Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A05
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 100714657
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 3970000 characters in sequence are not A, C, G, or T
File 110 of 318
Found at i:35258402 original size:6 final size:6
Alignment explanation
Indices: 35258373--35258424 Score: 59
Period size: 6 Copynumber: 8.3 Consensus size: 6
35258363 AGAGGAGACG
* * *
35258373 GATTTA GATTTA GATCTTT GGATTTT GATTCT GATTTT GATTTT GATTTT
1 GATTTT GATTTT GAT-TTT -GATTTT GATTTT GATTTT GATTTT GATTTT
35258423 GA
1 GA
35258425 AATTGGAGAT
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
6 33 0.80
7 5 0.12
8 3 0.07
ACGTcount: A:0.21, C:0.04, G:0.19, T:0.56
Consensus pattern (6 bp):
GATTTT
Found at i:35260753 original size:208 final size:206
Alignment explanation
Indices: 35260397--35260808 Score: 763
Period size: 208 Copynumber: 2.0 Consensus size: 206
35260387 ACTTATGAAT
35260397 ACTATGAACACTGCATATTTGTTCGAGATAAATTTACTGGCTGCTATGGCATCAACAGATGAACA
1 ACTATGAACACTGCATATTTGTTCGAGATAAATTTACTGGCTGCTATGGCATCAACAGATGAACA
35260462 AGAGATAAGTATATCAGGTAAATCCTATGTGGAAGAATGTGTGGAGATTAAAGCTTCCTTTTCAA
66 AGAGATAAGTATATCAGGTAAATCCTATGTGGAAGAATGTGTGGAGATTAAAGCTTCCTTTTCAA
35260527 CTAATCATCATTCTATGGAAAGTGTGTACCAACAATCTACCAGTAGATCAGACTTTACGAGGAGA
131 CTAATCATCATTCTATGGAAAGTGTGTACCAACAATCTACCAGTAGATCAGACTTTACGAGGAGA
35260592 AACACAAATGC
196 AACACAAATGC
35260603 ACTATGAACACTGCATATTTGTTCGAGATAAATATTTACTGGCTGCTATGGCATCAACAGACT-A
1 ACTATGAACACTGCATATTTGTTCGAGAT-AA-ATTTACTGGCTGCTATGGCATCAACAGA-TGA
* *
35260667 ACAAGAGATAAGTGTATCAGGTAAATCCTATGTGGAAGAATGTGTGGAGATTAAAGCTTCTTTTT
63 ACAAGAGATAAGTATATCAGGTAAATCCTATGTGGAAGAATGTGTGGAGATTAAAGCTTCCTTTT
*
35260732 CAACTAATCATCATTCTATGGAAAGTGTGTACCAACAATCTACTAGTAGATCAGACTTTACGAGG
128 CAACTAATCATCATTCTATGGAAAGTGTGTACCAACAATCTACCAGTAGATCAGACTTTACGAGG
35260797 AGAAACACAAAT
193 AGAAACACAAAT
35260809 ACTTCAGGTG
Statistics
Matches: 200, Mismatches: 3, Indels: 4
0.97 0.01 0.02
Matches are distributed among these distances:
206 29 0.14
207 2 0.01
208 168 0.84
209 1 0.00
ACGTcount: A:0.36, C:0.17, G:0.19, T:0.28
Consensus pattern (206 bp):
ACTATGAACACTGCATATTTGTTCGAGATAAATTTACTGGCTGCTATGGCATCAACAGATGAACA
AGAGATAAGTATATCAGGTAAATCCTATGTGGAAGAATGTGTGGAGATTAAAGCTTCCTTTTCAA
CTAATCATCATTCTATGGAAAGTGTGTACCAACAATCTACCAGTAGATCAGACTTTACGAGGAGA
AACACAAATGC
Found at i:35263024 original size:15 final size:16
Alignment explanation
Indices: 35262997--35263049 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 16
35262987 ATTTTTTTGA
*
35262997 TTTAATCTA-ATTATT
1 TTTAATATATATTATT
35263012 TTTAA-ATATATTATTT
1 TTTAATATATATTA-TT
*
35263028 TTTAATTTATATTATT
1 TTTAATATATATTATT
*
35263044 TGTAAT
1 TTTAAT
35263050 CCCTTTAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
14 2 0.06
15 9 0.28
16 14 0.44
17 7 0.22
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (16 bp):
TTTAATATATATTATT
Found at i:35263038 original size:17 final size:17
Alignment explanation
Indices: 35262997--35263044 Score: 57
Period size: 17 Copynumber: 3.0 Consensus size: 17
35262987 ATTTTTTTGA
*
35262997 TTTAATCTA-ATTA-TT
1 TTTAATATATATTATTT
35263012 TTTAA-ATATATTATTT
1 TTTAATATATATTATTT
*
35263028 TTTAATTTATATTATTT
1 TTTAATATATATTATTT
35263045 GTAATCCCTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
14 2 0.07
15 9 0.32
16 7 0.25
17 10 0.36
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (17 bp):
TTTAATATATATTATTT
Found at i:35266615 original size:31 final size:31
Alignment explanation
Indices: 35266580--35266642 Score: 92
Period size: 31 Copynumber: 2.0 Consensus size: 31
35266570 TACAATTTGG
* *
35266580 TCACTGAACTATTCAAAAGGTTTCT-TTTAAA
1 TCACTAAACTATTCAAAA-GCTTCTATTTAAA
35266611 TCACTAAACTATTCAAAAGCTTCTATTTAAA
1 TCACTAAACTATTCAAAAGCTTCTATTTAAA
35266642 T
1 T
35266643 AAAGTTCCAC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 5 0.17
31 24 0.83
ACGTcount: A:0.38, C:0.17, G:0.06, T:0.38
Consensus pattern (31 bp):
TCACTAAACTATTCAAAAGCTTCTATTTAAA
Found at i:35267319 original size:16 final size:17
Alignment explanation
Indices: 35267286--35267323 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
35267276 ATTAATAGAT
35267286 TTTTATGTAAAAAAATA
1 TTTTATGTAAAAAAATA
**
35267303 TTTTAT-TAAAATCATA
1 TTTTATGTAAAAAAATA
35267319 TTTTA
1 TTTTA
35267324 ACCAAAATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 13 0.68
17 6 0.32
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.50
Consensus pattern (17 bp):
TTTTATGTAAAAAAATA
Found at i:35268502 original size:34 final size:34
Alignment explanation
Indices: 35268459--35268526 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
35268449 ACGATTATAA
35268459 CGGTAACAAGGCACGAGGCAATCAAGAATCAAAC
1 CGGTAACAAGGCACGAGGCAATCAAGAATCAAAC
35268493 CGGTAACAAGGCACGAGGCAATCAAGAATCAAAC
1 CGGTAACAAGGCACGAGGCAATCAAGAATCAAAC
35268527 TCTTCCAACA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.44, C:0.24, G:0.24, T:0.09
Consensus pattern (34 bp):
CGGTAACAAGGCACGAGGCAATCAAGAATCAAAC
Found at i:35274981 original size:29 final size:29
Alignment explanation
Indices: 35274915--35275003 Score: 81
Period size: 30 Copynumber: 3.0 Consensus size: 29
35274905 ATCTCAAAAC
*
35274915 TATACACGAACTATTG-TTTAATGTTCAATTG
1 TATACATGAACT-TTGATTTAATG-T-AATTG
* *
35274946 TATACATGAACTTTGATTTTATGTAATTT
1 TATACATGAACTTTGATTTAATGTAATTG
* * *
35274975 TATACATGAAATTTTGATTTGATCTAATT
1 TATACATG-AACTTTGATTTAATGTAATT
35275004 CTTGTAAATT
Statistics
Matches: 50, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
29 12 0.24
30 21 0.42
31 17 0.34
ACGTcount: A:0.33, C:0.09, G:0.11, T:0.47
Consensus pattern (29 bp):
TATACATGAACTTTGATTTAATGTAATTG
Found at i:35278448 original size:21 final size:21
Alignment explanation
Indices: 35278422--35278465 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
35278412 CCAAATATTC
35278422 AACATTATATTCCATTATAGT
1 AACATTATATTCCATTATAGT
* *
35278443 AACATTATATTTCATTTTAGT
1 AACATTATATTCCATTATAGT
35278464 AA
1 AA
35278466 TATCACTAGT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.39, C:0.11, G:0.05, T:0.45
Consensus pattern (21 bp):
AACATTATATTCCATTATAGT
Found at i:35280964 original size:35 final size:35
Alignment explanation
Indices: 35280918--35280988 Score: 133
Period size: 35 Copynumber: 2.0 Consensus size: 35
35280908 TCATCAGAAA
*
35280918 AACGCCATGGAGGAGTTCTATTAAGCTGGTTTTTC
1 AACGCCATGGAGGAGTTCTATTAAGCTGATTTTTC
35280953 AACGCCATGGAGGAGTTCTATTAAGCTGATTTTTC
1 AACGCCATGGAGGAGTTCTATTAAGCTGATTTTTC
35280988 A
1 A
35280989 TATTTTTACT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (35 bp):
AACGCCATGGAGGAGTTCTATTAAGCTGATTTTTC
Found at i:35282609 original size:39 final size:38
Alignment explanation
Indices: 35282559--35282682 Score: 194
Period size: 39 Copynumber: 3.2 Consensus size: 38
35282549 GCTCTGATGA
35282559 GCTTCAGTTAGCCTCTGGGCTTCCGTTTAGCACTTATGT
1 GCTTCAGTTAGCCT-TGGGCTTCCGTTTAGCACTTATGT
* *
35282598 GCTTCACTTAGCCTATGGGCTTCCATTTAGCACTTATGT
1 GCTTCAGTTAGCCT-TGGGCTTCCGTTTAGCACTTATGT
*
35282637 GCTTCAGTTAGCCTTCGGGCTGCCGTTTAGCACTTATGT
1 GCTTCAGTTAGCCTT-GGGCTTCCGTTTAGCACTTATGT
35282676 GCTTCAG
1 GCTTCAG
35282683 CTAGATTTCG
Statistics
Matches: 78, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
38 1 0.01
39 77 0.99
ACGTcount: A:0.15, C:0.26, G:0.23, T:0.37
Consensus pattern (38 bp):
GCTTCAGTTAGCCTTGGGCTTCCGTTTAGCACTTATGT
Found at i:35282693 original size:39 final size:39
Alignment explanation
Indices: 35282575--35282697 Score: 160
Period size: 39 Copynumber: 3.2 Consensus size: 39
35282565 GTTAGCCTCT
*
35282575 GGGCTTCCGTTTAGCACTTATGTGCTTCA-CTTAGCCTAT-
1 GGGCTTCCGTTTAGCACTTATGTGCTTCAGC-TAG-CTTTC
* * *
35282614 GGGCTTCCATTTAGCACTTATGTGCTTCAGTTAGCCTTC
1 GGGCTTCCGTTTAGCACTTATGTGCTTCAGCTAGCTTTC
* *
35282653 GGGCTGCCGTTTAGCACTTATGTGCTTCAGCTAGATTTC
1 GGGCTTCCGTTTAGCACTTATGTGCTTCAGCTAGCTTTC
35282692 GGGCTT
1 GGGCTT
35282698 TAGATCACGA
Statistics
Matches: 72, Mismatches: 10, Indels: 4
0.84 0.12 0.05
Matches are distributed among these distances:
38 2 0.03
39 70 0.97
ACGTcount: A:0.15, C:0.24, G:0.24, T:0.37
Consensus pattern (39 bp):
GGGCTTCCGTTTAGCACTTATGTGCTTCAGCTAGCTTTC
Found at i:35283715 original size:13 final size:13
Alignment explanation
Indices: 35283697--35283721 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
35283687 CTCAATGGGC
35283697 AATTGGACTTGAA
1 AATTGGACTTGAA
35283710 AATTGGACTTGA
1 AATTGGACTTGA
35283722 GATCATAAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.08, G:0.24, T:0.32
Consensus pattern (13 bp):
AATTGGACTTGAA
Found at i:35284099 original size:62 final size:59
Alignment explanation
Indices: 35284027--35284140 Score: 149
Period size: 62 Copynumber: 1.9 Consensus size: 59
35284017 AGTGATTATC
* * *
35284027 TTAATATTAAATTTAAT-TTAATGTTTATCTTGTAGATAAATATTCTATTAATTTAATAAGAT
1 TTAATATTAAATTTAATCTT-ATATTTA-CCT-TA-ATAAATATTATATTAATTTAATAAGAT
*
35284089 TTAATTTTAAATTTAATCTTATATTTACCTTAATAAATATTATATTAATTTA
1 TTAATATTAAATTTAATCTTATATTTACCTTAATAAATATTATATTAATTTA
35284141 CTATTAAAGT
Statistics
Matches: 47, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
59 19 0.40
60 2 0.04
61 2 0.04
62 22 0.47
63 2 0.04
ACGTcount: A:0.40, C:0.04, G:0.04, T:0.52
Consensus pattern (59 bp):
TTAATATTAAATTTAATCTTATATTTACCTTAATAAATATTATATTAATTTAATAAGAT
Found at i:35294866 original size:7 final size:6
Alignment explanation
Indices: 35294825--35294862 Score: 51
Period size: 6 Copynumber: 6.3 Consensus size: 6
35294815 CTCTATAATT
*
35294825 AATTTA AATTT- AATCTTT AATTTA AATTTA AATTTA AA
1 AATTTA AATTTA AAT-TTA AATTTA AATTTA AATTTA AA
35294863 ATTTTAAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
5 3 0.10
6 23 0.79
7 3 0.10
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (6 bp):
AATTTA
Found at i:35294888 original size:13 final size:13
Alignment explanation
Indices: 35294870--35294912 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
35294860 AAAATTTTAA
35294870 AATATTTAGTGAT
1 AATATTTAGTGAT
*
35294883 AATATTTA-AGAT
1 AATATTTAGTGAT
35294895 --TATTTAGTGAT
1 AATATTTAGTGAT
35294906 AATATTT
1 AATATTT
35294913 TTTAAAAATC
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
10 6 0.24
11 3 0.12
12 3 0.12
13 13 0.52
ACGTcount: A:0.40, C:0.00, G:0.12, T:0.49
Consensus pattern (13 bp):
AATATTTAGTGAT
Found at i:35294889 original size:23 final size:24
Alignment explanation
Indices: 35294863--35294913 Score: 79
Period size: 23 Copynumber: 2.2 Consensus size: 24
35294853 TAAATTTAAA
35294863 ATTTTAA-AATATTTAGTGATAAT
1 ATTTTAAGAATATTTAGTGATAAT
*
35294886 A-TTTAAGATTATTTAGTGATAAT
1 ATTTTAAGAATATTTAGTGATAAT
35294909 ATTTT
1 ATTTT
35294914 TTAAAAATCT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
