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 184 of 187
Found at i:55084190 original size:29 final size:30
Alignment explanation
Indices: 55084128--55084190 Score: 94
Period size: 28 Copynumber: 2.2 Consensus size: 30
55084118 ATTAAATTTC
*
55084128 ATTTTTTAAGAAAATTTTAAAATTTTTTAT
1 ATTTTTTAAGAAAATTTTAAAATTTTTAAT
*
55084158 -TTTTTTAA-ATAATTTTAAAATTTTTAAT
1 ATTTTTTAAGAAAATTTTAAAATTTTTAAT
55084186 ATTTT
1 ATTTT
55084191 CAACAATGGC
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
28 18 0.60
29 12 0.40
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (30 bp):
ATTTTTTAAGAAAATTTTAAAATTTTTAAT
Found at i:55084302 original size:16 final size:15
Alignment explanation
Indices: 55084281--55084316 Score: 54
Period size: 16 Copynumber: 2.3 Consensus size: 15
55084271 AAATTTTAAA
55084281 TTTTATTTAAGATATT
1 TTTTATTTAAG-TATT
*
55084297 TTTTATTTATGTATT
1 TTTTATTTAAGTATT
55084312 TTTTA
1 TTTTA
55084317 GATATTTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 9 0.47
16 10 0.53
ACGTcount: A:0.25, C:0.00, G:0.06, T:0.69
Consensus pattern (15 bp):
TTTTATTTAAGTATT
Found at i:55084311 original size:15 final size:15
Alignment explanation
Indices: 55084281--55084330 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
55084271 AAATTTTAAA
*
55084281 TTTTATTTAAGATATT
1 TTTTATTTATG-TATT
55084297 TTTTATTTATGTATT
1 TTTTATTTATGTATT
** *
55084312 TTTTAGATATTTATT
1 TTTTATTTATGTATT
55084327 TTTT
1 TTTT
55084331 GTTATAAAAG
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
15 20 0.67
16 10 0.33
ACGTcount: A:0.24, C:0.00, G:0.06, T:0.70
Consensus pattern (15 bp):
TTTTATTTATGTATT
Found at i:55086030 original size:84 final size:84
Alignment explanation
Indices: 55085889--55086091 Score: 379
Period size: 84 Copynumber: 2.4 Consensus size: 84
55085879 CAAACTTGCT
*
55085889 ACTGTAGCAAAATCGCGTCCACGAGGGCGCGATTTGACACTATTTGCTCAGAAACGTCAAAAAAA
1 ACTGTAGCGAAATCGCGTCCACGAGGGCGCGATTTGACACTATTTGCTCAGAAACGTCAAAAAAA
*
55085954 ATTATTTCCTACATGATCA
66 ATTATTTCCTACATGACCA
55085973 ACTGTAGCGAAATCGCGTCCACGAGGGCGCGATTTGACACTATTTGCTCAGAAACGTCAAAAAAA
1 ACTGTAGCGAAATCGCGTCCACGAGGGCGCGATTTGACACTATTTGCTCAGAAACGTCAAAAAAA
55086038 ATTATTTCCTACATGACCA
66 ATTATTTCCTACATGACCA
*
55086057 ACTGTAGCGAAATCGCGTCCACGAGGGCGCAATTT
1 ACTGTAGCGAAATCGCGTCCACGAGGGCGCGATTT
55086092 CACAATTTCT
Statistics
Matches: 116, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
84 116 1.00
ACGTcount: A:0.33, C:0.24, G:0.20, T:0.24
Consensus pattern (84 bp):
ACTGTAGCGAAATCGCGTCCACGAGGGCGCGATTTGACACTATTTGCTCAGAAACGTCAAAAAAA
ATTATTTCCTACATGACCA
Found at i:55086221 original size:124 final size:124
Alignment explanation
Indices: 55086001--55086280 Score: 420
Period size: 124 Copynumber: 2.3 Consensus size: 124
55085991 CCACGAGGGC
55086001 GCGATTTGACACTATTTGCTCAGAAACGTCAAAAAAAATTATTTCCTACATGACCAACTGTAGCG
1 GCGATTTGACACTATTTGCTCAGAAACGTCAAAAAAAATTATTTCCTACATGACCAACTGTAGCG
* * * **
55086066 AAATCGCGTCCACGAGGGCGCAATTTCACAATTTCTTCTCATATAGCATCCTGGTATCA
66 AAATCGCGTCCACGAGGCCACAATTTCACAATTTCTTCTCAAATAGCATCCTGGTAGAA
* * *
55086125 GCGATTTTATACTATTTGCTCAGAAAACGTCAAAAAAAATTATTTCTTACATGACC-ACTGTAGC
1 GCGATTTGACACTATTTGCTCAG-AAACGTCAAAAAAAATTATTTCCTACATGACCAACTGTAGC
*
55086189 GAAATCGCGTCCACGAGGCCACTATTTCACAATTTCTTCTCAAATAGCATCCTGGTAGAA
65 GAAATCGCGTCCACGAGGCCACAATTTCACAATTTCTTCTCAAATAGCATCCTGGTAGAA
** *
55086249 GCGATTTCCCACTATTTGAC-CAGATACGTCAA
1 GCGATTTGACACTATTTG-CTCAGAAACGTCAA
55086281 CTCGAAAAAA
Statistics
Matches: 141, Mismatches: 13, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
123 8 0.06
124 101 0.72
125 32 0.23
ACGTcount: A:0.32, C:0.24, G:0.15, T:0.29
Consensus pattern (124 bp):
GCGATTTGACACTATTTGCTCAGAAACGTCAAAAAAAATTATTTCCTACATGACCAACTGTAGCG
AAATCGCGTCCACGAGGCCACAATTTCACAATTTCTTCTCAAATAGCATCCTGGTAGAA
Found at i:55086910 original size:20 final size:22
Alignment explanation
Indices: 55086867--55086912 Score: 60
Period size: 20 Copynumber: 2.2 Consensus size: 22
55086857 AAGAGTAGAT
55086867 ATTATCTTATATTAGTTATAAA
1 ATTATCTTATATTAGTTATAAA
* *
55086889 ATTATTTTA-ATTA-TTATTAA
1 ATTATCTTATATTAGTTATAAA
55086909 ATTA
1 ATTA
55086913 CATTATAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 10 0.45
21 4 0.18
22 8 0.36
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.54
Consensus pattern (22 bp):
ATTATCTTATATTAGTTATAAA
Found at i:55106459 original size:18 final size:18
Alignment explanation
Indices: 55106416--55106462 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
55106406 TTCGCTGCCC
* * *
55106416 CTTCTTCTTCACCTGTAT
1 CTTCTTCCTCAACTGCAT
*
55106434 CTTTTTCCTCAACTGCAT
1 CTTCTTCCTCAACTGCAT
55106452 CTTCTTCCTCA
1 CTTCTTCCTCA
55106463 TTTATTCCTT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.13, C:0.36, G:0.04, T:0.47
Consensus pattern (18 bp):
CTTCTTCCTCAACTGCAT
Found at i:55108881 original size:15 final size:15
Alignment explanation
Indices: 55108861--55108892 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
55108851 CATTTCACTA
*
55108861 TTATGTCTTTTGTAT
1 TTATGTCTTTTATAT
55108876 TTATGTCTTTTATAT
1 TTATGTCTTTTATAT
55108891 TT
1 TT
55108893 TGCATGTATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.16, C:0.06, G:0.09, T:0.69
Consensus pattern (15 bp):
TTATGTCTTTTATAT
Found at i:55118295 original size:37 final size:37
Alignment explanation
Indices: 55118245--55118318 Score: 121
