTATAAACCTAGCAGGCTAAGTGCCGGT
1 GATCTGAATCAGGTTATAAACCTAGCAGGCTAAGTGCCGGT
*
28142228 GATCTGAATCAGGTTATAAACCTAGCAGGCTAAGTGCTGGT
1 GATCTGAATCAGGTTATAAACCTAGCAGGCTAAGTGCCGGT
* * * *
28142269 GATCTGAATCCGGCTATAAGCCTAGCAGGCTAAGTGCTGGT
1 GATCTGAATCAGGTTATAAACCTAGCAGGCTAAGTGCCGGT
28142310 GAATCTG
1 G-ATCTG
28142317 TTAAATTAAG
Statistics
Matches: 161, Mismatches: 9, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
41 156 0.97
42 5 0.03
ACGTcount: A:0.28, C:0.19, G:0.27, T:0.25
Consensus pattern (41 bp):
GATCTGAATCAGGTTATAAACCTAGCAGGCTAAGTGCCGGT
Found at i:28154895 original size:3 final size:3
Alignment explanation
Indices: 28154878--28154972 Score: 70
Period size: 3 Copynumber: 31.3 Consensus size: 3
28154868 CTTAGCAATT
28154878 TTA TTA TTTA GTTA TTA TTA TT- TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA -TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
** * * * * *
28154924 TCT- TCC CTA TTA TTA TTT TTA -TA TTTA TTA ATA TTA TTG TTA CTA
1 T-TA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA
28154969 TTA T
1 TTA T
28154973 ATTCATTTAT
Statistics
Matches: 72, Mismatches: 14, Indels: 12
0.73 0.14 0.12
Matches are distributed among these distances:
2 4 0.06
3 59 0.82
4 9 0.12
ACGTcount: A:0.28, C:0.05, G:0.02, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:28154897 original size:14 final size:13
Alignment explanation
Indices: 28154878--28154924 Score: 69
Period size: 14 Copynumber: 3.5 Consensus size: 13
28154868 CTTAGCAATT
28154878 TTATTATTTAGTTA
1 TTATTATTTA-TTA
28154892 TTATTATTTTATTA
1 TTATTA-TTTATTA
28154906 TTATTA-TTATTA
1 TTATTATTTATTA
28154918 TTATTAT
1 TTATTAT
28154925 CTTCCCTATT
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
12 12 0.39
14 15 0.48
15 4 0.13
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (13 bp):
TTATTATTTATTA
Found at i:28155186 original size:22 final size:20
Alignment explanation
Indices: 28155152--28155195 Score: 52
Period size: 22 Copynumber: 2.1 Consensus size: 20
28155142 TTATCTTATT
*
28155152 TTTTTATCCACATATGCATATA
1 TTTTCATCCACATA--CATATA
*
28155174 TTTTCATCTACATACATATA
1 TTTTCATCCACATACATATA
28155194 TT
1 TT
28155196 CTTATGTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 8 0.40
22 12 0.60
ACGTcount: A:0.32, C:0.18, G:0.02, T:0.48
Consensus pattern (20 bp):
TTTTCATCCACATACATATA
Found at i:28156528 original size:17 final size:18
Alignment explanation
Indices: 28156506--28156546 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
28156496 TTTTGGAATT
*
28156506 ATATTTTTAA-CTTTATA
1 ATATTTTTAATCTTTAAA
*
28156523 ATATTTTTAATTTTTAAA
1 ATATTTTTAATCTTTAAA
28156541 ATATTT
1 ATATTT
28156547 ATTGGATAGC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 10 0.48
18 11 0.52
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (18 bp):
ATATTTTTAATCTTTAAA
Found at i:28160900 original size:27 final size:27
Alignment explanation
Indices: 28160876--28160927 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
28160866 GTGCAGTATA
*
28160876 TGTGGCAAAGCCACCAGTAATAGTAAT
1 TGTGGCAAAGCCACCAGTAACAGTAAT
* *
28160903 TGTGGCAGAGCCACTAGTAACAGTA
1 TGTGGCAAAGCCACCAGTAACAGTA
28160928 CTTCCTCTAC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.35, C:0.19, G:0.25, T:0.21
Consensus pattern (27 bp):
TGTGGCAAAGCCACCAGTAACAGTAAT
Found at i:28161129 original size:26 final size:26
Alignment explanation
Indices: 28161109--28161255 Score: 167
Period size: 26 Copynumber: 5.7 Consensus size: 26
28161099 GACCCTTCGG
*
28161109 GGGTATTTCGATAATTTACCCATCGA
1 GGGTATTTCGATAATTTACCCATCAA
*
28161135 GGGTATTTC-AGTAATTTACCTATCAA
1 GGGTATTTCGA-TAATTTACCCATCAA
*
28161161 GGGTATTTTGATAATTTACCCATCAA
1 GGGTATTTCGATAATTTACCCATCAA
*
28161187 GGGTATCTC-AGTAATTTACCCATC-A
1 GGGTATTTCGA-TAATTTACCCATCAA
* *
28161212 GGGATATTTCGATAATTTTCTCATCGAA
1 GGG-TATTTCGATAATTTACCCATC-AA
*
28161240 -GGTATTTCGGTAATTT
1 GGGTATTTCGATAATTT
28161256 TTATCCGTGT
Statistics
Matches: 104, Mismatches: 10, Indels: 14
0.81 0.08 0.11
Matches are distributed among these distances:
25 6 0.06
26 93 0.89
27 4 0.04
28 1 0.01
ACGTcount: A:0.28, C:0.16, G:0.18, T:0.38
Consensus pattern (26 bp):
GGGTATTTCGATAATTTACCCATCAA
Found at i:28161190 original size:52 final size:51
Alignment explanation
Indices: 28161109--28161255 Score: 197
Period size: 52 Copynumber: 2.8 Consensus size: 51
28161099 GACCCTTCGG
* *
28161109 GGGTATTTCGATAATTTACCCATCGAGGGTATTTCAGTAATTTACCTATCAA
1 GGGTATTTCGATAATTTACCCATCAAGGGTATTTCAGTAATTTACCCATC-A
* *
28161161 GGGTATTTTGATAATTTACCCATCAAGGGTATCTCAGTAATTTACCCATCA
1 GGGTATTTCGATAATTTACCCATCAAGGGTATTTCAGTAATTTACCCATCA
* * *
28161212 GGGATATTTCGATAATTTTCTCATCGAA-GGTATTTCGGTAATTT
1 GGG-TATTTCGATAATTTACCCATC-AAGGGTATTTCAGTAATTT
28161256 TTATCCGTGT
Statistics
Matches: 84, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
51 4 0.05
52 78 0.93
53 2 0.02
ACGTcount: A:0.28, C:0.16, G:0.18, T:0.38