22 5 0.20
23 17 0.68
24 3 0.12
ACGTcount: A:0.39, C:0.00, G:0.10, T:0.51
Consensus pattern (24 bp):
ATTTTAAGAATATTTAGTGATAAT
Found at i:35295092 original size:16 final size:16
Alignment explanation
Indices: 35295071--35295102 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
35295061 TTCTATTTTA
35295071 TTTATTTATTTACTTT
1 TTTATTTATTTACTTT
*
35295087 TTTATTTTTTTACTTT
1 TTTATTTATTTACTTT
35295103 CAACCCTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.16, C:0.06, G:0.00, T:0.78
Consensus pattern (16 bp):
TTTATTTATTTACTTT
Found at i:35295290 original size:20 final size:18
Alignment explanation
Indices: 35295255--35295308 Score: 54
Period size: 20 Copynumber: 2.8 Consensus size: 18
35295245 TTATTTATCT
35295255 ATTTATTTTATTTTTTTAA
1 ATTTATTTT-TTTTTTTAA
*
35295274 ATTTATTTTTTAGTTTTTGA
1 ATTTATTTTTT--TTTTTAA
*
35295294 ATTTGTTTTTATTTT
1 ATTTATTTTT-TTTT
35295309 ATTTTATTAC
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
18 2 0.07
19 12 0.40
20 15 0.50
21 1 0.03
ACGTcount: A:0.20, C:0.00, G:0.06, T:0.74
Consensus pattern (18 bp):
ATTTATTTTTTTTTTTAA
Found at i:35298898 original size:21 final size:22
Alignment explanation
Indices: 35298872--35298912 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
35298862 TATTAATAGT
35298872 TCTCAAATTTA-AGATTTAGGG
1 TCTCAAATTTAGAGATTTAGGG
* *
35298893 TCTCAAGTTTAGAGTTTTAG
1 TCTCAAATTTAGAGATTTAG
35298913 CATTTAGTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.29, C:0.10, G:0.20, T:0.41
Consensus pattern (22 bp):
TCTCAAATTTAGAGATTTAGGG
Found at i:35304623 original size:16 final size:18
Alignment explanation
Indices: 35304588--35304625 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
35304578 ATCTTTATTT
35304588 AAATAAAATACAATAGTA
1 AAATAAAATACAATAGTA
35304606 AAATAAAATA-AA-AGTA
1 AAATAAAATACAATAGTA
35304622 AAAT
1 AAAT
35304626 TCATATAGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 8 0.40
17 2 0.10
18 10 0.50
ACGTcount: A:0.71, C:0.03, G:0.05, T:0.21
Consensus pattern (18 bp):
AAATAAAATACAATAGTA
Found at i:35306816 original size:43 final size:43
Alignment explanation
Indices: 35306662--35306820 Score: 162
Period size: 43 Copynumber: 3.7 Consensus size: 43
35306652 CAATTCCATA
* ** * *
35306662 TCCCAAATATGGTCTTACATGTTATCACAT-ATCGATGCCGATAG
1 TCCCAGATATGGTCTTACACATAATCACATAAT-GATGCCAAT-G
* * * *
35306706 -CCCAGCTATGGTCTTACACGA-AACCAAATAACGATGCCAATG
1 TCCCAGATATGGTCTTACAC-ATAATCACATAATGATGCCAATG
* *
35306748 TCCCAGATATGGTCTTATACGTAATCACATAATGATGCCAATG
1 TCCCAGATATGGTCTTACACATAATCACATAATGATGCCAATG
*
35306791 TCCCAGATATGATCTTACACATAATCACAT
1 TCCCAGATATGGTCTTACACATAATCACAT
35306821 CTCGTTAATC
Statistics
Matches: 93, Mismatches: 18, Indels: 9
0.77 0.15 0.08
Matches are distributed among these distances:
42 1 0.01
43 91 0.98
44 1 0.01
ACGTcount: A:0.33, C:0.25, G:0.14, T:0.28
Consensus pattern (43 bp):
TCCCAGATATGGTCTTACACATAATCACATAATGATGCCAATG
Found at i:35310216 original size:6 final size:6
Alignment explanation
Indices: 35310198--35310365 Score: 94
Period size: 6 Copynumber: 27.3 Consensus size: 6
35310188 AAGAAACATT
* *
35310198 ATCAGA A-CTAGA ATCAGA ATCAGA ATTAGA ATCAGA ACCAGA ATCAGA
1 ATCAGA ATC-AGA ATCAGA ATCAGA ATCAGA ATCAGA ATCAGA ATCAGA
* * * * * * *
35310246 ATTAG- GTGACAGA ATCAGA ATCAGA GTCAGT ATTAGGTA A-CCGA ATCAAA
1 ATCAGA AT--CAGA ATCAGA ATCAGA ATCAGA ATCA-G-A ATCAGA ATCAGA
* * * *
35310296 ATCAAA ATCAGC ATCAGGTA A-CAGA ATCAAA ATCAGA ATCAGT ATCAGGTA
1 ATCAGA ATCAGA ATCA-G-A ATCAGA ATCAGA ATCAGA ATCAGA ATCA-G-A
*
35310347 A-CAGA ATCAAA ATCAGA AT
1 ATCAGA ATCAGA ATCAGA AT
35310366 GTGAATGCAA
Statistics
Matches: 122, Mismatches: 26, Indels: 28
0.69 0.15 0.16
Matches are distributed among these distances:
5 8 0.07
6 100 0.82
7 10 0.08
8 4 0.03
ACGTcount: A:0.48, C:0.16, G:0.17, T:0.19
Consensus pattern (6 bp):
ATCAGA
Found at i:35310263 original size:31 final size:31
Alignment explanation
Indices: 35310225--35310365 Score: 183
Period size: 31 Copynumber: 4.5 Consensus size: 31
35310215 AATCAGAATT
* * * * *
35310225 AGAATCAGAACCAGAATCAGAATTAGGTGAC
1 AGAATCAAAATCAGAATCAGTATCAGGTAAC
* * *
35310256 AGAATCAGAATCAGAGTCAGTATTAGGTAAC
1 AGAATCAAAATCAGAATCAGTATCAGGTAAC
* * *
35310287 CGAATCAAAATCAAAATCAGCATCAGGTAAC
1 AGAATCAAAATCAGAATCAGTATCAGGTAAC
35310318 AGAATCAAAATCAGAATCAGTATCAGGTAAC
1 AGAATCAAAATCAGAATCAGTATCAGGTAAC
35310349 AGAATCAAAATCAGAAT
1 AGAATCAAAATCAGAAT
35310366 GTGAATGCAA
Statistics
Matches: 97, Mismatches: 13, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 97 1.00
ACGTcount: A:0.48, C:0.16, G:0.18, T:0.18
Consensus pattern (31 bp):
AGAATCAAAATCAGAATCAGTATCAGGTAAC
Found at i:35310565 original size:26 final size:27
Alignment explanation
Indices: 35310501--35310574 Score: 96
Period size: 27 Copynumber: 2.8 Consensus size: 27
35310491 GCTCAGTTAT
* *
35310501 CAGATATTGTGACAGAGTCACCAGATA
1 CAGATATTGTGGCAGAGCCACCAGATA
35310528 CAGATATTGTGGCAGAGCCACCAGA-A
1 CAGATATTGTGGCAGAGCCACCAGATA
* * *
35310554 TAGATAATGTGGCAAAGCCAC
1 CAGATATTGTGGCAGAGCCAC
35310575 TTAACAAAAT
Statistics
Matches: 42, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
26 19 0.45
27 23 0.55
ACGTcount: A:0.36, C:0.20, G:0.24, T:0.19
Consensus pattern (27 bp):
CAGATATTGTGGCAGAGCCACCAGATA
Found at i:35310761 original size:22 final size:22
Alignment explanation
Indices: 35310733--35310797 Score: 69
Period size: 22 Copynumber: 3.0 Consensus size: 22
35310723 GCAAATACAT
*
35310733 TTGGCACACAGCCATAATCAGG
1 TTGGCACAAAGCCATAATCAGG
* *
35310755 TTGGCACAGAGCCAT-ATGTAGG
1 TTGGCACAAAGCCATAAT-CAGG
**
35310777 TTAACACAAAGCCATAATCAG
1 TTGGCACAAAGCCATAATCAG
35310798 AAGGCTTTAA
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
21 2 0.06
22 31 0.89
23 2 0.06
ACGTcount: A:0.35, C:0.23, G:0.22, T:0.20
Consensus pattern (22 bp):
TTGGCACAAAGCCATAATCAGG
Found at i:35311281 original size:27 final size:27
Alignment explanation
Indices: 35311224--35311553 Score: 448
Period size: 27 Copynumber: 12.3 Consensus size: 27
35311214 GGGGCAAAAT
* * *
35311224 GGTAATTTTACCCCACA-AGGTA-TCTC
1 GGTAATTCTACCCTACAGGGGTATTC-C
* **
35311250 GGTAATTCCACCCTACAGGGGTATTTT
1 GGTAATTCTACCCTACAGGGGTATTCC
* *
35311277 AGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTCC
* *
35311304 AGTAATTCTACCCTACAAGGGTATTCC
1 GGTAATTCTACCCTACAGGGGTATTCC
35311331 GGTAATTCTACCCTACAGGGGTATTCC
1 GGTAATTCTACCCTACAGGGGTATTCC
*
35311358 GGTAATTCTACCCTACAGGGGTATTCT
1 GGTAATTCTACCCTACAGGGGTATTCC
35311385 GGTAATTCTACCCTACAGGGGTATTCC
1 GGTAATTCTACCCTACAGGGGTATTCC
* *
35311412 GGTAATTCTACCCTACAGGGATATTTC
1 GGTAATTCTACCCTACAGGGGTATTCC
* * *
35311439 GGTAATTCTACCTTACAGAGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTCC
* *
35311466 GGTAATTCTACCCTATAGGGATATTCC
1 GGTAATTCTACCCTACAGGGGTATTCC
*
35311493 GGTAATTCTACCTTACAGGGGTATTCC
1 GGTAATTCTACCCTACAGGGGTATTCC
* *
35311520 GGTAATTCTACCCTATAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTCC
35311547 GGTAATT
1 GGTAATT
35311554 TTGTAAATCG
Statistics
Matches: 271, Mismatches: 31, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
26 14 0.05
27 256 0.94
28 1 0.00
ACGTcount: A:0.25, C:0.22, G:0.20, T:0.33
Consensus pattern (27 bp):
GGTAATTCTACCCTACAGGGGTATTCC
Found at i:35311633 original size:27 final size:27
Alignment explanation
Indices: 35311603--35311680 Score: 77
Period size: 27 Copynumber: 2.9 Consensus size: 27
35311593 GGTACTTTGG
* *
35311603 TAATTCTATAAGTCGAGGGTATTTCAA
1 TAATTCTACAAGTCAAGGGTATTTCAA
* * *
35311630 TAATTTTACAGGTCAAGGGTATTTCAG
1 TAATTCTACAAGTCAAGGGTATTTCAA
* *
35311657 TAATT-TCACAAATCAAGGATATTT
1 TAATTCT-ACAAGTCAAGGGTATTT
35311681 TAGTACATTT
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
26 1 0.02
27 41 0.98
ACGTcount: A:0.35, C:0.12, G:0.17, T:0.37
Consensus pattern (27 bp):
TAATTCTACAAGTCAAGGGTATTTCAA
Found at i:35311685 original size:27 final size:26
Alignment explanation
Indices: 35311618--35311821 Score: 151
Period size: 27 Copynumber: 7.6 Consensus size: 26
35311608 CTATAAGTCG
* * **
35311618 AGGGTATTTCAATAATTTTACAGGTCA
1 AGGGTATTTTAGTAATTTTACA-AACA
* *
35311645 AGGGTATTTCAGTAATTTCACAAATCA
1 AGGGTATTTTAGTAATTTTACAAA-CA
*
35311672 AGGATATTTTAGTACA-TTTACAAACTA
1 AGGGTATTTTAGTA-ATTTTACAAAC-A
* *
35311699 AGGCTATTTT-GATGATTTTACAAACCA
1 AGGGTATTTTAG-TAATTTTACAAA-CA
* *
35311726 GGGGTATTTTGGTAATTTTACAAACCA
1 AGGGTATTTTAGTAATTTTACAAA-CA
* * * *
35311753 GGGGTATTTTGGTGATTTTATAAACTA
1 AGGGTATTTTAGTAATTTTACAAAC-A
* *
35311780 AGGGTATTCTAGTAATTTTACAAACC
1 AGGGTATTTTAGTAATTTTACAAACA
*
35311806 AGTGGTATTTTGGTAA
1 AG-GGTATTTTAGTAA
35311822 ACTAAAGTAT
Statistics
Matches: 146, Mismatches: 22, Indels: 18
0.78 0.12 0.10
Matches are distributed among these distances:
26 6 0.04
27 137 0.94
28 3 0.02
ACGTcount: A:0.33, C:0.11, G:0.19, T:0.38
Consensus pattern (26 bp):
AGGGTATTTTAGTAATTTTACAAACA
Found at i:35311731 original size:81 final size:81
Alignment explanation
Indices: 35311646--35311815 Score: 191
Period size: 81 Copynumber: 2.1 Consensus size: 81
35311636 TACAGGTCAA
* *
35311646 GGGTATTTCAGTAATTTCACAAATCAAGGATATTTTAGT-ACATTTACAAACTAAGGCTATT-TT
1 GGGTATTTCAGTAATTTCACAAACCAAGGATATTTTAGTGA-ATTTACAAACTAAGGCTATTCTA
*
35311709 GATGATTTTACAAACCAG
65 G-TAATTTTACAAACCAG
** * * * * * * *
35311727 GGGTATTTTGGTAATTTTACAAACCAGGGGTATTTTGGTGATTTTATAAACTAAGGGTATTCTAG
1 GGGTATTTCAGTAATTTCACAAACCAAGGATATTTTAGTGAATTTACAAACTAAGGCTATTCTAG
35311792 TAATTTTACAAACCAG
66 TAATTTTACAAACCAG
*
35311808 TGGTATTT
1 GGGTATTT
35311816 TGGTAAACTA
Statistics
Matches: 74, Mismatches: 13, Indels: 4
0.81 0.14 0.04
Matches are distributed among these distances:
81 71 0.96
82 3 0.04
ACGTcount: A:0.32, C:0.11, G:0.18, T:0.38
Consensus pattern (81 bp):
GGGTATTTCAGTAATTTCACAAACCAAGGATATTTTAGTGAATTTACAAACTAAGGCTATTCTAG
TAATTTTACAAACCAG
Found at i:35311807 original size:54 final size:54
Alignment explanation
Indices: 35311618--35311819 Score: 190
Period size: 54 Copynumber: 3.7 Consensus size: 54
35311608 CTATAAGTCG
* * *** * ** * * *
35311618 AGGGTATTTCAATAATTTTACAGGTCAAGGGTATTTCAGTAATTTCACAAATCA
1 AGGGTATTTTAGTAATTTTACAAACCAGGGGTATTTTGGTGATTTTACAAACCA
* * * * *
35311672 AGGATATTTTAGTACA-TTTACAAACTAAGGCTATTTTGATGATTTTACAAACCA
1 AGGGTATTTTAGTA-ATTTTACAAACCAGGGGTATTTTGGTGATTTTACAAACCA
* * * *
35311726 GGGGTATTTTGGTAATTTTACAAACCAGGGGTATTTTGGTGATTTTATAAACTA
1 AGGGTATTTTAGTAATTTTACAAACCAGGGGTATTTTGGTGATTTTACAAACCA
* *
35311780 AGGGTATTCTAGTAATTTTACAAACCAGTGGTATTTTGGT
1 AGGGTATTTTAGTAATTTTACAAACCAGGGGTATTTTGGT
35311820 AAACTAAAGT
Statistics
Matches: 119, Mismatches: 27, Indels: 4
0.79 0.18 0.03
Matches are distributed among these distances:
53 1 0.01
54 117 0.98
55 1 0.01
ACGTcount: A:0.32, C:0.11, G:0.19, T:0.38