Period size: 37 Copynumber: 2.0 Consensus size: 37
55118235 CACATGCTAA
* *
55118245 TTATGATCAATGGCCCATTTATCCTCTAAGTTTTTTT
1 TTATGATCAATGGCCCACTGATCCTCTAAGTTTTTTT
*
55118282 TTATGATCAATGGCCTACTGATCCTCTAAGTTTTTTT
1 TTATGATCAATGGCCCACTGATCCTCTAAGTTTTTTT
55118319 GTATTTAACG
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.22, C:0.19, G:0.12, T:0.47
Consensus pattern (37 bp):
TTATGATCAATGGCCCACTGATCCTCTAAGTTTTTTT
Found at i:55120493 original size:13 final size:13
Alignment explanation
Indices: 55120477--55120508 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
55120467 AATCATAAAA
55120477 TCCCTTTTAATGG
1 TCCCTTTTAATGG
55120490 TCCCTTTTAATGG
1 TCCCTTTTAATGG
*
55120503 ACCCTT
1 TCCCTT
55120509 GAGGTTAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.16, C:0.28, G:0.12, T:0.44
Consensus pattern (13 bp):
TCCCTTTTAATGG
Found at i:55121506 original size:23 final size:21
Alignment explanation
Indices: 55121450--55121526 Score: 73
Period size: 21 Copynumber: 3.6 Consensus size: 21
55121440 TATGACACAT
* *
55121450 AAGTGCCTGAAACGACACACG
1 AAGTGCCTGATACAACACACG
55121471 AAGTGCCTGATACAACACACG
1 AAGTGCCTGATACAACACACG
* * * **
55121492 AGGTGCTTGACATACGACACATA
1 AAGTGCCTG--ATACAACACACG
55121515 AAGTGCCTGATA
1 AAGTGCCTGATA
55121527 TACGACACAT
Statistics
Matches: 45, Mismatches: 9, Indels: 4
0.78 0.16 0.07
Matches are distributed among these distances:
21 29 0.64
23 16 0.36
ACGTcount: A:0.36, C:0.25, G:0.22, T:0.17
Consensus pattern (21 bp):
AAGTGCCTGATACAACACACG
Found at i:55121529 original size:23 final size:22
Alignment explanation
Indices: 55121443--55121545 Score: 95
Period size: 23 Copynumber: 4.7 Consensus size: 22
55121433 ATCAGTATAT
55121443 GACACAT-AAGTGCCTGAA-AC
1 GACACATAAAGTGCCTGAATAC
**
55121463 GACACACGAAGTGCCTG-ATAC
1 GACACATAAAGTGCCTGAATAC
* ** * *
55121484 AACACACGAGGTGCTTGACATAC
1 GACACATAAAGTGCCTGA-ATAC
55121507 GACACATAAAGTGCCTGATATAC
1 GACACATAAAGTGCCTGA-ATAC
*
55121530 GACACATATAGTGCCT
1 GACACATAAAGTGCCT
55121546 AATCGGCAAA
Statistics
Matches: 68, Mismatches: 11, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
20 7 0.10
21 25 0.37
23 36 0.53
ACGTcount: A:0.36, C:0.25, G:0.20, T:0.18
Consensus pattern (22 bp):
GACACATAAAGTGCCTGAATAC
Found at i:55122525 original size:14 final size:14
Alignment explanation
Indices: 55122508--55122537 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
55122498 TTTGTTTCGT
55122508 TTTTATTTACTTTA
1 TTTTATTTACTTTA
55122522 TTTTATTTACTTTA
1 TTTTATTTACTTTA
55122536 TT
1 TT
55122538 GTTTTAATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.20, C:0.07, G:0.00, T:0.73
Consensus pattern (14 bp):
TTTTATTTACTTTA
Found at i:55124318 original size:36 final size:36
Alignment explanation
Indices: 55124237--55124307 Score: 106
Period size: 36 Copynumber: 2.0 Consensus size: 36
55124227 TTATATAAAT
* *
55124237 ACATATACTTCCATAAACTTCCATTCACTTGAATTA
1 ACATATACATCCATAAACTTCCATTCAATTGAATTA
**
55124273 ACATATACATCCATAAACTTTTATTCAATTGAATT
1 ACATATACATCCATAAACTTCCATTCAATTGAATT
55124308 GACAATTACA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.38, C:0.21, G:0.03, T:0.38
Consensus pattern (36 bp):
ACATATACATCCATAAACTTCCATTCAATTGAATTA
Found at i:55131527 original size:35 final size:36
Alignment explanation
Indices: 55131475--55131544 Score: 106
Period size: 35 Copynumber: 2.0 Consensus size: 36
55131465 CATTATAATC
* * *
55131475 ACTGTCACATTGTATGAA-AACATACCTACATATTT
1 ACTGTCACATGGCATGAATAACATACCCACATATTT
55131510 ACTGTCACATGGCATGAATAACATACCCACATATT
1 ACTGTCACATGGCATGAATAACATACCCACATATT
55131545 CTCTTTCACA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
35 16 0.52
36 15 0.48
ACGTcount: A:0.37, C:0.23, G:0.10, T:0.30
Consensus pattern (36 bp):
ACTGTCACATGGCATGAATAACATACCCACATATTT
Found at i:55134795 original size:78 final size:76
Alignment explanation
Indices: 55134666--55134890 Score: 279
Period size: 78 Copynumber: 3.0 Consensus size: 76
55134656 CTTCTGACTT
55134666 TCACCTTGGACTTTTCTACTAAATCTTTACGCAAATTCAACCAATTTGATGCTCTTTATGAATGC
1 TCACCTTGGACTTTTCTACTAAAT-TTTACGCAAATTCAACCAATTTGATGCTCTTTATGAATGC
55134731 AATGCTTAGAGGA
65 AATGCTTA-AGGA
* *
55134744 TCACCTTGGACTTTTCTAGTAAATTTTCACACAAATTCAACCAATTTGATGCTCTTTATGAATGC
1 TCACCTTGGACTTTTCTACTAAATTTT-ACGCAAATTCAACCAATTTGATGCTCTTTATGAATGC
*
55134809 AATTCTT----A
65 AATGCTTAAGGA
* * * *
55134817 -CA----GGACTTTTCTATTAAATTTTTACGCATATTCATCCAAATTGATGCTCTTTATGAATGC
1 TCACCTTGGACTTTTCTACTAAA-TTTTACGCAAATTCAACCAATTTGATGCTCTTTATGAATGC
55134877 AATGCTTATAGGA
65 AATGCTTA-AGGA
55134890 T
1 T
55134891 GAACAAATTC
Statistics
Matches: 130, Mismatches: 9, Indels: 20
0.82 0.06 0.13
Matches are distributed among these distances:
68 54 0.42
69 4 0.03
72 2 0.02
73 2 0.02
77 3 0.02
78 65 0.50
ACGTcount: A:0.30, C:0.19, G:0.12, T:0.39
Consensus pattern (76 bp):
TCACCTTGGACTTTTCTACTAAATTTTACGCAAATTCAACCAATTTGATGCTCTTTATGAATGCA
ATGCTTAAGGA
Found at i:55134861 original size:68 final size:68
Alignment explanation
Indices: 55134751--55134889 Score: 206
Period size: 68 Copynumber: 2.0 Consensus size: 68
55134741 GGATCACCTT
* *
55134751 GGACTTTTCTAGTAAATTTTCACACAAATTCAACCAATTTGATGCTCTTTATGAATGCAATTCTT
1 GGACTTTTCTAGTAAATTTTCACACAAATTCAACCAAATTGATGCTCTTTATGAATGCAATGCTT
55134816 ACA
66 ACA
* * * * *
55134819 GGACTTTTCTATTAAATTTTTACGCATATTCATCCAAATTGATGCTCTTTATGAATGCAATGCTT
