Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr01 ID=Chr01-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: 55868233
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 983842 characters in sequence are not A, C, G, or T
File 119 of 187
Found at i:35796836 original size:17 final size:19
Alignment explanation
Indices: 35796803--35796837 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
35796793 GCATGTTATT
35796803 TAATTAACCATTTCAATAA
1 TAATTAACCATTTCAATAA
35796822 TAATT-ACCA-TTCAATA
1 TAATTAACCATTTCAATA
35796838 TACCACATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 4 0.25
19 5 0.31
ACGTcount: A:0.46, C:0.17, G:0.00, T:0.37
Consensus pattern (19 bp):
TAATTAACCATTTCAATAA
Found at i:35803289 original size:27 final size:27
Alignment explanation
Indices: 35803258--35803315 Score: 116
Period size: 27 Copynumber: 2.1 Consensus size: 27
35803248 AGTTTCCTTA
35803258 TCTTGTACAAGTGGAATAACAGTTATT
1 TCTTGTACAAGTGGAATAACAGTTATT
35803285 TCTTGTACAAGTGGAATAACAGTTATT
1 TCTTGTACAAGTGGAATAACAGTTATT
35803312 TCTT
1 TCTT
35803316 TGGGAGTGAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.31, C:0.12, G:0.17, T:0.40
Consensus pattern (27 bp):
TCTTGTACAAGTGGAATAACAGTTATT
Found at i:35805916 original size:21 final size:23
Alignment explanation
Indices: 35805868--35805916 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
35805858 TAGATGCTCT
*
35805868 TTGGCCATATGTATGATGTTCAG
1 TTGGCCATATGTAGGATGTTCAG
35805891 TTGGCCACTA-GTAGGA-GTTC-G
1 TTGGCCA-TATGTAGGATGTTCAG
35805912 TTGGC
1 TTGGC
35805917 ATGCTCTCTA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
21 6 0.25
22 4 0.17
23 12 0.50
24 2 0.08
ACGTcount: A:0.18, C:0.16, G:0.31, T:0.35
Consensus pattern (23 bp):
TTGGCCATATGTAGGATGTTCAG
Found at i:35810611 original size:14 final size:14
Alignment explanation
Indices: 35810592--35810618 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
35810582 AAAAAACCAT
35810592 AGAGTATAAGACAC
1 AGAGTATAAGACAC
35810606 AGAGTATAAGACA
1 AGAGTATAAGACA
35810619 TCCCATTTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.11, G:0.22, T:0.15
Consensus pattern (14 bp):
AGAGTATAAGACAC
Found at i:35810838 original size:23 final size:23
Alignment explanation
Indices: 35810810--35810854 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
35810800 CCACTATACC
*
35810810 AAATGAACATGCAAAATGCAACA
1 AAATGAACATACAAAATGCAACA
*
35810833 AAATGATCATACAAAATGCAAC
1 AAATGAACATACAAAATGCAAC
35810855 CTAGATGCAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.56, C:0.18, G:0.11, T:0.16
Consensus pattern (23 bp):
AAATGAACATACAAAATGCAACA
Found at i:35818346 original size:19 final size:19
Alignment explanation
Indices: 35818322--35818358 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
35818312 TGTTGTCACT
*
35818322 GTTTAATAATAGATCATTC
1 GTTTAATAATAAATCATTC
35818341 GTTTAATAATAAATCATT
1 GTTTAATAATAAATCATT
35818359 GTTGTCATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.41, C:0.08, G:0.08, T:0.43
Consensus pattern (19 bp):
GTTTAATAATAAATCATTC
Found at i:35824354 original size:26 final size:25
Alignment explanation
Indices: 35824286--35824380 Score: 70
Period size: 26 Copynumber: 3.8 Consensus size: 25
35824276 TAAGATATGC
** **
35824286 AAAAATATGTATGTACGTGCAT-AT
1 AAAAATATGTATGTATATAAATAAT
* *
35824310 AAAAATATATATACT-TATAAA-AAT
1 AAAAATATGTAT-GTATATAAATAAT
35824334 AAAAGGATATGTATGTATATAAATTAAT
1 AAAA--ATATGTATGTATATAAA-TAAT
*
35824362 AATAATATGTATGTATATA
1 AAAAATATGTATGTATATA
35824381 CGGATTTATA
Statistics
Matches: 55, Mismatches: 9, Indels: 12
0.72 0.12 0.16
Matches are distributed among these distances:
24 19 0.35
25 2 0.04
26 28 0.51
28 6 0.11
ACGTcount: A:0.51, C:0.03, G:0.11, T:0.36
Consensus pattern (25 bp):
AAAAATATGTATGTATATAAATAAT
Found at i:35824568 original size:19 final size:18
Alignment explanation
Indices: 35824524--35824569 Score: 51
Period size: 19 Copynumber: 2.6 Consensus size: 18
35824514 ATATATATAT
35824524 ATATATGT-TATAAAACA
1 ATATATGTATATAAAACA
*
35824541 ATGTATGTATATCACAAA-A
1 ATATATGTATAT-A-AAACA
35824560 ATATATGTAT
1 ATATATGTAT
35824570 GTACATATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
17 7 0.29
18 3 0.12
19 11 0.46
20 3 0.12
ACGTcount: A:0.48, C:0.07, G:0.09, T:0.37
Consensus pattern (18 bp):
ATATATGTATATAAAACA
Found at i:35824627 original size:3 final size:3
Alignment explanation
Indices: 35824619--35824665 Score: 85
Period size: 3 Copynumber: 15.7 Consensus size: 3
35824609 AACAAATAGG
*
35824619 TAA TAA TAA TAA TAA CAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
35824666 GGACTAAATC
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:35825406 original size:20 final size:20
Alignment explanation
Indices: 35825368--35825406 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
35825358 TGCAAAGAAA
*
35825368 AAAATAAAACAAAATAAGAT
1 AAAATAAAACAAAAGAAGAT
35825388 AAAATAAAA-AACAAGAAGA
1 AAAATAAAACAA-AAGAAGA
35825407 AATAGTAAGG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 2 0.12
20 15 0.88
ACGTcount: A:0.77, C:0.05, G:0.08, T:0.10
Consensus pattern (20 bp):
AAAATAAAACAAAAGAAGAT
Found at i:35826079 original size:6 final size:6
Alignment explanation
Indices: 35826056--35826103 Score: 78
Period size: 6 Copynumber: 7.7 Consensus size: 6
35826046 TGTCTAAATG
35826056 TTTTCA TTTCTCCA TTTTCA TTTTCA TTTTCA TTTTCA TTTTCA TTTT
1 TTTTCA TTT-T-CA TTTTCA TTTTCA TTTTCA TTTTCA TTTTCA TTTT
35826104 GAAGAAAACC
Statistics
Matches: 40, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
6 33 0.82
7 2 0.05
8 5 0.12
ACGTcount: A:0.15, C:0.19, G:0.00, T:0.67
Consensus pattern (6 bp):
TTTTCA
Found at i:35840956 original size:69 final size:69
Alignment explanation
Indices: 35840863--35841305 Score: 539
Period size: 69 Copynumber: 6.4 Consensus size: 69
35840853 AGGTCCATTG
* * * *
35840863 TTTGCAGATTCTGTTCCAAGCACCCCTGCCTACGCAGGTGACATGTTCCAA-GGGAAGAGCTCAT
1 TTTGCAGATTCTGTTCCAAGCACTCCTGCCTATGCAGATAACATGTT-CAAGGGGAAGAGCTCAT
*
35840927 CTGTT
65 CTATT
** * * * * *
35840932 TTTGGGGAATCTGTTCCAAGCACCCCTGCTTATGCAGATAACATGTTCCAGGGGAAGGGCTCATC
1 TTTGCAGATTCTGTTCCAAGCACTCCTGCCTATGCAGATAACATGTTCAAGGGGAAGAGCTCATC
*
35840997 TGTT
66 TATT
* * * * *
35841001 TTTGCAGATTCTGTTCCAAGCACTCCGGCCTATGCAGATAGCATGTTTAAGGGGAAGAGTTCGTC
1 TTTGCAGATTCTGTTCCAAGCACTCCTGCCTATGCAGATAACATGTTCAAGGGGAAGAGCTCAT-
*
35841066 CT-TG
65 CTATT
* * ** * *
35841070 TTTGCAGATTCTGTTCCAAGCACTCCTGCCTATGCAGATAACTTGTTTAAGGGTCAGGGTTCATC
1 TTTGCAGATTCTGTTCCAAGCACTCCTGCCTATGCAGATAACATGTTCAAGGGGAAGAGCTCATC
* *
35841135 CATA
66 TATT
* * * * *
35841139 TTTGGAGATTCTGTTCCAAGCACTCCTGCCTATGCAGATAACTTGTTCAAGGGGAAGGGTTCGTC
1 TTTGCAGATTCTGTTCCAAGCACTCCTGCCTATGCAGATAACATGTTCAAGGGGAAGAGCTCATC
* *
35841204 CATA
66 TATT
35841208 TTTGCAGATTCTGTTCCAAGCACTCCTGCCTATGCAGATAACATGTTCAAGGGGAAGAGCTCATC
1 TTTGCAGATTCTGTTCCAAGCACTCCTGCCTATGCAGATAACATGTTCAAGGGGAAGAGCTCATC
35841273 TATT
66 TATT
*
35841277 TTTGCAGATTCTGTTCCAAGCACCCCTGC
1 TTTGCAGATTCTGTTCCAAGCACTCCTGC
35841306 TTATCATTAT
Statistics
Matches: 327, Mismatches: 44, Indels: 6
0.87 0.12 0.02
Matches are distributed among these distances:
68 3 0.01
69 322 0.98
70 2 0.01
ACGTcount: A:0.23, C:0.24, G:0.23, T:0.30
Consensus pattern (69 bp):
TTTGCAGATTCTGTTCCAAGCACTCCTGCCTATGCAGATAACATGTTCAAGGGGAAGAGCTCATC
TATT
Found at i:35841215 original size:207 final size:207
Alignment explanation
Indices: 35840855--35841305 Score: 600
Period size: 207 Copynumber: 2.2 Consensus size: 207
35840845 CCTGGGAAAG
* *
35840855 GTCCATTGTTTGCAGATTCTGTTCCAAGCACCCCTGCCTACGCAGGTGACATGTTCCAAGGGAAG
1 GTCC-TTGTTTGCAGATTCTGTTCCAAGCACCCCTGCCTACGCAGATAACATGTTCCAAGGGAAG
** * * * *
35840920 AGCTCATCTGTTTTTGGGGAATCTGTTCCAAGCACCCCTGCTTATGCAGATAACATGTTCCAGGG
65 AGCTCATCCATATTTGGAGAATCTGTTCCAAGCACCCCTGCCTATGCAGATAACATGTTCAAGGG
** * * *
35840985 GAAGGGCTCATCTGTTTTTGCAGATTCTGTTCCAAGCACTCCGGCCTATGCAGATAGCATGTTTA
130 GAAGGGCTCATCCATATTTGCAGATTCTGTTCCAAGCACTCCGGCCTATGCAGATAACATGTTCA
*
35841050 AGGGGAAGAGTTC
195 AGGGGAAGAGCTC
* * * * *
35841063 GTCCTTGTTTGCAGATTCTGTTCCAAGCACTCCTGCCTATGCAGATAACTTGTT-TAAGGGTCAG
1 GTCCTTGTTTGCAGATTCTGTTCCAAGCACCCCTGCCTACGCAGATAACATGTTCCAAGGG-AAG
* * * * *
35841127 GGTTCATCCATATTTGGAGATTCTGTTCCAAGCACTCCTGCCTATGCAGATAACTTGTTCAAGGG
65 AGCTCATCCATATTTGGAGAATCTGTTCCAAGCACCCCTGCCTATGCAGATAACATGTTCAAGGG
* * *
35841192 GAAGGGTTCGTCCATATTTGCAGATTCTGTTCCAAGCACTCCTGCCTATGCAGATAACATGTTCA
130 GAAGGGCTCATCCATATTTGCAGATTCTGTTCCAAGCACTCCGGCCTATGCAGATAACATGTTCA
35841257 AGGGGAAGAGCTC
195 AGGGGAAGAGCTC
* *
35841270 AT-CTATTTTTGCAGATTCTGTTCCAAGCACCCCTGC
1 GTCCT-TGTTTGCAGATTCTGTTCCAAGCACCCCTGC
35841306 TTATCATTAT
Statistics
Matches: 211, Mismatches: 30, Indels: 5
0.86 0.12 0.02
Matches are distributed among these distances:
206 7 0.03
207 200 0.95
208 4 0.02
ACGTcount: A:0.22, C:0.24, G:0.23, T:0.30
Consensus pattern (207 bp):
GTCCTTGTTTGCAGATTCTGTTCCAAGCACCCCTGCCTACGCAGATAACATGTTCCAAGGGAAGA
GCTCATCCATATTTGGAGAATCTGTTCCAAGCACCCCTGCCTATGCAGATAACATGTTCAAGGGG
AAGGGCTCATCCATATTTGCAGATTCTGTTCCAAGCACTCCGGCCTATGCAGATAACATGTTCAA
GGGGAAGAGCTC
Found at i:35850494 original size:15 final size:15
Alignment explanation
Indices: 35850469--35850504 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
35850459 GGAACCATAT
35850469 TTTAGAACCTTTTCTG
1 TTTA-AACCTTTTCTG
*
35850485 TTTAAACCTTTTTTG
1 TTTAAACCTTTTCTG
35850500 TTTAA
1 TTTAA
35850505 TAAAAGGTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 15 0.79
16 4 0.21
ACGTcount: A:0.22, C:0.14, G:0.08, T:0.56
Consensus pattern (15 bp):
TTTAAACCTTTTCTG
Found at i:35862011 original size:94 final size:92
Alignment explanation
Indices: 35861799--35862344 Score: 438
Period size: 94 Copynumber: 5.8 Consensus size: 92
35861789 TCACAGTTAC
* * * * * *
35861799 ATCTTGCTTCATTGCAACTTCAAGGAGATAAGATTTGCTGTTGTAGTTTCACTCCAACCCACT--
1 ATCTTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCT-ATGTAATTTCA-TCCCACCCACTAC
* * **
35861862 -ACTTCAGAGG-TATAGAATTTATAATTTT
64 AACTTCA-AGGATATAGGATTTGTAGCTTT
* * * * *
35861890 ATCTTGCTCCACTGCAACTTTAAGGAGATAAGATTTGCCATGGTAACTTCATCCCGACCCACTGC
1 ATCTTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCTAT-GTAATTTCATCCC-ACCCACTAC
*
35861955 AACTTCAAGGGTATAGGATTTGTAGCTTT
64 AACTTCAAGGATATAGGATTTGTAGCTTT
* * * * * ** *
35861984 ACCTTGCTCCATTGCACCTTCAGGGAGATAGGATTTGCTACTGTAATTTTAATCCCTGCCACTAT
1 ATCTTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCTA-TGTAA-TTTCATCCCACCCACTAC
* * * * * *
35862049 AATTTTAAGGATATAGGGTTTCTAACTTC
64 AACTTCAAGGATATAGGATTTGTAGCTTT
* * ** * *
35862078 ATCTTGCTCCACTGTAACTTCAGGGAGATAATATTTGCTACAATAATTTCAAT-CCATTCCACTG
1 ATCTTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCTA-TGTAATTTC-ATCCCA-CCCACTA
* *
35862142 CAACTTTAAGGATATAGGATTTGTAGCTTC
63 CAACTTCAAGGATATAGGATTTGTAGCTTT
* * *