Consensus pattern (54 bp):
AGGGTATTTTAGTAATTTTACAAACCAGGGGTATTTTGGTGATTTTACAAACCA
Found at i:35313815 original size:6 final size:6
Alignment explanation
Indices: 35313766--35313933 Score: 103
Period size: 6 Copynumber: 27.3 Consensus size: 6
35313756 AAGAAACATT
* * *
35313766 ATCAGA A-CTAGA ATCAGA ATCAGA ATTAGA ATTAGA ACCAGA ATCAGA
1 ATCAGA ATC-AGA ATCAGA ATCAGA ATCAGA ATCAGA ATCAGA ATCAGA
* * * * * *
35313814 ATTA-A GTGACAGA ATCAAA ATCAGA ATCAGT ATCAGGTA A-CCGA ATCAAA
1 ATCAGA AT--CAGA ATCAGA ATCAGA ATCAGA ATCA-G-A ATCAGA ATCAGA
* * *
35313864 ATCAGA ATCAGC ATCAGGTA A-CAGA ATCAAA ATCAGA ATCAGT ATCAGGTA
1 ATCAGA ATCAGA ATCA-G-A ATCAGA ATCAGA ATCAGA ATCAGA ATCA-G-A
*
35313915 A-CAGA ATCAAA ATCAGA AT
1 ATCAGA ATCAGA ATCAGA AT
35313934 GTGAATGCAA
Statistics
Matches: 124, Mismatches: 24, Indels: 28
0.70 0.14 0.16
Matches are distributed among these distances:
5 9 0.07
6 100 0.81
7 10 0.08
8 5 0.04
ACGTcount: A:0.49, C:0.16, G:0.16, T:0.19
Consensus pattern (6 bp):
ATCAGA
Found at i:35313839 original size:31 final size:31
Alignment explanation
Indices: 35313804--35313933 Score: 206
Period size: 31 Copynumber: 4.2 Consensus size: 31
35313794 GAATTAGAAC
* * * *
35313804 CAGAATCAGAATTAAGTGACAGAATCAAAAT
1 CAGAATCAGTATCAGGTAACAGAATCAAAAT
*
35313835 CAGAATCAGTATCAGGTAACCGAATCAAAAT
1 CAGAATCAGTATCAGGTAACAGAATCAAAAT
*
35313866 CAGAATCAGCATCAGGTAACAGAATCAAAAT
1 CAGAATCAGTATCAGGTAACAGAATCAAAAT
35313897 CAGAATCAGTATCAGGTAACAGAATCAAAAT
1 CAGAATCAGTATCAGGTAACAGAATCAAAAT
35313928 CAGAAT
1 CAGAAT
35313934 GTGAATGCAA
Statistics
Matches: 91, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 91 1.00
ACGTcount: A:0.48, C:0.17, G:0.16, T:0.18
Consensus pattern (31 bp):
CAGAATCAGTATCAGGTAACAGAATCAAAAT
Found at i:35314128 original size:26 final size:27
Alignment explanation
Indices: 35314066--35314138 Score: 103
Period size: 26 Copynumber: 2.7 Consensus size: 27
35314056 CTCAGTTATC
* *
35314066 AGATATTGTGACAGAGTCACCAGAAAT
1 AGATATTGTGGCAGAGCCACCAGAAAT
35314093 AGATATTGTGGCAGAGCCACCAG-AAT
1 AGATATTGTGGCAGAGCCACCAGAAAT
* *
35314119 AGATAATGTGGCAAAGCCAC
1 AGATATTGTGGCAGAGCCAC
35314139 TTAACAGAAT
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
26 21 0.50
27 21 0.50
ACGTcount: A:0.38, C:0.18, G:0.25, T:0.19
Consensus pattern (27 bp):
AGATATTGTGGCAGAGCCACCAGAAAT
Found at i:35314325 original size:22 final size:22
Alignment explanation
Indices: 35314297--35314361 Score: 69
Period size: 22 Copynumber: 3.0 Consensus size: 22
35314287 GTAAATACGT
*
35314297 TTGGCACACAGCCATAATCAGG
1 TTGGCACAAAGCCATAATCAGG
* *
35314319 TTGGCACAGAGCCAT-ATGTAGG
1 TTGGCACAAAGCCATAAT-CAGG
**
35314341 TTAACACAAAGCCATAATCAG
1 TTGGCACAAAGCCATAATCAG
35314362 AAGGCTTTAA
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
21 2 0.06
22 31 0.89
23 2 0.06
ACGTcount: A:0.35, C:0.23, G:0.22, T:0.20
Consensus pattern (22 bp):
TTGGCACAAAGCCATAATCAGG
Found at i:35314844 original size:27 final size:27
Alignment explanation
Indices: 35314788--35315090 Score: 371
Period size: 27 Copynumber: 11.3 Consensus size: 27
35314778 GGGGCAAAAT
* * * *
35314788 GGTAATTTTACCCCACA-AGGTATCTC
1 GGTAATTCTACCCTACAGGGGTATTTC
* * *
35314814 AGTAATTCCACCCTACAGGGGTATTTT
1 GGTAATTCTACCCTACAGGGGTATTTC
* *
35314841 AGTAATTCTACCCTACAAGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
* * *
35314868 AGTAATTCTACCTTACAGGGGTATTCC
1 GGTAATTCTACCCTACAGGGGTATTTC
*
35314895 GGTAATTCTACCCTATAGGGGTA-TTC
1 GGTAATTCTACCCTACAGGGGTATTTC
*
35314921 TGGTAATTCTACCCTATAGGGGTA-TTC
1 -GGTAATTCTACCCTACAGGGGTATTTC
*
35314948 TGGTAATTCTACCCTACAGGGGTATTCC
1 -GGTAATTCTACCCTACAGGGGTATTTC
*
35314976 GGTAATTCTACCCTACAGGGATATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
* *
35315003 GGTAATTCTACCTTACAGAGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
35315030 GGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
**
35315057 GGTAATTCTACCCTTTAGGGGTATTTTC
1 GGTAATTCTACCCTACAGGGGTA-TTTC
35315085 -GTAATT
1 GGTAATT
35315091 TTGTAAATCG
Statistics
Matches: 245, Mismatches: 28, Indels: 7
0.88 0.10 0.03
Matches are distributed among these distances:
26 15 0.06
27 224 0.91
28 6 0.02
ACGTcount: A:0.24, C:0.21, G:0.19, T:0.35
Consensus pattern (27 bp):
GGTAATTCTACCCTACAGGGGTATTTC
Found at i:35315105 original size:27 final size:26
Alignment explanation
Indices: 35315075--35315231 Score: 100
Period size: 27 Copynumber: 5.8 Consensus size: 26
35315065 TACCCTTTAG
**
35315075 GGGTATTTTCGTAATTTTGTAAATCGA
1 GGGTA-TTTCGTAATTTTACAAATCGA
** * * ** *
35315102 GGGTAAAATGGTAATTCTGTAAATCAA
1 GGGT-ATTTCGTAATTTTACAAATCGA
* * *
35315129 GGGTACTTTGGTAATTCTACAAGTCGA
1 GGGTA-TTTCGTAATTTTACAAATCGA
* **
35315156 GGGTATTTCAATAATTTTACAGGTCGA
1 GGGTATTTC-GTAATTTTACAAATCGA
35315183 GGGTATTTCAGTAATTTTACAAATC-A
1 GGGTATTTC-GTAATTTTACAAATCGA
*
35315209 GGGATATTTTGGTAATTTTACAA
1 GGG-TA-TTTCGTAATTTTACAA
35315232 GCTAGGGATA
Statistics
Matches: 106, Mismatches: 19, Indels: 10
0.79 0.14 0.07
Matches are distributed among these distances:
26 8 0.08
27 94 0.89
28 4 0.04
ACGTcount: A:0.31, C:0.10, G:0.22, T:0.38
Consensus pattern (26 bp):
GGGTATTTCGTAATTTTACAAATCGA
Found at i:35315115 original size:81 final size:80
Alignment explanation
Indices: 35314869--35315119 Score: 237
Period size: 81 Copynumber: 3.1 Consensus size: 80
35314859 GGGTATTTCA
* * *
35314869 GTAATTCTACCTTACAGGGGTATTCCGGTAATTCTACCCTATAGGGGTATTCTGGTAATTCTACC
1 GTAATTCTACCCTACAGGGGTATTCCGGTAATTCTACCCTATAGGGGTATTTTCGTAATTCT---
* * * *
35314934 CTATA-G-GGGTATTCTG
63 TTAAATGAGGGTAATATG
* *
35314950 GTAATTCTACCCTACAGGGGTATTCCGGTAATTCTACCCTACAGGGATA-TTTCGGTAATTCTAC
1 GTAATTCTACCCTACAGGGGTATTCCGGTAATTCTACCCTATAGGGGTATTTTC-GTAATTCT--
* *
35315014 CTTACA-GA-GGT-ATTTCG
63 -TTAAATGAGGGTAATAT-G
* *
35315031 GTAATTCTACCCTACAGGGGTATTTCGGTAATTCTACCCTTTAGGGGTATTTTCGTAATT-TTGT
1 GTAATTCTACCCTACAGGGGTATTCCGGTAATTCTACCCTATAGGGGTATTTTCGTAATTCTT-T
*
35315095 AAATCGAGGGTAAAATG
65 AAAT-GAGGGTAATATG
35315112 GTAATTCT
1 GTAATTCT
35315120 GTAAATCAAG
Statistics
Matches: 145, Mismatches: 16, Indels: 18
0.81 0.09 0.10
Matches are distributed among these distances:
77 1 0.01
78 3 0.02
80 7 0.05
81 128 0.88
82 6 0.04
ACGTcount: A:0.24, C:0.19, G:0.21, T:0.36
Consensus pattern (80 bp):
GTAATTCTACCCTACAGGGGTATTCCGGTAATTCTACCCTATAGGGGTATTTTCGTAATTCTTTA
AATGAGGGTAATATG
Found at i:35315238 original size:27 final size:26
Alignment explanation
Indices: 35315128--35315275 Score: 102
Period size: 27 Copynumber: 5.6 Consensus size: 26
35315118 CTGTAAATCA
* * *
35315128 AGGGTACTTTGGTAATTCTACAAGTCG
1 AGGGTATTTTGGTAATTTTACAAG-CT
*** * *
35315155 AGGGTATTTCAATAATTTTACAGGTCG
1 AGGGTATTTTGGTAATTTTACAAG-CT
** *
35315182 AGGGTATTTCAGTAATTTTACAA-AT
1 AGGGTATTTTGGTAATTTTACAAGCT
35315207 CAGGGATATTTTGGTAATTTTACAAGCT
1 -AGGG-TATTTTGGTAATTTTACAAGCT
* * **
35315235 AGGG-ATATTGATAATTTTACAAATT
1 AGGGTATTTTGGTAATTTTACAAGCT
35315260 AGCGGTATTTTGGTAA
1 AG-GGTATTTTGGTAA
35315276 ACTAAAGTAT
Statistics
Matches: 97, Mismatches: 19, Indels: 10
0.77 0.15 0.08
Matches are distributed among these distances:
25 19 0.20
26 6 0.06
27 71 0.73
28 1 0.01
ACGTcount: A:0.31, C:0.09, G:0.22, T:0.38
Consensus pattern (26 bp):
AGGGTATTTTGGTAATTTTACAAGCT
Found at i:35327195 original size:25 final size:24
Alignment explanation
Indices: 35327167--35327228 Score: 81
Period size: 25 Copynumber: 2.5 Consensus size: 24
35327157 ATTATCAGGC
35327167 TGCTAACACTAGCTTCGGATT-AGGT
1 TGCTAACACTAGCTT-GG-TTAAGGT
*
35327192 TGCTAACACTAGCTTGGTTCAATGT
1 TGCTAACACTAGCTTGGTT-AAGGT
35327217 TGCTAACACTAG
1 TGCTAACACTAG
35327229 TTTTAGAGAA
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
23 2 0.06
24 2 0.06
25 30 0.88
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.32
Consensus pattern (24 bp):
TGCTAACACTAGCTTGGTTAAGGT
Found at i:35329099 original size:39 final size:40
Alignment explanation
Indices: 35329045--35329126 Score: 130
Period size: 40 Copynumber: 2.1 Consensus size: 40
35329035 CACCTTGAGA
*
35329045 ATTCAGTACCCATTTGAAG-AAAACCATGAAAAGGAAAAG
1 ATTCAATACCCATTTGAAGAAAAACCATGAAAAGGAAAAG
* *
35329084 ATTCAATATCCATTTGAAGAAAAACCATGAAAAGGATAAG
1 ATTCAATACCCATTTGAAGAAAAACCATGAAAAGGAAAAG
35329124 ATT
1 ATT
35329127 TGGAAAGGGA
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
39 17 0.44
40 22 0.56
ACGTcount: A:0.49, C:0.13, G:0.16, T:0.22
Consensus pattern (40 bp):
ATTCAATACCCATTTGAAGAAAAACCATGAAAAGGAAAAG
Found at i:35331236 original size:159 final size:159
Alignment explanation
Indices: 35330994--35331601 Score: 953
Period size: 159 Copynumber: 3.9 Consensus size: 159
35330984 TTTTTCCGTC
* * * *
35330994 TTTTGGGAAAACGGCAACGTTTTATAGTATATT-T-AATACAGAATTC--A--AAGAAGTCAACG
1 TTTTGGGAAAACGGCAACGTTTTATATTAT-TTATAAAAACAGAACTCAGAGTAAGAAATCAACG
35331053 GCCTATTAGCTCAGCTGGTTAGAGCGTCGTGCTAATAACGCGAAGGTCGCAGGTTCGAGACCTGC
65 GCCTATTAGCTCAGCTGGTTAGAGCGTCGTGCTAATAACGCGAAGGTCGCAGGTTCGAGACCTGC
35331118 ATGGGCCAGTGAAAGCAACTGT-CTCTAATT
130 ATGGGCCAGTGAAAGCAACT-TCCTCTAATT
35331148 TTTTGGGAAAACGGCAACGTTTTATATTATTTATAAAAACAGAACTCAGAGTAAGAAATCAACGG
1 TTTTGGGAAAACGGCAACGTTTTATATTATTTATAAAAACAGAACTCAGAGTAAGAAATCAACGG
35331213 CCTATTAGCTCAGCTGGTTAGAGCGTCGTGCTAATAACGCGAAGGTCGCAGGTTCGAGACCTGCA
66 CCTATTAGCTCAGCTGGTTAGAGCGTCGTGCTAATAACGCGAAGGTCGCAGGTTCGAGACCTGCA
35331278 TGGGCCAGTGAAAGCAACTTCCTCTAATT
131 TGGGCCAGTGAAAGCAACTTCCTCTAATT
* * * *
35331307 TTTTGGGAGAACGGAAACGTTTTATATTATTTATAAAAACAAAACTCAGAGTAAGATATCAACGG
1 TTTTGGGAAAACGGCAACGTTTTATATTATTTATAAAAACAGAACTCAGAGTAAGAAATCAACGG
* *
35331372 CCTATTAGCTCAGCTGGTTAGATCGTCGTGCTAATAACGCGAAGGTCGCAGGTTCGGGACCTGCA
66 CCTATTAGCTCAGCTGGTTAGAGCGTCGTGCTAATAACGCGAAGGTCGCAGGTTCGAGACCTGCA
* *
35331437 TGGGCCACTAAAAGCAACTTCCTCTAATT
131 TGGGCCAGTGAAAGCAACTTCCTCTAATT
* * * ** ** *
35331466 TTTTGGGAAAACGGCAACGTTTTATATTATCTATTAAAA-AGAATTTTGAGTAAGAAGCCAATGG
1 TTTTGGGAAAACGGCAACGTTTTATATTATTTATAAAAACAGAACTCAGAGTAAGAAATCAACGG
*
35331530 CCTATTAGCTCAGTTGGTTAGAGCGTCGTGCTAATAACGCGAAGGTCGCAGGTTCGAGACCTGCA
66 CCTATTAGCTCAGCTGGTTAGAGCGTCGTGCTAATAACGCGAAGGTCGCAGGTTCGAGACCTGCA
35331595 TGGGCCA
131 TGGGCCA
35331602 CTTAAGATAT
Statistics
Matches: 420, Mismatches: 27, Indels: 10
0.92 0.06 0.02
Matches are distributed among these distances:
153 2 0.00
154 30 0.07
155 10 0.02
157 1 0.00
158 87 0.21
159 290 0.69
ACGTcount: A:0.31, C:0.19, G:0.24, T:0.27
Consensus pattern (159 bp):
TTTTGGGAAAACGGCAACGTTTTATATTATTTATAAAAACAGAACTCAGAGTAAGAAATCAACGG
CCTATTAGCTCAGCTGGTTAGAGCGTCGTGCTAATAACGCGAAGGTCGCAGGTTCGAGACCTGCA
TGGGCCAGTGAAAGCAACTTCCTCTAATT
Found at i:35332328 original size:43 final size:43
Alignment explanation
Indices: 35332267--35332352 Score: 145
Period size: 43 Copynumber: 2.0 Consensus size: 43