1 GGACTTTTCTAGTAAATTTTCACACAAATTCAACCAAATTGATGCTCTTTATGAATGCAATGCTT
*
55134884 ATA
66 ACA
55134887 GGA
1 GGA
55134890 TGAACAAATT
Statistics
Matches: 63, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
68 63 1.00
ACGTcount: A:0.31, C:0.17, G:0.12, T:0.40
Consensus pattern (68 bp):
GGACTTTTCTAGTAAATTTTCACACAAATTCAACCAAATTGATGCTCTTTATGAATGCAATGCTT
ACA
Found at i:55138897 original size:2 final size:2
Alignment explanation
Indices: 55138890--55138921 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
55138880 GCAAGCGTGT
55138890 GA GA GA GA GA GA GA GA GA GA GA -A GA GA -A GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
55138922 AAAGCCCACA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 26 0.93
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (2 bp):
GA
Found at i:55142919 original size:3 final size:3
Alignment explanation
Indices: 55142911--55142951 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
55142901 CTCAAGCTGT
55142911 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
55142952 TATATTCTTA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:55170657 original size:2 final size:2
Alignment explanation
Indices: 55170645--55170708 Score: 51
Period size: 2 Copynumber: 32.5 Consensus size: 2
55170635 ATAATTTATT
* * * *
55170645 TA TA TA AA TA TA TA TA CT- TA TA TA TA T- TT TA TA TA CA TA TC
1 TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
55170686 TA TA TA TA TA TC TA TA TA CA TA T
1 TA TA TA TA TA TA TA TA TA TA TA T
55170709 TTTTTATTTT
Statistics
Matches: 48, Mismatches: 11, Indels: 6
0.74 0.17 0.09
Matches are distributed among these distances:
1 2 0.04
2 45 0.94
3 1 0.02
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:55170665 original size:29 final size:29
Alignment explanation
Indices: 55170643--55170696 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
55170633 TTATAATTTA
55170643 TTTATATAAATATATATACTTATATATAT
1 TTTATATAAATATATATACTTATATATAT
* *
55170672 TTTATATACATATCTATA--TATATAT
1 TTTATATAAATATATATACTTATATAT
55170697 CTATATACAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 7 0.30
29 16 0.70
ACGTcount: A:0.43, C:0.06, G:0.00, T:0.52
Consensus pattern (29 bp):
TTTATATAAATATATATACTTATATATAT
Found at i:55170672 original size:41 final size:40
Alignment explanation
Indices: 55170627--55170762 Score: 113
Period size: 39 Copynumber: 3.5 Consensus size: 40
55170617 ATACACGTAC
*
55170627 ATATTTTTATAATTTATTTATATAAATATATATACTTATAT
1 ATATTTTTATAATTTATATATAT-AATATATATACTTATAT
** * *
55170668 ATA-TTTTAT-ATACATATCTAT-ATATATAT-CTATATAC
1 ATATTTTTATAATTTATATATATAATATATATACT-TATAT
* * *
55170705 ATATTTTT-TATTTTCATAAATAT-ATATACATACTTATAT
1 ATATTTTTATAATTT-ATATATATAATATATATACTTATAT
*
55170744 ATATTTTTTATATTTTATA
1 ATA-TTTTTATAATTTATA
55170763 ATTTTCATAT
Statistics
Matches: 76, Mismatches: 12, Indels: 15
0.74 0.12 0.15
Matches are distributed among these distances:
36 2 0.03
37 16 0.21
38 5 0.07
39 28 0.37
40 16 0.21
41 9 0.12
ACGTcount: A:0.39, C:0.06, G:0.00, T:0.55
Consensus pattern (40 bp):
ATATTTTTATAATTTATATATATAATATATATACTTATAT
Found at i:55170695 original size:39 final size:38
Alignment explanation
Indices: 55170608--55170755 Score: 106
Period size: 39 Copynumber: 3.9 Consensus size: 38
55170598 TATGTAGATG
* * **
55170608 TATATATATATACACGTACATAT-TTTTATA-ATTTATT
1 TATATATATATATACTTACATATATTTTATATACATA-T
*
55170645 TATATAAATATATATACTTATATATATTTTATATACATAT
1 TATAT--ATATATATACTTACATATATTTTATATACATAT
* * * *
55170685 CTATATATATATCTA-TATACATATTTTTTATTTTCATA-
1 -TATATATATATATACT-TACATATATTTTATATACATAT
* * * *
55170723 AATATATATACATACTTATATATATTTTTTATA
1 TATATATATATATACTTACATATATTTTATATA
55170756 TTTTATAATT
Statistics
Matches: 86, Mismatches: 18, Indels: 14
0.73 0.15 0.12
Matches are distributed among these distances:
37 28 0.33
38 2 0.02
39 40 0.47
40 8 0.09
41 8 0.09
ACGTcount: A:0.40, C:0.07, G:0.01, T:0.52
Consensus pattern (38 bp):
TATATATATATATACTTACATATATTTTATATACATAT
Found at i:55170696 original size:12 final size:12
Alignment explanation
Indices: 55170652--55170708 Score: 64
Period size: 12 Copynumber: 4.8 Consensus size: 12
55170642 ATTTATATAA
55170652 ATATATATA-CT
1 ATATATATATCT
*
55170663 -TATATATATTTT
1 ATATATATA-TCT
*
55170675 ATATACATATCT
1 ATATATATATCT
55170687 ATATATATATCT
1 ATATATATATCT
*
55170699 ATATACATAT
1 ATATATATAT
55170709 TTTTTATTTT
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
10 8 0.21
12 23 0.61
13 7 0.18
ACGTcount: A:0.42, C:0.09, G:0.00, T:0.49
Consensus pattern (12 bp):
ATATATATATCT
Found at i:55170788 original size:39 final size:39
Alignment explanation
Indices: 55170652--55170786 Score: 123
Period size: 39 Copynumber: 3.5 Consensus size: 39
55170642 ATTTATATAA
* * * **
55170652 ATATATATACTTATATATA--TTTTATATACATATCTAT
1 ATATACATACTTATATATATTTTTTATTTTCATAAATAT
* *
55170689 ATATATAT-CTATATACATATTTTTTATTTTCATAAATAT
1 ATATACATACT-TATATATATTTTTTATTTTCATAAATAT
* * *
55170728 ATATACATACTTATATATATTTTTTATATTTTATAATTTT
1 ATATACATACTTATATATATTTTTTAT-TTTCATAAATAT
*
55170768 CATATACATATTTATATAT
1 -ATATACATACTTATATAT
55170787 TTACGTACAT
Statistics
Matches: 81, Mismatches: 11, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
36 2 0.02
37 15 0.19
39 36 0.44
40 11 0.14
41 17 0.21
ACGTcount: A:0.39, C:0.07, G:0.00, T:0.54
Consensus pattern (39 bp):
ATATACATACTTATATATATTTTTTATTTTCATAAATAT