Consensus pattern (51 bp):
GGGTATTTCGATAATTTACCCATCAAGGGTATTTCAGTAATTTACCCATCA
Found at i:28162080 original size:29 final size:29
Alignment explanation
Indices: 28162046--28162118 Score: 100
Period size: 25 Copynumber: 2.7 Consensus size: 29
28162036 AAAAAGAGGA
28162046 ATTTTGACAGAAAAGAGAAAGAGGATTCG
1 ATTTTGACAGAAAAGAGAAAGAGGATTCG
*
28162075 GTTTTGAC--AAAAGAG--AGAGGATTCG
1 ATTTTGACAGAAAAGAGAAAGAGGATTCG
*
28162100 ATTTTGACAGAAGAGAGAA
1 ATTTTGACAGAAAAGAGAA
28162119 GGAGAGAAGA
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
25 17 0.46
27 13 0.35
29 7 0.19
ACGTcount: A:0.42, C:0.07, G:0.29, T:0.22
Consensus pattern (29 bp):
ATTTTGACAGAAAAGAGAAAGAGGATTCG
Found at i:28165816 original size:10 final size:10
Alignment explanation
Indices: 28165790--28165830 Score: 55
Period size: 10 Copynumber: 4.1 Consensus size: 10
28165780 CTTAACTCCC
28165790 TTTTTTTAAA
1 TTTTTTTAAA
** *
28165800 TAATTTTAAT
1 TTTTTTTAAA
28165810 TTTTTTTAAA
1 TTTTTTTAAA
28165820 TTTTTTTAAA
1 TTTTTTTAAA
28165830 T
1 T
28165831 CGTAAAAATT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
10 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (10 bp):
TTTTTTTAAA
Found at i:28167590 original size:18 final size:18
Alignment explanation
Indices: 28167564--28167602 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
28167554 AGGTGCGTTC
* *
28167564 CCTAGCCCTTATATGTAT
1 CCTAACCCTTATACGTAT
28167582 CCTAACCCTTATACGTAT
1 CCTAACCCTTATACGTAT
28167600 CCT
1 CCT
28167603 TTTCCGAGTC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.23, C:0.33, G:0.08, T:0.36
Consensus pattern (18 bp):
CCTAACCCTTATACGTAT
Found at i:28168070 original size:45 final size:45
Alignment explanation
Indices: 28168021--28168108 Score: 149
Period size: 45 Copynumber: 2.0 Consensus size: 45
28168011 ATATTTTGAA
* *
28168021 TATTTTGATATTATTTTATGTAATAAAATAGAAATTTTTTTGAGT
1 TATTTTGATATTATTTGATGTAATAAAATAGAAATTTATTTGAGT
*
28168066 TATTTTGATATTATTTGATGTAATAAAATAGAAGTTTATTTGA
1 TATTTTGATATTATTTGATGTAATAAAATAGAAATTTATTTGA
28168109 TGTAATAAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 40 1.00
ACGTcount: A:0.36, C:0.00, G:0.12, T:0.51
Consensus pattern (45 bp):
TATTTTGATATTATTTGATGTAATAAAATAGAAATTTATTTGAGT
Found at i:28168104 original size:25 final size:24
Alignment explanation
Indices: 28168076--28168132 Score: 96
Period size: 25 Copynumber: 2.3 Consensus size: 24
28168066 TATTTTGATA
28168076 TTATTTGATGTAATAAAATAGAAGT
1 TTATTTGATGTAATAAAATAGAA-T
28168101 TTATTTGATGTAATAAAATAGAAT
1 TTATTTGATGTAATAAAATAGAAT
*
28168125 TTTTTTGA
1 TTATTTGA
28168133 GTTATTTTGA
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
24 8 0.26
25 23 0.74
ACGTcount: A:0.40, C:0.00, G:0.14, T:0.46
Consensus pattern (24 bp):
TTATTTGATGTAATAAAATAGAAT
Found at i:28168149 original size:69 final size:70
Alignment explanation
Indices: 28168031--28168160 Score: 235
Period size: 69 Copynumber: 1.9 Consensus size: 70
28168021 TATTTTGATA
* *
28168031 TTATTTTATGTAATAAAATAGAAATTTTTTTGAGTTATTTTGATATTATTTGATGTAATAAAATA
1 TTATTTGATGTAATAAAATAGAAATTTTTTTGAGTTATTTTGATATTATTCGATGTAATAAAATA
28168096 GAAGT
66 GAAGT
28168101 TTATTTGATGTAATAAAATAG-AATTTTTTTGAGTTATTTTGATATTATTCGATGTAATAA
1 TTATTTGATGTAATAAAATAGAAATTTTTTTGAGTTATTTTGATATTATTCGATGTAATAA
28168161 CATGAACTTA
Statistics
Matches: 58, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
69 38 0.66
70 20 0.34
ACGTcount: A:0.37, C:0.01, G:0.13, T:0.49
Consensus pattern (70 bp):
TTATTTGATGTAATAAAATAGAAATTTTTTTGAGTTATTTTGATATTATTCGATGTAATAAAATA
GAAGT
Found at i:28174909 original size:321 final size:322
Alignment explanation
Indices: 28174298--28174942 Score: 1148
Period size: 321 Copynumber: 2.0 Consensus size: 322
28174288 GAGCCCTGTT
*
28174298 TAAGGTATGACCTTTGCTTCGAGAAAATATTTTTTGGTCAATTGGAAATGGTAATAACATTAGGT
1 TAAGGTATGACCTTTGCTTCGAGAAAATATTTTTTGGTCAATTGGAAATGGTAATAACATCAGGT
*
28174363 GTTAGAAGGACAGTTGGATTCCAAAGGTTGATCCCCTAATCAATCTAATCCCAACTAATGCAAAC
66 GTTAGAAGGACAGTTGGATTCCAAAGGTTGATACCCTAATCAATCTAATCCCAACTAATGCAAAC
* * * *
28174428 ATTGCTACTAATTATTTTCTTAAGGAGATGGTTATAGAAGAAGATTTGTGGAATCTGGAACTCTT
131 ATTGCTACTAATTATTTTCTTAAGGAAATAGTTATAGAAGAAGATTTATGGAATCTGAAACTCTT
* * *
28174493 TCAAGTTTGGTTGTCAGAAGAAATTATTGGACGTATTATTAGTATTCCACCTCCACAACCCTTGG
196 TCAAGTTTGATTGCCAGAAGAAATTATTGGACGTATTACTAGTATTCCACCTCCACAACCCTTGG
* *
28174558 CAGGATTTGACAAGATTGCCTGGGTTGGTACTTCTTCAGGTTATTTTTCTGTTAAGAGTGTC
261 CAGGATTTGACAAGATTGCCTGGGTTGGTACTTCTTCAGGTTAGTTTTCTGTTAAAAGTGTC
* *
28174620 TAAGGTATGGCCTTTGCTTTGAGAAAAT-TTTTTTGGTCAATTGGAAATGGTAATAACATCAGGT
1 TAAGGTATGACCTTTGCTTCGAGAAAATATTTTTTGGTCAATTGGAAATGGTAATAACATCAGGT
28174684 GTTAGAAGGACAGTTGGATTCCAAAGGTTGATACCCTAATCAATCTAATCCCAACTAATGCAAAC
66 GTTAGAAGGACAGTTGGATTCCAAAGGTTGATACCCTAATCAATCTAATCCCAACTAATGCAAAC
28174749 ATTGCTACTAATTATTTTCTTAAGGAAATAGTTATAGAAGAAGATTTATGGAATCTGAAACTCTT
131 ATTGCTACTAATTATTTTCTTAAGGAAATAGTTATAGAAGAAGATTTATGGAATCTGAAACTCTT