35332257 ACGGTATTTG
** *
35332267 ATCGGCAAACCTTGATAAGGATGTCAGCCAGGCATTGTAAAAA
1 ATCGGCAAACCTTGATAAGGAAATCAGCCAGGCATTATAAAAA
35332310 ATCGGCAAACCTTGATAAGGAAATCAGCCAGGCATTATAAAAA
1 ATCGGCAAACCTTGATAAGGAAATCAGCCAGGCATTATAAAAA
35332353 TTAAATTCAT
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 40 1.00
ACGTcount: A:0.41, C:0.19, G:0.21, T:0.20
Consensus pattern (43 bp):
ATCGGCAAACCTTGATAAGGAAATCAGCCAGGCATTATAAAAA
Found at i:35336692 original size:17 final size:18
Alignment explanation
Indices: 35336670--35336705 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
35336660 TAAATGAGTT
35336670 AATTAGGAT-TAAATTGG
1 AATTAGGATATAAATTGG
*
35336687 AATTAGGGTATAAATTGG
1 AATTAGGATATAAATTGG
35336705 A
1 A
35336706 TAGAAATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.42, C:0.00, G:0.25, T:0.33
Consensus pattern (18 bp):
AATTAGGATATAAATTGG
Found at i:35337025 original size:18 final size:18
Alignment explanation
Indices: 35337002--35337038 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
35336992 TTTGTGATCA
*
35337002 AAATTGAAGGTGAAAGTG
1 AAATTGAAAGTGAAAGTG
*
35337020 AAATTGAAATTGAAAGTG
1 AAATTGAAAGTGAAAGTG
35337038 A
1 A
35337039 CAGGAATTGC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.49, C:0.00, G:0.27, T:0.24
Consensus pattern (18 bp):
AAATTGAAAGTGAAAGTG
Found at i:35338961 original size:198 final size:198
Alignment explanation
Indices: 35338613--35339009 Score: 677
Period size: 198 Copynumber: 2.0 Consensus size: 198
35338603 ACTAGTCACA
*
35338613 GCATTTTACTCGGTGAGATTGTTCCAATATAACTCATTTGTGGTGCATGATACAATAGGTGTTGA
1 GCATGTTACTCGGTGAGATTGTTCCAATATAACTCATTTGTGGTGCATGATACAATAGGTGTTGA
*
35338678 GTTGATGGTTATACACTCAAGATCTTTTAGTTAAATAACTCCCCAAGGAGTTATGCTTAAGTTAG
66 GTTGATGGTTATACACTCAAGATCTTTTAGTTAAATAACTCCCCAAAGAGTTATGCTTAAGTTAG
** *
35338743 AAAGATGGTCAAACGTTACACAATTATTAGTACATGCAAATGCCTAAGGAATTAGGCTCGTCTAA
131 AAAGATCATCAAACGTTACACAATTATTAGTACATGCAAATGCCTAAGGAATTAAGCTCGTCTAA
35338808 TTG
196 TTG
*
35338811 GCATGTTACTCGGTGAGATTGTTCCAATATAACTCATTTGTGGTGCATGATACGATAGGTGTTGA
1 GCATGTTACTCGGTGAGATTGTTCCAATATAACTCATTTGTGGTGCATGATACAATAGGTGTTGA
*
35338876 GTTGATGGTTATACACTCAAGATCTTTTAGTTAAATAACTTCCCAAAGAGTTATGCTTAAGTTAG
66 GTTGATGGTTATACACTCAAGATCTTTTAGTTAAATAACTCCCCAAAGAGTTATGCTTAAGTTAG
* ** * * *
35338941 AAAGATCATCAAATGTTACACGGTTATTAGTACGTGCGAATGCCTAAGGAATTAAGTTCGTCTAA
131 AAAGATCATCAAACGTTACACAATTATTAGTACATGCAAATGCCTAAGGAATTAAGCTCGTCTAA
35339006 TTG
196 TTG
35339009 G
1 G
35339010 ATGAAATTAT
Statistics
Matches: 186, Mismatches: 13, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
198 186 1.00
ACGTcount: A:0.31, C:0.15, G:0.21, T:0.34
Consensus pattern (198 bp):
GCATGTTACTCGGTGAGATTGTTCCAATATAACTCATTTGTGGTGCATGATACAATAGGTGTTGA
GTTGATGGTTATACACTCAAGATCTTTTAGTTAAATAACTCCCCAAAGAGTTATGCTTAAGTTAG
AAAGATCATCAAACGTTACACAATTATTAGTACATGCAAATGCCTAAGGAATTAAGCTCGTCTAA
TTG
Found at i:35339932 original size:47 final size:47
Alignment explanation
Indices: 35339879--35339972 Score: 179
Period size: 47 Copynumber: 2.0 Consensus size: 47
35339869 TTATATTTTC
35339879 TTTCAAATCACTTTTAAAATGGACAAAAATTTAATTTTTTTAACTTT
1 TTTCAAATCACTTTTAAAATGGACAAAAATTTAATTTTTTTAACTTT
*
35339926 TTTCAAATCACTTTTAAAATGGACAAAAATTTATTTTTTTTAACTTT
1 TTTCAAATCACTTTTAAAATGGACAAAAATTTAATTTTTTTAACTTT
35339973 ATTGACATAA
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 46 1.00
ACGTcount: A:0.37, C:0.11, G:0.04, T:0.48
Consensus pattern (47 bp):
TTTCAAATCACTTTTAAAATGGACAAAAATTTAATTTTTTTAACTTT
Found at i:35342025 original size:25 final size:25
Alignment explanation
Indices: 35341997--35342047 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
35341987 AAATTGCTCC
35341997 CTAACTCAAAGTATCAATGCTTATA
1 CTAACTCAAAGTATCAATGCTTATA
35342022 CTAACTCAAAGTATCAATGCTTATA
1 CTAACTCAAAGTATCAATGCTTATA
35342047 C
1 C
35342048 CAAGAATCGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.39, C:0.22, G:0.08, T:0.31
Consensus pattern (25 bp):
CTAACTCAAAGTATCAATGCTTATA
Found at i:35343790 original size:26 final size:26
Alignment explanation
Indices: 35343754--35343863 Score: 184
Period size: 26 Copynumber: 4.2 Consensus size: 26
35343744 TGATACAAAT
35343754 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
35343780 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
* *
35343806 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCA
* *
35343832 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCA
35343858 TGATAA
1 TGATAA
35343864 GAATTTCATG
Statistics
Matches: 82, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 82 1.00
ACGTcount: A:0.34, C:0.05, G:0.25, T:0.36
Consensus pattern (26 bp):
TGATAATAGGTTAGGTAAATGTTCCA
Found at i:35351421 original size:13 final size:13
Alignment explanation
Indices: 35351403--35351427 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
35351393 TCCTCTTATA
35351403 TTAATAAATTGAG
1 TTAATAAATTGAG
35351416 TTAATAAATTGA
1 TTAATAAATTGA
35351428 ACTCAATTGG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.00, G:0.12, T:0.40
Consensus pattern (13 bp):
TTAATAAATTGAG
Found at i:35353068 original size:11 final size:11
Alignment explanation
Indices: 35353052--35353078 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
35353042 ACCTATCTCT
35353052 TAATATTTACA
1 TAATATTTACA
35353063 TAATATTTACA
1 TAATATTTACA
35353074 TAATA
1 TAATA
35353079 AACTAAATCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.44
Consensus pattern (11 bp):
TAATATTTACA
Found at i:35353492 original size:15 final size:16
Alignment explanation
Indices: 35353468--35353506 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
35353458 TAATTCATGC
*
35353468 AAAATAATAA-TATTT
1 AAAATAATAATTAATT
*
35353483 AAAATGATAATTAATT
1 AAAATAATAATTAATT
35353499 AAAATAAT
1 AAAATAAT
35353507 TAAAATATAC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
15 9 0.45
16 11 0.55
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.36
Consensus pattern (16 bp):
AAAATAATAATTAATT
Found at i:35358156 original size:11 final size:11
Alignment explanation
Indices: 35358140--35358182 Score: 50
Period size: 11 Copynumber: 3.7 Consensus size: 11
35358130 TAATAACGTG
35358140 TTTAATTAGGC
1 TTTAATTAGGC
*
35358151 TTTAATTAAGTGA
1 TTTAATT-AG-GC
*
35358164 ATTAATTAGGC
1 TTTAATTAGGC
35358175 TTTAATTA
1 TTTAATTA
35358183 AGTGAACTTA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
11 15 0.58
12 4 0.15
13 7 0.27
ACGTcount: A:0.35, C:0.05, G:0.14, T:0.47
Consensus pattern (11 bp):
TTTAATTAGGC
Found at i:35358168 original size:24 final size:24
Alignment explanation
Indices: 35358141--35358188 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
35358131 AATAACGTGT
35358141 TTAATTAGGCTTTAATTAAGTGAA
1 TTAATTAGGCTTTAATTAAGTGAA
35358165 TTAATTAGGCTTTAATTAAGTGAA
1 TTAATTAGGCTTTAATTAAGTGAA
35358189 CTTAGCTCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.38, C:0.04, G:0.17, T:0.42
Consensus pattern (24 bp):
TTAATTAGGCTTTAATTAAGTGAA
Found at i:35358366 original size:16 final size:17
Alignment explanation
Indices: 35358341--35358390 Score: 59
Period size: 16 Copynumber: 3.1 Consensus size: 17
35358331 TTTTCTTACT
35358341 TTAT-TAAATTATTATA
1 TTATATAAATTATTATA
*
35358357 TTATAT-AATTATTATT
1 TTATATAAATTATTATA
* *
35358373 TTATTTAAATTATAATA
1 TTATATAAATTATTATA
35358390 T
1 T
35358391 GAATTATAGA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
16 18 0.64
17 10 0.36
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
TTATATAAATTATTATA
Found at i:35359338 original size:51 final size:51
Alignment explanation
Indices: 35359257--35359379 Score: 167
Period size: 51 Copynumber: 2.4 Consensus size: 51
35359247 AGAACTAAGT
* * **
35359257 TATCCGGATGAAATATGAAGTTCTTGTTGAAACTAGAGTAATAAAGTAATA
1 TATCCGGATGAAATATGAAGTTCTTATTGAAACCAGAACAATAAAGTAATA
* *
35359308 TATCAGGATGAAATATGAAGTTCTTATTGAAGCCAGAACAATAAAGTAATA
1 TATCCGGATGAAATATGAAGTTCTTATTGAAACCAGAACAATAAAGTAATA
*
35359359 -AGTCCGGATGAAGTATGAAGT
1 TA-TCCGGATGAAATATGAAGT
35359380 AAGTTTGGGA
Statistics
Matches: 63, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
50 1 0.02
51 62 0.98
ACGTcount: A:0.41, C:0.09, G:0.21, T:0.28
Consensus pattern (51 bp):
TATCCGGATGAAATATGAAGTTCTTATTGAAACCAGAACAATAAAGTAATA
Found at i:35360016 original size:23 final size:23
Alignment explanation
Indices: 35359985--35360034 Score: 82
Period size: 23 Copynumber: 2.2 Consensus size: 23
35359975 TTCGGATGTA
* *
35359985 TTTGGGTTGGATATTCTGGTGTG
1 TTTGAGTTGGACATTCTGGTGTG
35360008 TTTGAGTTGGACATTCTGGTGTG
1 TTTGAGTTGGACATTCTGGTGTG
35360031 TTTG
1 TTTG
35360035 GGTGGAATCC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.10, C:0.06, G:0.36, T:0.48
Consensus pattern (23 bp):
TTTGAGTTGGACATTCTGGTGTG
Found at i:35360208 original size:7 final size:7
Alignment explanation
Indices: 35360196--35360224 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
35360186 TAAAATATGA
35360196 ATTTAAG
1 ATTTAAG
35360203 ATTTAAG
1 ATTTAAG
35360210 ATTTAAG
1 ATTTAAG
35360217 ATTTAAG
1 ATTTAAG
35360224 A
1 A
35360225 ACTAATATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.45, C:0.00, G:0.14, T:0.41
Consensus pattern (7 bp):
ATTTAAG
Found at i:35364577 original size:20 final size:20
Alignment explanation
Indices: 35364552--35364603 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
35364542 AGGGGCACAC
*
35364552 GCCCGTGTGGCCTGGGACAT
1 GCCCGTGTGGCCTGGAACAT
35364572 GCCCGTGTGGCCTGGAACAT
1 GCCCGTGTGGCCTGGAACAT
* *
35364592 GGCCGTGGGGCC
1 GCCCGTGTGGCC
35364604 AGGCCGCGGG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.10, C:0.31, G:0.42, T:0.17
Consensus pattern (20 bp):
GCCCGTGTGGCCTGGAACAT
Found at i:35364614 original size:13 final size:13
Alignment explanation
Indices: 35364592--35364621 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
35364582 CCTGGAACAT
*
35364592 GGCCGTGGGGCCA
1 GGCCGCGGGGCCA
35364605 GGCCGCGGGGCCA
1 GGCCGCGGGGCCA
35364618 GGCC
1 GGCC
35364622 ATGGGCAGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.07, C:0.37, G:0.53, T:0.03
Consensus pattern (13 bp):
GGCCGCGGGGCCA
Found at i:35366372 original size:19 final size:17
Alignment explanation
Indices: 35366339--35366377 Score: 60
Period size: 19 Copynumber: 2.2 Consensus size: 17
35366329 CCTAAATTTT
35366339 CCTTTTCTTTTTCTTTC
1 CCTTTTCTTTTTCTTTC
35366356 CCTTTTCTTTCTTTCTTTC
1 CCTTTTC-TT-TTTCTTTC
35366375 CCT
1 CCT
35366378 GCTCTATTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 7 0.35
18 2 0.10
19 11 0.55
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (17 bp):
CCTTTTCTTTTTCTTTC
Found at i:35366434 original size:14 final size:14
Alignment explanation
Indices: 35366395--35366436 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