Found at i:55172088 original size:120 final size:120
Alignment explanation
Indices: 55171955--55172539 Score: 1091
Period size: 120 Copynumber: 4.9 Consensus size: 120
55171945 TTTAAACATA
*
55171955 ATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATCAATATTCTTAT
1 ATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAATATTCTTAT
*
55172020 ATGAATTTACTCAAATCATAATATATGATACTATAAAATATAATTTAACATAATT
66 ATGAATTTACTCAAATCATAATATATGATACTATAAAAGATAATTTAACATAATT
55172075 ATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAATATTCTTAT
1 ATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAATATTCTTAT
55172140 ATGAATTTACTCAAATCATAATATATGATACTATAAAAGATAATTTAACATAATT
66 ATGAATTTACTCAAATCATAATATATGATACTATAAAAGATAATTTAACATAATT
* *
55172195 ATTATTAAATATATTTTAATTAAAATATATGATTTAATAAAATTCTTAATAATTAATATTCTTAT
1 ATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAATATTCTTAT
55172260 ATGAATTTACTCAAATCATAATATATGATACTATAAAAGATAATTTAACATAATT
66 ATGAATTTACTCAAATCATAATATATGATACTATAAAAGATAATTTAACATAATT
55172315 ATTATTAAATATA-TATTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAATATTCTTA
1 ATTATTAAATATATTA-TAATTAAAATATATAATTTAATAAAATTCTTAATAATTAATATTCTTA
55172379 TATGAATTTACTCAAATCATAATATATGATACTATAAAAGATAATTTAACATAATT
65 TATGAATTTACTCAAATCATAATATATGATACTATAAAAGATAATTTAACATAATT
* *
55172435 ATTATTAAATATATTTTAATTAAAATATATGATTTAATAAAATTCTTAATAATTAATATTCTTAT
1 ATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAATATTCTTAT
*
55172500 ATGAATTTACTCAAATCATAGTATATGATACTATAAAAGA
66 ATGAATTTACTCAAATCATAATATATGATACTATAAAAGA
55172540 AAACTGATCA
Statistics
Matches: 454, Mismatches: 9, Indels: 4
0.97 0.02 0.01
Matches are distributed among these distances:
119 1 0.00
120 452 1.00
121 1 0.00
ACGTcount: A:0.48, C:0.06, G:0.03, T:0.43
Consensus pattern (120 bp):
ATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAATATTCTTAT
ATGAATTTACTCAAATCATAATATATGATACTATAAAAGATAATTTAACATAATT
Found at i:55172102 original size:16 final size:16
Alignment explanation
Indices: 55172058--55172104 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
55172048 TACTATAAAA
*
55172058 TATAATTTAACATA-AT
1 TATAA-TTAAAATATAT
*
55172074 TATTATT-AAATATAT
1 TATAATTAAAATATAT
55172089 TATAATTAAAATATAT
1 TATAATTAAAATATAT
55172105 AATTTAATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
14 4 0.15
15 10 0.38
16 12 0.46
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (16 bp):
TATAATTAAAATATAT
Found at i:55172224 original size:18 final size:17
Alignment explanation
Indices: 55172201--55172237 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 17
55172191 AATTATTATT
55172201 AAATATAT--TTTAATTA
1 AAATATATGATTTAA-TA
55172217 AAATATATGATTTAATA
1 AAATATATGATTTAATA
55172234 AAAT
1 AAAT
55172238 TCTTAATAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 8 0.42
17 6 0.32
18 5 0.26
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (17 bp):
AAATATATGATTTAATA
Found at i:55172342 original size:14 final size:15
Alignment explanation
Indices: 55172314--55172353 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 15
55172304 TTAACATAAT
55172314 TATT-ATTAAATATA
1 TATTAATTAAATATA
55172328 TATTAATTAAA-ATA
1 TATTAATTAAATATA
*
55172342 TA-TAATTTAATA
1 TATTAATTAAATA
55172354 AAATTCTTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
13 7 0.30
14 10 0.43
15 6 0.26
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
TATTAATTAAATATA
Found at i:55172344 original size:18 final size:17
Alignment explanation
Indices: 55172321--55172357 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 17
55172311 AATTATTATT
55172321 AAATATAT-A-TTAATTA
1 AAATATATAATTTAA-TA
55172337 AAATATATAATTTAATA
1 AAATATATAATTTAATA
55172354 AAAT
1 AAAT
55172358 TCTTAATAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 8 0.42
17 7 0.37
18 4 0.21
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
AAATATATAATTTAATA
Found at i:55172464 original size:18 final size:17
Alignment explanation
Indices: 55172441--55172477 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 17
55172431 AATTATTATT
55172441 AAATATAT--TTTAATTA
1 AAATATATGATTTAA-TA
55172457 AAATATATGATTTAATA
1 AAATATATGATTTAATA
55172474 AAAT
1 AAAT
55172478 TCTTAATAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 8 0.42
17 6 0.32
18 5 0.26
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (17 bp):
AAATATATGATTTAATA
Found at i:55205086 original size:16 final size:15
Alignment explanation
Indices: 55205057--55205089 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 15
55205047 TATATTGTCA
55205057 ATATAAAAATATATT
1 ATATAAAAATATATT
55205072 ATATAAAATATATATT
1 ATATAAAA-ATATATT
55205088 AT
1 AT
55205090 TTATTTCGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
ATATAAAAATATATT
Found at i:55207516 original size:74 final size:72
Alignment explanation
Indices: 55207381--55207550 Score: 191
Period size: 74 Copynumber: 2.3 Consensus size: 72
55207371 ACGAGCTGTA
* * *
55207381 TAATAGGAAGCTCATAAGAGCCATAATCAAGAAGCTCATGCGAGCCAATAATGGGTAGCTTCGAA
1 TAATAGGAAGCTCATAAGAGCCATAATCAAGAAGCTCAAGCGAGCCAATAATGAGAAGCTTCGAA
*
55207446 GAGCCAT
66 AAGCCAT
* * * *
55207453 TAATCAGGAAGCTC-TAGATAGTCATATATCAGGAAGTTCAAGCGAGCCAAT-ATCGAGAAGCTT
1 TAAT-AGGAAGCTCATA-AGAGCCATA-ATCAAGAAGCTCAAGCGAGCCAATAAT-GAGAAGCTT
55207516 CGAAAAGCCAT
62 CGAAAAGCCAT
*
55207527 TAATTAGGAAGCTCACAAAGAGCC