*
28174814 TCAGGTTTGATTGCCAGAAGAAATTATTGGACGTATTACTAGTATTCCACCTCCACAACCCTTGG
196 TCAAGTTTGATTGCCAGAAGAAATTATTGGACGTATTACTAGTATTCCACCTCCACAACCCTTGG
*
28174879 CAGGATTTGACAAGATTGCTTGGGTTGGTACTTCTTCAGGTTAGTTTTCTGTTAAAAGTGTC
261 CAGGATTTGACAAGATTGCCTGGGTTGGTACTTCTTCAGGTTAGTTTTCTGTTAAAAGTGTC
28174941 TA
1 TA
28174943 TCGTATAGTT
Statistics
Matches: 308, Mismatches: 15, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
321 282 0.92
322 26 0.08
ACGTcount: A:0.30, C:0.15, G:0.20, T:0.35
Consensus pattern (322 bp):
TAAGGTATGACCTTTGCTTCGAGAAAATATTTTTTGGTCAATTGGAAATGGTAATAACATCAGGT
GTTAGAAGGACAGTTGGATTCCAAAGGTTGATACCCTAATCAATCTAATCCCAACTAATGCAAAC
ATTGCTACTAATTATTTTCTTAAGGAAATAGTTATAGAAGAAGATTTATGGAATCTGAAACTCTT
TCAAGTTTGATTGCCAGAAGAAATTATTGGACGTATTACTAGTATTCCACCTCCACAACCCTTGG
CAGGATTTGACAAGATTGCCTGGGTTGGTACTTCTTCAGGTTAGTTTTCTGTTAAAAGTGTC
Found at i:28176184 original size:6 final size:6
Alignment explanation
Indices: 28176175--28176205 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
28176165 ATAATAATAA
28176175 TATATT TATATT TATATT TATATT TATATT T
1 TATATT TATATT TATATT TATATT TATATT T
28176206 GATGAAATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (6 bp):
TATATT
Found at i:28184739 original size:13 final size:13
Alignment explanation
Indices: 28184721--28184746 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
28184711 AAAAATAAAA
28184721 CAAAAAGTTGTAG
1 CAAAAAGTTGTAG
28184734 CAAAAAGTTGTAG
1 CAAAAAGTTGTAG
28184747 AATAACTCAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.08, G:0.23, T:0.23
Consensus pattern (13 bp):
CAAAAAGTTGTAG
Found at i:28185417 original size:17 final size:17
Alignment explanation
Indices: 28185397--28185430 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
28185387 TTTGTTAATT
28185397 ATTAAAATAAAAATAAA
1 ATTAAAATAAAAATAAA
*
28185414 ATTAAAATTAAAATAAA
1 ATTAAAATAAAAATAAA
28185431 TAAAAATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (17 bp):
ATTAAAATAAAAATAAA
Found at i:28186036 original size:14 final size:14
Alignment explanation
Indices: 28185995--28186042 Score: 64
Period size: 14 Copynumber: 3.5 Consensus size: 14
28185985 TTTCAACCAG
*
28185995 AATA-ATAATAAAT
1 AATATATAATAATT
28186008 AATATATAATAATT
1 AATATATAATAATT
28186022 AATATATAACT-ATT
1 AATATATAA-TAATT
28186036 AATATAT
1 AATATAT
28186043 TATAGATTAT
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
13 4 0.12
14 27 0.84
15 1 0.03
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (14 bp):
AATATATAATAATT
Found at i:28186619 original size:23 final size:26
Alignment explanation
Indices: 28186593--28186645 Score: 67
Period size: 23 Copynumber: 2.2 Consensus size: 26
28186583 TTATTTTGAG
28186593 TTTGGGTAATAA-TGAGTATA-T-TA
1 TTTGGGTAATAACTGAGTATAGTATA
* *
28186616 TTTGGGTTATAACTTAGTATAGTATA
1 TTTGGGTAATAACTGAGTATAGTATA
28186642 TTTG
1 TTTG
28186646 AGTTTTGAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 11 0.44
24 7 0.28
25 1 0.04
26 6 0.24
ACGTcount: A:0.30, C:0.02, G:0.21, T:0.47
Consensus pattern (26 bp):
TTTGGGTAATAACTGAGTATAGTATA
Found at i:28187137 original size:14 final size:15
Alignment explanation
Indices: 28187110--28187139 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
28187100 GAGCCCGCTC
28187110 TAGTTTTAAAATATA
1 TAGTTTTAAAATATA
28187125 TAGTTTT-AAATATA
1 TAGTTTTAAAATATA
28187139 T
1 T
28187140 GAACAAAAAT
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:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (15 bp):
TAGTTTTAAAATATA
Found at i:28189821 original size:2 final size:2
Alignment explanation
Indices: 28189814--28189840 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
28189804 TCATAAAAAC
28189814 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
28189841 ATCCTACCCC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:28197494 original size:9 final size:9
Alignment explanation
Indices: 28197480--28197509 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
28197470 ACGACATGAG
28197480 AAATAAAAA
1 AAATAAAAA
28197489 AAATAAAAA
1 AAATAAAAA
*
28197498 AAAGAAAAA
1 AAATAAAAA
28197507 AAA
1 AAA
28197510 AAACACCCCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.90, C:0.00, G:0.03, T:0.07
Consensus pattern (9 bp):
AAATAAAAA
Found at i:28198680 original size:15 final size:15
Alignment explanation
Indices: 28198652--28198690 Score: 64
Period size: 15 Copynumber: 2.7 Consensus size: 15
28198642 TATGACTCAA
28198652 ATAAT-TTA-TAATT
1 ATAATATTATTAATT
28198665 ATAATATTATTAATT
1 ATAATATTATTAATT
28198680 ATAATATTATT
1 ATAATATTATT
28198691 TAGTCACAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 5 0.21
14 3 0.12
15 16 0.67
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (15 bp):
ATAATATTATTAATT
Found at i:28200851 original size:3 final size:3
Alignment explanation
Indices: 28200843--28200910 Score: 136
Period size: 3 Copynumber: 22.7 Consensus size: 3