35366385 TTTGTTTTCA
*
35366395 TTCTCTCTTTTA-T
1 TTCTTTCTTTTATT
35366408 TTCTTTCTTTTATT
1 TTCTTTCTTTTATT
* *
35366422 TTTTTTGTTTTATT
1 TTCTTTCTTTTATT
35366436 T
1 T
35366437 AATTACTTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
13 11 0.44
14 14 0.56
ACGTcount: A:0.07, C:0.12, G:0.02, T:0.79
Consensus pattern (14 bp):
TTCTTTCTTTTATT
Found at i:35369986 original size:22 final size:20
Alignment explanation
Indices: 35369960--35370000 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 20
35369950 TAAATGAAAT
35369960 AAAAGAAACAAAAGCATAAAAC
1 AAAAGAAAC-AAAGC-TAAAAC
35369982 AAAAGAAACAAAGCTAAAA
1 AAAAGAAACAAAGCTAAAA
35370001 AGAAACAGAG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.26
21 5 0.26
22 9 0.47
ACGTcount: A:0.73, C:0.12, G:0.10, T:0.05
Consensus pattern (20 bp):
AAAAGAAACAAAGCTAAAAC
Found at i:35370051 original size:16 final size:16
Alignment explanation
Indices: 35370030--35370062 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
35370020 ACAAGGGAAG
35370030 GAAAGAAAGAA-GAAAA
1 GAAAGAAA-AAGGAAAA
35370046 GAAAGAAAAAGGAAAA
1 GAAAGAAAAAGGAAAA
35370062 G
1 G
35370063 GAAAAATTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 2 0.12
16 14 0.88
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (16 bp):
GAAAGAAAAAGGAAAA
Found at i:35370459 original size:17 final size:18
Alignment explanation
Indices: 35370437--35370470 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
35370427 TAAATGAGTT
35370437 AATTAGGAT-TAAATTGG
1 AATTAGGATATAAATTGG
*
35370454 AATTAGGGTATAAATTG
1 AATTAGGATATAAATTG
35370471 AATAGAAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.41, C:0.00, G:0.24, T:0.35
Consensus pattern (18 bp):
AATTAGGATATAAATTGG
Found at i:35370974 original size:21 final size:21
Alignment explanation
Indices: 35370950--35371010 Score: 88
Period size: 21 Copynumber: 3.0 Consensus size: 21
35370940 GTTGTATTTG
*
35370950 AGGCACCTCGTGTGTCGTATC
1 AGGCACCTTGTGTGTCGTATC
*
35370971 AGGCACCTTGTGTGTCGTTTC
1 AGGCACCTTGTGTGTCGTATC
*
35370992 AGGCA-CTTATGTGTCGTAT
1 AGGCACCTTGTGTGTCGTAT
35371011 ACTGATCAGG
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
20 12 0.33
21 24 0.67
ACGTcount: A:0.15, C:0.23, G:0.28, T:0.34
Consensus pattern (21 bp):
AGGCACCTTGTGTGTCGTATC
Found at i:35384230 original size:24 final size:23
Alignment explanation
Indices: 35384188--35384302 Score: 73
Period size: 22 Copynumber: 5.0 Consensus size: 23
35384178 TATATGCATG
35384188 AAAATATATATA-TAAGATAATATA
1 AAAATATATA-ACT-AGATAATATA
*
35384212 AAAATATATAACTATGAT-A-CT-
1 AAAATATATAACTA-GATAATATA
* * *
35384233 AAAGTATATACACGAAATAGTATATA
1 AAAATATATA-ACTAGATA--ATATA
*
35384259 AAAATATATAACTA-ATAATATC
1 AAAATATATAACTAGATAATATA
35384281 AAAATATAT-AC-ATGATAATATA
1 AAAATATATAACTA-GATAATATA
35384303 TATAAAAAAA
Statistics
Matches: 72, Mismatches: 9, Indels: 22
0.70 0.09 0.21
Matches are distributed among these distances:
20 1 0.01
21 13 0.18
22 24 0.33
23 3 0.04
24 18 0.25
25 4 0.06
26 9 0.12
ACGTcount: A:0.57, C:0.06, G:0.05, T:0.31
Consensus pattern (23 bp):
AAAATATATAACTAGATAATATA
Found at i:35384301 original size:22 final size:22
Alignment explanation
Indices: 35384204--35384290 Score: 79
Period size: 22 Copynumber: 3.8 Consensus size: 22
35384194 TATATATAAG
35384204 ATAATATAAAAATATATAACT-
1 ATAATATAAAAATATATAACTA
* * *
35384225 ATGATACT-AAAGTATATACACGAA
1 ATAATA-TAAAAATATATA-AC-TA
35384249 ATAGTATATAAAAATATATAACTA
1 ATA--ATATAAAAATATATAACTA
*
35384273 ATAATATCAAAATATATA
1 ATAATATAAAAATATATA
35384291 CATGATAATA
Statistics
Matches: 52, Mismatches: 7, Indels: 13
0.72 0.10 0.18
Matches are distributed among these distances:
21 14 0.27
22 17 0.33
24 6 0.12
25 3 0.06
26 12 0.23
ACGTcount: A:0.57, C:0.07, G:0.05, T:0.31
Consensus pattern (22 bp):
ATAATATAAAAATATATAACTA
Found at i:35384308 original size:48 final size:47
Alignment explanation
Indices: 35384207--35384315 Score: 141
Period size: 48 Copynumber: 2.3 Consensus size: 47
35384197 ATATAAGATA
* *
35384207 ATATAAAAATATATAACTATGATACTAAAGTATATACACGAAATAGT
1 ATATAAAAATATATAACTATAATACTAAAATATATACACGAAATAGT
*
35384254 ATATAAAAATATATAACTAATAATA-TCAAAATATATACATGATAATA-T
1 ATATAAAAATATATAACT-ATAATACT-AAAATATATACACGA-AATAGT
*
35384302 ATATAAAAAAATAT
1 ATATAAAAATATAT
35384316 TAGAAAATAT
Statistics
Matches: 55, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
47 19 0.35
48 32 0.58
49 4 0.07
ACGTcount: A:0.58, C:0.06, G:0.05, T:0.31
Consensus pattern (47 bp):
ATATAAAAATATATAACTATAATACTAAAATATATACACGAAATAGT
Found at i:35384356 original size:24 final size:25
Alignment explanation
Indices: 35384298--35384372 Score: 89
Period size: 24 Copynumber: 2.9 Consensus size: 25
35384288 ATACATGATA
* *
35384298 ATATATATAAAAAAATATTAGAAAAT
1 ATATACATAATAAAATATT-GAAAAT
35384324 ATATGTACATAATAAAATA-TGAAAAT
1 ATA--TACATAATAAAATATTGAAAAT
*
35384350 ATATACATAATATAATATTGAAA
1 ATATACATAATAAAATATTGAAA
35384373 CATAATAATA
Statistics
Matches: 43, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
24 13 0.30
25 5 0.12
26 12 0.28
27 1 0.02
28 12 0.28
ACGTcount: A:0.60, C:0.03, G:0.05, T:0.32
Consensus pattern (25 bp):
ATATACATAATAAAATATTGAAAAT
Found at i:35384408 original size:9 final size:9
Alignment explanation
Indices: 35384393--35384465 Score: 57
Period size: 9 Copynumber: 8.4 Consensus size: 9
35384383 CAACATTAAA
35384393 AATATATAT
1 AATATATAT
*
35384402 GATATATAT
1 AATATATAT
35384411 -A-ATATAT
1 AATATATAT
*
35384418 AATAT-TAA
1 AATATATAT
35384426 AAGTATATAT
1 AA-TATATAT
*
35384436 AACATATA-
1 AATATATAT
*
35384444 AAAATATAT
1 AATATATAT
35384453 -ATATAATAT
1 AATAT-ATAT
35384462 AATA
1 AATA
35384466 CCTAAGTATA
Statistics
Matches: 51, Mismatches: 6, Indels: 13
0.73 0.09 0.19
Matches are distributed among these distances:
7 6 0.12
8 16 0.31
9 22 0.43
10 7 0.14
ACGTcount: A:0.58, C:0.01, G:0.03, T:0.38
Consensus pattern (9 bp):
AATATATAT
Found at i:35384433 original size:34 final size:35
Alignment explanation
Indices: 35384387--35384453 Score: 91
Period size: 34 Copynumber: 1.9 Consensus size: 35
35384377 ATAATACAAC
* * *
35384387 ATTAAAAATATATATGATATAT-ATAATATATAAT
1 ATTAAAAATATATATAACATATAAAAATATATAAT
*
35384421 ATTAAAAGTATATATAACATATAAAAATATATA
1 ATTAAAAATATATATAACATATAAAAATATATA
35384454 TATAATATAA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
34 19 0.68
35 9 0.32
ACGTcount: A:0.58, C:0.01, G:0.03, T:0.37
Consensus pattern (35 bp):
ATTAAAAATATATATAACATATAAAAATATATAAT
Found at i:35384462 original size:53 final size:58
Alignment explanation
Indices: 35384340--35384462 Score: 154
Period size: 53 Copynumber: 2.2 Consensus size: 58
35384330 ACATAATAAA
*
35384340 ATATGAAAATATATACATAATATAATATTGAAACATAATAATACAACATTAAAAATAT
1 ATATGATAATATATACATAATATAATATTGAAACATAATAATACAACATTAAAAATAT
*
35384398 ATATGAT-ATATATA-AT-ATATAATATT-AAA-AGT-AT-ATATAACATATAAAAATAT
1 ATATGATAATATATACATAATATAATATTGAAACA-TAATAATACAACAT-TAAAAATAT
35384451 ATAT-ATAATATA
1 ATATGATAATATA
35384463 ATACCTAAGT
Statistics
Matches: 60, Mismatches: 2, Indels: 11
0.82 0.03 0.15
Matches are distributed among these distances:
52 10 0.17
53 21 0.35
54 4 0.07
55 10 0.17
56 2 0.03
57 7 0.12
58 6 0.10
ACGTcount: A:0.58, C:0.04, G:0.03, T:0.35
Consensus pattern (58 bp):
ATATGATAATATATACATAATATAATATTGAAACATAATAATACAACATTAAAAATAT
Found at i:35384496 original size:53 final size:53
Alignment explanation
Indices: 35384384--35384499 Score: 134
Period size: 52 Copynumber: 2.2 Consensus size: 53
35384374 ATAATAATAC
* *
35384384 AACAT-TAAAAATATATATGATATATATAATATATAATATTAAAAGTATATAT
1 AACATATAAAAATATATATGATATATATAATACATAATATTAAAAGTACATAT
* *
35384436 AACATATAAAAATATATAT-ATA-ATATAATACCTAAGTA-TACTAAGTACATAT
1 AACATATAAAAATATATATGATATATATAATACATAA-TATTA-AAAGTACATAT
35384488 -ACATATATAAAA
1 AACATATA-AAAA
35384500 GATCCTATAC
Statistics
Matches: 56, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
51 20 0.36
52 23 0.41
53 13 0.23
ACGTcount: A:0.56, C:0.06, G:0.03, T:0.34
Consensus pattern (53 bp):
AACATATAAAAATATATATGATATATATAATACATAATATTAAAAGTACATAT
Found at i:35386232 original size:45 final size:44
Alignment explanation
Indices: 35386134--35386233 Score: 110
Period size: 45 Copynumber: 2.2 Consensus size: 44
35386124 GATATCCTCG
* * *
35386134 ATCAGCTCCACTGCAACTTCAGGGAGGCAAGACTTGCAACTTTA
1 ATCAGCTCCACTGCAACTTCAGGGAGGCAAAACTGGCAACTTCA
* * ***
35386178 ATCTTGCTCCACTGCAACTTCAGGGATGCAAAATCTGGTGTCTTCA
1 ATC-AGCTCCACTGCAACTTCAGGGAGGCAAAA-CTGGCAACTTCA
35386224 ATCAGCTCCA
1 ATCAGCTCCA
35386234 ATCTTTATTC
Statistics
Matches: 45, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
44 3 0.07
45 32 0.71
46 10 0.22
ACGTcount: A:0.27, C:0.28, G:0.19, T:0.26
Consensus pattern (44 bp):
ATCAGCTCCACTGCAACTTCAGGGAGGCAAAACTGGCAACTTCA
Found at i:35386317 original size:12 final size:12
Alignment explanation
Indices: 35386300--35386329 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
35386290 AATTGACTCT
*
35386300 TTAAAACAGACA
1 TTAAAACAGAAA
35386312 TTAAAACAGAAA
1 TTAAAACAGAAA
35386324 TTAAAA
1 TTAAAA
35386330 ATACCTCAGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.63, C:0.10, G:0.07, T:0.20
Consensus pattern (12 bp):
TTAAAACAGAAA
Found at i:35386544 original size:89 final size:87
Alignment explanation
Indices: 35386433--35386740 Score: 404
Period size: 87 Copynumber: 3.5 Consensus size: 87
35386423 ATGTGACCCA
*
35386433 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGACAAATATAAATTGAAAGAACAGGAA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTGAAAAATATAAATTGAAA-AACAGGAA
* *
35386498 TTGAAAATACCTAATCGTGTCCTG
64 TTGAAAATACCTCAGCGTGTCCTG
* * *
35386522 AGGCTCAACTCACCTCTCGCAATATGAGTCGATTTTTGAAAAACAAAAATTGAAAAACA-GATAT
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAATATAAATTGAAAAACAGGA-AT
35386586 TGAAAATACCTCAGCGTGTCCTG
65 TGAAAATACCTCAGCGTGTCCTG
* * * *
35386609 AGGCTCAACTCACCTCTCACAATATGAGTTGATTTTCGAAAAATATAAATTGAAAAAATAGAAAT
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAATATAAATTG-AAAAACAGGAAT
* **
35386674 TGAAAACT-CCTCAGCATGTGAGTCG
65 TGAAAA-TACCTCAGCGTGT-CCT-G
* *
35386699 AGGCTCAACTCACCTCTCGCAATATAAGTTGAATTTTGAAAA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAA
35386741 TAAACATCAA
Statistics
Matches: 193, Mismatches: 20, Indels: 11
0.86 0.09 0.05
Matches are distributed among these distances:
86 2 0.01
87 74 0.38
88 44 0.23
89 34 0.18
90 39 0.20
ACGTcount: A:0.38, C:0.19, G:0.16, T:0.27
Consensus pattern (87 bp):
AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAATATAAATTGAAAAACAGGAATT
GAAAATACCTCAGCGTGTCCTG
Found at i:35386576 original size:14 final size:14
Alignment explanation
Indices: 35386557--35386591 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