1 TAA-TAGGAAGCTCA-TAAGAGCC
55207551 TTTAATCGGG
Statistics
Matches: 80, Mismatches: 11, Indels: 11
0.78 0.11 0.11
Matches are distributed among these distances:
72 6 0.08
73 18 0.22
74 50 0.62
75 5 0.06
76 1 0.01
ACGTcount: A:0.38, C:0.19, G:0.22, T:0.20
Consensus pattern (72 bp):
TAATAGGAAGCTCATAAGAGCCATAATCAAGAAGCTCAAGCGAGCCAATAATGAGAAGCTTCGAA
AAGCCAT
Found at i:55207555 original size:26 final size:26
Alignment explanation
Indices: 55207521--55207578 Score: 89
Period size: 26 Copynumber: 2.2 Consensus size: 26
55207511 AGCTTCGAAA
*
55207521 AGCCATTAATTAGGAAGCTCACAAAG
1 AGCCATTAATCAGGAAGCTCACAAAG
* *
55207547 AGCCTTTAATCGGGAAGCTCACAAAG
1 AGCCATTAATCAGGAAGCTCACAAAG
55207573 AGCCAT
1 AGCCAT
55207579 ATATCGGGAC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.38, C:0.22, G:0.21, T:0.19
Consensus pattern (26 bp):
AGCCATTAATCAGGAAGCTCACAAAG
Found at i:55207584 original size:26 final size:26
Alignment explanation
Indices: 55207533--55207593 Score: 88
Period size: 26 Copynumber: 2.3 Consensus size: 26
55207523 CCATTAATTA
*
55207533 GGAAGCTCACAAAGAGCCTTTAATCG
1 GGAAGCTCACAAAGAGCCTATAATCG
55207559 GGAAGCTCACAAAGAGCC-ATATATCG
1 GGAAGCTCACAAAGAGCCTATA-ATCG
*
55207585 GGACGCTCA
1 GGAAGCTCA
55207594 TAAGAGTTGT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
25 2 0.06
26 30 0.94
ACGTcount: A:0.34, C:0.25, G:0.25, T:0.16
Consensus pattern (26 bp):
GGAAGCTCACAAAGAGCCTATAATCG
Found at i:55207666 original size:24 final size:25
Alignment explanation
Indices: 55207651--55207697 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
55207641 GGATGCTCCG
55207651 AAGAACTAT-TAACGGGAAGCTCGC
1 AAGAACTATATAACGGGAAGCTCGC
**
55207675 AAGAACTATATAACATGAAGCTC
1 AAGAACTATATAACGGGAAGCTC
55207698 AAGAGGGCCA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 9 0.45
25 11 0.55
ACGTcount: A:0.43, C:0.19, G:0.19, T:0.19
Consensus pattern (25 bp):
AAGAACTATATAACGGGAAGCTCGC
Found at i:55207991 original size:18 final size:18
Alignment explanation
Indices: 55207958--55208006 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
55207948 ATTCATCTAA
*
55207958 ACCCAATCCAAACCCAAGT
1 ACCCAA-CCCAACCCAAGT
** *
55207977 ATTCAACCCAACCCAATT
1 ACCCAACCCAACCCAAGT
55207995 ACCCAACCCAAC
1 ACCCAACCCAAC
55208007 TCAACCCAAT
Statistics
Matches: 24, Mismatches: 6, Indels: 1
0.77 0.19 0.03
Matches are distributed among these distances:
18 20 0.83
19 4 0.17
ACGTcount: A:0.41, C:0.45, G:0.02, T:0.12
Consensus pattern (18 bp):
ACCCAACCCAACCCAAGT
Found at i:55208133 original size:9 final size:9
Alignment explanation
Indices: 55208119--55208183 Score: 71
Period size: 9 Copynumber: 7.2 Consensus size: 9
55208109 GTAGCGATTC
55208119 AATTCGGTT
1 AATTCGGTT
55208128 AATTCGGTT
1 AATTCGGTT
55208137 AATTCAGG-T
1 AATTC-GGTT
55208146 AATTC-GTGT
1 AATTCGGT-T
*
55208155 AATCCGGTT
1 AATTCGGTT
**
55208164 AATTAAGTT
1 AATTCGGTT
55208173 AATTCGGTT
1 AATTCGGTT
55208182 AA
1 AA
55208184 CCGACCGAAT
Statistics
Matches: 46, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
7 1 0.02
9 41 0.89
10 4 0.09
ACGTcount: A:0.29, C:0.11, G:0.20, T:0.40
Consensus pattern (9 bp):
AATTCGGTT
Found at i:55208151 original size:27 final size:27
Alignment explanation
Indices: 55208119--55208183 Score: 87
Period size: 27 Copynumber: 2.4 Consensus size: 27
55208109 GTAGCGATTC
* *
55208119 AATTCGGTTAATTCGGTTAATTCAGGT
1 AATTCGGTTAATCCGGTTAATTAAGGT
*
55208146 AATTC-GTGTAATCCGGTTAATTAAGTT
1 AATTCGGT-TAATCCGGTTAATTAAGGT
55208173 AATTCGGTTAA
1 AATTCGGTTAA
55208184 CCGACCGAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
26 2 0.06
27 29 0.88
28 2 0.06
ACGTcount: A:0.29, C:0.11, G:0.20, T:0.40
Consensus pattern (27 bp):
AATTCGGTTAATCCGGTTAATTAAGGT
Found at i:55216644 original size:15 final size:15
Alignment explanation
Indices: 55216618--55216663 Score: 60
Period size: 15 Copynumber: 3.1 Consensus size: 15
55216608 TTTCATTTTT
*
55216618 TTTCACTTTATTATTA
1 TTTCATTTTATTA-TA
55216634 TTTC-TTTTATTATA
1 TTTCATTTTATTATA
55216648 TTTCATTTTATT-TA
1 TTTCATTTTATTATA
55216662 TT
1 TT
55216664 CTTTTTCTTC
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
14 10 0.36
15 14 0.50
16 4 0.14
ACGTcount: A:0.22, C:0.09, G:0.00, T:0.70
Consensus pattern (15 bp):
TTTCATTTTATTATA
Found at i:55216649 original size:14 final size:14
Alignment explanation
Indices: 55216624--55216668 Score: 58
Period size: 15 Copynumber: 3.2 Consensus size: 14
55216614 TTTTTTTCAC
55216624 TTTATTATTATTTCT
1 TTTATTA-TATTTCT
55216639 TTTATTATATTTCAT
1 TTTATTATATTTC-T
55216654 TTTATT-TA-TTCT
1 TTTATTATATTTCT
55216666 TTT
1 TTT
55216669 TCTTCTTCTT
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
12 4 0.14
13 3 0.10
14 8 0.28
15 14 0.48
ACGTcount: A:0.20, C:0.07, G:0.00, T:0.73
Consensus pattern (14 bp):
TTTATTATATTTCT
Found at i:55224556 original size:29 final size:29
Alignment explanation
Indices: 55224490--55224557 Score: 70
Period size: 29 Copynumber: 2.4 Consensus size: 29
55224480 TTTGCCTCAA
* *
55224490 TAGTT-TTTGAATTTTTAAAATTTAGTGC
1 TAGTTATTTTAATTTTTAAAAATTAGTGC
*
55224518 -ATTTACTTTTAATTTTTAAAAATTAGT-C
1 TAGTTA-TTTTAATTTTTAAAAATTAGTGC
55224546 TTAGTTATTTTA
1 -TAGTTATTTTA
55224558 TTTAAAAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 7
0.74 0.09 0.16
Matches are distributed among these distances:
27 3 0.09
28 1 0.03
29 24 0.75
30 4 0.12