28200833 GACCATGATC
28200843 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
28200891 AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AA
28200911 ATGTAGCAAT
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 65 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:28205078 original size:25 final size:25
Alignment explanation
Indices: 28205050--28205134 Score: 62
Period size: 25 Copynumber: 3.2 Consensus size: 25
28205040 AATTAATTTA
*
28205050 TATTTTATGTATCATTATATTAAAT
1 TATTTTATATATCATTATATTAAAT
* * *
28205075 TATTTAAATATTTCATGTATTATATTAAAA
1 TATTT---TATAT-AT-CATTATATTAAAT
* * *
28205105 TATTTAAAATACCATTATATTAAAT
1 TATTTTATATATCATTATATTAAAT
28205130 TATTT
1 TATTT
28205135 AAATATTATT
Statistics
Matches: 46, Mismatches: 9, Indels: 10
0.71 0.14 0.15
Matches are distributed among these distances:
25 21 0.46
26 1 0.02
27 2 0.04
28 4 0.09
29 2 0.04
30 16 0.35
ACGTcount: A:0.41, C:0.05, G:0.02, T:0.52
Consensus pattern (25 bp):
TATTTTATATATCATTATATTAAAT
Found at i:28205121 original size:55 final size:56
Alignment explanation
Indices: 28205062--28205171 Score: 163
Period size: 55 Copynumber: 2.0 Consensus size: 56
28205052 TTTTATGTAT
28205062 CATTATATTAAATTATTTAAATA-T-TTCATGTATTATA-TTAAAATATTTAAAATAC
1 CATTATATTAAATTATTTAAATATTATTCAT-TATTATACTTAAAAT-TTTAAAATAC
* *
28205117 CATTATATTAAATTATTTAAATATTATTTATTATTTTACTTAAAATTTTAAAATA
1 CATTATATTAAATTATTTAAATATTATTCATTATTATACTTAAAATTTTAAAATA
28205172 TTTCATGTAT
Statistics
Matches: 50, Mismatches: 2, Indels: 5
0.88 0.04 0.09
Matches are distributed among these distances:
55 23 0.46
56 16 0.32
57 11 0.22
ACGTcount: A:0.45, C:0.05, G:0.01, T:0.50
Consensus pattern (56 bp):
CATTATATTAAATTATTTAAATATTATTCATTATTATACTTAAAATTTTAAAATAC
Found at i:28205147 original size:25 final size:25
Alignment explanation
Indices: 28205064--28205147 Score: 80
Period size: 25 Copynumber: 3.2 Consensus size: 25
28205054 TTATGTATCA
28205064 TTATATTAAATTATTTAAATATTTCATGT
1 TTATATTAAATTATTTAAATA-TT-A--T
* **
28205093 ATTATATTAAAATATTTAAAATACCA-
1 -TTATATTAAATTATTT-AAATATTAT
28205119 TTATATTAAATTATTTAAATATTAT
1 TTATATTAAATTATTTAAATATTAT
28205144 TTAT
1 TTAT
28205148 TATTTTACTT
Statistics
Matches: 46, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
24 6 0.13
25 19 0.41
29 1 0.02
30 15 0.33
31 5 0.11
ACGTcount: A:0.44, C:0.04, G:0.01, T:0.51
Consensus pattern (25 bp):
TTATATTAAATTATTTAAATATTAT
Found at i:28211676 original size:22 final size:21
Alignment explanation
Indices: 28211641--28211698 Score: 53
Period size: 22 Copynumber: 2.7 Consensus size: 21
28211631 AAAGGGTACC
* * *
28211641 TACAAATTAAATCTCTAAGAT
1 TACAAATCATATCTCCAAGAT
28211662 TACAAAATCATATCTTCCAAGAT
1 TAC-AAATCATATC-TCCAAGAT
* *
28211685 TGCATATCATATCT
1 TACAAATCATATCT
28211699 AAGATTGCAT
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
21 4 0.13
22 17 0.57
23 9 0.30
ACGTcount: A:0.41, C:0.19, G:0.05, T:0.34
Consensus pattern (21 bp):
TACAAATCATATCTCCAAGAT
Found at i:28212242 original size:88 final size:88
Alignment explanation
Indices: 28212072--28212886 Score: 919
Period size: 88 Copynumber: 9.3 Consensus size: 88
28212062 GCTTGATCTG
* * * * *
28212072 CTGCAACTCAGGGAGGCAAGGCTGGTGTTTTCGATCTACTTCACTGTCGGTGCAGGAAGGCAATA
1 CTGCAACCCAGGGAGGCAAGGCTGGTGTCTTCGATCTGCTTCACTGTTGGTGCAGGAAGGCAAGA
* * *
28212137 TCTGCTATTTTTAACCTGCTCCG
66 TCTGCTATCTTCAACCTGCTCCA
* * * * * * * *
28212160 TTGTAGCCCAGAGAGGTAAGACTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGA
1 CTGCAACCCAGGGAGGCAAGGCTGGTGTCTTCGATCTGCTTCACTGTTGGTGCAGGAAGGCAAGA
* * *
28212225 TCTGCTATTTTTAACCTGCTCCG
66 TCTGCTATCTTCAACCTGCTCCA
* * ** * * *
28212248 CTGCAACCCAGAGTGGCAAGGCTACTGTCTTCGATCTGCTTTACTGTTGGTGCAAGAAGGAAAGA
1 CTGCAACCCAGGGAGGCAAGGCTGGTGTCTTCGATCTGCTTCACTGTTGGTGCAGGAAGGCAAGA
* * *
28212313 TCTGCTATTTTTAACCTGCTCCG
66 TCTGCTATCTTCAACCTGCTCCA
* * * * ** *
28212336 CTGCAACCCAGGGAGGCAAGACTAGTGTCTTCAATCTGTTTCACTGTCAGTACAGGAAGGCAAGA
1 CTGCAACCCAGGGAGGCAAGGCTGGTGTCTTCGATCTGCTTCACTGTTGGTGCAGGAAGGCAAGA
* *
28212401 TCTACTATCTTTAACCTGCTCCA
66 TCTGCTATCTTCAACCTGCTCCA
* * * * * * *
28212424 CTGCCACCGAGGGAGGCAAGGCTAGTGTCTTCAATCTGTTTCACTGTTAGTACAGGAAGGCAAGA
1 CTGCAACCCAGGGAGGCAAGGCTGGTGTCTTCGATCTGCTTCACTGTTGGTGCAGGAAGGCAAGA
28212489 TCTGCTATCTTCAACCTGCTCCA
66 TCTGCTATCTTCAACCTGCTCCA
* * * * * * *
28212512 CTACGACCCAGGGAGGCAAGGCTGTTATCTTCGATCTGCTTCACTGTCGGTACAAGAAGGCAAGA
1 CTGCAACCCAGGGAGGCAAGGCTGGTGTCTTCGATCTGCTTCACTGTTGGTGCAGGAAGGCAAGA
*
28212577 TCTGCTATCTTCAACCTACTCCA
66 TCTGCTATCTTCAACCTGCTCCA
* ** * * * * * *
28212600 CTACGGCCCAGGGAGGCAAGGATGGTATCTTCGATCTACTTCGCTGTTGATGTAGGAAGGCAAGA
1 CTGCAACCCAGGGAGGCAAGGCTGGTGTCTTCGATCTGCTTCACTGTTGGTGCAGGAAGGCAAGA
28212665 TCTGCTATCTTCAACCTGCTCCA
66 TCTGCTATCTTCAACCTGCTCCA
* * * * *
28212688 CTACAACCCAGGGAGGCAAGGCTGGTATCTTCGATCTACTTCGCTGTTGATGCAGGAAGGCAAGA
1 CTGCAACCCAGGGAGGCAAGGCTGGTGTCTTCGATCTGCTTCACTGTTGGTGCAGGAAGGCAAGA