35386547 GAGTCGATTT
35386557 TTGAAAAACAAAAA
1 TTGAAAAACAAAAA
* *
35386571 TTGAAAAACAGATA
1 TTGAAAAACAAAAA
35386585 TTGAAAA
1 TTGAAAA
35386592 TACCTCAGCG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.63, C:0.06, G:0.11, T:0.20
Consensus pattern (14 bp):
TTGAAAAACAAAAA
Found at i:35386667 original size:15 final size:15
Alignment explanation
Indices: 35386647--35386679 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
35386637 TTGATTTTCG
*
35386647 AAAAATATAAATTGA
1 AAAAATAGAAATTGA
35386662 AAAAATAGAAATTGA
1 AAAAATAGAAATTGA
35386677 AAA
1 AAA
35386680 CTCCTCAGCA
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:0.70, C:0.00, G:0.09, T:0.21
Consensus pattern (15 bp):
AAAAATAGAAATTGA
Found at i:35395072 original size:4 final size:4
Alignment explanation
Indices: 35395026--35395053 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
35395016 TGGGATATGC
35395026 AATG AATG AATG AATG AATG AATG AATG
1 AATG AATG AATG AATG AATG AATG AATG
35395054 CATAAATGTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.25, T:0.25
Consensus pattern (4 bp):
AATG
Found at i:35399253 original size:47 final size:48
Alignment explanation
Indices: 35399190--35399305 Score: 141
Period size: 48 Copynumber: 2.4 Consensus size: 48
35399180 AAATATATAT
* * *
35399190 ATAAGATAGTATAAAAATATATAACT-ATGATA-CTAAAGTATATACACG
1 ATAATATA-TATAAAAATATATAACTAATAATATC-AAAATATATACACG
*
35399238 A-AATAGTATATAAAAATATATAACTAATAATATCAAAATATATACATG
1 ATAATA-TATATAAAAATATATAACTAATAATATCAAAATATATACACG
35399286 ATAATATATATAAAAA-ATAT
1 ATAATATATATAAAAATATAT
35399306 TAGAAAATAT
Statistics
Matches: 60, Mismatches: 4, Indels: 9
0.82 0.05 0.12
Matches are distributed among these distances:
47 24 0.40
48 31 0.52
49 5 0.08
ACGTcount: A:0.57, C:0.06, G:0.06, T:0.31
Consensus pattern (48 bp):
ATAATATATATAAAAATATATAACTAATAATATCAAAATATATACACG
Found at i:35399266 original size:24 final size:23
Alignment explanation
Indices: 35399176--35399293 Score: 77
Period size: 22 Copynumber: 5.1 Consensus size: 23
35399166 AAATATATGC
* *
35399176 ATAAAAATATATATA-TAAGATAGT
1 ATAAAAATATATACACT-A-ATAAT
*
35399200 ATAAAAATATATA-ACT-ATGAT
1 ATAAAAATATATACACTAATAAT
* *
35399221 ACT-AAAGTATATACACGAAATAGTAT
1 A-TAAAAATATATACAC-TAATA--AT
35399247 ATAAAAATATATA-ACTAATAAT
1 ATAAAAATATATACACTAATAAT
* *
35399269 ATCAAAATATATACA-TGATAAT
1 ATAAAAATATATACACTAATAAT
35399291 ATA
1 ATA
35399294 TATAAAAAAT
Statistics
Matches: 75, Mismatches: 10, Indels: 20
0.71 0.10 0.19
Matches are distributed among these distances:
21 13 0.17
22 25 0.33
23 2 0.03
24 20 0.27
25 3 0.04
26 12 0.16
ACGTcount: A:0.57, C:0.06, G:0.06, T:0.31
Consensus pattern (23 bp):
ATAAAAATATATACACTAATAAT
Found at i:35399292 original size:22 final size:22
Alignment explanation
Indices: 35399176--35399281 Score: 74
Period size: 24 Copynumber: 4.6 Consensus size: 22
35399166 AAATATATGC
*
35399176 ATAAAAATATATATA-TAAGATAGT
1 ATAAAAATATATA-ACT-A-ATAAT
*
35399200 ATAAAAATATATAACT-ATGAT
1 ATAAAAATATATAACTAATAAT
* *
35399221 ACT-AAAGTATATACACGAAATAGTAT
1 A-TAAAAATATATA-AC-TAATA--AT
35399247 ATAAAAATATATAACTAATAAT
1 ATAAAAATATATAACTAATAAT
*
35399269 ATCAAAATATATA
1 ATAAAAATATATA
35399282 CATGATAATA
Statistics
Matches: 66, Mismatches: 8, Indels: 18
0.72 0.09 0.20
Matches are distributed among these distances:
21 13 0.20
22 17 0.26
23 1 0.02
24 20 0.30
25 3 0.05
26 12 0.18
ACGTcount: A:0.58, C:0.06, G:0.06, T:0.31
Consensus pattern (22 bp):
ATAAAAATATATAACTAATAAT
Found at i:35399346 original size:24 final size:25
Alignment explanation
Indices: 35399308--35399362 Score: 85
Period size: 24 Copynumber: 2.2 Consensus size: 25
35399298 AAAAATATTA
35399308 GAAAATATATGTACATAATATAATAT
1 GAAAATATA-GTACATAATATAATAT
35399334 GAAAATATA-TACATAATATAATAT
1 GAAAATATAGTACATAATATAATAT
*
35399358 TAAAA
1 GAAAA
35399363 CATAATAATA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
24 19 0.68
26 9 0.32
ACGTcount: A:0.58, C:0.04, G:0.05, T:0.33
Consensus pattern (25 bp):
GAAAATATAGTACATAATATAATAT
Found at i:35399372 original size:21 final size:22
Alignment explanation
Indices: 35399319--35399383 Score: 69
Period size: 21 Copynumber: 2.9 Consensus size: 22
35399309 AAAATATATG
* *
35399319 TACATAATATAATATGAAAATATA
1 TACATAATATAATAT-TAAA-ACA
35399343 TACATAATATAATATTAAAACA
1 TACATAATATAATATTAAAACA
* *
35399365 TA-ATAATACAACATTAAAA
1 TACATAATATAATATTAAAA
35399384 ATATATATAT
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
21 15 0.41
22 4 0.11
23 3 0.08
24 15 0.41
ACGTcount: A:0.60, C:0.08, G:0.02, T:0.31
Consensus pattern (22 bp):
TACATAATATAATATTAAAACA
Found at i:35399400 original size:9 final size:9
Alignment explanation
Indices: 35399386--35399452 Score: 59
Period size: 9 Copynumber: 7.6 Consensus size: 9
35399376 CATTAAAAAT
*
35399386 ATATATATG
1 ATATATATA
35399395 ATATATAT-
1 ATATATATA
35399403 A-ATATATA
1 ATATATATA
*
35399411 ATAT-TAAA
1 ATATATATA
35399419 AGTATATATA
1 A-TATATATA
* *
35399429 ACATATAAAA
1 ATATAT-ATA
35399439 ATATATATA
1 ATATATATA
35399448 ATATA
1 ATATA
35399453 ATACCTAAGT
Statistics
Matches: 47, Mismatches: 6, Indels: 10
0.75 0.10 0.16
Matches are distributed among these distances:
7 6 0.13
8 6 0.13
9 24 0.51
10 11 0.23
ACGTcount: A:0.57, C:0.01, G:0.03, T:0.39
Consensus pattern (9 bp):
ATATATATA
Found at i:35399438 original size:55 final size:60
Alignment explanation
Indices: 35399324--35399447 Score: 163
Period size: 55 Copynumber: 2.2 Consensus size: 60
35399314 ATATGTACAT
35399324 AATATA-ATATGAAAATATATACATAATATAATATTAAAACATAATAATACAACATTAAA
1 AATATATATATGAAAATATATACATAATATAATATTAAAACATAATAATACAACATTAAA
* * *
35399383 AATATATATATG-ATATATATA-AT-ATATAATATTAAAA-GT-AT-ATATAACATATAAA
1 AATATATATATGAAAATATATACATAATATAATATTAAAACATAATAATACAACAT-TAAA
35399438 AATATATATA
1 AATATATATA
35399448 ATATAATACC
Statistics
Matches: 60, Mismatches: 3, Indels: 8
0.85 0.04 0.11
Matches are distributed among these distances:
54 8 0.13
55 16 0.27
56 1 0.02
57 14 0.23
58 2 0.03
59 14 0.23
60 5 0.08
ACGTcount: A:0.59, C:0.04, G:0.02, T:0.35
Consensus pattern (60 bp):
AATATATATATGAAAATATATACATAATATAATATTAAAACATAATAATACAACATTAAA
Found at i:35401095 original size:21 final size:22
Alignment explanation
Indices: 35401066--35401108 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
35401056 TTACATGTAA
* *
35401066 TTATTTAG-TAAATTATATTGT
1 TTATGTAGTTAAATAATATTGT
35401087 TTATGTAGTTAAATAATATTGT
1 TTATGTAGTTAAATAATATTGT
35401109 ACTTCGTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (22 bp):
TTATGTAGTTAAATAATATTGT
Found at i:35405066 original size:41 final size:42
Alignment explanation
Indices: 35404999--35405080 Score: 112
Period size: 41 Copynumber: 2.0 Consensus size: 42
35404989 CATTATTAAA
* ** * *
35404999 ACAGAGCCCAAAAAACTGAAGGGGCCCAACGCACACGGAAAG
1 ACAGAGCCCAAAAAACTAAACAGGCCCAAAGCACAAGGAAAG
35405041 ACAGAGCCC-AAAAACTAAACAGGCCCAAAGCACAAGGAAA
1 ACAGAGCCCAAAAAACTAAACAGGCCCAAAGCACAAGGAAA
35405081 AGTCAAAAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
41 26 0.74
42 9 0.26
ACGTcount: A:0.48, C:0.28, G:0.22, T:0.02
Consensus pattern (42 bp):
ACAGAGCCCAAAAAACTAAACAGGCCCAAAGCACAAGGAAAG
Found at i:35411051 original size:11 final size:11
Alignment explanation
Indices: 35411025--35411080 Score: 51
Period size: 11 Copynumber: 4.9 Consensus size: 11
35411015 ATTAAAGAGG
*
35411025 AAAGAAAATAGA
1 AAAGAAAA-ATA
*
35411037 AAAGAAAAATC
1 AAAGAAAAATA
35411048 AAAGTAAAAGA-A
1 AAAG-AAAA-ATA
*
35411060 AAAGAAAAAAA
1 AAAGAAAAATA
35411071 AAAGAAAAAT
1 AAAGAAAAAT
35411081 TCAAAGAAAG
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
10 1 0.03
11 19 0.51
12 16 0.43
13 1 0.03
ACGTcount: A:0.79, C:0.02, G:0.12, T:0.07
Consensus pattern (11 bp):
AAAGAAAAATA
Found at i:35411058 original size:17 final size:17
Alignment explanation
Indices: 35411036--35411089 Score: 63
Period size: 17 Copynumber: 3.1 Consensus size: 17
35411026 AAGAAAATAG
*
35411036 AAAAGAAAAATCAAAGT
1 AAAAGAAAAATCAAAGA
** *
35411053 AAAAGAAAAAGAAAAAA
1 AAAAGAAAAATCAAAGA
35411070 AAAAGAAAAATTCAAAGA
1 AAAAGAAAAA-TCAAAGA
35411088 AA
1 AA
35411090 GTATATACTA
Statistics
Matches: 29, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
17 23 0.79
18 6 0.21
ACGTcount: A:0.78, C:0.04, G:0.11, T:0.07
Consensus pattern (17 bp):
AAAAGAAAAATCAAAGA
Found at i:35411079 original size:6 final size:6
Alignment explanation
Indices: 35411025--35411079 Score: 53
Period size: 6 Copynumber: 9.5 Consensus size: 6
35411015 ATTAAAGAGG
** *
35411025 AAAGAA AATAG-A AAAGAA AAA-TC AAAGTA AAAGAA AAAGAA AAA-AA
1 AAAGAA AA-AGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA
35411071 AAAGAA AAA
1 AAAGAA AAA
35411080 TTCAAAGAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
5 10 0.24
6 29 0.71
7 2 0.05
ACGTcount: A:0.80, C:0.02, G:0.13, T:0.05
Consensus pattern (6 bp):
AAAGAA
Found at i:35413234 original size:15 final size:16
Alignment explanation
Indices: 35413214--35413247 Score: 61
Period size: 15 Copynumber: 2.2 Consensus size: 16
35413204 AATTTTTTAA
35413214 AAATTATTAAAAT-AT
1 AAATTATTAAAATAAT
35413229 AAATTATTAAAATAAT
1 AAATTATTAAAATAAT
35413245 AAA
1 AAA
35413248 ATTACAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 13 0.72
16 5 0.28
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (16 bp):
AAATTATTAAAATAAT
Found at i:35413598 original size:31 final size:31
Alignment explanation
Indices: 35413561--35413619 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
35413551 TTTAATTTGA
*
35413561 TCAATTTTACTTATTCTACTTTTTGAATCGG
1 TCAATTTTACTCATTCTACTTTTTGAATCGG
* *
35413592 TCAATTTTAGTCATTGTACTTTTTGAAT
1 TCAATTTTACTCATTCTACTTTTTGAAT
35413620 TTTGAAGTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.24, C:0.14, G:0.10, T:0.53
Consensus pattern (31 bp):
TCAATTTTACTCATTCTACTTTTTGAATCGG
Found at i:35414187 original size:3 final size:3
Alignment explanation
Indices: 35414179--35414212 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
35414169 ATCCATCACA
*
35414179 AAT AAT AAT AAC AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
35414213 CAATTTCCTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:35415266 original size:15 final size:15
Alignment explanation
Indices: 35415237--35415299 Score: 65
Period size: 15 Copynumber: 4.0 Consensus size: 15
35415227 TTAAACTTTA
35415237 TATTA-TAAAATATT
1 TATTATTAAAATATT
*
35415251 TATTATTAATATATT
1 TATTATTAAAATATT
*
35415266 TATAATTGTAATAACTATT
1 TATTA-T-TAA-AA-TATT
35415285 TATTATTAAAATATT
1 TATTATTAAAATATT
35415300 AATATTGAAT
Statistics
Matches: 40, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
14 5 0.12
15 16 0.40
16 3 0.08
17 6 0.15
18 2 0.05
19 8 0.20