35862172 ATCTTGCTCCACTGCAACTTTAGGGAGATAAGATTCGCTACTGTAATTTCAAT-CCATTCCACTA
1 ATCTTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCTA-TGTAATTTC-ATCCCA-CCCACTA
*
35862236 CAACTTCAAGGATATAGGATTTGTAGTTTT
63 CAACTTCAAGGATATAGGATTTGTAGCTTT
* * * * * * * ** *
35862266 ATCTTACTCCACTACAACTTTAGGGAGGTAAGATTTTCAATTGTAATTTTGATCTGATCCACTAC
1 ATCTTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCTA-TGTAA-TTTCATCCCACCCACTAC
*
35862331 ATCTTCAAGGATAT
64 AACTTCAAGGATAT
35862345 GGGAGTCACT
Statistics
Matches: 373, Mismatches: 70, Indels: 21
0.80 0.15 0.05
Matches are distributed among these distances:
90 4 0.01
91 49 0.13
93 8 0.02
94 300 0.80
95 12 0.03
ACGTcount: A:0.28, C:0.21, G:0.16, T:0.35
Consensus pattern (92 bp):
ATCTTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCTATGTAATTTCATCCCACCCACTACAA
CTTCAAGGATATAGGATTTGTAGCTTT
Found at i:35862164 original size:50 final size:49
Alignment explanation
Indices: 35862110--35862258 Score: 130
Period size: 50 Copynumber: 3.1 Consensus size: 49
35862100 GGGAGATAAT
35862110 ATTTGCTACAATAATTTCAATCCATTCCACTGCAACTTTAAGGATATAGG
1 ATTTGCTAC-ATAATTTCAATCCATTCCACTGCAACTTTAAGGATATAGG
* * * * * * *
35862160 ATTTG-TAGCTTCA--TC-TTGC--TCCACTGCAACTTTAGGGAGATAAG
1 ATTTGCTA-CATAATTTCAATCCATTCCACTGCAACTTTAAGGATATAGG
* * * *
35862204 ATTCGCTACTGTAATTTCAATCCATTCCACTACAACTTCAAGGATATAGG
1 ATTTGCTAC-ATAATTTCAATCCATTCCACTGCAACTTTAAGGATATAGG
35862254 ATTTG
1 ATTTG
35862259 TAGTTTTATC
Statistics
Matches: 73, Mismatches: 18, Indels: 16
0.68 0.17 0.15
Matches are distributed among these distances:
44 27 0.37
45 4 0.05
46 2 0.03
47 4 0.05
48 2 0.03
49 4 0.05
50 30 0.41
ACGTcount: A:0.30, C:0.21, G:0.15, T:0.34
Consensus pattern (49 bp):
ATTTGCTACATAATTTCAATCCATTCCACTGCAACTTTAAGGATATAGG
Found at i:35862278 original size:188 final size:188
Alignment explanation
Indices: 35861798--35862301 Score: 552
Period size: 188 Copynumber: 2.7 Consensus size: 188
35861788 ATCACAGTTA
* * ** * *
35861798 CATCTTGCTTCATTGCAACTTCAAGGAGATAAGATTTGCTGTTGTAGTTTCACTCCA-ACC-C-A
1 CATCTTGCTCCATTGCAACTTCAGGGAGATAAGATTTGCTACTGTAATTTCAATCCATACCACTA
* * *
35861860 CTACTTCAGAGG-TATAGAATTTATAATTTTATCTTGCTCCACTGCAACTTTAAGGAGATAAGAT
66 CAACTTCA-AGGATATAGGATTTATAATTTTATCTTGCTCCACTGCAACTTTAGGGAGATAAGAT
*** *
35861924 TTGCCATGGTAACTTCATCCCGACCCACTGCAACTTCAAGGGTATAGGATTTGTAGCTT
130 TTGCCACAATAACTTCATCCCGACCCACTGCAACTTCAAGGATATAGGATTTGTAGCTT
* * * * * * *
35861983 TACCTTGCTCCATTGCACCTTCAGGGAGATAGGATTTGCTACTGTAATTTTAATCCCTGCCACTA
1 CATCTTGCTCCATTGCAACTTCAGGGAGATAAGATTTGCTACTGTAATTTCAATCCATACCACTA
* * * * * * * * * *
35862048 TAATTTTAAGGATATAGGGTTTCTAACTTCATCTTGCTCCACTGTAACTTCAGGGAGATAATATT
66 CAACTTCAAGGATATAGGATTTATAATTTTATCTTGCTCCACTGCAACTTTAGGGAGATAAGATT
* * * *
35862113 TGCTACAATAATTTCAAT-CC-ATTCCACTGCAACTTTAAGGATATAGGATTTGTAGCTT
131 TGCCACAATAACTTC-ATCCCGA-CCCACTGCAACTTCAAGGATATAGGATTTGTAGCTT
* * * *
35862171 CATCTTGCTCCACTGCAACTTTAGGGAGATAAGATTCGCTACTGTAATTTCAATCCATTCCACTA
1 CATCTTGCTCCATTGCAACTTCAGGGAGATAAGATTTGCTACTGTAATTTCAATCCATACCACTA
* * * * *
35862236 CAACTTCAAGGATATAGGATTTGTAGTTTTATCTTACTCCACTACAACTTTAGGGAGGTAAGATT
66 CAACTTCAAGGATATAGGATTTATAATTTTATCTTGCTCCACTGCAACTTTAGGGAGATAAGATT
35862301 T
131 T
35862302 TCAATTGTAA
Statistics
Matches: 255, Mismatches: 58, Indels: 9
0.79 0.18 0.03
Matches are distributed among these distances:
185 45 0.18
186 2 0.01
187 5 0.02
188 201 0.79
189 2 0.01
ACGTcount: A:0.28, C:0.21, G:0.16, T:0.35
Consensus pattern (188 bp):
CATCTTGCTCCATTGCAACTTCAGGGAGATAAGATTTGCTACTGTAATTTCAATCCATACCACTA
CAACTTCAAGGATATAGGATTTATAATTTTATCTTGCTCCACTGCAACTTTAGGGAGATAAGATT
TGCCACAATAACTTCATCCCGACCCACTGCAACTTCAAGGATATAGGATTTGTAGCTT
Found at i:35862301 original size:44 final size:44
Alignment explanation
Indices: 35862135--35862301 Score: 120
Period size: 44 Copynumber: 3.7 Consensus size: 44
35862125 TTCAATCCAT
* * * * * *
35862135 TCCACTGCAACTTTAAGGATATAGGATTTGTAGCTTCATCTTGC
1 TCCACTACAACTTTAAGGAGATAAGATTTGTAGTTTTATCTTAC
* * * * *
35862179 TCCACTGCAACTTTAGGGAGATAAGATTCGCTACTGTAATTTCAATC-CAT
1 TCCACTACAACTTTAAGGAGATAAGATTTG-TA--GT--TTT--ATCTTAC
* * *
35862229 TCCACTACAACTTCAAGGATATAGGATTTGTAGTTTTATCTTAC
1 TCCACTACAACTTTAAGGAGATAAGATTTGTAGTTTTATCTTAC
* *
35862273 TCCACTACAACTTTAGGGAGGTAAGATTT
1 TCCACTACAACTTTAAGGAGATAAGATTT
35862302 TCAATTGTAA
Statistics
Matches: 93, Mismatches: 22, Indels: 16
0.71 0.17 0.12
Matches are distributed among these distances:
43 3 0.03
44 51 0.55
45 5 0.05
47 3 0.03
49 4 0.04
50 24 0.26
51 3 0.03
ACGTcount: A:0.29, C:0.20, G:0.17, T:0.35
Consensus pattern (44 bp):
TCCACTACAACTTTAAGGAGATAAGATTTGTAGTTTTATCTTAC
Found at i:35865566 original size:22 final size:22
Alignment explanation
Indices: 35865540--35865584 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
35865530 ATTATATGTA
*
35865540 TTAATTCATAATATAA-TTAATT
1 TTAATTCAT-ATACAATTTAATT
*
35865562 TTAATTTATATACAATTTAATT
1 TTAATTCATATACAATTTAATT
35865584 T
1 T
35865585 GGGTTAATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 5 0.25
22 15 0.75
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.53
Consensus pattern (22 bp):
TTAATTCATATACAATTTAATT
Found at i:35865649 original size:14 final size:14
Alignment explanation
Indices: 35865630--35865656 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
35865620 GTGGTCCAGT
35865630 TGAACTGAACCGAG
1 TGAACTGAACCGAG
35865644 TGAACTGAACCGA
1 TGAACTGAACCGA
35865657 CCAAGAAAGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.22, G:0.26, T:0.15
Consensus pattern (14 bp):
TGAACTGAACCGAG
Found at i:35869286 original size:236 final size:236
Alignment explanation
Indices: 35868873--35869344 Score: 926
Period size: 236 Copynumber: 2.0 Consensus size: 236
35868863 AATCACATGG
35868873 ACTTAAAAACGTTAAATGTTACCTGGTCATCCTGAACAGACATAGTAAGCTCGCCCTTCTGCACA
1 ACTTAAAAACGTTAAATGTTACCTGGTCATCCTGAACAGACATAGTAAGCTCGCCCTTCTGCACA
35868938 TCAATAAGGGTCCTTCCGGTTGCTAAGAATGGTCTTCTTAGGATGATTGACACCTCTTTGTCTGC
66 TCAATAAGGGTCCTTCCGGTTGCTAAGAATGGTCTTCTTAGGATGATTGACACCTCTTTGTCTGC
35869003 TTCAAAGTCTAGAATCACAAAGTCAACAGGAAAGATAAATTTATCTACACGTACCAATACGTCAT
131 TTCAAAGTCTAGAATCACAAAGTCAACAGGAAAGATAAATTTATCTACACGTACCAATACGTCAT
35869068 CGATTTTTCCTTCTGGATGTGCTAAGAATCGATCTGCTAAT
196 CGATTTTTCCTTCTGGATGTGCTAAGAATCGATCTGCTAAT
* *
35869109 ACTTAAAAACGTTAAATGTTACCTGGTCATCCTGAACAGGCATAGTAAGCTCGCCTTTCTGCACA
1 ACTTAAAAACGTTAAATGTTACCTGGTCATCCTGAACAGACATAGTAAGCTCGCCCTTCTGCACA
35869174 TCAATAAGGGTCCTTCCGGTTGCTAAGAATGGTCTTCTTAGGATGATTGACACCTCTTTGTCTGC
66 TCAATAAGGGTCCTTCCGGTTGCTAAGAATGGTCTTCTTAGGATGATTGACACCTCTTTGTCTGC
35869239 TTCAAAGTCTAGAATCACAAAGTCAACAGGAAAGATAAATTTATCTACACGTACCAATACGTCAT
131 TTCAAAGTCTAGAATCACAAAGTCAACAGGAAAGATAAATTTATCTACACGTACCAATACGTCAT
35869304 CGATTTTTCCTTCTGGATGTGCTAAGAATCGATCTGCTAAT
196 CGATTTTTCCTTCTGGATGTGCTAAGAATCGATCTGCTAAT
35869345 TGAAGTGTAA
Statistics
Matches: 234, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
236 234 1.00
ACGTcount: A:0.30, C:0.22, G:0.18, T:0.31
Consensus pattern (236 bp):
ACTTAAAAACGTTAAATGTTACCTGGTCATCCTGAACAGACATAGTAAGCTCGCCCTTCTGCACA
TCAATAAGGGTCCTTCCGGTTGCTAAGAATGGTCTTCTTAGGATGATTGACACCTCTTTGTCTGC
TTCAAAGTCTAGAATCACAAAGTCAACAGGAAAGATAAATTTATCTACACGTACCAATACGTCAT
CGATTTTTCCTTCTGGATGTGCTAAGAATCGATCTGCTAAT
Found at i:35881216 original size:31 final size:31
Alignment explanation
Indices: 35881154--35881216 Score: 74
Period size: 31 Copynumber: 2.0 Consensus size: 31
35881144 TAGTCCGGTA
* * *
35881154 ACTTAAACTAAAACTTTTAAATAGTTTAATG
1 ACTTAAACTAAAACTTTCAAATAATTCAATG
*
35881185 ACTTAAA-TAAAAACTTTCGAATAATTCAATG
1 ACTTAAACT-AAAACTTTCAAATAATTCAATG
35881216 A
1 A
35881217 TCAAATTGTA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
30 1 0.04
31 26 0.96
ACGTcount: A:0.48, C:0.11, G:0.06, T:0.35
Consensus pattern (31 bp):
ACTTAAACTAAAACTTTCAAATAATTCAATG
Found at i:35883735 original size:16 final size:16
Alignment explanation
Indices: 35883716--35883748 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
35883706 CCCAAATATA
35883716 TCCCTCAAAAAATTTC
1 TCCCTCAAAAAATTTC
35883732 TCCCTCAAAAAATTTC
1 TCCCTCAAAAAATTTC
35883748 T
1 T
35883749 TAGAATTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.36, C:0.30, G:0.00, T:0.33
Consensus pattern (16 bp):
TCCCTCAAAAAATTTC
Found at i:35886152 original size:51 final size:50
Alignment explanation
Indices: 35886088--35886265 Score: 216
Period size: 51 Copynumber: 3.5 Consensus size: 50
35886078 CCGGTTCACA
*
35886088 TAGTAGCCTGCACATAGTACTACACATGTGACCATTTTCATCCGATACACG
1 TAGTAGCCTGCACATAGTACTACACATGTGACCA-TATCATCCGATACACG
* * * * *
35886139 TAGTAGCCTGCACATAGTACTACACACGTGATCGA-AGCTATCCGATACGCA
1 TAGTAGCCTGCACATAGTACTACACATGTGA-CCATATC-ATCCGATACACG
* * *
35886190 TAGTAGCCTGCACATAGTACTACACATGCGACC-TATCATCCCGGTACAAG
1 TAGTAGCCTGCACATAGTACTACACATGTGACCATATCAT-CCGATACACG
*
35886240 TAGTAGCCTGCACACAGTACTACACA
1 TAGTAGCCTGCACATAGTACTACACA
35886266 CATGACCTAG
Statistics
Matches: 108, Mismatches: 15, Indels: 9
0.82 0.11 0.07
Matches are distributed among these distances:
49 2 0.02
50 35 0.32
51 69 0.64
52 2 0.02
ACGTcount: A:0.31, C:0.29, G:0.17, T:0.23
Consensus pattern (50 bp):
TAGTAGCCTGCACATAGTACTACACATGTGACCATATCATCCGATACACG
Found at i:35889067 original size:42 final size:42
Alignment explanation
Indices: 35888987--35889068 Score: 103
Period size: 42 Copynumber: 2.0 Consensus size: 42
35888977 CGTTTTCTCT
* * **
35888987 ATGCCATAGTCCAACTATGGTCTTACATATATTTACATATTG
1 ATGCCATAGCCCAACTATGGTCTTACACATATGCACATATTG
*
35889029 ATGCCATAGCCCAGCTATGGTCTTACACAGTA-GCACATAT
1 ATGCCATAGCCCAACTATGGTCTTACACA-TATGCACATAT
35889069 CACACCAATG
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
42 32 0.94
43 2 0.06
ACGTcount: A:0.30, C:0.23, G:0.15, T:0.32
Consensus pattern (42 bp):
ATGCCATAGCCCAACTATGGTCTTACACATATGCACATATTG
Found at i:35891935 original size:51 final size:50
Alignment explanation
Indices: 35891871--35892048 Score: 216
Period size: 51 Copynumber: 3.5 Consensus size: 50
35891861 CCGGTTCACA
*
35891871 TAGTAGCCTGCACATAGTACTACACATGTGACCATTTTCATCCGATACACG
1 TAGTAGCCTGCACATAGTACTACACATGTGACCA-TATCATCCGATACACG
* * * * *
35891922 TAGTAGCCTGCACATAGTACTACACACGTGATCGA-AGCTATCCGATACGCA
1 TAGTAGCCTGCACATAGTACTACACATGTGA-CCATATC-ATCCGATACACG
* * *
35891973 TAGTAGCCTGCACATAGTACTACACATGCGACC-TATCATCCCGGTACAAG
1 TAGTAGCCTGCACATAGTACTACACATGTGACCATATCAT-CCGATACACG
*
35892023 TAGTAGCCTGCACACAGTACTACACA
1 TAGTAGCCTGCACATAGTACTACACA
35892049 CATGACCTAG
Statistics
Matches: 108, Mismatches: 15, Indels: 9
0.82 0.11 0.07
Matches are distributed among these distances:
49 2 0.02
50 35 0.32
51 69 0.64
52 2 0.02
ACGTcount: A:0.31, C:0.29, G:0.17, T:0.23
Consensus pattern (50 bp):
TAGTAGCCTGCACATAGTACTACACATGTGACCATATCATCCGATACACG
Found at i:35894851 original size:42 final size:42
Alignment explanation