28212753 TCTGCTATCTTCAACCTGCTCCA
66 TCTGCTATCTTCAACCTGCTCCA
* * * * * * *
28212776 CTACAACCCAGGGAGGCAAGGTTGGTATCTTCGATCTGCTTCGCCGTTAGTACAGGAAGGCAAGA
1 CTGCAACCCAGGGAGGCAAGGCTGGTGTCTTCGATCTGCTTCACTGTTGGTGCAGGAAGGCAAGA
* * *
28212841 TCTGTTATTTTCAACCTGCTCCG
66 TCTGCTATCTTCAACCTGCTCCA
* *
28212864 CTGCAAACCAGGAAGGCAAGGCT
1 CTGCAACCCAGGGAGGCAAGGCT
28212887 TTGCGATTTC
Statistics
Matches: 642, Mismatches: 85, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
88 642 1.00
ACGTcount: A:0.23, C:0.25, G:0.25, T:0.27
Consensus pattern (88 bp):
CTGCAACCCAGGGAGGCAAGGCTGGTGTCTTCGATCTGCTTCACTGTTGGTGCAGGAAGGCAAGA
TCTGCTATCTTCAACCTGCTCCA
Found at i:28212676 original size:45 final size:45
Alignment explanation
Indices: 28212625--28212764 Score: 140
Period size: 45 Copynumber: 3.2 Consensus size: 45
28212615 GCAAGGATGG
*
28212625 TATCTTCGATCTACTTCGCTGTTGATGTAGGAAGGCAAGATCTGC
1 TATCTTCGATCTACTTCGCTGTTGATGCAGGAAGGCAAGATCTGC
* * * * * *** ** * * *
28212670 TATCTTCAACCTGCTCCACT-ACAACCCAGGGAGGCAAG-GCTGG
1 TATCTTCGATCTACTTCGCTGTTGATGCAGGAAGGCAAGATCTGC
28212713 TATCTTCGATCTACTTCGCTGTTGATGCAGGAAGGCAAGATCTGC
1 TATCTTCGATCTACTTCGCTGTTGATGCAGGAAGGCAAGATCTGC
28212758 TATCTTC
1 TATCTTC
28212765 AACCTGCTCC
Statistics
Matches: 66, Mismatches: 27, Indels: 4
0.68 0.28 0.04
Matches are distributed among these distances:
43 18 0.27
44 23 0.35
45 25 0.38
ACGTcount: A:0.23, C:0.25, G:0.23, T:0.29
Consensus pattern (45 bp):
TATCTTCGATCTACTTCGCTGTTGATGCAGGAAGGCAAGATCTGC
Found at i:28212876 original size:44 final size:44
Alignment explanation
Indices: 28212303--28212883 Score: 191
Period size: 44 Copynumber: 13.2 Consensus size: 44
28212293 GTTGGTGCAA
* * * *
28212303 GAAGGAAAGATCTGCTATTTTTAACCTGCTCCGCTGCAACCCAG
1 GAAGGCAAGATCTGCTATCTTCAACCTGCTCCGCTGCAAACCAG
* * * * * * *
28212347 GGAGGCAAGA-CTAG-TGTCTTCAATCTGTTTCACTGTCAGTA-CAG
1 GAAGGCAAGATCT-GCTATCTTCAACCTGCTCCGCTG-CA-AACCAG
* * * *
28212391 GAAGGCAAGATCTACTATCTTTAACCTGCTCCACTGC-CACCGAG
1 GAAGGCAAGATCTGCTATCTTCAACCTGCTCCGCTGCAAACC-AG
* * * * * * * * *
28212435 GGAGGCAAG-GCTAG-TGTCTTCAATCTGTTTCACTGTTAGTA-CAG
1 GAAGGCAAGATCT-GCTATCTTCAACCTGCTCCGCTG-CA-AACCAG
* * * *
28212479 GAAGGCAAGATCTGCTATCTTCAACCTGCTCCACTACGACCCAG
1 GAAGGCAAGATCTGCTATCTTCAACCTGCTCCGCTGCAAACCAG
* * * * * * * ** *
28212523 GGAGGCAAG-GCTGTTATCTTCGATCTGCTTCACTGTCGGTA-CAA
1 GAAGGCAAGATCTGCTATCTTCAACCTGCTCCGCTG-C-AAACCAG
* * * ***
28212567 GAAGGCAAGATCTGCTATCTTCAACCTACTCCACTACGGCCCAG
1 GAAGGCAAGATCTGCTATCTTCAACCTGCTCCGCTGCAAACCAG
* * * * * * ** ***
28212611 GGAGGCAAGGA--TGGTATCTTCGATCTACTTCGCTGTTGATGTAG
1 GAAGGCAA-GATCTGCTATCTTCAACCTGCTCCGCTG-CAAACCAG
* * *
28212655 GAAGGCAAGATCTGCTATCTTCAACCTGCTCCACTACAACCCAG
1 GAAGGCAAGATCTGCTATCTTCAACCTGCTCCGCTGCAAACCAG
* * * * * * * ** **
28212699 GGAGGCAAG-GCTGGTATCTTCGATCTACTTCGCTGTTGATGCAG
1 GAAGGCAAGATCTGCTATCTTCAACCTGCTCCGCTG-CAAACCAG
* * *
28212743 GAAGGCAAGATCTGCTATCTTCAACCTGCTCCACTACAACCCAG
1 GAAGGCAAGATCTGCTATCTTCAACCTGCTCCGCTGCAAACCAG
* * * * * * * * *
28212787 GGAGGCAAGGT-TGGTATCTTCGATCTGCTTCGCCGTTAGTA-CAG
1 GAAGGCAAGATCTGCTATCTTCAACCTGCTCCGCTG-CA-AACCAG
* *
28212831 GAAGGCAAGATCTGTTATTTTCAACCTGCTCCGCTGCAAACCAG
1 GAAGGCAAGATCTGCTATCTTCAACCTGCTCCGCTGCAAACCAG
28212875 GAAGGCAAG
1 GAAGGCAAG
28212884 GCTTTGCGAT
Statistics
Matches: 375, Mismatches: 134, Indels: 56
0.66 0.24 0.10
Matches are distributed among these distances:
42 1 0.00
43 112 0.30
44 149 0.40
45 112 0.30
46 1 0.00
ACGTcount: A:0.25, C:0.26, G:0.24, T:0.25
Consensus pattern (44 bp):
GAAGGCAAGATCTGCTATCTTCAACCTGCTCCGCTGCAAACCAG
Found at i:28219816 original size:21 final size:21
Alignment explanation
Indices: 28219782--28219833 Score: 90
Period size: 21 Copynumber: 2.6 Consensus size: 21
28219772 CATATCTTCC
28219782 AAGATTGC--ATATCATATCT
1 AAGATTGCATATATCATATCT
28219801 AAGATTGCATATATCATATCT
1 AAGATTGCATATATCATATCT
28219822 AAGATTGCATAT
1 AAGATTGCATAT
28219834 CCTTGAAGAT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
19 8 0.26
21 23 0.74
ACGTcount: A:0.38, C:0.13, G:0.12, T:0.37
Consensus pattern (21 bp):
AAGATTGCATATATCATATCT
Found at i:28223904 original size:12 final size:13
Alignment explanation
Indices: 28223883--28223911 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
28223873 TGTTGATGGA
28223883 TTTTATTTTTTAT
1 TTTTATTTTTTAT
28223896 TTTTA-TTTTTAT
1 TTTTATTTTTTAT
28223908 TTTT
1 TTTT
28223912 TGTTTTGTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.69
13 5 0.31
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (13 bp):
TTTTATTTTTTAT
Found at i:28224193 original size:69 final size:72
Alignment explanation
Indices: 28224120--28224253 Score: 193
Period size: 73 Copynumber: 1.9 Consensus size: 72
28224110 AATTCTGTTA
* * *
28224120 TCTTTGTTTAGTTTA-TT-TTT-TTATTTGTTTAATCATTATCTTTCCTCTGTTTTGCCATCAAT
1 TCTTTGTTTAGTTTATTTGTTTATTATTTGTTTAATCATCATCCTGCCTCTGTTTTGCCATCAAT