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (15 bp):
TATTATTAAAATATT
Found at i:35415876 original size:44 final size:44
Alignment explanation
Indices: 35415825--35415910 Score: 145
Period size: 44 Copynumber: 2.0 Consensus size: 44
35415815 TTTGTGAGCA
* *
35415825 ATGTCACCAGAATCTCATCAAAAGTTGTTGAAATTTGACAAACT
1 ATGTCACCAGAATCTCATCAAAAATGGTTGAAATTTGACAAACT
*
35415869 ATGTCACCAGAGTCTCATCAAAAATGGTTGAAATTTGACAAA
1 ATGTCACCAGAATCTCATCAAAAATGGTTGAAATTTGACAAA
35415911 TTATAAAACT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 39 1.00
ACGTcount: A:0.40, C:0.17, G:0.15, T:0.28
Consensus pattern (44 bp):
ATGTCACCAGAATCTCATCAAAAATGGTTGAAATTTGACAAACT
Found at i:35424481 original size:164 final size:164
Alignment explanation
Indices: 35424210--35425294 Score: 1904
Period size: 164 Copynumber: 6.6 Consensus size: 164
35424200 CTGTAAAACA
**
35424210 AAAACAAAAACGAAACAAAAAAGCACTTAATGGCCCATGCAGGTCTCGAACCTGCGACCTTCGCG
1 AAAACAAAAACGAAAGTAAAAAGCACTTAATGGCCCATGCAGGTCTCGAACCTGCGACCTTCGCG
35424275 TTATTAGCACGACGCTCTAACCAGCTGAGCTAATAGGCCATTGGTGTTCACGCCCAAATTCTGTT
66 TTATTAGCACGACGCTCTAACCAGCTGAGCTAATAGGCCATTGGTGTTCACGCCCAAATTCTGTT
*
35424340 CTAATAAATAGTGTAAAACGGTGCCGTTTTCCAG
131 CTAATAAATACTGTAAAACGGTGCCGTTTTCCAG
*
35424374 AAAACAAAAACGAAAGTAAAAAGCACTAAATGGCCCATGCAGGTCTCGAACCTGCGACCTTCGCG
1 AAAACAAAAACGAAAGTAAAAAGCACTTAATGGCCCATGCAGGTCTCGAACCTGCGACCTTCGCG
*
35424439 TTATTAGCACGACGCTCTAACCAGCTGAGCTAATAGGCCATTGGTGTTCACGCCCAAATTCAGTT
66 TTATTAGCACGACGCTCTAACCAGCTGAGCTAATAGGCCATTGGTGTTCACGCCCAAATTCTGTT
* * * *
35424504 TTACTAAATACTGTAAAACGTTGCCGTTTCCCAG
131 CTAATAAATACTGTAAAACGGTGCCGTTTTCCAG
*
35424538 AAAACAAAAACGAAAGAAAAAAGCACTTAATGGCCCATGCAGGTCTCGAACCTGCGACCTTCGCG
1 AAAACAAAAACGAAAGTAAAAAGCACTTAATGGCCCATGCAGGTCTCGAACCTGCGACCTTCGCG
*
35424603 TTATTAGCACGACGCTCTAACCATCTGAGCTAATAGGCCATTGGTGTTCACGCCCAAATTCTGTT
66 TTATTAGCACGACGCTCTAACCAGCTGAGCTAATAGGCCATTGGTGTTCACGCCCAAATTCTGTT
* * *
35424668 CT-ATGAAATATTGTAAAACGCTGCCGTTTTCTAG
131 CTAAT-AAATACTGTAAAACGGTGCCGTTTTCCAG
35424702 AAAACAAAAACGAAAGTAAAAAGCACTTAATGGCCCATGCAGGTCTCGAACCTGCGACCTTCGCG
1 AAAACAAAAACGAAAGTAAAAAGCACTTAATGGCCCATGCAGGTCTCGAACCTGCGACCTTCGCG
*
35424767 TTATTAGCACGACGCTCTAACCAGCTGAGCTAATAGGCCATTGTTGTTCACGCCCAAATTCTGTT
66 TTATTAGCACGACGCTCTAACCAGCTGAGCTAATAGGCCATTGGTGTTCACGCCCAAATTCTGTT
*
35424832 CTAATAAATAGTGTAAAACGGTGCCGTTTTCCAG
131 CTAATAAATACTGTAAAACGGTGCCGTTTTCCAG
35424866 AAAACAAAAACGAAAGTAAAAAGCACTTAATGGCCCATGCAGGTCTCGAACCTGCGACCTTCGCG
1 AAAACAAAAACGAAAGTAAAAAGCACTTAATGGCCCATGCAGGTCTCGAACCTGCGACCTTCGCG
*
35424931 TTATTAGCACGACGCTCTAACCAGCTGAGCTAATAGGCCATTGGTGTTCACGCCCAAATTCAGTT
66 TTATTAGCACGACGCTCTAACCAGCTGAGCTAATAGGCCATTGGTGTTCACGCCCAAATTCTGTT
* * * *
35424996 TTACTAAATACTGTAAAACGTTGCCGTTTCCCAG
131 CTAATAAATACTGTAAAACGGTGCCGTTTTCCAG
*
35425030 AAAACAAAAACGAAAGAAAAAAGCACTTAATGGCCCATGCAGGTCTCGAACCTGCGACCTTCGCG
1 AAAACAAAAACGAAAGTAAAAAGCACTTAATGGCCCATGCAGGTCTCGAACCTGCGACCTTCGCG
*
35425095 TTATTAGCACGACGCTCTAACCATCTGAGCTAATAGGCCATTGGTGTTCACGCCCAAATTCTGTT
66 TTATTAGCACGACGCTCTAACCAGCTGAGCTAATAGGCCATTGGTGTTCACGCCCAAATTCTGTT
* *
35425160 CT-ATGAAATATTGTAAAACGGTGCCGTTTTCTAG
131 CTAAT-AAATACTGTAAAACGGTGCCGTTTTCCAG
35425194 AAAACAAAAACGAAAGTAAAAAGCACTTAATGGCCCATGCAGGTCTCGAACCTGCGACCTTCGCG
1 AAAACAAAAACGAAAGTAAAAAGCACTTAATGGCCCATGCAGGTCTCGAACCTGCGACCTTCGCG
*
35425259 TTATTAGCACGACGCTCTAACCAGCTGAGTTAATAG
66 TTATTAGCACGACGCTCTAACCAGCTGAGCTAATAG
35425295 ACCTTTATGT
Statistics
Matches: 874, Mismatches: 44, Indels: 6
0.95 0.05 0.01
Matches are distributed among these distances:
163 2 0.00
164 870 1.00
165 2 0.00
ACGTcount: A:0.32, C:0.25, G:0.19, T:0.24
Consensus pattern (164 bp):
AAAACAAAAACGAAAGTAAAAAGCACTTAATGGCCCATGCAGGTCTCGAACCTGCGACCTTCGCG
TTATTAGCACGACGCTCTAACCAGCTGAGCTAATAGGCCATTGGTGTTCACGCCCAAATTCTGTT
CTAATAAATACTGTAAAACGGTGCCGTTTTCCAG
Found at i:35424949 original size:492 final size:491
Alignment explanation
Indices: 35423936--35425294 Score: 2216
Period size: 492 Copynumber: 2.8 Consensus size: 491
35423926 ATTTGAATCT
* * * * * *
35423936 TGCAGGACTCGAAACTG-G-CCTTCGCGTTATTAGCACGACGATCTAACCAGCAGACCTAATAAG
1 TGCAGGTCTCGAACCTGCGACCTTCGCGTTATTAGCACGACGCTCTAACCAGCTGAGCTAATAGG
* * *** * * * * * * * * *
35423999 CCGTT-ATGTTGTTGTCTAAATTCTA-TTTTATTAACTAATATAAAACGCTGCCGTTTTCCAAAA
66 CCATTGGTGTTCACGCCCAAATTC-AGTTTTACTAAATACTGTAAAACGTTGCCGTTTCCCAGAA
* * * * *
35424062 AACCAAAA-GAAAAGAAAATAGCGCATAATGGCCCACGCAGGTCTCGAACCTGCGACCTTCGCGT
130 AACAAAAACG-AAAGAAAAAAGCACTTAATGGCCCATGCAGGTCTCGAACCTGCGACCTTCGCGT
* * * * *
35424126 TATTAGCACGACGCTCTAACCAGCTGAGCTAATAGACCGTTGGTGTTCACGACCAAATTCTGTTT
194 TATTAGCACGACGCTCTAACCATCTGAGCTAATAGGCCATTGGTGTTCACGCCCAAATTCTGTTC
* **
35424191 TACT-AAATACTGTAAAA-----------C-A-AAAACAAAAACGAAACAAAAAAGCACTTAATG
259 TA-TGAAATATTGTAAAACGTGCCGTTTTCTAGAAAACAAAAACGAAAGTAAAAAGCACTTAATG
35424242 GCCCATGCAGGTCTCGAACCTGCGACCTTCGCGTTATTAGCACGACGCTCTAACCAGCTGAGCTA
323 GCCCATGCAGGTCTCGAACCTGCGACCTTCGCGTTATTAGCACGACGCTCTAACCAGCTGAGCTA
35424307 ATAGGCCATTGGTGTTCACGCCCAAATTCTGTTCTAATAAATAGTGTAAAACGGTGCCGTTTTCC
388 ATAGGCCATTGGTGTTCACGCCCAAATTCTGTTCTAATAAATAGTGTAAAACGGTGCCGTTTTCC
35424372 AGAAAACAAAAACGAAAGTAAAAAGCACTAAATGGCCCA
453 AGAAAACAAAAACGAAAGTAAAAAGCACTAAATGGCCCA
35424411 TGCAGGTCTCGAACCTGCGACCTTCGCGTTATTAGCACGACGCTCTAACCAGCTGAGCTAATAGG
1 TGCAGGTCTCGAACCTGCGACCTTCGCGTTATTAGCACGACGCTCTAACCAGCTGAGCTAATAGG
35424476 CCATTGGTGTTCACGCCCAAATTCAGTTTTACTAAATACTGTAAAACGTTGCCGTTTCCCAGAAA
66 CCATTGGTGTTCACGCCCAAATTCAGTTTTACTAAATACTGTAAAACGTTGCCGTTTCCCAGAAA
35424541 ACAAAAACGAAAGAAAAAAGCACTTAATGGCCCATGCAGGTCTCGAACCTGCGACCTTCGCGTTA
131 ACAAAAACGAAAGAAAAAAGCACTTAATGGCCCATGCAGGTCTCGAACCTGCGACCTTCGCGTTA
35424606 TTAGCACGACGCTCTAACCATCTGAGCTAATAGGCCATTGGTGTTCACGCCCAAATTCTGTTCTA
196 TTAGCACGACGCTCTAACCATCTGAGCTAATAGGCCATTGGTGTTCACGCCCAAATTCTGTTCTA
35424671 TGAAATATTGTAAAACGCTGCCGTTTTCTAGAAAACAAAAACGAAAGTAAAAAGCACTTAATGGC
261 TGAAATATTGTAAAACG-TGCCGTTTTCTAGAAAACAAAAACGAAAGTAAAAAGCACTTAATGGC
35424736 CCATGCAGGTCTCGAACCTGCGACCTTCGCGTTATTAGCACGACGCTCTAACCAGCTGAGCTAAT
325 CCATGCAGGTCTCGAACCTGCGACCTTCGCGTTATTAGCACGACGCTCTAACCAGCTGAGCTAAT
*
35424801 AGGCCATTGTTGTTCACGCCCAAATTCTGTTCTAATAAATAGTGTAAAACGGTGCCGTTTTCCAG
390 AGGCCATTGGTGTTCACGCCCAAATTCTGTTCTAATAAATAGTGTAAAACGGTGCCGTTTTCCAG
*
35424866 AAAACAAAAACGAAAGTAAAAAGCACTTAATGGCCCA
455 AAAACAAAAACGAAAGTAAAAAGCACTAAATGGCCCA
35424903 TGCAGGTCTCGAACCTGCGACCTTCGCGTTATTAGCACGACGCTCTAACCAGCTGAGCTAATAGG
1 TGCAGGTCTCGAACCTGCGACCTTCGCGTTATTAGCACGACGCTCTAACCAGCTGAGCTAATAGG
35424968 CCATTGGTGTTCACGCCCAAATTCAGTTTTACTAAATACTGTAAAACGTTGCCGTTTCCCAGAAA
66 CCATTGGTGTTCACGCCCAAATTCAGTTTTACTAAATACTGTAAAACGTTGCCGTTTCCCAGAAA
35425033 ACAAAAACGAAAGAAAAAAGCACTTAATGGCCCATGCAGGTCTCGAACCTGCGACCTTCGCGTTA
131 ACAAAAACGAAAGAAAAAAGCACTTAATGGCCCATGCAGGTCTCGAACCTGCGACCTTCGCGTTA
35425098 TTAGCACGACGCTCTAACCATCTGAGCTAATAGGCCATTGGTGTTCACGCCCAAATTCTGTTCTA
196 TTAGCACGACGCTCTAACCATCTGAGCTAATAGGCCATTGGTGTTCACGCCCAAATTCTGTTCTA
35425163 TGAAATATTGTAAAACGGTGCCGTTTTCTAGAAAACAAAAACGAAAGTAAAAAGCACTTAATGGC
261 TGAAATATTGTAAAAC-GTGCCGTTTTCTAGAAAACAAAAACGAAAGTAAAAAGCACTTAATGGC
*
35425228 CCATGCAGGTCTCGAACCTGCGACCTTCGCGTTATTAGCACGACGCTCTAACCAGCTGAGTTAAT
325 CCATGCAGGTCTCGAACCTGCGACCTTCGCGTTATTAGCACGACGCTCTAACCAGCTGAGCTAAT
35425293 AG
390 AG
35425295 ACCTTTATGT
Statistics
Matches: 827, Mismatches: 36, Indels: 25
0.93 0.04 0.03
Matches are distributed among these distances:
475 15 0.02
476 1 0.00
477 47 0.06
478 174 0.21
479 1 0.00
490 1 0.00
491 1 0.00
492 586 0.71
493 1 0.00
ACGTcount: A:0.32, C:0.25, G:0.19, T:0.24
Consensus pattern (491 bp):
TGCAGGTCTCGAACCTGCGACCTTCGCGTTATTAGCACGACGCTCTAACCAGCTGAGCTAATAGG
CCATTGGTGTTCACGCCCAAATTCAGTTTTACTAAATACTGTAAAACGTTGCCGTTTCCCAGAAA
ACAAAAACGAAAGAAAAAAGCACTTAATGGCCCATGCAGGTCTCGAACCTGCGACCTTCGCGTTA
TTAGCACGACGCTCTAACCATCTGAGCTAATAGGCCATTGGTGTTCACGCCCAAATTCTGTTCTA
TGAAATATTGTAAAACGTGCCGTTTTCTAGAAAACAAAAACGAAAGTAAAAAGCACTTAATGGCC
CATGCAGGTCTCGAACCTGCGACCTTCGCGTTATTAGCACGACGCTCTAACCAGCTGAGCTAATA
GGCCATTGGTGTTCACGCCCAAATTCTGTTCTAATAAATAGTGTAAAACGGTGCCGTTTTCCAGA
AAACAAAAACGAAAGTAAAAAGCACTAAATGGCCCA
Found at i:35426223 original size:100 final size:101
Alignment explanation
Indices: 35426116--35426319 Score: 250
Period size: 100 Copynumber: 2.0 Consensus size: 101
35426106 TAATTGATTG
* * ** * * *
35426116 GTGGTTTTGATGAAAGGATTGTCTTTGTTTCTTCGTTTCAAGCTATAAAGCATCTAATTTGTTAA
1 GTGGTTTTGATAAAAGGATTGTCCTCCTTTCTTCATCTCAAGCTATAAAGCATCTAATTTGGTAA
* *
35426181 TTTCATGTAAAA-AAATTG-CAATTTGAAAAGAAGTT
66 CTTCATGGAAAAGAAATTGTCAATTT-AAAAGAAGTT
* * *
35426216 GTGGTTTTGATAAAAGGATTGTCCTCCTTTCTTCATCTCATGCTATAAAGCGTCTACTTTGGTAA
1 GTGGTTTTGATAAAAGGATTGTCCTCCTTTCTTCATCTCAAGCTATAAAGCATCTAATTTGGTAA
* *
35426281 CTTCATGGAAAAGTTACTTGTCAATTTAAAAGAAGTT
66 CTTCATGGAAAAG-AAATTGTCAATTTAAAAGAAGTT
35426318 GT
1 GT
35426320 ATAGTTTCAT
Statistics
Matches: 87, Mismatches: 14, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
100 65 0.75
102 16 0.18
103 6 0.07
ACGTcount: A:0.30, C:0.12, G:0.18, T:0.40
Consensus pattern (101 bp):
GTGGTTTTGATAAAAGGATTGTCCTCCTTTCTTCATCTCAAGCTATAAAGCATCTAATTTGGTAA
CTTCATGGAAAAGAAATTGTCAATTTAAAAGAAGTT
Found at i:35433310 original size:8 final size:8
Alignment explanation
Indices: 35433297--35433346 Score: 100
Period size: 8 Copynumber: 6.2 Consensus size: 8
35433287 ATCCTCAAAA
35433297 AGAGTGAG
1 AGAGTGAG
35433305 AGAGTGAG
1 AGAGTGAG
35433313 AGAGTGAG
1 AGAGTGAG
35433321 AGAGTGAG
1 AGAGTGAG
35433329 AGAGTGAG
1 AGAGTGAG
35433337 AGAGTGAG
1 AGAGTGAG
35433345 AG
1 AG
35433347 CGAACGCAAG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 42 1.00
ACGTcount: A:0.38, C:0.00, G:0.50, T:0.12
Consensus pattern (8 bp):
AGAGTGAG
Found at i:35435360 original size:21 final size:21
Alignment explanation
Indices: 35435334--35435373 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
35435324 CAAAATGATG
35435334 TAGTTTTG-CATTTTAACTTAA
1 TAGTTTTGAC-TTTTAACTTAA
35435355 TAGTTTTGACTTTTAACTT
1 TAGTTTTGACTTTTAACTT
35435374 TGAAAAAGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 17 0.94
22 1 0.06
ACGTcount: A:0.25, C:0.10, G:0.10, T:0.55
Consensus pattern (21 bp):
TAGTTTTGACTTTTAACTTAA
Found at i:35448741 original size:17 final size:17
Alignment explanation
Indices: 35448715--35448748 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
35448705 GATTTAATTT
*
35448715 ATATATTTTAAATTTTA
1 ATATAATTTAAATTTTA
*
35448732 ATATAATTTAATTTTTA
1 ATATAATTTAAATTTTA
35448749 TATTTTTATC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
ATATAATTTAAATTTTA
Found at i:35448751 original size:16 final size:17
Alignment explanation
Indices: 35448712--35448751 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