Indices: 35894771--35894852 Score: 103
Period size: 42 Copynumber: 2.0 Consensus size: 42
35894761 CGTTTTCTCT
* * **
35894771 ATGCCATAGTCCAACTATGGTCTTACATATATTTACATATTG
1 ATGCCATAGCCCAACTATGGTCTTACACATATGCACATATTG
*
35894813 ATGCCATAGCCCAGCTATGGTCTTACACAGTA-GCACATAT
1 ATGCCATAGCCCAACTATGGTCTTACACA-TATGCACATAT
35894853 CACACCAATG
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
42 32 0.94
43 2 0.06
ACGTcount: A:0.30, C:0.23, G:0.15, T:0.32
Consensus pattern (42 bp):
ATGCCATAGCCCAACTATGGTCTTACACATATGCACATATTG
Found at i:35897147 original size:102 final size:101
Alignment explanation
Indices: 35897028--35897212 Score: 300
Period size: 101 Copynumber: 1.8 Consensus size: 101
35897018 ACCCGGTTCA
* *
35897028 CATAGTAGCCTGCACATAGTACTACACATGTGACCATTTTCA-TCCGATACACGTAGTAGCCTGC
1 CATAGTAGCCTGCACATAATACTACACATGTGACC--TATCATTCCGATACACGTAGTAGCCTGC
35897092 ACATAGTACTACACACGTGATCGAAGCTCTCCGGTACG
64 ACATAGTACTACACACGTGATCGAAGCTCTCCGGTACG
* *
35897130 CATAGTAGCCTGCACATAATACTACACATGTGACCTATCATTCCGGTACATGTAGTAGCCTGCAC
1 CATAGTAGCCTGCACATAATACTACACATGTGACCTATCATTCCGATACACGTAGTAGCCTGCAC
*
35897195 ATGGTACTACACACGTGA
66 ATAGTACTACACACGTGA
35897213 CCTAGCAACT
Statistics
Matches: 77, Mismatches: 5, Indels: 3
0.91 0.06 0.04
Matches are distributed among these distances:
100 4 0.05
101 39 0.51
102 34 0.44
ACGTcount: A:0.29, C:0.28, G:0.18, T:0.25
Consensus pattern (101 bp):
CATAGTAGCCTGCACATAATACTACACATGTGACCTATCATTCCGATACACGTAGTAGCCTGCAC
ATAGTACTACACACGTGATCGAAGCTCTCCGGTACG
Found at i:35897196 original size:50 final size:50
Alignment explanation
Indices: 35897020--35897216 Score: 218
Period size: 51 Copynumber: 3.9 Consensus size: 50
35897010 TAAATGGTAC
* * * *
35897020 CCGGTTCACATAGTAGCCTGCACATAGTACTACACATGTGACCATTTTCA-T
1 CCGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGACC--TATCATT
* ** *
35897071 CCGATACACGTAGTAGCCTGCACATAGTACTACACACGTGATCGAAGC-TCT
1 CCGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGA-CCTATCAT-T
* * * *
35897122 CCGGTACGCATAGTAGCCTGCACATAATACTACACATGTGACCTATCATT
1 CCGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGACCTATCATT
* *
35897172 CCGGTACATGTAGTAGCCTGCACATGGTACTACACACGTGACCTA
1 CCGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGACCTA
35897217 GCAACTTCAC
Statistics
Matches: 120, Mismatches: 22, Indels: 9
0.79 0.15 0.06
Matches are distributed among these distances:
50 44 0.37
51 75 0.62
52 1 0.01
ACGTcount: A:0.28, C:0.28, G:0.18, T:0.25
Consensus pattern (50 bp):
CCGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGACCTATCATT
Found at i:35904715 original size:22 final size:22
Alignment explanation
Indices: 35904688--35904742 Score: 83
Period size: 22 Copynumber: 2.5 Consensus size: 22
35904678 ATATTAATTA
*
35904688 TCAATAAAATTTTATAGGTATT
1 TCAATAAAATTTTATAGGTAGT
* *
35904710 TGAATAAAATGTTATAGGTAGT
1 TCAATAAAATTTTATAGGTAGT
35904732 TCAATAAAATT
1 TCAATAAAATT
35904743 AATCATGTAT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.44, C:0.04, G:0.13, T:0.40
Consensus pattern (22 bp):
TCAATAAAATTTTATAGGTAGT
Found at i:35906137 original size:20 final size:20
Alignment explanation
Indices: 35906097--35906150 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
35906087 AGGAAAAACT
* *
35906097 TTTACCAAAATATTTCTAAAAC
1 TTTACCAAAATA--CCTAAAAA
*
35906119 TTTACTAAAATACCTAAAAA
1 TTTACCAAAATACCTAAAAA
35906139 TTTACCAAAATA
1 TTTACCAAAATA
35906151 AATCCTTAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 17 0.61
22 11 0.39
ACGTcount: A:0.50, C:0.17, G:0.00, T:0.33
Consensus pattern (20 bp):
TTTACCAAAATACCTAAAAA
Found at i:35911682 original size:17 final size:16
Alignment explanation
Indices: 35911657--35911697 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
35911647 TTATTTTCTC
35911657 AAAAAATTAATTAATTT
1 AAAAAATTAA-TAATTT
*
35911674 AAAATATTAATAATTT
1 AAAAAATTAATAATTT
*
35911690 AATAAATT
1 AAAAAATT
35911698 GAAAAATTAG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
16 12 0.57
17 9 0.43
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
AAAAAATTAATAATTT
Found at i:35911697 original size:25 final size:25
Alignment explanation
Indices: 35911663--35911713 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
35911653 TCTCAAAAAA
* *
35911663 TTAATTAATTTAAAATATTA-ATAAT
1 TTAATAAATTGAAAA-ATTAGATAAT
35911688 TTAATAAATTGAAAAATTAGATAAT
1 TTAATAAATTGAAAAATTAGATAAT
35911713 T
1 T
35911714 AAATTAAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 4 0.17
25 19 0.83
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (25 bp):
TTAATAAATTGAAAAATTAGATAAT
Found at i:35919150 original size:19 final size:21
Alignment explanation
Indices: 35919112--35919152 Score: 59
Period size: 19 Copynumber: 2.0 Consensus size: 21
35919102 TGAAATGCTA
35919112 TCAACCTAACATGAATTAAAT
1 TCAACCTAACATGAATTAAAT
*
35919133 TCAAGCTAA-ATG-ATTAAAT
1 TCAACCTAACATGAATTAAAT
35919152 T
1 T
35919153 AATCATTCTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 8 0.42
20 3 0.16
21 8 0.42
ACGTcount: A:0.46, C:0.15, G:0.07, T:0.32
Consensus pattern (21 bp):
TCAACCTAACATGAATTAAAT
Found at i:35922492 original size:41 final size:41
Alignment explanation
Indices: 35922395--35922492 Score: 142
Period size: 41 Copynumber: 2.4 Consensus size: 41
35922385 AATCACAATG
* *
35922395 CTCACACGAGCTGTCGGTCGAAACGTAGCTACACGATACTG
1 CTCACACGAGCTGTGGGTCGAAACGTAGCTACACGATACTA
* * * *
35922436 CTCACACAAGTTGTGGGTTGAAACGTAGCTACACGATGCTA
1 CTCACACGAGCTGTGGGTCGAAACGTAGCTACACGATACTA
35922477 CTCACACGAGCTGTGG
1 CTCACACGAGCTGTGG
35922493 AGTATCCGTA
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 49 1.00
ACGTcount: A:0.27, C:0.27, G:0.26, T:0.21
Consensus pattern (41 bp):
CTCACACGAGCTGTGGGTCGAAACGTAGCTACACGATACTA
Found at i:35927615 original size:18 final size:17
Alignment explanation
Indices: 35927573--35927616 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 17
35927563 TAGAAACCTA
35927573 TAAGTTTAGAAAAAGGAC
1 TAAGTTT-GAAAAAGGAC
*
35927591 TAA-TTTGTAAAAAGGTC
1 TAAGTTTG-AAAAAGGAC
35927608 TAAGTTTGA
1 TAAGTTTGA
35927617 GTCTTTATGA
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
16 1 0.04
17 15 0.65
18 7 0.30
ACGTcount: A:0.43, C:0.05, G:0.20, T:0.32
Consensus pattern (17 bp):
TAAGTTTGAAAAAGGAC
Found at i:35932522 original size:50 final size:50
Alignment explanation
Indices: 35932406--35932651 Score: 228
Period size: 50 Copynumber: 4.8 Consensus size: 50
35932396 GATAATAACA
* ** * * *
35932406 TGCCAAAGCCATGTCCCAGACATGGTCTTACAT-GGATGTTTCTTGTAC--
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATAT-CGG
* * * **
35932454 TGCCAATGCCATATCCCAGATATGGTATTACATGGGAGTTCTCATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
* ** *
35932504 TGCCCATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
* * *
35932554 TGCCAACGCTATGTCCCAGACATGGTCTTACATGGGACCTCTCATAACCTCAATGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCAT-A--TC---GG
* *
35932610 TGCTAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
35932652 TTCCCCAAAT
Statistics
Matches: 160, Mismatches: 29, Indels: 10
0.80 0.15 0.05
Matches are distributed among these distances:
48 30 0.19
49 8 0.05
50 81 0.51
53 2 0.01
56 39 0.24
ACGTcount: A:0.23, C:0.28, G:0.22, T:0.28
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
Found at i:35939799 original size:21 final size:21
Alignment explanation
Indices: 35939775--35939842 Score: 70
Period size: 21 Copynumber: 3.4 Consensus size: 21
35939765 GTTGTTGAGA
*
35939775 AGGAAGTTGATGCTGTAGAAG
1 AGGAAGTTGATGCTGAAGAAG
* *
35939796 AGGAAGTT-CT--TGCAGAAG
1 AGGAAGTTGATGCTGAAGAAG
* *
35939814 AGGAAGTTGTTGCTGAAAAAG
1 AGGAAGTTGATGCTGAAGAAG
35939835 AGGAAGTT
1 AGGAAGTT
35939843 ATTGAAAATG
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
18 15 0.38
19 1 0.03
20 1 0.03
21 22 0.56
ACGTcount: A:0.35, C:0.06, G:0.35, T:0.24
Consensus pattern (21 bp):
AGGAAGTTGATGCTGAAGAAG
Found at i:35939814 original size:18 final size:18
Alignment explanation
Indices: 35939791--35939826 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
35939781 TTGATGCTGT
35939791 AGAAGAGGAAGTTCTTGC
1 AGAAGAGGAAGTTCTTGC
*
35939809 AGAAGAGGAAGTTGTTGC
1 AGAAGAGGAAGTTCTTGC
35939827 TGAAAAAGAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.33, C:0.08, G:0.36, T:0.22
Consensus pattern (18 bp):
AGAAGAGGAAGTTCTTGC
Found at i:35939850 original size:18 final size:18
Alignment explanation
Indices: 35939793--35939850 Score: 53
Period size: 18 Copynumber: 3.1 Consensus size: 18
35939783 GATGCTGTAG
* * *
35939793 AAGAGGAAGTTCTTGCAG
1 AAGAGGAAGTTATTGAAA
*
35939811 AAGAGGAAGTTGTTGCTGAAA
1 AAGAGGAAGTT-AT--TGAAA
35939832 AAGAGGAAGTTATTGAAA
1 AAGAGGAAGTTATTGAAA
35939850 A
1 A
35939851 TGAGAAAGAA
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
18 17 0.52
19 1 0.03
20 1 0.03
21 14 0.42
ACGTcount: A:0.41, C:0.05, G:0.31, T:0.22
Consensus pattern (18 bp):
AAGAGGAAGTTATTGAAA
Found at i:35943240 original size:67 final size:67
Alignment explanation
Indices: 35943157--35943303 Score: 204
Period size: 67 Copynumber: 2.2 Consensus size: 67
35943147 CTCAAGTGCC
* * * *
35943157 AATTATCTTAAATTATGAGTATGTGTGTATTGTGATATGTGTTTATATGACACGCGACCATTATG
1 AATTATCTTAAATTATGAATATGTGTGTATTATGATATGTGTTTATACGACACGCGACCACTATG
35943222 CA
66 CA
* * * *
35943224 AATTATCTTAACTTATGAATATGTGTGTATTATGATATGTGTTTTTACGACATGTGACCACTATG
1 AATTATCTTAAATTATGAATATGTGTGTATTATGATATGTGTTTATACGACACGCGACCACTATG
35943289 CA
66 CA
*
35943291 ATTTATCTATAAA
1 AATTATCT-TAAA
35943304 ATGTTTTAGA
Statistics
Matches: 69, Mismatches: 10, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
67 66 0.96
68 3 0.04
ACGTcount: A:0.31, C:0.11, G:0.16, T:0.41
Consensus pattern (67 bp):
AATTATCTTAAATTATGAATATGTGTGTATTATGATATGTGTTTATACGACACGCGACCACTATG
CA
Found at i:35943367 original size:39 final size:38
Alignment explanation
Indices: 35943307--35943409 Score: 89
Period size: 39 Copynumber: 2.7 Consensus size: 38
35943297 CTATAAAATG
* ** * * * *
35943307 TTTTAGAGTATTGTGGTATATGTTTGAATGTTATGTGA
1 TTTTAGAGTATTCTGACATATGCTTAAACGTTATGAGA
35943345 TTTTACGAGTATTCTGACATATGCTTAAACGTTATGAGA
1 TTTTA-GAGTATTCTGACATATGCTTAAACGTTATGAGA
* ** *
35943384 TTATATGAGTATGGTGATATATGCTT
1 TTTTA-GAGTATTCTGACATATGCTT
35943410 TTATCTTAGG
Statistics
Matches: 52, Mismatches: 12, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
38 5 0.10
39 47 0.90
ACGTcount: A:0.27, C:0.06, G:0.22, T:0.45
Consensus pattern (38 bp):
TTTTAGAGTATTCTGACATATGCTTAAACGTTATGAGA
Found at i:35949350 original size:22 final size:22
Alignment explanation
Indices: 35949324--35949372 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
35949314 TCAAAACATC
*
35949324 TAATACTTATACATATTACCAA
1 TAATAATTATACATATTACCAA
* *
35949346 TAATAATTCTACCTATTACCAA
1 TAATAATTATACATATTACCAA
35949368 TAATA
1 TAATA