ACGTcount: A:0.31, C:0.04, G:0.09, T:0.56
Consensus pattern (29 bp):
TAGTTATTTTAATTTTTAAAAATTAGTGC
Found at i:55227171 original size:20 final size:18
Alignment explanation
Indices: 55227131--55227193 Score: 72
Period size: 20 Copynumber: 3.3 Consensus size: 18
55227121 TTTTAAAAAT
*
55227131 AATTTTAACTTTGATTGAA
1 AATTTTAAC-TTGATTAAA
55227150 AATGTTTAACTTGATTTAAAA
1 AAT-TTTAACTTGA-TT-AAA
*
55227171 AATTTTGACTTGATTAAA
1 AATTTTAACTTGATTAAA
55227189 AATTT
1 AATTT
55227194 ATTCAAAAAG
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
18 8 0.21
19 9 0.23
20 17 0.44
21 5 0.13
ACGTcount: A:0.40, C:0.05, G:0.10, T:0.46
Consensus pattern (18 bp):
AATTTTAACTTGATTAAA
Found at i:55229787 original size:41 final size:41
Alignment explanation
Indices: 55229722--55229833 Score: 172
Period size: 41 Copynumber: 2.7 Consensus size: 41
55229712 AACATATTCA
* *
55229722 CGGCACTTAGCCTGCTGGGCTTATAGCCTGATTCAGATCAC
1 CGGCACTTAGCCTGCTAGGTTTATAGCCTGATTCAGATCAC
*
55229763 CGGCA-TGTAGCCTGCTAGGTTTATAACCTGATTCAGATCAC
1 CGGCACT-TAGCCTGCTAGGTTTATAGCCTGATTCAGATCAC
*
55229804 CGGCACTTAGCCTGCTAGGTTCATAGCCTG
1 CGGCACTTAGCCTGCTAGGTTTATAGCCTG
55229834 NNNNNNNNNN
Statistics
Matches: 64, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
40 1 0.02
41 62 0.97
42 1 0.02
ACGTcount: A:0.21, C:0.28, G:0.24, T:0.28
Consensus pattern (41 bp):
CGGCACTTAGCCTGCTAGGTTTATAGCCTGATTCAGATCAC
Found at i:55230362 original size:2 final size:2
Alignment explanation
Indices: 55230357--55230401 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
55230347 ATTCGGCTAA
55230357 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
55230399 AT A
1 AT A
55230402 GAATCTATGC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:55231472 original size:36 final size:35
Alignment explanation
Indices: 55231432--55231503 Score: 108
Period size: 36 Copynumber: 2.0 Consensus size: 35
55231422 CATCTCCGGA
55231432 GCTTGGCAAATAAGGAAAGTGATCTTATGAAGATAT
1 GCTTGGCAAATAAGGAAAGTGATCTTATG-AGATAT
* * *
55231468 GCTTGGCAAATATGGAAGGTGATCTTTTGAGATAT
1 GCTTGGCAAATAAGGAAAGTGATCTTATGAGATAT
55231503 G
1 G
55231504 TGATCCTAGA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
35 7 0.21
36 26 0.79
ACGTcount: A:0.33, C:0.08, G:0.28, T:0.31
Consensus pattern (35 bp):
GCTTGGCAAATAAGGAAAGTGATCTTATGAGATAT
Found at i:55231876 original size:48 final size:48
Alignment explanation
Indices: 55231801--55231896 Score: 138
Period size: 48 Copynumber: 2.0 Consensus size: 48
55231791 TAAGGGAATT
** **
55231801 CTGTTGAATCCTTTATTGTTGTGAGTTAAGCTGACTTAGGCATTTTTA
1 CTGTTGAATCCTTTATTACTGCAAGTTAAGCTGACTTAGGCATTTTTA
* *
55231849 CTGTTGAATCCTTTATTACTGCAAGTTAGGCTGACTTAGGCGTTTTTA
1 CTGTTGAATCCTTTATTACTGCAAGTTAAGCTGACTTAGGCATTTTTA
55231897 AGCAAAGAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
48 42 1.00
ACGTcount: A:0.21, C:0.15, G:0.21, T:0.44
Consensus pattern (48 bp):
CTGTTGAATCCTTTATTACTGCAAGTTAAGCTGACTTAGGCATTTTTA
Found at i:55236662 original size:36 final size:35
Alignment explanation
Indices: 55236622--55236693 Score: 108
Period size: 36 Copynumber: 2.0 Consensus size: 35
55236612 CATCTCCGGA
55236622 GCTTGGCAAATAAGGAAAGTGATCTTATGAAGATAT
1 GCTTGGCAAATAAGGAAAGTGATCTTATG-AGATAT
* * *
55236658 GCTTGGCAAATATGGAAGGTGATCTTTTGAGATAT
1 GCTTGGCAAATAAGGAAAGTGATCTTATGAGATAT
55236693 G
1 G
55236694 TGATCCTAGA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
35 7 0.21
36 26 0.79
ACGTcount: A:0.33, C:0.08, G:0.28, T:0.31
Consensus pattern (35 bp):
GCTTGGCAAATAAGGAAAGTGATCTTATGAGATAT
Found at i:55237066 original size:48 final size:48
Alignment explanation
Indices: 55236991--55237086 Score: 156
Period size: 48 Copynumber: 2.0 Consensus size: 48
55236981 TAAGGGAATT
** *
55236991 CTGTTGAATCCTTTATTGTTGCGAGTTAAGCTGACTTAGGCGTTTTTA
1 CTGTTGAATCCTTTATTACTGCAAGTTAAGCTGACTTAGGCGTTTTTA
*
55237039 CTGTTGAATCCTTTATTACTGCAAGTTAGGCTGACTTAGGCGTTTTTA
1 CTGTTGAATCCTTTATTACTGCAAGTTAAGCTGACTTAGGCGTTTTTA
55237087 AGCAAAGAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
48 44 1.00
ACGTcount: A:0.20, C:0.16, G:0.22, T:0.43
Consensus pattern (48 bp):
CTGTTGAATCCTTTATTACTGCAAGTTAAGCTGACTTAGGCGTTTTTA
Found at i:55240372 original size:28 final size:28
Alignment explanation
Indices: 55240336--55240433 Score: 99
Period size: 28 Copynumber: 3.5 Consensus size: 28
55240326 ACAAATTTCA
*
55240336 AATAACGATAAGCATCAAAGTGCAAAAT
1 AATAACGATAAGCACCAAAGTGCAAAAT
* *
55240364 AATAACGATAAGCACCAAAGTACAAATTTT
1 AATAACGATAAGCACCAAAGTGCAAA--AT
* * * * *
55240394 TACAACGATAAGCACCGAAGCGCGAAAT
1 AATAACGATAAGCACCAAAGTGCAAAAT
55240422 AAT-ACGATAAGC
1 AATAACGATAAGC
55240434 GCGCTAATTT
Statistics
Matches: 56, Mismatches: 12, Indels: 5
0.77 0.16 0.07
Matches are distributed among these distances:
27 9 0.16
28 26 0.46
30 21 0.38
ACGTcount: A:0.49, C:0.18, G:0.15, T:0.17
Consensus pattern (28 bp):
AATAACGATAAGCACCAAAGTGCAAAAT
Found at i:55247608 original size:15 final size:14
Alignment explanation
Indices: 55247589--55247657 Score: 50
Period size: 15 Copynumber: 4.7 Consensus size: 14
55247579 AAAATCATAT
55247589 TTTAATAATAATTA
1 TTTAATAATAATTA
*
55247603 TATTAATTATATATTA
1 T-TTAATAATA-ATTA
* * * *
55247619 TTTTATTAGACTTTA
1 TTTAATAATA-ATTA
55247634 TTTAATAATAATTA
1 TTTAATAATAATTA
55247648 TGTTAA-AATA
1 T-TTAATAATA
55247658 TGATTAAATA
Statistics
Matches: 43, Mismatches: 9, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