35448702 TAAGATTTAA
*
35448712 TTTATATATTTTAAATT
1 TTTATATAATTTAAATT
*
35448729 TTAATATAATTT-AATT
1 TTTATATAATTTAAATT
35448745 TTTATAT
1 TTTATAT
35448752 TTTTATCATA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
16 10 0.50
17 10 0.50
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
TTTATATAATTTAAATT
Found at i:35453068 original size:3 final size:3
Alignment explanation
Indices: 35453056--35453096 Score: 73
Period size: 3 Copynumber: 13.7 Consensus size: 3
35453046 TTCCTCCTCC
*
35453056 TCT TCC TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
35453097 ACCTCAGCAT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.00, C:0.37, G:0.00, T:0.63
Consensus pattern (3 bp):
TCT
Found at i:35460592 original size:19 final size:20
Alignment explanation
Indices: 35460568--35460605 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
35460558 TAATTTCTTT
*
35460568 TATATTTTT-TAAAATTAAA
1 TATATTTTTAAAAAATTAAA
35460587 TATATTTTTAAAAAATTAA
1 TATATTTTTAAAAAATTAA
35460606 TGTGATAACG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
TATATTTTTAAAAAATTAAA
Found at i:35465782 original size:12 final size:12
Alignment explanation
Indices: 35465765--35465808 Score: 88
Period size: 12 Copynumber: 3.7 Consensus size: 12
35465755 AAAGGGATCG
35465765 TATTTTAAAATT
1 TATTTTAAAATT
35465777 TATTTTAAAATT
1 TATTTTAAAATT
35465789 TATTTTAAAATT
1 TATTTTAAAATT
35465801 TATTTTAA
1 TATTTTAA
35465809 CTTTCGACAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 32 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (12 bp):
TATTTTAAAATT
Found at i:35468774 original size:23 final size:23
Alignment explanation
Indices: 35468744--35468788 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
35468734 TAAGGATGGT
35468744 AGAGTAAGATGAAAACAGATCTC
1 AGAGTAAGATGAAAACAGATCTC
35468767 AGAGTAAGATGAAAACAGATCT
1 AGAGTAAGATGAAAACAGATCT
35468789 TACCTTACAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.49, C:0.11, G:0.22, T:0.18
Consensus pattern (23 bp):
AGAGTAAGATGAAAACAGATCTC
Found at i:35472809 original size:39 final size:40
Alignment explanation
Indices: 35472755--35472832 Score: 113
Period size: 40 Copynumber: 2.0 Consensus size: 40
35472745 TATTACCGAT
** * *
35472755 TCAGATACAGTTTA-GGCCTTAGCCCATTCAGATACAGTC
1 TCAGATACAAATTAGGGCCTTAACCCATTCAAATACAGTC
35472794 TCAGATACAAATTAGGGCCTTAACCCATTCAAATACAGT
1 TCAGATACAAATTAGGGCCTTAACCCATTCAAATACAGT
35472833 ATGTATACAG
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 12 0.35
40 22 0.65
ACGTcount: A:0.33, C:0.24, G:0.15, T:0.27
Consensus pattern (40 bp):
TCAGATACAAATTAGGGCCTTAACCCATTCAAATACAGTC
Found at i:35493455 original size:17 final size:17
Alignment explanation
Indices: 35493410--35493461 Score: 59
Period size: 19 Copynumber: 2.9 Consensus size: 17
35493400 ATTTGACAAA
*
35493410 GCCCGATAAATGATAAT
1 GCCCAATAAATGATAAT
*
35493427 GCCTGAAATAAATGATAAT
1 GCC--CAATAAATGATAAT
*
35493446 GCCCAATAAACGATAA
1 GCCCAATAAATGATAA
35493462 ATGATAAAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
17 14 0.48
19 15 0.52
ACGTcount: A:0.46, C:0.17, G:0.15, T:0.21
Consensus pattern (17 bp):
GCCCAATAAATGATAAT
Found at i:35497588 original size:7 final size:7
Alignment explanation
Indices: 35497576--35497600 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
35497566 GTTGTGTGTC
35497576 CCTTGCA
1 CCTTGCA
35497583 CCTTGCA
1 CCTTGCA
35497590 CCTTGCA
1 CCTTGCA
35497597 CCTT
1 CCTT
35497601 AAATTTGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.12, C:0.44, G:0.12, T:0.32
Consensus pattern (7 bp):
CCTTGCA
Found at i:35498443 original size:22 final size:23
Alignment explanation
Indices: 35498416--35498482 Score: 68
Period size: 22 Copynumber: 3.0 Consensus size: 23
35498406 GGGTGTTACA
*
35498416 TAAATCTGTTTAGAACACTTAAG
1 TAAATCTATTTAGAACACTTAAG
* *
35498439 T-AATCATATTATA-AACA-TAAAT
1 TAAATC-TATT-TAGAACACTTAAG
35498461 TAAATCTATTTAGAACACTTAA
1 TAAATCTATTTAGAACACTTAA
35498483 TTAACCATAA
Statistics
Matches: 35, Mismatches: 4, Indels: 10
0.71 0.08 0.20
Matches are distributed among these distances:
21 2 0.06
22 16 0.46
23 15 0.43
24 2 0.06
ACGTcount: A:0.46, C:0.12, G:0.06, T:0.36
Consensus pattern (23 bp):
TAAATCTATTTAGAACACTTAAG
Found at i:35498484 original size:23 final size:23
Alignment explanation
Indices: 35498416--35498486 Score: 76
Period size: 23 Copynumber: 3.1 Consensus size: 23
35498406 GGGTGTTACA
* *
35498416 TAAATCTGTTTAGAACACTTAAG
1 TAAATCTATTTAGAACACTTAAT
*
35498439 T-AATCATATTATA-AACA-TAAAT
1 TAAATC-TATT-TAGAACACTTAAT
35498461 TAAATCTATTTAGAACACTTAAT
1 TAAATCTATTTAGAACACTTAAT
35498484 TAA
1 TAA
35498487 CCATAATTTA
Statistics
Matches: 39, Mismatches: 4, Indels: 10
0.74 0.08 0.19
Matches are distributed among these distances:
21 2 0.05
22 16 0.41
23 19 0.49
24 2 0.05
ACGTcount: A:0.46, C:0.11, G:0.06, T:0.37
Consensus pattern (23 bp):
TAAATCTATTTAGAACACTTAAT
Found at i:35504713 original size:43 final size:43
Alignment explanation
Indices: 35504654--35504880 Score: 221
Period size: 43 Copynumber: 5.3 Consensus size: 43
35504644 GTTTTCCCAC
*
35504654 AAACGCCGCTAAAGAACATGACCTTTAGCAGCGTTTTTACTAA
1 AAACGCCGCTAAAGAACATGACCTTTAGCAGCGCTTTTACTAA
** * *
35504697 AAACGGTGCTATAGAACATGACCTTTAG-AGACGCTTCT-CATAA
1 AAACGCCGCTAAAGAACATGACCTTTAGCAG-CGCTTTTAC-TAA
* * ** *
35504740 AAACGCCGCTCAAGAATATGACCTTTAGTGGCACTTTTACTAA
1 AAACGCCGCTAAAGAACATGACCTTTAGCAGCGCTTTTACTAA
* * * * * *
35504783 AAACGCCACTATAGAACATAACCTTTAGCGGCACTTCT-C-AA
1 AAACGCCGCTAAAGAACATGACCTTTAGCAGCGCTTTTACTAA
*
35504824 AAACGCCGCTAAAGAACATGACCTTTAGC-GTCGATTTTACTAA
1 AAACGCCGCTAAAGAACATGACCTTTAGCAG-CGCTTTTACTAA
* *
35504867 AAATGCTGCTAAAG
1 AAACGCCGCTAAAG
35504881 GTCATGTTCT
Statistics
Matches: 149, Mismatches: 28, Indels: 14
0.78 0.15 0.07
Matches are distributed among these distances:
40 1 0.01
41 32 0.21
42 5 0.03
43 109 0.73
44 2 0.01
ACGTcount: A:0.35, C:0.23, G:0.16, T:0.25
Consensus pattern (43 bp):
AAACGCCGCTAAAGAACATGACCTTTAGCAGCGCTTTTACTAA
Found at i:35504894 original size:84 final size:84
Alignment explanation
Indices: 35504654--35504877 Score: 281
Period size: 86 Copynumber: 2.6 Consensus size: 84
35504644 GTTTTCCCAC
* *
35504654 AAACGCCGCTAAAGAACATGACCTTTAGCAGCGTTTTTACTAAAAACGGTGCTATAGAACATGAC
1 AAACGCCGCTAAAGAACATGACCTTTAGC-GCGATTTTACTAAAAACGCTGCTATAGAACATGAC
* *
35504719 CTTTAGAGACGCTTCTCATAA
65 CTTTAGAGGCACTTCTCA-AA
* * * ** *
35504740 AAACGCCGCTCAAGAATATGACCTTTAGTG-GCACTTTTACTAAAAACGCCACTATAGAACATAA
1 AAACGCCGCTAAAGAACATGACCTTTAGCGCG-A-TTTTACTAAAAACGCTGCTATAGAACATGA
*
35504804 CCTTTAGCGGCACTTCTC-AA
64 CCTTTAGAGGCACTTCTCAAA
*
35504824 AAACGCCGCTAAAGAACATGACCTTTAGCGTCGATTTTACTAAAAATGCTGCTA
1 AAACGCCGCTAAAGAACATGACCTTTAGCG-CGATTTTACTAAAAACGCTGCTA
35504878 AAGGTCATGT
Statistics
Matches: 117, Mismatches: 17, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
84 47 0.40
85 2 0.02
86 68 0.58
ACGTcount: A:0.35, C:0.24, G:0.16, T:0.25
Consensus pattern (84 bp):
AAACGCCGCTAAAGAACATGACCTTTAGCGCGATTTTACTAAAAACGCTGCTATAGAACATGACC
TTTAGAGGCACTTCTCAAA
Found at i:35505082 original size:43 final size:43
Alignment explanation
Indices: 35505026--35505193 Score: 164
Period size: 43 Copynumber: 4.0 Consensus size: 43
35505016 ACAAATGTCT
* * *
35505026 CTAAAAAACATGACATTTAGCGGCGCTTCTCA-TAAAAACGCCA
1 CTAAAGAACATGACCTTTAGCGGCACTT-TCACTAAAAACGCCA
* ** * *
35505069 CTAAAGAATATGACCTTTAATGGCACTTTTACTAAAAACGCCG
1 CTAAAGAACATGACCTTTAGCGGCACTTTCACTAAAAACGCCA
* * *
35505112 CTATAGAACATGACCTTTAGCTGCAC-TTCTC-AAAAACG-CA
1 CTAAAGAACATGACCTTTAGCGGCACTTTCACTAAAAACGCCA
* * *
35505152 GCCAAAGAACATGACCTTTAGCGGCGCTTTTACTAAAAACGC
1 -CTAAAGAACATGACCTTTAGCGGCACTTTCACTAAAAACGC
35505194 TGCTAAAAGT
Statistics
Matches: 98, Mismatches: 22, Indels: 9
0.76 0.17 0.07
Matches are distributed among these distances:
40 1 0.01
41 29 0.30
42 8 0.08
43 60 0.61
ACGTcount: A:0.36, C:0.25, G:0.15, T:0.24
Consensus pattern (43 bp):
CTAAAGAACATGACCTTTAGCGGCACTTTCACTAAAAACGCCA
Found at i:35505182 original size:84 final size:85
Alignment explanation
Indices: 35505032--35505198 Score: 221
Period size: 84 Copynumber: 2.0 Consensus size: 85
35505022 GTCTCTAAAA
* * * *
35505032 AACATGACATTTAGCGGCGCTTCTCATAAAAACGCCACTAAAGAATATGACCTTTAATGGCACTT
1 AACATGACATTTAGCGGCACTTCTCA-AAAAACGCCACCAAAGAACATGACCTTTAACGGCACTT
35505097 TTACTAAAAACGCCGCTATAG
65 TTACTAAAAACGCCGCTATAG
* * * *
35505118 AACATGACCTTTAGCTGCACTTCTC-AAAAACG-CAGCCAAAGAACATGACCTTTAGCGGCGCTT
1 AACATGACATTTAGCGGCACTTCTCAAAAAACGCCA-CCAAAGAACATGACCTTTAACGGCACTT
*
35505181 TTACTAAAAACGCTGCTA
65 TTACTAAAAACGCCGCTA
35505199 AAAGTCATGT
Statistics
Matches: 71, Mismatches: 9, Indels: 4
0.85 0.11 0.05
Matches are distributed among these distances:
83 2 0.03
84 47 0.66
86 22 0.31
ACGTcount: A:0.35, C:0.25, G:0.16, T:0.25
Consensus pattern (85 bp):
AACATGACATTTAGCGGCACTTCTCAAAAAACGCCACCAAAGAACATGACCTTTAACGGCACTTT
TACTAAAAACGCCGCTATAG
Found at i:35505548 original size:27 final size:23
Alignment explanation
Indices: 35505504--35505568 Score: 64
Period size: 26 Copynumber: 2.8 Consensus size: 23
35505494 AAAATAGTTT
35505504 AAAAA-TT-ATAAAAA-TATTCAA
1 AAAAAGTTAATAAAAATTATT-AA
*
35505525 AAAAATGTATAATTAAAAATTATTAT
1 AAAAA-GT-TAA-TAAAAATTATTAA
35505551 AAAAAGTTAATAAAAATT
1 AAAAAGTTAATAAAAATT
35505569 CCAAAAAAAT
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
21 5 0.14
23 9 0.24
24 4 0.11
25 3 0.08
26 12 0.32
27 4 0.11
ACGTcount: A:0.63, C:0.02, G:0.03, T:0.32
Consensus pattern (23 bp):
AAAAAGTTAATAAAAATTATTAA
Found at i:35515212 original size:23 final size:22
Alignment explanation
Indices: 35515143--35515205 Score: 85
Period size: 21 Copynumber: 2.9 Consensus size: 22
35515133 TATGACACAT
*
35515143 AAGTGCCTGAA-ACAACACACG
1 AAGTGCCTGAATACGACACACG
*
35515164 AGGTGCCTG-ATACGACACACG
1 AAGTGCCTGAATACGACACACG
35515185 AAGTGCCTGATATACGACACA
1 AAGTGCCTGA-ATACGACACA
35515206 TAAAGTGTCT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 1 0.03
21 25 0.69
23 10 0.28
ACGTcount: A:0.37, C:0.27, G:0.22, T:0.14
Consensus pattern (22 bp):
AAGTGCCTGAATACGACACACG
Found at i:35516434 original size:26 final size:26
Alignment explanation
Indices: 35516405--35516512 Score: 198
Period size: 26 Copynumber: 4.2 Consensus size: 26
35516395 TGATACAAAT
35516405 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
35516431 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
35516457 TAATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
35516483 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
35516509 TGAT
1 TGAT
35516513 GGGAATTTCA
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 78 1.00
ACGTcount: A:0.31, C:0.06, G:0.26, T:0.36
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Done.