35949373 GTTCAATTCT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.45, C:0.18, G:0.00, T:0.37
Consensus pattern (22 bp):
TAATAATTATACATATTACCAA
Found at i:35953125 original size:51 final size:50
Alignment explanation
Indices: 35953015--35953204 Score: 195
Period size: 51 Copynumber: 3.8 Consensus size: 50
35953005 GTACTCGATT
* * * **
35953015 CACATAGCAGCCTGCACATTGTACTACACATGTGACCATTTCCA-TCTGATA
1 CACATAGTAGCCTGCACATAGTACTACACACGTGACCA--AGCATTCTGATA
* * *
35953066 CACGTAGTAGCCTGCACATAGTACTACACACGTGATCGAAGCTATTC-GGTA
1 CACATAGTAGCCTGCACATAGTACTACACACGTGA-CCAAGC-ATTCTGATA
* * * * *
35953117 CGCATAGTAGCCTGCACATAGTACTACACATGCGACCCATCATTCTGATA
1 CACATAGTAGCCTGCACATAGTACTACACACGTGACCAAGCATTCTGATA
* *
35953167 CACGTAGTAGCCTGCACATAGTACTACATACGTGACCA
1 CACATAGTAGCCTGCACATAGTACTACACACGTGACCA
35953205 TCACTTTCAC
Statistics
Matches: 113, Mismatches: 22, Indels: 9
0.78 0.15 0.06
Matches are distributed among these distances:
49 4 0.04
50 39 0.35
51 66 0.58
52 4 0.04
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.24
Consensus pattern (50 bp):
CACATAGTAGCCTGCACATAGTACTACACACGTGACCAAGCATTCTGATA
Found at i:35953193 original size:101 final size:101
Alignment explanation
Indices: 35953017--35953201 Score: 293
Period size: 101 Copynumber: 1.8 Consensus size: 101
35953007 ACTCGATTCA
* *
35953017 CATAGCAGCCTGCACATTGTACTACACATGTGACCATTTCCATCTGATACACGTAGTAGCCTGCA
1 CATAGCAGCCTGCACATAGTACTACACATGCGACCA-TTCCATCTGATACACGTAGTAGCCTGCA
35953082 CATAGTACTACACACGTGATCGAAGCTATTCGGTACG
65 CATAGTACTACACACGTGATCGAAGCTATTCGGTACG
*
35953119 CATAGTAGCCTGCACATAGTACTACACATGCGACCCA-T-CATTCTGATACACGTAGTAGCCTGC
1 CATAGCAGCCTGCACATAGTACTACACATGCGA-CCATTCCA-TCTGATACACGTAGTAGCCTGC
*
35953182 ACATAGTACTACATACGTGA
64 ACATAGTACTACACACGTGA
35953202 CCATCACTTT
Statistics
Matches: 77, Mismatches: 4, Indels: 5
0.90 0.05 0.06
Matches are distributed among these distances:
100 2 0.03
101 42 0.55
102 30 0.39
103 3 0.04
ACGTcount: A:0.30, C:0.28, G:0.18, T:0.25
Consensus pattern (101 bp):
CATAGCAGCCTGCACATAGTACTACACATGCGACCATTCCATCTGATACACGTAGTAGCCTGCAC
ATAGTACTACACACGTGATCGAAGCTATTCGGTACG
Found at i:35956661 original size:28 final size:28
Alignment explanation
Indices: 35956629--35956715 Score: 122
Period size: 28 Copynumber: 3.1 Consensus size: 28
35956619 GAGAAAAACG
*
35956629 TATGAAAATTGAAGCCTTTGTGGAAATC
1 TATGAAAATTGAAGCCTTTGTGGCAATC
*
35956657 TATGAAAATGGAAGCC-TTGTGGCAATC
1 TATGAAAATTGAAGCCTTTGTGGCAATC
* * *
35956684 TATGAAAATTGAAGTCTTCGTGGCGATC
1 TATGAAAATTGAAGCCTTTGTGGCAATC
35956712 TATG
1 TATG
35956716 GAATGGAACG
Statistics
Matches: 52, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
27 24 0.46
28 28 0.54
ACGTcount: A:0.32, C:0.13, G:0.24, T:0.31
Consensus pattern (28 bp):
TATGAAAATTGAAGCCTTTGTGGCAATC
Found at i:35956684 original size:27 final size:27
Alignment explanation
Indices: 35956629--35956723 Score: 111
Period size: 27 Copynumber: 3.5 Consensus size: 27
35956619 GAGAAAAACG
* *
35956629 TATGAAAATTGAAGCCTTTGTGGAAATC
1 TATGAAAATGGAAGCC-TTGTGGCAATC
35956657 TATGAAAATGGAAGCCTTGTGGCAATC
1 TATGAAAATGGAAGCCTTGTGGCAATC
* * *
35956684 TATGAAAATTGAAGTCTTCGTGGCGATC
1 TATGAAAATGGAAGCCTT-GTGGCAATC
*
35956712 TATG-GAATGGAA
1 TATGAAAATGGAA
35956724 CGCATTCATG
Statistics
Matches: 59, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
27 32 0.54
28 27 0.46
ACGTcount: A:0.34, C:0.12, G:0.25, T:0.29
Consensus pattern (27 bp):
TATGAAAATGGAAGCCTTGTGGCAATC
Found at i:35961663 original size:18 final size:17
Alignment explanation
Indices: 35961635--35961672 Score: 58
Period size: 18 Copynumber: 2.2 Consensus size: 17
35961625 AGTTTTAAGT
35961635 ATTTGTTAAGTATAAAA
1 ATTTGTTAAGTATAAAA
*
35961652 ATTTGATTAAGTATAAGA
1 ATTTG-TTAAGTATAAAA
35961670 ATT
1 ATT
35961673 CTTTGAACAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 5 0.26
18 14 0.74
ACGTcount: A:0.45, C:0.00, G:0.13, T:0.42
Consensus pattern (17 bp):
ATTTGTTAAGTATAAAA
Found at i:35963110 original size:28 final size:28
Alignment explanation
Indices: 35963031--35963138 Score: 139
Period size: 28 Copynumber: 3.9 Consensus size: 28
35963021 CGTGAAAAAG
* * *
35963031 TATGAAAATGGAAGTCTTTGGGGCAATA
1 TATGAAAATGGAAGCCTTTGTGGCAATC
35963059 TATGAAAATGGAAGCCTTTGTGGCAATC
1 TATGAAAATGGAAGCCTTTGTGGCAATC
35963087 TATGAAAATGGAAGCCTTCT-TGGCAATC
1 TATGAAAATGGAAGCCTT-TGTGGCAATC
* *
35963115 TATGGAAAT-GAATGCCTTCGTGGC
1 TATGAAAATGGAA-GCCTTTGTGGC
35963139 GCACTCCAAT
Statistics
Matches: 72, Mismatches: 5, Indels: 6
0.87 0.06 0.07
Matches are distributed among these distances:
27 3 0.04
28 68 0.94
29 1 0.01
ACGTcount: A:0.31, C:0.14, G:0.26, T:0.29
Consensus pattern (28 bp):
TATGAAAATGGAAGCCTTTGTGGCAATC
Found at i:35963793 original size:19 final size:19
Alignment explanation
Indices: 35963771--35963832 Score: 69
Period size: 19 Copynumber: 3.4 Consensus size: 19
35963761 CAAGACATCA
35963771 AAACCAATTCAATAACCTT
1 AAACCAATTCAATAACCTT
*
35963790 AAACCAA-TC---AACCAAT
1 AAACCAATTCAATAACC-TT
*
35963806 CAACCAATTCAATAACCTT
1 AAACCAATTCAATAACCTT
35963825 AAACCAAT
1 AAACCAAT
35963833 CAACCAATAT
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
15 4 0.12
16 7 0.21
17 2 0.06
18 2 0.06
19 15 0.44
20 4 0.12
ACGTcount: A:0.50, C:0.29, G:0.00, T:0.21
Consensus pattern (19 bp):
AAACCAATTCAATAACCTT
Found at i:35963852 original size:35 final size:35
Alignment explanation
Indices: 35963772--35963840 Score: 138
Period size: 35 Copynumber: 2.0 Consensus size: 35
35963762 AAGACATCAA
35963772 AACCAATTCAATAACCTTAAACCAATCAACCAATC
1 AACCAATTCAATAACCTTAAACCAATCAACCAATC
35963807 AACCAATTCAATAACCTTAAACCAATCAACCAAT
1 AACCAATTCAATAACCTTAAACCAATCAACCAAT
35963841 ATTCCATTTC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.49, C:0.30, G:0.00, T:0.20
Consensus pattern (35 bp):
AACCAATTCAATAACCTTAAACCAATCAACCAATC
Found at i:35965050 original size:19 final size:19
Alignment explanation
Indices: 35965026--35965066 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
35965016 GTCTATCTTG
35965026 ATCTAAATAGAAAAATTCA
1 ATCTAAATAGAAAAATTCA
35965045 ATCTAAATAGAAAAATTCA
1 ATCTAAATAGAAAAATTCA
35965064 ATC
1 ATC
35965067 CATTTAATAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.56, C:0.12, G:0.05, T:0.27
Consensus pattern (19 bp):
ATCTAAATAGAAAAATTCA
Found at i:35973308 original size:16 final size:15
Alignment explanation
Indices: 35973283--35973316 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
35973273 AAAGTTGATA
*
35973283 ATAATTAATATACATT
1 ATAATAAATATA-ATT
35973299 ATAATAAATATAATT
1 ATAATAAATATAATT
35973314 ATA
1 ATA
35973317 TATTAGTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (15 bp):
ATAATAAATATAATT
Found at i:35975557 original size:25 final size:25
Alignment explanation
Indices: 35975490--35975559 Score: 95
Period size: 25 Copynumber: 2.8 Consensus size: 25
35975480 CTGAACATGT
* * *
35975490 ATGCTCTCACGAGCTGTAAATCAGA
1 ATGCTCACACGAGCTGTGAATCAAA
*
35975515 ATGCTCACATGAGCTGTGAATCAAA
1 ATGCTCACACGAGCTGTGAATCAAA
*
35975540 ATGCTCACACAAGCTGTGAA
1 ATGCTCACACGAGCTGTGAA
35975560 AATGGGCCTG
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 39 1.00
ACGTcount: A:0.34, C:0.23, G:0.20, T:0.23
Consensus pattern (25 bp):
ATGCTCACACGAGCTGTGAATCAAA
Found at i:35983469 original size:21 final size:20
Alignment explanation
Indices: 35983436--35983474 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
35983426 AATATGCGTT
35983436 TGTTTGTCAGAACATTTTGTC
1 TGTTTGTCAGAAC-TTTTGTC
**
35983457 TGTTTGTGTGAACTTTTG
1 TGTTTGTCAGAACTTTTG
35983475 GTTATTGACA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 5 0.31
21 11 0.69
ACGTcount: A:0.15, C:0.10, G:0.23, T:0.51
Consensus pattern (20 bp):
TGTTTGTCAGAACTTTTGTC
Found at i:35983862 original size:32 final size:32
Alignment explanation
Indices: 35983826--35983891 Score: 105
Period size: 32 Copynumber: 2.1 Consensus size: 32
35983816 TTAAGTCGGT
*
35983826 TTGTAAAATGATTATATAAATTGCGGTACAAG
1 TTGTAAAATGATTATATAAACTGCGGTACAAG
* *
35983858 TTGTACAATGATTATATAAACTGTGGTACAAG
1 TTGTAAAATGATTATATAAACTGCGGTACAAG
35983890 TT
1 TT
35983892 TTTATGGTGG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.38, C:0.08, G:0.18, T:0.36
Consensus pattern (32 bp):
TTGTAAAATGATTATATAAACTGCGGTACAAG
Found at i:35986746 original size:21 final size:22
Alignment explanation
Indices: 35986717--35986767 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 22
35986707 TCTCTCTCGC
*
35986717 TTTCCTTTTCGCCTTTTTCA-T
1 TTTCATTTTCGCCTTTTTCACT
**
35986738 TTTCATTTTCTTCTTTTTCACT
1 TTTCATTTTCGCCTTTTTCACT
35986760 TTT-ATTTT
1 TTTCATTTT
35986768 TCTCTTCTCC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
21 22 0.85
22 4 0.15
ACGTcount: A:0.08, C:0.22, G:0.02, T:0.69
Consensus pattern (22 bp):
TTTCATTTTCGCCTTTTTCACT
Found at i:35988291 original size:40 final size:41
Alignment explanation
Indices: 35988235--35988316 Score: 107
Period size: 40 Copynumber: 2.0 Consensus size: 41
35988225 TGAAGTGCTT
35988235 TGTCCACGTGGAGACAAAGTACGC-CCTCAAGGAAGCGTTTTC
1 TGTCCACGTGGAGACAAAG--CGCTCCTCAAGGAAGCGTTTTC
*
35988277 TGTCCACGT-G-GACAAAGCGCTTCCTTAAGGAAGCGTTTTC
1 TGTCCACGTGGAGACAAAGCGC-TCCTCAAGGAAGCGTTTTC
35988317 CTGCTTTATC
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
38 3 0.08
40 24 0.65
41 1 0.03
42 9 0.24
ACGTcount: A:0.24, C:0.26, G:0.26, T:0.24
Consensus pattern (41 bp):
TGTCCACGTGGAGACAAAGCGCTCCTCAAGGAAGCGTTTTC
Found at i:35995628 original size:26 final size:26
Alignment explanation
Indices: 35995599--35995705 Score: 133
Period size: 26 Copynumber: 4.1 Consensus size: 26
35995589 TGGAGGAAGT
* *
35995599 ATACTGTTACTAGCAGCTTTGCGGCG
1 ATACTATTACTAGCAGCTTTGCTGCG
** * *
35995625 ATACTGGTACTGGTAGCTTTGCTGCG
1 ATACTATTACTAGCAGCTTTGCTGCG
* * *
35995651 ATACTATTACTAGCAGTTTTACTGTG
1 ATACTATTACTAGCAGCTTTGCTGCG
35995677 ATACTATTACTAGCAGCTTTGCTGCG
1 ATACTATTACTAGCAGCTTTGCTGCG
35995703 ATA
1 ATA
35995706 TTGGTGTGTT
Statistics
Matches: 67, Mismatches: 14, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 67 1.00
ACGTcount: A:0.22, C:0.20, G:0.22, T:0.36
Consensus pattern (26 bp):
ATACTATTACTAGCAGCTTTGCTGCG
Found at i:35997073 original size:51 final size:50
Alignment explanation
Indices: 35996828--35997073 Score: 282
Period size: 50 Copynumber: 4.9 Consensus size: 50
35996818 GTGAAGTTGC
* * * *
35996828 TAGGTCACGTGTGTAGTACTATGTGCATGCTACTGCGTGTACCGGAATGA
1 TAGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGAATGA
* *
35996878 TAGGTCGCATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGAATGA
1 TAGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGAATGA
* * * * *
35996928 TAGGTCTCATGTGTAGTACTATGTGCAGGCTAC-ATGCGTATAGG-ATAGCT
1 TAGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGAAT-G-A
* * *
35996978 TCGATCACATGTGTAGTACTATGTGCAGGCTACTACCTGTATCGGAA-GAA