14 9 0.21
15 29 0.67
16 5 0.12
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.52
Consensus pattern (14 bp):
TTTAATAATAATTA
Found at i:55254020 original size:22 final size:21
Alignment explanation
Indices: 55253969--55254024 Score: 58
Period size: 22 Copynumber: 2.6 Consensus size: 21
55253959 CCCCTGCTCC
* * *
55253969 AATGTCGCGACACTGGGGGTT
1 AATGTCGTGACACTGAGGGTG
*
55253990 AGATATCGTGACACTGAGGGTCG
1 A-ATGTCGTGACACTGAGGGT-G
55254013 AATGTCGTGACA
1 AATGTCGTGACA
55254025 TTGAAGATAG
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
21 1 0.04
22 26 0.93
23 1 0.04
ACGTcount: A:0.25, C:0.18, G:0.34, T:0.23
Consensus pattern (21 bp):
AATGTCGTGACACTGAGGGTG
Found at i:55255872 original size:116 final size:116
Alignment explanation
Indices: 55255668--55255906 Score: 469
Period size: 116 Copynumber: 2.1 Consensus size: 116
55255658 TACACTCAAT
55255668 TTCAATATCCTCCACTATTTATTCTACTCTTTTCATATTATTGCCCTTCTAGTCCTTCCTCTATT
1 TTCAATATCCTCCACTATTTATTCTACTCTTTTCATATTATTGCCCTTCTAGTCCTTCCTCTATT
55255733 TCTCATTTATCTAATCAAGTCATTTCTTCTTTTTAATTTTCACACTTTTAC
66 TCTCATTTATCTAATCAAGTCATTTCTTCTTTTTAATTTTCACACTTTTAC
*
55255784 TTCAATATCCTCCACTATTTATTCTACTCTTTTCATATTATTTCCCTTCTAGTCCTTCCTCTATT
1 TTCAATATCCTCCACTATTTATTCTACTCTTTTCATATTATTGCCCTTCTAGTCCTTCCTCTATT
55255849 TCTCATTTATCTAATCAAGTCATTTCTTCTTTTTAATTTTCACACTTTTAC
66 TCTCATTTATCTAATCAAGTCATTTCTTCTTTTTAATTTTCACACTTTTAC
55255900 TTCAATA
1 TTCAATA
55255907 CTTTTCACTC
Statistics
Matches: 122, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
116 122 1.00
ACGTcount: A:0.21, C:0.26, G:0.02, T:0.51
Consensus pattern (116 bp):
TTCAATATCCTCCACTATTTATTCTACTCTTTTCATATTATTGCCCTTCTAGTCCTTCCTCTATT
TCTCATTTATCTAATCAAGTCATTTCTTCTTTTTAATTTTCACACTTTTAC
Found at i:55256075 original size:20 final size:20
Alignment explanation
Indices: 55256050--55256090 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
55256040 AACATGTGTT
55256050 CAACCCAAAATGACACGGTC
1 CAACCCAAAATGACACGGTC
*
55256070 CAACCCGAAATGACACGGTC
1 CAACCCAAAATGACACGGTC
55256090 C
1 C
55256091 CATTTTAGGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.37, C:0.37, G:0.17, T:0.10
Consensus pattern (20 bp):
CAACCCAAAATGACACGGTC
Found at i:55261370 original size:31 final size:32
Alignment explanation
Indices: 55261318--55261393 Score: 86
Period size: 31 Copynumber: 2.4 Consensus size: 32
55261308 TACACTCAAG
*
55261318 GTCACTAAACTATTATTAAGTTTAT-ATTTT-A
1 GTCACTAAACTATTATAAAGTTT-TCATTTTAA
*
55261349 GTCACTCAACTATTCA-AAAGTTTTCATTTTAA
1 GTCACTAAACTATT-ATAAAGTTTTCATTTTAA
*
55261381 GTTACTAAACTAT
1 GTCACTAAACTAT
55261394 ACAAGTTTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
30 1 0.03
31 24 0.63
32 13 0.34
ACGTcount: A:0.36, C:0.14, G:0.07, T:0.43
Consensus pattern (32 bp):
GTCACTAAACTATTATAAAGTTTTCATTTTAA
Found at i:55266383 original size:31 final size:29
Alignment explanation
Indices: 55266345--55266414 Score: 86
Period size: 29 Copynumber: 2.3 Consensus size: 29
55266335 ACTATCAAAA
* *
55266345 TAGTCACTTTTGTTTGACTCAGGTTACATTT
1 TAGTCACTTATGTTTGA--AAGGTTACATTT
* *
55266376 TAGTCACTTATGTTTGAAATGTTACGTTT
1 TAGTCACTTATGTTTGAAAGGTTACATTT
55266405 TAGTCACTTA
1 TAGTCACTTA
55266415 CGTTATCGTG
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 19 0.54
31 16 0.46
ACGTcount: A:0.23, C:0.14, G:0.16, T:0.47
Consensus pattern (29 bp):
TAGTCACTTATGTTTGAAAGGTTACATTT
Found at i:55266999 original size:31 final size:29
Alignment explanation
Indices: 55266961--55267037 Score: 91
Period size: 29 Copynumber: 2.6 Consensus size: 29
55266951 CTAACGGCTC
* *
55266961 AGTGACTAAAATGTTACAACATGATAACATA
1 AGTGACTAAAATGTAAC-ACATCA-AACATA
* **
55266992 AGTGACTAAAACGTAACATTTCAAACATA
1 AGTGACTAAAATGTAACACATCAAACATA
55267021 AGTGACTAAAATGTAAC
1 AGTGACTAAAATGTAAC
55267038 TTGAGTCAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
29 22 0.55
30 3 0.08
31 15 0.38
ACGTcount: A:0.48, C:0.14, G:0.13, T:0.25
Consensus pattern (29 bp):
AGTGACTAAAATGTAACACATCAAACATA
Found at i:55267055 original size:31 final size:29
Alignment explanation
Indices: 55266986--55267059 Score: 96
Period size: 29 Copynumber: 2.5 Consensus size: 29
55266976 ACAACATGAT
55266986 AACATAAGTGACTAAAACGTAACATTTCA
1 AACATAAGTGACTAAAACGTAACATTTCA
*
55267015 AACATAAGTGACTAAAATGTAAC-TTGAGTCA
1 AACATAAGTGACTAAAACGTAACATT---TCA
*
55267046 AACAAAAGTGACTA
1 AACATAAGTGACTA
55267060 TTTTGGTAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
28 2 0.05
29 22 0.55
31 16 0.40
ACGTcount: A:0.49, C:0.15, G:0.14, T:0.23
Consensus pattern (29 bp):
AACATAAGTGACTAAAACGTAACATTTCA
Found at i:55268247 original size:7 final size:7
Alignment explanation
Indices: 55268235--55268259 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
55268225 CTTGATTAAA
55268235 ATTTATT
1 ATTTATT
55268242 ATTTATT
1 ATTTATT
55268249 ATTTATT
1 ATTTATT
55268256 ATTT
1 ATTT
55268260 CACTTAGGAA
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:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (7 bp):
ATTTATT
Found at i:55268381 original size:22 final size:24
Alignment explanation
Indices: 55268354--55268399 Score: 69
Period size: 22 Copynumber: 2.0 Consensus size: 24
55268344 TTTTATAGTT
55268354 GTTGTTATAGA-TG-AAAAATAAA
1 GTTGTTATAGAGTGTAAAAATAAA
*
55268376 GTTGTTATGGAGTGTAAAAATAAA
1 GTTGTTATAGAGTGTAAAAATAAA
55268400 ACATGAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 10 0.48