28224182 TCCCTTG
66 TCCCTTG
* *
28224189 TCTTTGTTTTGTTTATTTTGTTTATTATTTGTTTAATCGTCATCCTGCCTCTGTTTTGCCATCAA
1 TCTTTGTTTAGTTTA-TTTGTTTATTATTTGTTTAATCATCATCCTGCCTCTGTTTTGCCATCAA
28224254 CTCTGTGGTG
Statistics
Matches: 56, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
69 14 0.25
71 2 0.04
72 3 0.05
73 37 0.66
ACGTcount: A:0.14, C:0.17, G:0.10, T:0.58
Consensus pattern (72 bp):
TCTTTGTTTAGTTTATTTGTTTATTATTTGTTTAATCATCATCCTGCCTCTGTTTTGCCATCAAT
TCCCTTG
Found at i:28224743 original size:29 final size:28
Alignment explanation
Indices: 28224699--28224755 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 28
28224689 GTGTGATTAT
* *
28224699 ATGGGCAATTCGGGTAGGTCATGTAGGGC
1 ATGGGCAAATCAGGTAGGTCATGT-GGGC
*
28224728 ATGGGCAAATCAGGTAGGTCGTGTGGGC
1 ATGGGCAAATCAGGTAGGTCATGTGGGC
28224756 TACATAGGCT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
28 4 0.16
29 21 0.84
ACGTcount: A:0.21, C:0.14, G:0.42, T:0.23
Consensus pattern (28 bp):
ATGGGCAAATCAGGTAGGTCATGTGGGC
Found at i:28227996 original size:20 final size:19
Alignment explanation
Indices: 28227971--28228089 Score: 65
Period size: 20 Copynumber: 6.4 Consensus size: 19
28227961 ATATATTTAG
28227971 AATTTTTTAGAATTTTTATA
1 AATTTTTT-GAATTTTTATA
* *
28227991 AATTTTAT-AA---ATATA
1 AATTTTTTGAATTTTTATA
*
28228006 AA-ATT-TGAAATTTTTATA
1 AATTTTTTGA-ATTTTTATA
* *
28228024 AATATTTTGAA-TTTTAAA
1 AATTTTTTGAATTTTTATA
**
28228042 AATTATTTTGAATTTTTGGA
1 AATT-TTTTGAATTTTTATA
28228062 AATTATTTTGAATTATTCTAT-
1 AATT-TTTTGAATT-TT-TATA
28228083 AATTTTT
1 AATTTTT
28228090 GTTGAGAGAG
Statistics
Matches: 78, Mismatches: 10, Indels: 22
0.71 0.09 0.20
Matches are distributed among these distances:
13 1 0.01
14 3 0.04
15 7 0.09
18 17 0.22
19 11 0.14
20 32 0.41
21 6 0.08
22 1 0.01
ACGTcount: A:0.39, C:0.01, G:0.06, T:0.55
Consensus pattern (19 bp):
AATTTTTTGAATTTTTATA
Found at i:28228005 original size:42 final size:40
Alignment explanation
Indices: 28227954--28228058 Score: 99
Period size: 42 Copynumber: 2.6 Consensus size: 40
28227944 ACTTTTTATA
* *
28227954 TATATATATATATTTAGAATTTTT-TAGAATTTTTATAAATTT
1 TATAAATATATATTT-GAATTTTTATA-AATATTT-TAAATTT
* *
28227996 TATAAATATAAAATTTGAAATTTTTATAAATATTTTGAATTT
1 TATAAATAT-ATATTTG-AATTTTTATAAATATTTTAAATTT
*
28228038 TAAAAAT-TAT-TTTGAATTTTT
1 TATAAATATATATTTGAATTTTT
28228059 GGAAATTATT
Statistics
Matches: 54, Mismatches: 6, Indels: 10
0.77 0.09 0.14
Matches are distributed among these distances:
38 7 0.13
39 4 0.07
40 1 0.02
41 1 0.02
42 21 0.39
43 18 0.33
44 2 0.04
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (40 bp):
TATAAATATATATTTGAATTTTTATAAATATTTTAAATTT
Found at i:28235622 original size:17 final size:17
Alignment explanation
Indices: 28235569--28235623 Score: 53
Period size: 17 Copynumber: 3.2 Consensus size: 17
28235559 GCCTGAAGTT
*
28235569 AGAAGGAGAGAGGAAGAG
1 AGAA-GAGAGAGAAAGAG
28235587 -GAAG-GAG-GACAAGATG
1 AGAAGAGAGAGA-AAGA-G
28235603 AGAAGAGAGAGAAAGAG
1 AGAAGAGAGAGAAAGAG
28235620 AGAA
1 AGAA
28235624 AAGGGGAGTG
Statistics
Matches: 31, Mismatches: 1, Indels: 11
0.72 0.02 0.26
Matches are distributed among these distances:
14 1 0.03
15 7 0.23
16 2 0.06
17 12 0.39
18 7 0.23
19 2 0.06
ACGTcount: A:0.53, C:0.02, G:0.44, T:0.02
Consensus pattern (17 bp):
AGAAGAGAGAGAAAGAG
Found at i:28241820 original size:54 final size:54
Alignment explanation
Indices: 28241758--28241906 Score: 158
Period size: 54 Copynumber: 2.8 Consensus size: 54
28241748 TGTCACATAT
*
28241758 CCGTGTGACTCAAGTCAGAGAGTTACACGGTCAGACACACGGCCTCA-CACATGC
1 CCGTGTGACTCAAGTCAGAGAGTTACACGGTCAGACACACGGCCT-AGCACACGC
** * * * * *
28241812 CCGTGTGACTTTAGTTAGAGAGTTACACGCTCTGGCACACGGCCTAGCACACGT
1 CCGTGTGACTCAAGTCAGAGAGTTACACGGTCAGACACACGGCCTAGCACACGC
* * * *
28241866 CTGTGTGACTCAAGCCAAAGAGTTACATAGG-CAGACACACG
1 CCGTGTGACTCAAGTCAGAGAGTTACA-CGGTCAGACACACG
28241907 CCCATATGAT
Statistics
Matches: 75, Mismatches: 18, Indels: 4
0.77 0.19 0.04
Matches are distributed among these distances:
53 1 0.01
54 73 0.97
55 1 0.01
ACGTcount: A:0.28, C:0.28, G:0.25, T:0.19
Consensus pattern (54 bp):
CCGTGTGACTCAAGTCAGAGAGTTACACGGTCAGACACACGGCCTAGCACACGC
Found at i:28242098 original size:8 final size:8
Alignment explanation
Indices: 28242085--28242109 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
28242075 TAAAAAAAAC
28242085 CAATTAAA
1 CAATTAAA
28242093 CAATTAAA
1 CAATTAAA
28242101 CAATTAAA
1 CAATTAAA
28242109 C
1 C
28242110 GAACCAAAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.60, C:0.16, G:0.00, T:0.24
Consensus pattern (8 bp):
CAATTAAA
Found at i:28255785 original size:20 final size:21
Alignment explanation
Indices: 28255760--28255799 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
28255750 TTTTTTTTTA
*
28255760 ATTT-AATTAACTATCCAAAC
1 ATTTAAATTAACTAACCAAAC
*
28255780 ATTTAAATTACCTAACCAAA
1 ATTTAAATTAACTAACCAAA
28255800 TTTTTATATG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.47, C:0.20, G:0.00, T:0.33