1 TAGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGAATG-A
* * *
35997028 AATGGTCACATGTGTAGTACTATGTGCAGGCTACTATGTGAATCGG
1 TA-GGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTATCGG
35997074 TATCATTAAT
Statistics
Matches: 166, Mismatches: 25, Indels: 9
0.83 0.12 0.05
Matches are distributed among these distances:
48 2 0.01
49 8 0.05
50 109 0.66
51 46 0.28
52 1 0.01
ACGTcount: A:0.25, C:0.17, G:0.28, T:0.30
Consensus pattern (50 bp):
TAGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGAATGA
Found at i:36000364 original size:27 final size:27
Alignment explanation
Indices: 36000333--36000419 Score: 74
Period size: 27 Copynumber: 3.2 Consensus size: 27
36000323 TGTTTTGAGA
36000333 ATGTGAAATTAGTAATGAATTGGCTAT
1 ATGTGAAATTAGTAATGAATTGGCTAT
* * *
36000360 CTGTG--A-TAGT-ATGTGATATGCGCAAT
1 ATGTGAAATTAGTAATG-AAT-TG-GCTAT
36000386 AATGTGAAATTAGTAATGAATTGGCTAT
1 -ATGTGAAATTAGTAATGAATTGGCTAT
*
36000414 TTGTGA
1 ATGTGA
36000420 TAGTATGTGA
Statistics
Matches: 45, Mismatches: 7, Indels: 16
0.66 0.10 0.24
Matches are distributed among these distances:
23 3 0.07
24 6 0.13
25 3 0.07
26 4 0.09
27 13 0.29
28 4 0.09
29 3 0.07
30 6 0.13
31 3 0.07
ACGTcount: A:0.33, C:0.06, G:0.24, T:0.37
Consensus pattern (27 bp):
ATGTGAAATTAGTAATGAATTGGCTAT
Found at i:36000370 original size:24 final size:24
Alignment explanation
Indices: 36000342--36000424 Score: 60
Period size: 24 Copynumber: 3.2 Consensus size: 24
36000332 AATGTGAAAT
*
36000342 TAGTAATGAATTGGCTATCTGTGA
1 TAGTAATGAATTGGCTATATGTGA
* *
36000366 TAGT-ATGTGATATGCGCAATAATGTGAAA
1 TAGTAATG-AAT-TG-GCTAT-ATGTG--A
*
36000395 TTAGTAATGAATTGGCTATTTGTGA
1 -TAGTAATGAATTGGCTATATGTGA
36000420 TAGTA
1 TAGTA
36000425 TGTGATATGC
Statistics
Matches: 45, Mismatches: 6, Indels: 16
0.67 0.09 0.24
Matches are distributed among these distances:
23 3 0.07
24 11 0.24
25 3 0.07
26 4 0.09
27 8 0.18
28 4 0.09
29 3 0.07
30 6 0.13
31 3 0.07
ACGTcount: A:0.33, C:0.06, G:0.24, T:0.37
Consensus pattern (24 bp):
TAGTAATGAATTGGCTATATGTGA
Found at i:36000445 original size:54 final size:54
Alignment explanation
Indices: 36000332--36000437 Score: 203
Period size: 54 Copynumber: 2.0 Consensus size: 54
36000322 ATGTTTTGAG
36000332 AATGTGAAATTAGTAATGAATTGGCTATCTGTGATAGTATGTGATATGCGCAAT
1 AATGTGAAATTAGTAATGAATTGGCTATCTGTGATAGTATGTGATATGCGCAAT
*
36000386 AATGTGAAATTAGTAATGAATTGGCTATTTGTGATAGTATGTGATATGCGCA
1 AATGTGAAATTAGTAATGAATTGGCTATCTGTGATAGTATGTGATATGCGCA
36000438 TTTATGTGTA
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 51 1.00
ACGTcount: A:0.33, C:0.07, G:0.25, T:0.36
Consensus pattern (54 bp):
AATGTGAAATTAGTAATGAATTGGCTATCTGTGATAGTATGTGATATGCGCAAT
Found at i:36002964 original size:50 final size:50
Alignment explanation
Indices: 36002872--36002994 Score: 149
Period size: 50 Copynumber: 2.4 Consensus size: 50
36002862 GTGAAGTTGC
* * *
36002872 TAGGTCACGTGTGTAGTACTATGTGCAGGCTACTGCGTGTACCGGAATGA
1 TAGGTCACATGTGTAGTACTATGTGCAGGCTACTACGCGTACCGGAATGA
* * *
36002922 TAGGTCGCATGTGTAGTACTATGTGCAGGCTACTATGCGTACCGG-ATAGCT
1 TAGGTCACATGTGTAGTACTATGTGCAGGCTACTACGCGTACCGGAAT-G-A
* *
36002973 TCGATCACATGTGTAGTACTAT
1 TAGGTCACATGTGTAGTACTAT
36002995 CGAACGAAAA
Statistics
Matches: 62, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
49 2 0.03
50 41 0.66
51 19 0.31
ACGTcount: A:0.23, C:0.19, G:0.28, T:0.30
Consensus pattern (50 bp):
TAGGTCACATGTGTAGTACTATGTGCAGGCTACTACGCGTACCGGAATGA
Found at i:36003142 original size:46 final size:43
Alignment explanation
Indices: 36003051--36003151 Score: 105
Period size: 46 Copynumber: 2.2 Consensus size: 43
36003041 TCAACCGGTT
* *
36003051 TCATTAATTATAAGGTGGTTGCTATGTGCTAATCCCATCGGGTA
1 TCATT-ATTATAAGGTGGTTGCTATATGCTAATCCCACCGGGTA
* *
36003095 TCATTGATTATAAAGGGTGGTTGCTGTATGCTGAAT-CCACCGTGTA
1 TCATT-ATTAT-AA-GGTGGTTGCTATATGCT-AATCCCACCGGGTA
36003141 TCTATTATTAT
1 TC-ATTATTAT
36003152 TCCGAAGTGT
Statistics
Matches: 48, Mismatches: 5, Indels: 6
0.81 0.08 0.10
Matches are distributed among these distances:
44 10 0.21
45 2 0.04
46 30 0.62
47 6 0.12
ACGTcount: A:0.25, C:0.15, G:0.22, T:0.39
Consensus pattern (43 bp):
TCATTATTATAAGGTGGTTGCTATATGCTAATCCCACCGGGTA
Found at i:36005062 original size:27 final size:27
Alignment explanation
Indices: 36005002--36005063 Score: 83
Period size: 28 Copynumber: 2.3 Consensus size: 27
36004992 GTTCTGCTAT
36005002 TGTACTGGGCTAAGGCCCACATTGTTAC
1 TGTACTGGGCTAAGGCCCACA-TGTTAC
36005030 TGTACTGGGCTAAGGCCACACA-G-TAC
1 TGTACTGGGCTAAGGCC-CACATGTTAC
36005056 TGTTACTG
1 TG-TACTG
36005064 AATAAGGCTC
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
26 5 0.16
27 6 0.19
28 17 0.53
29 4 0.12
ACGTcount: A:0.23, C:0.24, G:0.26, T:0.27
Consensus pattern (27 bp):
TGTACTGGGCTAAGGCCCACATGTTAC
Found at i:36006132 original size:186 final size:187
Alignment explanation
Indices: 36005811--36006157 Score: 502
Period size: 186 Copynumber: 1.9 Consensus size: 187
36005801 CTTTAAAGCT
*
36005811 ATAGGGGACACATGACCGTGTCGCCTGGCCATGTGTCACACATGGCTAAGACACACGTTCGTGTC
1 ATAGGGGACACACGACCGTGTCGCCTGGCCATGTGTCACACATGGCTAAGACACACGTTCGTGTC
* * * * *
36005876 TCTAGCCGTGTGGATGAAAAATAAACTATTTCTAGGTCATTTTCCTCACCCAAAGACCAGCCACT
66 TCTAGCCATGTGGATGAAAAATAAACTATTTCCAAGCCATTTTCCTCACCCAAAGACCAGCCAAT
*
36005941 TGCACAACCC-ATTGTACCTATAATCATGCAACAACCTGCCTTGCAACCTTTTGAAG
131 TGCACAACCCAAATGTACCTATAATCATGCAACAACCTGCCTTGCAACCTTTTGAAG
* * *
36005997 ATAGGGGACACACGACCGTGTCGCCTGGCCTTGTGTCGCACATGGCTGAGACACACG-TCTGTGT
1 ATAGGGGACACACGACCGTGTCGCCTGGCCATGTGTCACACATGGCTAAGACACACGTTC-GTGT
* * ** * * *
36006061 CTTTGGCCATGTGG-TCGAAAAATAGGCTATTTCCAAGCCATTTTTCTCACCTAATGACCAGCCA
65 CTCTAGCCATGTGGAT-GAAAAATAAACTATTTCCAAGCCATTTTCCTCACCCAAAGACCAGCCA
36006125 ATTGCACAACCCAAATGTACCTATAATCATGCA
129 ATTGCACAACCCAAATGTACCTATAATCATGCA
36006158 TTCAAAACAC
Statistics
Matches: 141, Mismatches: 17, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
185 3 0.02
186 119 0.84
187 19 0.13
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.25
Consensus pattern (187 bp):
ATAGGGGACACACGACCGTGTCGCCTGGCCATGTGTCACACATGGCTAAGACACACGTTCGTGTC
TCTAGCCATGTGGATGAAAAATAAACTATTTCCAAGCCATTTTCCTCACCCAAAGACCAGCCAAT
TGCACAACCCAAATGTACCTATAATCATGCAACAACCTGCCTTGCAACCTTTTGAAG
Found at i:36023529 original size:27 final size:27
Alignment explanation
Indices: 36023484--36023566 Score: 130
Period size: 27 Copynumber: 3.1 Consensus size: 27
36023474 TATAACAGTT
*
36023484 ATTTTACCCTATGGGGGTATTTCGGTC
1 ATTTTACCCTATGAGGGTATTTCGGTC
* * *
36023511 ATTTTACCCTATCAAGGTATTTTGGTC
1 ATTTTACCCTATGAGGGTATTTCGGTC
36023538 ATTTTACCCTATGAGGGTATTTCGGTC
1 ATTTTACCCTATGAGGGTATTTCGGTC
36023565 AT
1 AT
36023567 AATAGTGTAA
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 49 1.00
ACGTcount: A:0.19, C:0.18, G:0.20, T:0.42
Consensus pattern (27 bp):
ATTTTACCCTATGAGGGTATTTCGGTC
Found at i:36045231 original size:16 final size:18
Alignment explanation
Indices: 36045205--36045237 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
36045195 TTCAATTAAC
36045205 TAAATTAA-TTTCTCAAT
1 TAAATTAATTTTCTCAAT
36045222 TAAA-TAATTTTCTCAA
1 TAAATTAATTTTCTCAA
36045238 GTCAGTTCTG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 3 0.20
17 12 0.80
ACGTcount: A:0.42, C:0.12, G:0.00, T:0.45
Consensus pattern (18 bp):
TAAATTAATTTTCTCAAT
Found at i:36047290 original size:30 final size:31
Alignment explanation
Indices: 36047254--36047322 Score: 88
Period size: 31 Copynumber: 2.3 Consensus size: 31
36047244 TGCTTTCAAT
*
36047254 TCAGTCACTCAAC-TT-TTGAAAAATAACAAA
1 TCAGTCACT-AACGTTATCGAAAAATAACAAA
* *
36047284 TCAGTCACTAACGTTATCGAAAAGTGACAAA
1 TCAGTCACTAACGTTATCGAAAAATAACAAA
36047315 TCAGTCAC
1 TCAGTCAC
36047323 CCATTAACAT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
29 3 0.09
30 11 0.32
31 20 0.59
ACGTcount: A:0.42, C:0.22, G:0.12, T:0.25
Consensus pattern (31 bp):
TCAGTCACTAACGTTATCGAAAAATAACAAA
Found at i:36048238 original size:3 final size:3
Alignment explanation
Indices: 36048230--36048280 Score: 79
Period size: 3 Copynumber: 17.3 Consensus size: 3
36048220 ACATCTCAAT
36048230 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TAT- TTC -TC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T-TC TTC TTC TTC
36048274 TTC TTC T
1 TTC TTC T
36048281 ACAGCCTAGT
Statistics
Matches: 45, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
2 3 0.07
3 41 0.91
4 1 0.02
ACGTcount: A:0.02, C:0.31, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:36053234 original size:39 final size:39
Alignment explanation
Indices: 36053180--36053259 Score: 151
Period size: 39 Copynumber: 2.1 Consensus size: 39
36053170 GGTACTAGTT
*
36053180 ATATTTCTGTGTTGCACTAGACAACCTTCCTTGCTGTTA
1 ATATTTATGTGTTGCACTAGACAACCTTCCTTGCTGTTA
36053219 ATATTTATGTGTTGCACTAGACAACCTTCCTTGCTGTTA
1 ATATTTATGTGTTGCACTAGACAACCTTCCTTGCTGTTA
36053258 AT
1 AT
36053260 GTGTCTGAAC
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.23, C:0.21, G:0.15, T:0.41
Consensus pattern (39 bp):
ATATTTATGTGTTGCACTAGACAACCTTCCTTGCTGTTA
Found at i:36058627 original size:21 final size:20
Alignment explanation
Indices: 36058580--36058628 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 20
36058570 TTTTGCGTTT
*
36058580 CTTTTTTGTTTATTTTCTTC
1 CTTTTTTGTTTATTTTCTTA
36058600 CTTTTTTTGTTTATTTTCTATAA
1 C-TTTTTTGTTTATTTTCT-T-A
36058623 CTTTTT
1 CTTTTT
36058629 AAACAAAACG
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
20 1 0.04
21 17 0.68
22 6 0.24
23 1 0.04
ACGTcount: A:0.10, C:0.12, G:0.04, T:0.73
Consensus pattern (20 bp):
CTTTTTTGTTTATTTTCTTA
Found at i:36063089 original size:17 final size:18
Alignment explanation
Indices: 36063067--36063103 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
36063057 TTATTCTTTT
36063067 ATTCTTTCATCCA-AATC
1 ATTCTTTCATCCATAATC
*
36063084 ATTCTTTCATTCATAATC
1 ATTCTTTCATCCATAATC
36063102 AT
1 AT
36063104 ACTGTGCAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 12 0.67
18 6 0.33
ACGTcount: A:0.30, C:0.24, G:0.00, T:0.46
Consensus pattern (18 bp):
ATTCTTTCATCCATAATC
Found at i:36063821 original size:11 final size:11
Alignment explanation
Indices: 36063805--36063850 Score: 55
Period size: 10 Copynumber: 4.5 Consensus size: 11
36063795 GAGTTCAGAC
36063805 TCAAAAAAAAA
1 TCAAAAAAAAA
36063816 TC---AAAAAA
1 TCAAAAAAAAA
36063824 TCAAAAAAAAAA
1 TC-AAAAAAAAA
36063836 T-AAAAAAAAA
1 TCAAAAAAAAA
36063846 TCAAA
1 TCAAA
36063851 GTCAAAATAG
Statistics
Matches: 30, Mismatches: 0, Indels: 10
0.75 0.00 0.25
Matches are distributed among these distances:
8 8 0.27
10 10 0.33
11 5 0.17
12 7 0.23
ACGTcount: A:0.80, C:0.09, G:0.00, T:0.11
Consensus pattern (11 bp):
TCAAAAAAAAA
Found at i:36063835 original size:22 final size:22
Alignment explanation
Indices: 36063818--36063868 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
36063808 AAAAAAAATC
36063818 AAAAAATCAAAAAAAAAATAAA
1 AAAAAATCAAAAAAAAAATAAA
***
36063840 AAAAAATCAAAGTCAAAATAGAA
1 AAAAAATCAAAAAAAAAATA-AA
36063863 AAAAAA
1 AAAAAA
36063869 AAGAGAAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
22 17 0.68
23 8 0.32
ACGTcount: A:0.80, C:0.06, G:0.04, T:0.10
Consensus pattern (22 bp):
AAAAAATCAAAAAAAAAATAAA
Found at i:36063865 original size:30 final size:28
Alignment explanation
Indices: 36063807--36063870 Score: 76
Period size: 28 Copynumber: 2.2 Consensus size: 28
36063797 GTTCAGACTC
36063807 AAAAAAAAATCAAAAAATCAAAAAAAAAA
1 AAAAAAAAATC-AAAAATCAAAAAAAAAA
* * *
36063836 TAAAAAAAAATC-AAAGTCAAAATAGAAA
1 -AAAAAAAAATCAAAAATCAAAAAAAAAA
36063864 AAAAAAA
1 AAAAAAA
36063871 GAGAAAAAGA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
27 7 0.23
28 13 0.42
30 11 0.35
ACGTcount: A:0.81, C:0.06, G:0.03, T:0.09
Consensus pattern (28 bp):
AAAAAAAAATCAAAAATCAAAAAAAAAA
Found at i:36065688 original size:8 final size:8
Alignment explanation
Indices: 36065675--36065699 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
36065665 AAACACCAAG
36065675 TGCTCACC
1 TGCTCACC
36065683 TGCTCACC
1 TGCTCACC
36065691 TGCTCACC
1 TGCTCACC
36065699 T
1 T
36065700 ACAACACGCA
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:0.12, C:0.48, G:0.12, T:0.28
Consensus pattern (8 bp):
TGCTCACC
Found at i:36065959 original size:22 final size:20
Alignment explanation
Indices: 36065911--36065960 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 20
36065901 TCTTGCGTTT
*
36065911 CTTTTTTGTTTATTTTCTTC
1 CTTTTTTGTTTATTTTCTTA
36065931 CTTTTTTTTGTTTATTTTCTATAA
1 C--TTTTTTGTTTATTTTCT-T-A
36065955 CTTTTT
1 CTTTTT
36065961 AAACAAAACG
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
20 1 0.04
22 22 0.88
23 1 0.04
24 1 0.04
ACGTcount: A:0.10, C:0.12, G:0.04, T:0.74
Consensus pattern (20 bp):
CTTTTTTGTTTATTTTCTTA
Found at i:36079034 original size:120 final size:121
Alignment explanation
Indices: 36078815--36079054 Score: 385
Period size: 120 Copynumber: 2.0 Consensus size: 121
36078805 TTCGTACTAC
* *
36078815 ATGTATTAACTATACCATTTTTCTGATCTTGGTACTTAATTGTTTTTTTGTCACAAGTGATACCC
1 ATGTATTAACTATACCATTTTTCTCATCTAGGTACTTAATTGTTTTTTTGTCACAAGTGATACCC
* * * *
36078880 TTTTTGCTCTAGTTAGTACCTCCGTTAGTTAAACAATTAAATCTTTTTTTAAAAAT
66 TTTTTGCTCTAGTTAGCACCTCCGTTAGTCAAACAATTAAATCTATTTTAAAAAAT
36078936 ATGTATTAACTATACCATTTTTCTCATCTAGGTACTTAATTG-TTTTTTGTCACAAGTGATACCC
1 ATGTATTAACTATACCATTTTTCTCATCTAGGTACTTAATTGTTTTTTTGTCACAAGTGATACCC
* *
36079000 TTTTTGC-CGTAGTTGGCACCTCCGTTAGTCAAACAGTTAAATCTATTTTAAAAAA
66 TTTTTGCTC-TAGTTAGCACCTCCGTTAGTCAAACAATTAAATCTATTTTAAAAAA
36079055 GGGTAAATTA
Statistics
Matches: 110, Mismatches: 8, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
119 1 0.01
120 69 0.63
121 40 0.36
ACGTcount: A:0.28, C:0.17, G:0.12, T:0.43
Consensus pattern (121 bp):
ATGTATTAACTATACCATTTTTCTCATCTAGGTACTTAATTGTTTTTTTGTCACAAGTGATACCC
TTTTTGCTCTAGTTAGCACCTCCGTTAGTCAAACAATTAAATCTATTTTAAAAAAT
Found at i:36079345 original size:6 final size:7
Alignment explanation
Indices: 36079326--36079376 Score: 61
Period size: 7 Copynumber: 7.4 Consensus size: 7
36079316 GTTTTACTTC
36079326 TTAAAAA
1 TTAAAAA
36079333 TTAAAAA
1 TTAAAAA
36079340 TTAAAAA
1 TTAAAAA
36079347 TTAAAAA
1 TTAAAAA
36079354 --AAAAA
1 TTAAAAA
*
36079359 CTTTAAAA
1 -TTAAAAA
*
36079367 CTAAAAA
1 TTAAAAA
36079374 TTA
1 TTA
36079377 TTTAAAAAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
5 5 0.14
7 28 0.76
8 4 0.11
ACGTcount: A:0.69, C:0.04, G:0.00, T:0.27
Consensus pattern (7 bp):
TTAAAAA
Found at i:36079358 original size:20 final size:20
Alignment explanation
Indices: 36079335--36079373 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
36079325 CTTAAAAATT
*
36079335 AAAAATTAAAAATTAAAAAA
1 AAAAATTAAAAACTAAAAAA
* *
36079355 AAAACTTTAAAACTAAAAA
1 AAAAATTAAAAACTAAAAA
36079374 TTATTTAAAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.74, C:0.05, G:0.00, T:0.21
Consensus pattern (20 bp):
AAAAATTAAAAACTAAAAAA
Found at i:36079500 original size:19 final size:20
Alignment explanation
Indices: 36079467--36079511 Score: 58
Period size: 19 Copynumber: 2.3 Consensus size: 20
36079457 ATTTATTTAT
36079467 TAAAATAATAC-TTTTATAAA
1 TAAAATAATACTTTTTA-AAA
*
36079487 TAAAA-AATATTTTTTAAAA
1 TAAAATAATACTTTTTAAAA
36079506 TAAAAT
1 TAAAAT
36079512 CGCACAAACA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
19 12 0.55
20 10 0.45
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (20 bp):
TAAAATAATACTTTTTAAAA
Found at i:36080752 original size:20 final size:20
Alignment explanation
Indices: 36080729--36080774 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
36080719 TATTTATAAA
*
36080729 TATTTTCAT-AATTTTGTATG
1 TATTTTCATAAACTTT-TATG
*
36080749 TATTTTTATAAACTTTTATG
1 TATTTTCATAAACTTTTATG
36080769 TATTTT
1 TATTTT
36080775 TATCGAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 18 0.78
21 5 0.22
ACGTcount: A:0.26, C:0.04, G:0.07, T:0.63
Consensus pattern (20 bp):
TATTTTCATAAACTTTTATG
Found at i:36081960 original size:16 final size:15
Alignment explanation
Indices: 36081927--36081973 Score: 53
Period size: 15 Copynumber: 3.1 Consensus size: 15
36081917 ATTATAAAGG
36081927 AAGAGAAAAGAAAAA
1 AAGAGAAAAGAAAAA
36081942 AAGAGGAAAA-AAAATA
1 AAGA-GAAAAGAAAA-A
*
36081958 AAGA-AATAGAAAAA
1 AAGAGAAAAGAAAAA
36081972 AA
1 AA
36081974 ATGGAGAAGG
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
14 6 0.21
15 12 0.43
16 10 0.36
ACGTcount: A:0.79, C:0.00, G:0.17, T:0.04
Consensus pattern (15 bp):
AAGAGAAAAGAAAAA
Found at i:36083861 original size:9 final size:9
Alignment explanation
Indices: 36083849--36083935 Score: 59
Period size: 9 Copynumber: 9.7 Consensus size: 9
36083839 TGCAGCACAT
*
36083849 TGCATGGAG
1 TGCATGGAA
*
36083858 TGCATGG-T
1 TGCATGGAA
*
36083866 TCGCATGAAA
1 T-GCATGGAA
*
36083876 TGCATGGAT
1 TGCATGGAA
*
36083885 TGCATGGGA
1 TGCATGGAA
*
36083894 TGCATGAAA
1 TGCATGGAA
***
36083903 TGCATGTTT
1 TGCATGGAA
36083912 TGCATGGAA
1 TGCATGGAA
* *
36083921 CGCATGGAG
1 TGCATGGAA
36083930 TGCATG
1 TGCATG
36083936 CCCAAACTCG
Statistics
Matches: 58, Mismatches: 18, Indels: 4
0.73 0.22 0.05
Matches are distributed among these distances:
8 1 0.02
9 56 0.97
10 1 0.02
ACGTcount: A:0.25, C:0.14, G:0.33, T:0.28
Consensus pattern (9 bp):
TGCATGGAA
Found at i:36083925 original size:27 final size:27
Alignment explanation
Indices: 36083849--36083935 Score: 93
Period size: 27 Copynumber: 3.2 Consensus size: 27
36083839 TGCAGCACAT
* **
36083849 TGCATGGAGTGCATGGTTCGCATGAAA
1 TGCATGGATTGCATGGAACGCATGAAA
* *
36083876 TGCATGGATTGCATGGGATGCATGAAA
1 TGCATGGATTGCATGGAACGCATGAAA
** * *
36083903 TGCATGTTTTGCATGGAACGCATGGAG
1 TGCATGGATTGCATGGAACGCATGAAA
36083930 TGCATG
1 TGCATG
36083936 CCCAAACTCG
Statistics
Matches: 50, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 50 1.00
ACGTcount: A:0.25, C:0.14, G:0.33, T:0.28
Consensus pattern (27 bp):
TGCATGGATTGCATGGAACGCATGAAA
Found at i:36088710 original size:39 final size:36
Alignment explanation
Indices: 36088629--36088714 Score: 118
Period size: 36 Copynumber: 2.4 Consensus size: 36
36088619 AGATCGAGCA
* *
36088629 CACACCACCACCACCAATAACATTCCTTTCGGGATG
1 CACACCACCACCACCAACAACATTCCTTTCGGGACG
* * * *
36088665 CACACCATCTCTACCAACAATATTCCTTTCGGGACG
1 CACACCACCACCACCAACAACATTCCTTTCGGGACG
36088701 CACACCACCACCAC
1 CACACCACCACCAC
36088715 TAGCGGTACT
Statistics
Matches: 41, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
36 41 1.00
ACGTcount: A:0.30, C:0.42, G:0.09, T:0.19
Consensus pattern (36 bp):
CACACCACCACCACCAACAACATTCCTTTCGGGACG
Found at i:36089167 original size:11 final size:11
Alignment explanation
Indices: 36089151--36089185 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
36089141 TTGTATTCTC
36089151 ATTTTTTTTAA
1 ATTTTTTTTAA
*
36089162 ATTTTTATTAA
1 ATTTTTTTTAA
*
36089173 ATTTTTTTGAA
1 ATTTTTTTTAA
36089184 AT
1 AT
36089186 ACCAATCCCA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (11 bp):
ATTTTTTTTAA
Found at i:36090495 original size:9 final size:9
Alignment explanation
Indices: 36090481--36090525 Score: 54
Period size: 9 Copynumber: 5.0 Consensus size: 9
36090471 CATGCAGCAC
36090481 ATTGCATGG
1 ATTGCATGG
*
36090490 AGTGCATGG
1 ATTGCATGG
* *
36090499 TTTGCATGA
1 ATTGCATGG
*
36090508 AATGCATGG
1 ATTGCATGG
36090517 ATTGCATGG
1 ATTGCATGG
36090526 GATGCATGAA
Statistics
Matches: 28, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
9 28 1.00
ACGTcount: A:0.24, C:0.11, G:0.33, T:0.31
Consensus pattern (9 bp):
ATTGCATGG
Found at i:36090505 original size:18 final size:18
Alignment explanation
Indices: 36090481--36090533 Score: 70
Period size: 18 Copynumber: 2.9 Consensus size: 18
36090471 CATGCAGCAC
*
36090481 ATTGCATGGAGTGCATGG
1 ATTGCATGGAATGCATGG
* *
36090499 TTTGCATGAAATGCATGG
1 ATTGCATGGAATGCATGG
*
36090517 ATTGCATGGGATGCATG
1 ATTGCATGGAATGCATG
36090534 AAATGCATGT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.25, C:0.11, G:0.34, T:0.30
Consensus pattern (18 bp):
ATTGCATGGAATGCATGG
Found at i:36090550 original size:27 final size:27
Alignment explanation
Indices: 36090483--36090542 Score: 93
Period size: 27 Copynumber: 2.2 Consensus size: 27
36090473 TGCAGCACAT
* **
36090483 TGCATGGAGTGCATGGTTTGCATGAAA
1 TGCATGGATTGCATGGGATGCATGAAA
36090510 TGCATGGATTGCATGGGATGCATGAAA
1 TGCATGGATTGCATGGGATGCATGAAA
36090537 TGCATG
1 TGCATG
36090543 TTTTGCATAG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.27, C:0.12, G:0.33, T:0.28
Consensus pattern (27 bp):
TGCATGGATTGCATGGGATGCATGAAA
Found at i:36090559 original size:27 final size:27
Alignment explanation
Indices: 36090502--36090569 Score: 73
Period size: 27 Copynumber: 2.5 Consensus size: 27
36090492 TGCATGGTTT
* * *
36090502 GCATGAAATGCATGGATTGCATGGGAT
1 GCATGAAATGCATGGATTGCATAGAAC
**
36090529 GCATGAAATGCATGTTTTGCATAGAAC
1 GCATGAAATGCATGGATTGCATAGAAC
* *
36090556 GCATGGAGTGCATG
1 GCATGAAATGCATG
36090570 CCCAAACTCG
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.29, C:0.13, G:0.31, T:0.26
Consensus pattern (27 bp):
GCATGAAATGCATGGATTGCATAGAAC
Found at i:36092045 original size:24 final size:24
Alignment explanation
Indices: 36092014--36092064 Score: 102
Period size: 24 Copynumber: 2.1 Consensus size: 24
36092004 AATTAAAGTA
36092014 AAAAAAGTTTAAATACCATTTTGT
1 AAAAAAGTTTAAATACCATTTTGT
36092038 AAAAAAGTTTAAATACCATTTTGT
1 AAAAAAGTTTAAATACCATTTTGT
36092062 AAA
1 AAA
36092065 TTAAACTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.49, C:0.08, G:0.08, T:0.35
Consensus pattern (24 bp):
AAAAAAGTTTAAATACCATTTTGT
Found at i:36093971 original size:95 final size:95
Alignment explanation
Indices: 36093808--36093979 Score: 317
Period size: 95 Copynumber: 1.8 Consensus size: 95
36093798 TTCAAATCAA
36093808 ATTATTCTTAAAAAGGGTTTAGTTCAACAAATATAAAATTATATTTCGAAATAGGATTACAATAA