Consensus pattern (21 bp):
ATTTAAATTAACTAACCAAAC
Found at i:28269450 original size:31 final size:31
Alignment explanation
Indices: 28269415--28269498 Score: 107
Period size: 31 Copynumber: 2.7 Consensus size: 31
28269405 GTATATGTTT
* * *
28269415 TATACATTGTCAAATTTTATTTTTATATAGA
1 TATACATTGCCAAATTTGATTTGTATATAGA
*
28269446 TATACATTGCCAAATTTGATTTGTATATGGA
1 TATACATTGCCAAATTTGATTTGTATATAGA
* *
28269477 TATATATTGCCGAA-TTGATTTG
1 TATACATTGCCAAATTTGATTTG
28269499 AGCATTGGAT
Statistics
Matches: 47, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
30 8 0.17
31 39 0.83
ACGTcount: A:0.32, C:0.08, G:0.13, T:0.46
Consensus pattern (31 bp):
TATACATTGCCAAATTTGATTTGTATATAGA
Found at i:28273392 original size:45 final size:45
Alignment explanation
Indices: 28273321--28273543 Score: 302
Period size: 45 Copynumber: 5.0 Consensus size: 45
28273311 GCTATACACC
* *
28273321 TAAAAATGAGTAAGACTATAGCTGAAAGATGTTATGGCATCATGA
1 TAAAAATGAGTAAGACCATAGCTGAAAGATGTTATGACATCATGA
* * *
28273366 TAAAAATAAGTAAGACCATAGTTGAAAGATGTTATGGCATCATGA
1 TAAAAATGAGTAAGACCATAGCTGAAAGATGTTATGACATCATGA
* *
28273411 TAAAAGTGAGTAAGACCATAGCTGAAAGATGCTATGACATCATGA
1 TAAAAATGAGTAAGACCATAGCTGAAAGATGTTATGACATCATGA
* *
28273456 TAAAAATGAGTAAGACCGTAGCTGAAAGATGATATGACATCATGA
1 TAAAAATGAGTAAGACCATAGCTGAAAGATGTTATGACATCATGA
* * * * * **
28273501 TAGATATGAGTAAGACGATAGATAAAAGATGCCATGACATCAT
1 TAAAAATGAGTAAGACCATAGCTGAAAGATGTTATGACATCAT
28273544 ATGAAAGCGC
Statistics
Matches: 159, Mismatches: 19, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
45 159 1.00
ACGTcount: A:0.43, C:0.11, G:0.22, T:0.24
Consensus pattern (45 bp):
TAAAAATGAGTAAGACCATAGCTGAAAGATGTTATGACATCATGA
Found at i:28276029 original size:18 final size:18
Alignment explanation
Indices: 28276002--28276046 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
28275992 ATAATAATAA
*
28276002 TTAATAAAATATTATTAT
1 TTAATAAAATATTATTAC
*
28276020 TTATTAAAATATTATTAC
1 TTAATAAAATATTATTAC
28276038 TTAATAAAA
1 TTAATAAAA
28276047 AATCATTTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (18 bp):
TTAATAAAATATTATTAC
Found at i:28280234 original size:20 final size:20
Alignment explanation
Indices: 28280209--28280255 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
28280199 TGTGCCCTAG
28280209 CCGTGTGGAGGTCTACACGC
1 CCGTGTGGAGGTCTACACGC
* *
28280229 CCGTGTGGTGGTCTACATGC
1 CCGTGTGGAGGTCTACACGC
*
28280249 CTGTGTG
1 CCGTGTG
28280256 CAAGATGCAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.11, C:0.26, G:0.36, T:0.28
Consensus pattern (20 bp):
CCGTGTGGAGGTCTACACGC
Found at i:28283412 original size:19 final size:20
Alignment explanation
Indices: 28283388--28283435 Score: 66
Period size: 19 Copynumber: 2.5 Consensus size: 20
28283378 GTCACATTGC
28283388 AAATATAAATAAA-AATTAA
1 AAATATAAATAAATAATTAA
28283407 AAATAT--ATAAATTAATTAA
1 AAATATAAATAAA-TAATTAA
28283426 AAATATAAAT
1 AAATATAAAT
28283436 TTTCACATCA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
17 5 0.20
19 18 0.72
21 2 0.08
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (20 bp):
AAATATAAATAAATAATTAA
Found at i:28283431 original size:17 final size:15
Alignment explanation
Indices: 28283394--28283436 Score: 50
Period size: 17 Copynumber: 2.7 Consensus size: 15
28283384 TTGCAAATAT
*
28283394 AAATAAAAATTAAAA
1 AAATATAAATTAAAA
*
28283409 ATATATAAATTAATTAA
1 AAATATAAATTAA--AA
28283426 AAATATAAATT
1 AAATATAAATT
28283437 TTCACATCAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
15 11 0.48
17 12 0.52
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (15 bp):
AAATATAAATTAAAA
Found at i:28283823 original size:25 final size:26
Alignment explanation
Indices: 28283793--28283849 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 26
28283783 TATTATAGGC
* *
28283793 TTTTTTATATATTTTTA-ATTGTATA
1 TTTTTTATAAATTTATATATTGTATA
*
28283818 TATTTTTATAAATTTATATTTTGTATA
1 T-TTTTTATAAATTTATATATTGTATA
28283845 TTTTT
1 TTTTT
28283850 AAAATAATAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
25 1 0.04
26 18 0.67
27 8 0.30
ACGTcount: A:0.28, C:0.00, G:0.04, T:0.68
Consensus pattern (26 bp):
TTTTTTATAAATTTATATATTGTATA
Found at i:28283987 original size:20 final size:20
Alignment explanation
Indices: 28283962--28284016 Score: 57
Period size: 20 Copynumber: 3.0 Consensus size: 20
28283952 AAAAAAATAC
28283962 TTTTTAAATTAATTTATATA
1 TTTTTAAATTAATTTATATA
*
28283982 TTTTTAAAGTTTATTT-TA-A
1 TTTTTAAA-TTAATTTATATA
28284001 TTTTT---TTAATTTATAT
1 TTTTTAAATTAATTTATAT
28284017 TTGTCATGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
15 6 0.20
16 2 0.07
19 6 0.20
20 10 0.33
21 6 0.20
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (20 bp):
TTTTTAAATTAATTTATATA
Found at i:28286095 original size:50 final size:51
Alignment explanation
Indices: 28285931--28286112 Score: 194
Period size: 51 Copynumber: 3.6 Consensus size: 51