1 ATTATTCTTAAAAAGGGTTTAGTTCAACAAATATAAAATTATATTTCGAAATAGGATTACAATAA
36093873 TATAATATTACATGCGATATCTTATCTTAT
66 TATAATATTACATGCGATATCTTATCTTAT
* * *
36093903 ATTATTCTTAAAAGGGGTTTAGTTCAACAAGTATAAGATTATATTTCGAAATAGGATTACAATAA
1 ATTATTCTTAAAAAGGGTTTAGTTCAACAAATATAAAATTATATTTCGAAATAGGATTACAATAA
36093968 TATAATATTACA
66 TATAATATTACA
36093980 ATAATATAAT
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
95 74 1.00
ACGTcount: A:0.42, C:0.09, G:0.11, T:0.38
Consensus pattern (95 bp):
ATTATTCTTAAAAAGGGTTTAGTTCAACAAATATAAAATTATATTTCGAAATAGGATTACAATAA
TATAATATTACATGCGATATCTTATCTTAT
Found at i:36093979 original size:16 final size:16
Alignment explanation
Indices: 36093958--36093992 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
36093948 TCGAAATAGG
36093958 ATTACAATAATATAAT
1 ATTACAATAATATAAT
36093974 ATTACAATAATATAAT
1 ATTACAATAATATAAT
36093990 ATT
1 ATT
36093993 TCGAAATAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.54, C:0.06, G:0.00, T:0.40
Consensus pattern (16 bp):
ATTACAATAATATAAT
Found at i:36100869 original size:40 final size:40
Alignment explanation
Indices: 36100811--36100973 Score: 159
Period size: 40 Copynumber: 4.1 Consensus size: 40
36100801 TTATTATCTG
*
36100811 AATGCACATACGTACCCCT-ATTTGTACTTCGGTACCCCTA
1 AATGCACATACGTGCCCCTGA-TTGTACTTCGGTACCCCTA
* * *
36100851 AATGCACATACGTGCCCCTGATTGTATTTCAGTACACCTA
1 AATGCACATACGTGCCCCTGATTGTACTTCGGTACCCCTA
* ** * * *
36100891 AATGCACATACGTGCCCTTGATTGCCCTTTGGTATCCCTG
1 AATGCACATACGTGCCCCTGATTGTACTTCGGTACCCCTA
* * * * *
36100931 AATGCACATGCATGCCCCT-ATTTATACTTTGGTAACCCTA
1 AATGCACATACGTGCCCCTGA-TTGTACTTCGGTACCCCTA
36100971 AAT
1 AAT
36100974 CAAATAGTAT
Statistics
Matches: 100, Mismatches: 21, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
39 1 0.01
40 98 0.98
41 1 0.01
ACGTcount: A:0.25, C:0.29, G:0.15, T:0.31
Consensus pattern (40 bp):
AATGCACATACGTGCCCCTGATTGTACTTCGGTACCCCTA
Found at i:36101785 original size:54 final size:53
Alignment explanation
Indices: 36101698--36101799 Score: 152
Period size: 54 Copynumber: 1.9 Consensus size: 53
36101688 GTGTTTAAAG
* *
36101698 TCAGCGAGTTACACGGCTTAGCACATGGCCTGG-CACACAGGTGTGTGTGGCAAC
1 TCAGAGAGTTACACGGCCTAGCACATGGCCTGGCCACAC-GGT-TGTGTGGCAAC
*
36101752 TCAGAGAGTTACATGGCCTAGCACATGGCCTGGCCACACGGTTGTGTG
1 TCAGAGAGTTACACGGCCTAGCACATGGCCTGGCCACACGGTTGTGTG
36101800 ACCCCTATTT
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
53 6 0.14
54 33 0.75
55 5 0.11
ACGTcount: A:0.22, C:0.25, G:0.31, T:0.22
Consensus pattern (53 bp):
TCAGAGAGTTACACGGCCTAGCACATGGCCTGGCCACACGGTTGTGTGGCAAC
Found at i:36103681 original size:26 final size:26
Alignment explanation
Indices: 36103652--36103708 Score: 60
Period size: 27 Copynumber: 2.2 Consensus size: 26
36103642 TTTAACTACA
* *
36103652 AGGGCATCACGATCATTTTATCCTAT
1 AGGGCATCACGATAATTTTACCCTAT
* **
36103678 AGGGGTATTTCGATAATTTTACCCTAT
1 A-GGGCATCACGATAATTTTACCCTAT
36103705 AGGG
1 AGGG
36103709 GTATTTCGGT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
26 4 0.16
27 21 0.84
ACGTcount: A:0.26, C:0.18, G:0.21, T:0.35
Consensus pattern (26 bp):
AGGGCATCACGATAATTTTACCCTAT
Found at i:36103697 original size:27 final size:27
Alignment explanation
Indices: 36103661--36103912 Score: 182
Period size: 27 Copynumber: 9.3 Consensus size: 27
36103651 AAGGGCATCA
* *
36103661 CGATCATTTTATCCTATAGGGGTATTT
1 CGATAATTTTACCCTATAGGGGTATTT
36103688 CGATAATTTTACCCTATAGGGGTATTT
1 CGATAATTTTACCCTATAGGGGTATTT
* *
36103715 CGGTAATTTTA-CCTATTGGGGGTATTT
1 CGATAATTTTACCCTA-TAGGGGTATTT
* * ** *
36103742 TGGTAAAATTACCCT-TCGAGGGTATTT
1 CGATAATTTTACCCTATAG-GGGTATTT
36103769 C-AGTAATTTTACCC-ATCAGGGGTATTT
1 CGA-TAATTTTACCCTAT-AGGGGTATTT
* *
36103796 TGATAATTTTACCC-ATCGAGGGTATTT
1 CGATAATTTTACCCTATAG-GGGTATTT
* *
36103823 CAATAATTTTACCCT-TCGAGGGTATTT
1 CGATAATTTTACCCTATAG-GGGTATTT
* *
36103850 C-AGTAATTTTATCC-ATCAAGGGTATTT
1 CGA-TAATTTTACCCTAT-AGGGGTATTT
* * *
36103877 TGGTAATTTTACCCT-TCGAGGGTATTT
1 CGATAATTTTACCCTATAG-GGGTATTT
36103904 C-AGTAATTT
1 CGA-TAATTT
36103913 ACTCATGAAT
Statistics
Matches: 182, Mismatches: 27, Indels: 32
0.76 0.11 0.13
Matches are distributed among these distances:
26 8 0.04
27 169 0.93
28 5 0.03
ACGTcount: A:0.25, C:0.15, G:0.19, T:0.41
Consensus pattern (27 bp):
CGATAATTTTACCCTATAGGGGTATTT
Found at i:36103890 original size:54 final size:54
Alignment explanation
Indices: 36103680--36103912 Score: 233
Period size: 54 Copynumber: 4.3 Consensus size: 54
36103670 TATCCTATAG
* * * *
36103680 GGGTATTTC-GATAATTTTACCCTAT-AGGGGTATTTCGGTAATTTTA-CCTATTGG
1 GGGTATTTCAG-TAATTTTACCC-ATCAAGGGTATTTCAGTAATTTTACCCT-TCGA
** ** * * *
36103734 GGGTATTTTGGTAAAATTACCCTTCGAGGGTATTTCAGTAATTTTACCCATC-A
1 GGGTATTTCAGTAATTTTACCCATCAAGGGTATTTCAGTAATTTTACCCTTCGA
* * *
36103787 GGGGTATTT-TGATAATTTTACCCATCGAGGGTATTTCAATAATTTTACCCTTCGA
1 -GGGTATTTCAG-TAATTTTACCCATCAAGGGTATTTCAGTAATTTTACCCTTCGA
* **
36103842 GGGTATTTCAGTAATTTTATCCATCAAGGGTATTTTGGTAATTTTACCCTTCGA
1 GGGTATTTCAGTAATTTTACCCATCAAGGGTATTTCAGTAATTTTACCCTTCGA
36103896 GGGTATTTCAGTAATTT
1 GGGTATTTCAGTAATTT
36103913 ACTCATGAAT
Statistics
Matches: 150, Mismatches: 22, Indels: 14
0.81 0.12 0.08
Matches are distributed among these distances:
53 2 0.01
54 143 0.95
55 5 0.03
ACGTcount: A:0.24, C:0.15, G:0.20, T:0.41
Consensus pattern (54 bp):
GGGTATTTCAGTAATTTTACCCATCAAGGGTATTTCAGTAATTTTACCCTTCGA
Found at i:36103911 original size:81 final size:81
Alignment explanation
Indices: 36103680--36103912 Score: 310
Period size: 81 Copynumber: 2.9 Consensus size: 81
36103670 TATCCTATAG
* * *
36103680 GGGTATTTC-GATAATTTTACCCTAT-AGGGGTATTTCGGTAATTTTA-CCTATTGGGGGTATTT
1 GGGTATTTCAG-TAATTTTACCC-ATCAGGGGTATTTTGGTAATTTTACCCT-TCGAGGGTATTT
** **
36103742 TGGTAAAATTACCCTTCGA
63 CAGTAATTTTACCCTTCGA
* * *
36103761 GGGTATTTCAGTAATTTTACCCATCAGGGGTATTTTGATAATTTTACCCATCGAGGGTATTTCAA
1 GGGTATTTCAGTAATTTTACCCATCAGGGGTATTTTGGTAATTTTACCCTTCGAGGGTATTTCAG
36103826 TAATTTTACCCTTCGA
66 TAATTTTACCCTTCGA
* *
36103842 GGGTATTTCAGTAATTTTATCCATCAAGGGTATTTTGGTAATTTTACCCTTCGAGGGTATTTCAG
1 GGGTATTTCAGTAATTTTACCCATCAGGGGTATTTTGGTAATTTTACCCTTCGAGGGTATTTCAG
36103907 TAATTT
66 TAATTT
36103913 ACTCATGAAT
Statistics
Matches: 134, Mismatches: 15, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
80 2 0.01
81 129 0.96
82 3 0.02
ACGTcount: A:0.24, C:0.15, G:0.20, T:0.41
Consensus pattern (81 bp):
GGGTATTTCAGTAATTTTACCCATCAGGGGTATTTTGGTAATTTTACCCTTCGAGGGTATTTCAG
TAATTTTACCCTTCGA
Found at i:36110506 original size:51 final size:51
Alignment explanation
Indices: 36110446--36110547 Score: 161
Period size: 51 Copynumber: 2.0 Consensus size: 51
36110436 TTTTGTGGTG
36110446 AATGTTGGTTAAACACTCTTCTACACCCTA-GAGTTTTATTTTATGATTCCT
1 AATGTTGGTTAAACACTCTTCTACACCCTAGGA-TTTTATTTTATGATTCCT
* * *
36110497 AATGTTGGTTAAACACTGTTCTGCACGCTAGGATTTTATTTTATGATTCCT
1 AATGTTGGTTAAACACTCTTCTACACCCTAGGATTTTATTTTATGATTCCT
36110548 TTCTTTTTAT
Statistics
Matches: 47, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
51 45 0.96
52 2 0.04
ACGTcount: A:0.25, C:0.18, G:0.15, T:0.43
Consensus pattern (51 bp):
AATGTTGGTTAAACACTCTTCTACACCCTAGGATTTTATTTTATGATTCCT
Found at i:36118476 original size:56 final size:50
Alignment explanation
Indices: 36118380--36118677 Score: 226
Period size: 50 Copynumber: 5.9 Consensus size: 50
36118370 ATTTGGGTAA
*
36118380 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTGAGATCATG
1 AGAGCTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCAT-C--GAGA-C--G
* * **
36118436 AGAGGTCTCATGTAAGACCATGTCTGGGACATGGTGTTGGCATCGAGACG
1 AGAGCTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGAGACG
* * * *
36118486 AGAGCTCCCATCTGAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
1 AGAGCTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGAGACG
* * ** * * * * *
36118536 TGAGATCCCCCGTAAGACCATGTCTAGGACATAGCATGGGCA-CTGATATG
1 AGAGCTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATC-GAGACG
* * * * * * * *
36118586 AGAACTCCCATGTAATACCATATCTGCGAGATGGCATCGGCA--GTACATG
1 AGAGCTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCG-AGACG
* * *
36118635 A-AACATCCCATGTAAAACCATGTCTGGGACATGGCTTTGGCAT
1 AGAGC-TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCAT
36118678 GTTATTATCA
Statistics
Matches: 197, Mismatches: 41, Indels: 14
0.78 0.16 0.06
Matches are distributed among these distances:
48 4 0.02
49 37 0.19
50 111 0.56
52 1 0.01
53 4 0.02
55 1 0.01
56 39 0.20
ACGTcount: A:0.27, C:0.23, G:0.27, T:0.23
Consensus pattern (50 bp):
AGAGCTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGAGACG
Found at i:36118606 original size:100 final size:104
Alignment explanation
Indices: 36118385--36118627 Score: 253
Period size: 100 Copynumber: 2.4 Consensus size: 104
36118375 GGTAAAGAGA
* *
36118385 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTGAGATCATGAGAGGTCTCATGTA
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCC-TGAGATCATGAGA-GTCCCACGTA
* * ** * *
36118450 AGACCATGTCTGGGACATGGTGTTGGCATCGAGACGAGAGC
64 AGACCATGTCTAGGACATAGCATGGGCATCGAGACGAGAAC
* * * *
36118491 TCCCATCTGAGACCATGTCTGGGACATGGCATTGGCA-CC-GAGAT-GTGAGA-TCCCCCGTAAG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTGAGATCATGAGAGTCCCACGTAAG
* *
36118552 ACCATGTCTAGGACATAGCATGGGCA-CTGATATGAGAAC
66 ACCATGTCTAGGACATAGCATGGGCATC-GAGACGAGAAC
* * * * *
36118591 TCCCATGTAATACCATATCTGCGAGATGGCATCGGCA
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
36118628 GTACATGAAA
Statistics
Matches: 115, Mismatches: 21, Indels: 8
0.80 0.15 0.06
Matches are distributed among these distances:
99 1 0.01
100 67 0.58
102 5 0.04
103 5 0.04
105 2 0.02
106 35 0.30
ACGTcount: A:0.26, C:0.23, G:0.28, T:0.23
Consensus pattern (104 bp):
TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTGAGATCATGAGAGTCCCACGTAAG
ACCATGTCTAGGACATAGCATGGGCATCGAGACGAGAAC
Found at i:36124144 original size:50 final size:50
Alignment explanation
Indices: 36124011--36124308 Score: 285
Period size: 50 Copynumber: 5.9 Consensus size: 50
36124001 ATTTGGGTAA
* * *
36124011 AGAGATCCCATGTAAGACCATGTCTTGGACATGGAATTGGCATCCTTGAGATCATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCAT-C--GAG---ATG
* * *
36124067 AGAGGTGCCATGTAAGACCATGTCTGGGACATGGCGTTGGCATCGAGACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGAGATG
* * * *
36124117 AGAGGTCCCATGTAAGACCATGCCTGGGACATGGCGTTGGCACCGGGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGAGATG
* ** * *
36124167 AGAAGTCCCCCGTAAGACCATGTCTGGGACATGGCATGGGCATCGATATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGAGATG
** * * * *
36124217 AGAACTCCCATGTAAGACCATATCTAGGATATGGCATTGGCA--GTACATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCG-AGATG
* ** * *
36124266 AAACATCCCATGTAAGACCATGTTTGGGACATGGCTTTGGCAT
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCAT
36124309 GTTATTATAA
Statistics
Matches: 204, Mismatches: 36, Indels: 10
0.82 0.14 0.04
Matches are distributed among these distances:
48 1 0.00
49 38 0.19
50 123 0.60
53 3 0.01
55 1 0.00
56 38 0.19
ACGTcount: A:0.27, C:0.21, G:0.29, T:0.23
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGAGATG
Found at i:36134779 original size:33 final size:33
Alignment explanation
Indices: 36134683--36134782 Score: 116
Period size: 33 Copynumber: 3.1 Consensus size: 33
36134673 GTTTAGTTTA
*
36134683 ATTAATTCTACAGCTTTTAATTATGTCTTGC-TT
1 ATTAA-TCTACATCTTTTAATTATGTCTTGCATT
* *
36134716 ATT-ATATGCATC-TTTAATTAATGTCTTGCATT
1 ATTAATCTACATCTTTTAATT-ATGTCTTGCATT
* *
36134748 ATTAATCTACATCTTTTAATTATGACATGCATT
1 ATTAATCTACATCTTTTAATTATGTCTTGCATT
36134781 AT
1 AT
36134783 GTGTTTTGCA
Statistics
Matches: 56, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
30 7 0.12
31 14 0.25
32 6 0.11
33 22 0.39
34 7 0.12
ACGTcount: A:0.29, C:0.14, G:0.08, T:0.49
Consensus pattern (33 bp):
ATTAATCTACATCTTTTAATTATGTCTTGCATT
Found at i:36134867 original size:50 final size:52
Alignment explanation
Indices: 36134804--36134922 Score: 161
Period size: 50 Copynumber: 2.3 Consensus size: 52
36134794 TAAATAAAGT
36134804 CATGCATTATGTAACTCTCATGTTAGTT-AAGTTTGCATCA-TAAATTAGGA
1 CATGCATTATGTAACTCTCATGTTAGTTAAAGTTTGCATCATTAAATTAGGA
* * * * *
36134854 CATGCTTTTTGTAACTCTCATGTTAGTTAAAGTTTGCATTATTAAATTAAGT
1 CATGCATTATGTAACTCTCATGTTAGTTAAAGTTTGCATCATTAAATTAGGA
* *
36134906 CATGGATTAAGTAACTC
1 CATGCATTATGTAACTC
36134923 ATTTGTTCAT
Statistics
Matches: 58, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
50 26 0.45
51 11 0.19
52 21 0.36
ACGTcount: A:0.31, C:0.13, G:0.15, T:0.40
Consensus pattern (52 bp):
CATGCATTATGTAACTCTCATGTTAGTTAAAGTTTGCATCATTAAATTAGGA
Found at i:36134924 original size:50 final size:50
Alignment explanation
Indices: 36134791--36134950 Score: 157
Period size: 50 Copynumber: 3.2 Consensus size: 50
36134781 ATGTGTTTTG
*
36134791 CATTAAATAAAGTCATGCATTATGTAACTCTCATGTTAGTTAAGTTTGCAT
1 CATTAAATTAAGTCATGCATTATGTAAC-CTCATGTTAGTTAAGTTTGCAT
* * * *
36134842 CA-TAAATTAGGACATGCTTTTTGTAACTCTCATGTTAGTTAAAGTTTGCAT
1 CATTAAATTAAGTCATGCATTATGTAAC-CTCATGTTAGTT-AAGTTTGCAT
* * * *
36134893 TATTAAATTAAGTCATGGATTAAGTAA-CTCATTTGTTCA-TTTAGTTTGCAT
1 CATTAAATTAAGTCATGCATTATGTAACCTCA--TGTT-AGTTAAGTTTGCAT
36134944 C-TTAAAT
1 CATTAAAT
36134951 CATGCATTTA
Statistics
Matches: 90, Mismatches: 14, Indels: 11
0.78 0.12 0.10
Matches are distributed among these distances:
50 43 0.48
51 22 0.24
52 24 0.27
53 1 0.01
ACGTcount: A:0.32, C:0.12, G:0.14, T:0.42
Consensus pattern (50 bp):
CATTAAATTAAGTCATGCATTATGTAACCTCATGTTAGTTAAGTTTGCAT
Found at i:36135286 original size:69 final size:69
Alignment explanation
Indices: 36135171--36135309 Score: 206
Period size: 69 Copynumber: 2.0 Consensus size: 69
36135161 CTATCTTGTA
* * *
36135171 GGTGACTATTCATATGACTAATTGAATTTTCAAGTTTGGATGTTTTTCAGGCCTTCAAAGATCAT
1 GGTGACTATTCATATGACTAATTGAATCTTCAAGTTTGGATATTTTTCAAGCCTTCAAAGATCAT
*
36135236 TATG
66 CATG
* * **
36135240 GGTGACTATTCATATGGCTAATTGACTCTTCAAGTTTTTATATTTTTCAAGCCTTCAAAGATCAT
1 GGTGACTATTCATATGACTAATTGAATCTTCAAGTTTGGATATTTTTCAAGCCTTCAAAGATCAT
36135305 CATG
66 CATG
36135309 G
1 G
36135310 TGGCTGTTCC
Statistics
Matches: 62, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
69 62 1.00
ACGTcount: A:0.27, C:0.15, G:0.17, T:0.40
Consensus pattern (69 bp):
GGTGACTATTCATATGACTAATTGAATCTTCAAGTTTGGATATTTTTCAAGCCTTCAAAGATCAT
CATG
Found at i:36138839 original size:11 final size:11
Alignment explanation
Indices: 36138823--36138850 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
36138813 ACAGTTGTGA
36138823 GGAGTTTGAAT
1 GGAGTTTGAAT
36138834 GGAGTTTGAAT
1 GGAGTTTGAAT
36138845 GGAGTT
1 GGAGTT
36138851 GTTGGGGGAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.25, C:0.00, G:0.39, T:0.36
Consensus pattern (11 bp):
GGAGTTTGAAT
Found at i:36139919 original size:27 final size:27
Alignment explanation
Indices: 36139881--36140022 Score: 169
Period size: 27 Copynumber: 5.3 Consensus size: 27
36139871 TTCGTGGGCT
36139881 AATGACCGAAATACCCTCGAAGGGTAA
1 AATGACCGAAATACCCTCGAAGGGTAA
*
36139908 AATGACCAAAATACCCTCGAAGGGTAA
1 AATGACCGAAATACCCTCGAAGGGTAA
* *
36139935 AATGACCTAAATACCCCCGAAGGGTAA
1 AATGACCGAAATACCCTCGAAGGGTAA
** * *
36139962 GGTGATCGAAATACCC-CCACAGGGTAA
1 AATGACCGAAATACCCTCGA-AGGGTAA
* * **
36139989 AATGATCGAAATACCTTCTTAGGGTAA
1 AATGACCGAAATACCCTCGAAGGGTAA
36140016 AATGACC
1 AATGACC
36140023 ATTACACCCC
Statistics
Matches: 99, Mismatches: 14, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
26 2 0.02
27 96 0.97
28 1 0.01
ACGTcount: A:0.39, C:0.23, G:0.20, T:0.18
Consensus pattern (27 bp):
AATGACCGAAATACCCTCGAAGGGTAA
Found at i:36140379 original size:28 final size:28
Alignment explanation
Indices: 36140358--36140531 Score: 159
Period size: 28 Copynumber: 6.0 Consensus size: 28
36140348 TGTTTCTATT
36140358 TTGGGCTAAGGCCCACACTGTTACTGTA
1 TTGGGCTAAGGCCCACACTGTTACTGTA
* ** * * *
36140386 ATAAGCTAAAGCCCACAATGTTACTGAA
1 TTGGGCTAAGGCCCACACTGTTACTGTA
* * * *
36140414 ATGGGCTAAAGCCCACACTATTTCTGTA
1 TTGGGCTAAGGCCCACACTGTTACTGTA
*
36140442 TTGGGCTAAGGCCCACATTGTTACTGTA
1 TTGGGCTAAGGCCCACACTGTTACTGTA
* **
36140470 TCGGGCTAAGGCCCACACTGTACTATTACTGCG
1 TTGGGCTAAGGCCCACACTG-----TTACTGTA
* *
36140503 TTGGGCTCAGGCCCAGACTGTTACTGTA
1 TTGGGCTAAGGCCCACACTGTTACTGTA
36140531 T
1 T
36140532 GTTGTATGCT
Statistics
Matches: 115, Mismatches: 26, Indels: 10
0.76 0.17 0.07
Matches are distributed among these distances:
28 92 0.80
33 23 0.20
ACGTcount: A:0.25, C:0.25, G:0.22, T:0.28
Consensus pattern (28 bp):
TTGGGCTAAGGCCCACACTGTTACTGTA
Found at i:36144451 original size:49 final size:49
Alignment explanation
Indices: 36144379--36144477 Score: 171
Period size: 49 Copynumber: 2.0 Consensus size: 49
36144369 TTGCTTGATT
*
36144379 GAATACCATCCTAGTAAGGCTAACGTGGTAGCTGACGCACTAAGCTGTA
1 GAATACCATCCTAGTAAGGCTAACATGGTAGCTGACGCACTAAGCTGTA
* *
36144428 GAATACCATCCTGGTAAGGCTAACATGGTAGCTGACGCACTGAGCTGTA
1 GAATACCATCCTAGTAAGGCTAACATGGTAGCTGACGCACTAAGCTGTA
36144477 G
1 G
36144478 GACTGTATCT
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
49 47 1.00
ACGTcount: A:0.29, C:0.22, G:0.26, T:0.22
Consensus pattern (49 bp):
GAATACCATCCTAGTAAGGCTAACATGGTAGCTGACGCACTAAGCTGTA
Found at i:36145533 original size:27 final size:27
Alignment explanation
Indices: 36145495--36145609 Score: 151
Period size: 27 Copynumber: 4.3 Consensus size: 27
36145485 TTCGTGGGCT
36145495 AATGACCGAAATACCCTCGAAGGGTAA
1 AATGACCGAAATACCCTCGAAGGGTAA
*
36145522 AATGACCGAAATACCCCCGAAGGGTAA
1 AATGACCGAAATACCCTCGAAGGGTAA
* * *
36145549 AATGACCAAAATACCC-CCAGAGGATAA
1 AATGACCGAAATACCCTCGA-AGGGTAA
* * *
36145576 AATGGCTGAAATACCCTCAAAGGGTAA
1 AATGACCGAAATACCCTCGAAGGGTAA
36145603 AATGACC
1 AATGACC
36145610 ATTACACCCC
Statistics
Matches: 75, Mismatches: 11, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
26 2 0.03
27 71 0.95
28 2 0.03
ACGTcount: A:0.43, C:0.23, G:0.20, T:0.14
Consensus pattern (27 bp):
AATGACCGAAATACCCTCGAAGGGTAA
Found at i:36145970 original size:28 final size:28
Alignment explanation
Indices: 36145929--36146132 Score: 237
Period size: 28 Copynumber: 7.3 Consensus size: 28
36145919 GTTGCATTAT
* *
36145929 CACACTGTTTCTGTTTTAGGCTAAGGCC
1 CACACTGTTTCTGTATTGGGCTAAGGCC
* *
36145957 CACACTGTTACTGTAATGGGCTAAGGCC
1 CACACTGTTTCTGTATTGGGCTAAGGCC
* *
36145985 CACACTATTTCTATATTGGGCTAAGGCC
1 CACACTGTTTCTGTATTGGGCTAAGGCC
* *
36146013 CACATTGTTTCTGTTTTGGGCTAAGGCC
1 CACACTGTTTCTGTATTGGGCTAAGGCC
* * * *
36146041 CACACTGTTACTATAATGGGATAAGGCC
1 CACACTGTTTCTGTATTGGGCTAAGGCC
* *
36146069 CATATTGTTTCTGTATTGGGCTAAGGCC
1 CACACTGTTTCTGTATTGGGCTAAGGCC
* * * *
36146097 CACATTGTTACCGTATCGGGCTAAGGCC
1 CACACTGTTTCTGTATTGGGCTAAGGCC
*
36146125 TACACTGT
1 CACACTGT
36146133 ACTATTACCG
Statistics
Matches: 146, Mismatches: 30, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 146 1.00
ACGTcount: A:0.22, C:0.24, G:0.23, T:0.32
Consensus pattern (28 bp):
CACACTGTTTCTGTATTGGGCTAAGGCC
Found at i:36146035 original size:84 final size:84
Alignment explanation
Indices: 36145929--36146137 Score: 294
Period size: 84 Copynumber: 2.5 Consensus size: 84
36145919 GTTGCATTAT
* * * *
36145929 CACACTGTTTCTGTTTTAGGCTAAGGCCCACACTGTTACTGTAATGGGCTAAGGCCCACACTATT
1 CACATTGTTTCTGTTTTGGGCTAAGGCCCACACTGTTACTATAATGGGATAAGGCCCACACTATT
36145994 TCTATATTGGGCTAAGGCC
66 TCTATATTGGGCTAAGGCC
* * *
36146013 CACATTGTTTCTGTTTTGGGCTAAGGCCCACACTGTTACTATAATGGGATAAGGCCCATATTGTT
1 CACATTGTTTCTGTTTTGGGCTAAGGCCCACACTGTTACTATAATGGGATAAGGCCCACACTATT
*
36146078 TCTGTATTGGGCTAAGGCC
66 TCTATATTGGGCTAAGGCC
* * * * *
36146097 CACATTGTTACCGTATCGGGCTAAGGCCTACACTG-TACTAT
1 CACATTGTTTCTGTTTTGGGCTAAGGCCCACACTGTTACTAT
36146138 TACCGCGTTG
Statistics
Matches: 112, Mismatches: 13, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
83 6 0.05
84 106 0.95
ACGTcount: A:0.22, C:0.23, G:0.22, T:0.32
Consensus pattern (84 bp):
CACATTGTTTCTGTTTTGGGCTAAGGCCCACACTGTTACTATAATGGGATAAGGCCCACACTATT
TCTATATTGGGCTAAGGCC
Found at i:36147232 original size:25 final size:26
Alignment explanation
Indices: 36147191--36147239 Score: 66
Period size: 25 Copynumber: 1.9 Consensus size: 26
36147181 TAGGATTATT
*
36147191 TTAAATTAAATAAAAATCATAATAAA
1 TTAAATTAAATAAAAATCAAAATAAA
36147217 TTAAA-TAAA-AACAAATCAAAATA
1 TTAAATTAAATAA-AAATCAAAATA
36147240 TTTATAAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 2 0.10
25 14 0.67
26 5 0.24
ACGTcount: A:0.67, C:0.06, G:0.00, T:0.27
Consensus pattern (26 bp):
TTAAATTAAATAAAAATCAAAATAAA
Found at i:36147906 original size:28 final size:28
Alignment explanation
Indices: 36147852--36147906 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 28
36147842 CAGTATAGTT
* * *
36147852 TGGGCCTTATCCCATTACAGTAACAGTG
1 TGGGCCCTATCCCAATACAGAAACAGTG
36147880 TGGGCCCTA-CCCAATACAGAAATCAGT
1 TGGGCCCTATCCCAATACAGAAA-CAGT
36147907 ACAATGTTGT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
27 11 0.48
28 12 0.52
ACGTcount: A:0.29, C:0.27, G:0.20, T:0.24
Consensus pattern (28 bp):
TGGGCCCTATCCCAATACAGAAACAGTG
Found at i:36148273 original size:27 final size:27
Alignment explanation
Indices: 36148243--36148327 Score: 73
Period size: 27 Copynumber: 3.1 Consensus size: 27
36148233 TATTTCAGTC
*
36148243 ATTTTACCCTTTGGGGGTAATTCGATT
1 ATTTTACCCTTTGGGGGTAATTCGATA
* * * *
36148270 ATTTTA-CCTTTCAGGGGTATTTTGGTA
1 ATTTTACCCTTT-GGGGGTAATTCGATA
** * *
36148297 ATTTTACCCTTTGAAGGTATTTCGGTA
1 ATTTTACCCTTTGGGGGTAATTCGATA
36148324 ATTT
1 ATTT
36148328 GTGGCCTATT
Statistics
Matches: 47, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
26 5 0.11
27 37 0.79
28 5 0.11
ACGTcount: A:0.20, C:0.13, G:0.20, T:0.47
Consensus pattern (27 bp):
ATTTTACCCTTTGGGGGTAATTCGATA
Done.