28285921 TATAAACACA
* * * * * *
28285931 TGTGTAGTACTAAGTGCAGGCTACTACGT-GTATC-GATAGATAATGGTCACA
1 TGTGTAGTACTATGTGCAGGCTACTACGTGGTA-CGGAAAGCT-TTGATCACG
* * *
28285982 TGTGTAGTACTATGTGCAAGCTACTATGT-GTACCGGAAGGCTTTGATCACG
1 TGTGTAGTACTATGTGCAGGCTACTACGTGGTA-CGGAAAGCTTTGATCACG
*
28286033 TGTGTAGTACTATGTGCAGGCTACCACGTGGTTA-GGAAAG-TTTGATCACG
1 TGTGTAGTACTATGTGCAGGCTACTACGTGG-TACGGAAAGCTTTGATCACG
*
28286083 TGTGTAGTACTATGTGAAGGCTACTACGTG
1 TGTGTAGTACTATGTGCAGGCTACTACGTG
28286113 TATCGAATGA
Statistics
Matches: 112, Mismatches: 16, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
50 38 0.34
51 67 0.60
52 5 0.04
53 2 0.02
ACGTcount: A:0.25, C:0.16, G:0.28, T:0.31
Consensus pattern (51 bp):
TGTGTAGTACTATGTGCAGGCTACTACGTGGTACGGAAAGCTTTGATCACG
Found at i:28287474 original size:20 final size:20
Alignment explanation
Indices: 28287451--28287505 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
28287441 AGTTAAATTC
28287451 AGCTCAATTTTAGCTCAATG
1 AGCTCAATTTTAGCTCAATG
*
28287471 AGCTC-GTTCTTAGCTCAATG
1 AGCTCAATT-TTAGCTCAATG
*
28287491 AGCTCATTTTTAGCT
1 AGCTCAATTTTAGCT
28287506 TACTTTAGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
19 2 0.06
20 27 0.87
21 2 0.06
ACGTcount: A:0.24, C:0.22, G:0.16, T:0.38
Consensus pattern (20 bp):
AGCTCAATTTTAGCTCAATG
Found at i:28288997 original size:12 final size:12
Alignment explanation
Indices: 28288977--28289008 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
28288967 TCGGAGTAAG
*
28288977 TTCGTAAAAAAA
1 TTCGAAAAAAAA
28288989 TTCGAAAAAAAA
1 TTCGAAAAAAAA
28289001 TTCGAAAA
1 TTCGAAAA
28289009 TTCAAAGTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.59, C:0.09, G:0.09, T:0.22
Consensus pattern (12 bp):
TTCGAAAAAAAA
Found at i:28290177 original size:21 final size:21
Alignment explanation
Indices: 28290133--28290173 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
28290123 AAAAGAACAT
**
28290133 TGAAAAAGAAATTGATAGAAA
1 TGAAAAAGAAAAAGATAGAAA
28290154 TGAAAAAGAAAAAGAT-GAAA
1 TGAAAAAGAAAAAGATAGAAA
28290174 ATGAGATTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.66, C:0.00, G:0.20, T:0.15
Consensus pattern (21 bp):
TGAAAAAGAAAAAGATAGAAA
Found at i:28290224 original size:12 final size:12
Alignment explanation
Indices: 28290207--28290274 Score: 52
Period size: 12 Copynumber: 5.7 Consensus size: 12
28290197 AGTGAAAAGC
28290207 AAAAAGAGATTG
1 AAAAAGAGATTG
*
28290219 AAAAAGAAATTG
1 AAAAAGAGATTG
*
28290231 --AAAGAGA-AG
1 AAAAAGAGATTG
*
28290240 AAAAAGAAAGAGTGG
1 AAAAAG--AGA-TTG
*
28290255 AAAAAGAAATTG
1 AAAAAGAGATTG
28290267 AAAAAGAG
1 AAAAAGAG
28290275 TCTGCAAAAG
Statistics
Matches: 43, Mismatches: 7, Indels: 12
0.69 0.11 0.19
Matches are distributed among these distances:
9 1 0.02
10 6 0.14
11 4 0.09
12 20 0.47
13 5 0.12
15 7 0.16
ACGTcount: A:0.65, C:0.00, G:0.25, T:0.10
Consensus pattern (12 bp):
AAAAAGAGATTG
Found at i:28290248 original size:15 final size:15
Alignment explanation
Indices: 28290230--28290263 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
28290220 AAAAGAAATT
28290230 GAAAGAGAAGAAAAA
1 GAAAGAGAAGAAAAA
**
28290245 GAAAGAGTGGAAAAA
1 GAAAGAGAAGAAAAA
28290260 GAAA
1 GAAA
28290264 TTGAAAAAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.68, C:0.00, G:0.29, T:0.03
Consensus pattern (15 bp):
GAAAGAGAAGAAAAA
Found at i:28290269 original size:21 final size:20
Alignment explanation
Indices: 28290217--28290269 Score: 53
Period size: 18 Copynumber: 2.9 Consensus size: 20
28290207 AAAAAGAGAT
28290217 TGAAAAAGAAATTGAAAGA-
1 TGAAAAAGAAATTGAAAGAG
*
28290236 -GAAGAA-AAA--GAAAGAG
1 TGAAAAAGAAATTGAAAGAG
28290252 TGGAAAAAGAAATTGAAA
1 T-GAAAAAGAAATTGAAA
28290270 AAGAGTCTGC
Statistics
Matches: 26, Mismatches: 2, Indels: 10
0.68 0.05 0.26
Matches are distributed among these distances:
15 6 0.23
17 3 0.12
18 10 0.38
19 3 0.12
21 4 0.15
ACGTcount: A:0.64, C:0.00, G:0.25, T:0.11
Consensus pattern (20 bp):
TGAAAAAGAAATTGAAAGAG
Found at i:28292082 original size:20 final size:20
Alignment explanation
Indices: 28292059--28292113 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
28292049 AGTTCAATTC
28292059 AGCTCAATTTTAGCTCAATG
1 AGCTCAATTTTAGCTCAATG
*
28292079 AGCTC-GTTCTTAGCTCAATG
1 AGCTCAATT-TTAGCTCAATG
*
28292099 AGCTCATTTTTAGCT
1 AGCTCAATTTTAGCT
28292114 TACTTTAGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
19 2 0.06
20 27 0.87
21 2 0.06
ACGTcount: A:0.24, C:0.22, G:0.16, T:0.38
Consensus pattern (20 bp):
AGCTCAATTTTAGCTCAATG
Found at i:28294822 original size:13 final size:13
Alignment explanation
Indices: 28294804--28294830 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
28294794 GAAATACGAC
28294804 AACCAGATTAATT
1 AACCAGATTAATT
28294817 AACCAGATTAATT
1 AACCAGATTAATT
28294830 A
1 A
28294831 TGATATAACT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.48, C:0.15, G:0.07, T:0.30
Consensus pattern (13 bp):
AACCAGATTAATT
Done.