23 2 0.10
24 9 0.43
ACGTcount: A:0.46, C:0.00, G:0.22, T:0.33
Consensus pattern (24 bp):
GTTGTTATAGAGTGTAAAAATAAA
Found at i:55268942 original size:21 final size:21
Alignment explanation
Indices: 55268918--55268961 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
55268908 AAGATGTGAC
*
55268918 TTGTATTGAATTGAATG-TAAA
1 TTGTATTAAATTG-ATGTTAAA
55268939 TTGTATTAAATTGATGTTAAA
1 TTGTATTAAATTGATGTTAAA
55268960 TT
1 TT
55268962 TACTCGAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 3 0.14
21 18 0.86
ACGTcount: A:0.36, C:0.00, G:0.16, T:0.48
Consensus pattern (21 bp):
TTGTATTAAATTGATGTTAAA
Found at i:55269542 original size:24 final size:24
Alignment explanation
Indices: 55269510--55269560 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
55269500 GTGCTTCCCA
55269510 TTAATTGCTCTTCAGAGCTACCCG
1 TTAATTGCTCTTCAGAGCTACCCG
**
55269534 TTAATTGCTCTTTGGAGCTACCCG
1 TTAATTGCTCTTCAGAGCTACCCG
55269558 TTA
1 TTA
55269561 TAGGCTTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.20, C:0.25, G:0.18, T:0.37
Consensus pattern (24 bp):
TTAATTGCTCTTCAGAGCTACCCG
Found at i:55269571 original size:24 final size:25
Alignment explanation
Indices: 55269524--55269577 Score: 67
Period size: 24 Copynumber: 2.2 Consensus size: 25
55269514 TTGCTCTTCA
*
55269524 GAGCTACCCGTTAATTGCTCTTTG-
1 GAGCTACCCGTTAATGGCTCTTTGT
*
55269548 GAGCTACCCGTT-ATAGGCTTTTTGT
1 GAGCTACCCGTTAAT-GGCTCTTTGT
55269573 GAGCT
1 GAGCT
55269578 TCTTGTTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
23 2 0.08
24 19 0.73
25 5 0.19
ACGTcount: A:0.17, C:0.22, G:0.24, T:0.37
Consensus pattern (25 bp):
GAGCTACCCGTTAATGGCTCTTTGT
Found at i:55270616 original size:24 final size:24
Alignment explanation
Indices: 55270589--55270635 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
55270579 ATTGAAATGG
55270589 ATTG-ATTTAGTATGTGA-TGAATTT
1 ATTGAATTTA-TAT-TGATTGAATTT
55270613 ATTGAATTTATATTGATTGAATT
1 ATTGAATTTATATTGATTGAATT
55270636 GGAATATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 3 0.14
24 13 0.62
25 5 0.24
ACGTcount: A:0.32, C:0.00, G:0.17, T:0.51
Consensus pattern (24 bp):
ATTGAATTTATATTGATTGAATTT
Found at i:55270657 original size:21 final size:21
Alignment explanation
Indices: 55270606--55270657 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 21
55270596 TAGTATGTGA
* *
55270606 TGAATTTATT-GAATTTATAT
1 TGAATATATTGGAATATATAT
*
55270626 TGATTGA-ATTGGAATATATAT
1 TGAAT-ATATTGGAATATATAT
55270647 TGAATATATTG
1 TGAATATATTG
55270658 ATTATTTGAA
Statistics
Matches: 25, Mismatches: 4, Indels: 5
0.74 0.12 0.15
Matches are distributed among these distances:
20 8 0.32
21 17 0.68
ACGTcount: A:0.37, C:0.00, G:0.15, T:0.48
Consensus pattern (21 bp):
TGAATATATTGGAATATATAT
Found at i:55270834 original size:39 final size:38
Alignment explanation
Indices: 55270791--55270924 Score: 121
Period size: 39 Copynumber: 3.5 Consensus size: 38
55270781 CGACTTCAAG
55270791 TCGATGAGACACTAGGTGTCAATTTAACTTCGGATTAA
1 TCGATGAGACACTAGGTGTCAATTTAACTTCGGATTAA
* * *
55270829 TTCGATGAGGCACTAGGTGCCAATTT-ACTTCGGTTTAA
1 -TCGATGAGACACTAGGTGTCAATTTAACTTCGGATTAA
* * * * *
55270867 CCAATGTGACACT-GAGTGTCAATTTATTACTTTGAATT-A
1 TCGATGAGACACTAG-GTGTCAATTTA--ACTTCGGATTAA
*
55270906 TCTGATGAGGCACTAGGTG
1 TC-GATGAGACACTAGGTG
55270925 CCAAACTGGT
Statistics
Matches: 74, Mismatches: 15, Indels: 11
0.74 0.15 0.11
Matches are distributed among these distances:
36 1 0.01
37 18 0.24
38 11 0.15
39 25 0.34
40 18 0.24
41 1 0.01
ACGTcount: A:0.28, C:0.16, G:0.22, T:0.34
Consensus pattern (38 bp):
TCGATGAGACACTAGGTGTCAATTTAACTTCGGATTAA
Found at i:55271093 original size:20 final size:20
Alignment explanation
Indices: 55271068--55271107 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
55271058 TTGAATATGG
*
55271068 TATGGATAAAGTAATTGCAT
1 TATGGATAAAGCAATTGCAT
55271088 TATGGATAAAGCAATTGCAT
1 TATGGATAAAGCAATTGCAT
55271108 AAATGAAATG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.40, C:0.07, G:0.20, T:0.33
Consensus pattern (20 bp):
TATGGATAAAGCAATTGCAT
Found at i:55272598 original size:21 final size:21
Alignment explanation
Indices: 55272574--55272619 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
55272564 TGTTTATTTT
55272574 TCAACAAAGATTCAAAA-TCTA
1 TCAACAAAGA-TCAAAACTCTA
* *
55272595 TCAACTAAGATCAAAACTCTT
1 TCAACAAAGATCAAAACTCTA
55272616 TCAA
1 TCAA
55272620 AATAATTCAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 6 0.27
21 16 0.73
ACGTcount: A:0.48, C:0.22, G:0.04, T:0.26
Consensus pattern (21 bp):
TCAACAAAGATCAAAACTCTA
Found at i:55277494 original size:32 final size:32
Alignment explanation
Indices: 55277458--55277529 Score: 92
Period size: 32 Copynumber: 2.2 Consensus size: 32
55277448 AGGAATATTG
* * *
55277458 TATCATTTAACAAAAT-TAAAGTTGATATTTGT
1 TATCATTTAAC-AAATGAAAAGGTGATATTAGT
*
55277490 TATCATTTCACAAATGAAAAGGTGATATTAGT
1 TATCATTTAACAAATGAAAAGGTGATATTAGT
55277522 TATCATTT
1 TATCATTT
55277530 TATAGAACTG
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
31 4 0.11
32 31 0.89
ACGTcount: A:0.39, C:0.08, G:0.11, T:0.42
Consensus pattern (32 bp):
TATCATTTAACAAATGAAAAGGTGATATTAGT
Found at i:55278619 original size:52 final size:52
Alignment explanation
Indices: 55278553--55278656 Score: 165
Period size: 52 Copynumber: 2.0 Consensus size: 52
55278543 TAATAGTTAG
* * *
55278553 ACGCAACGTGCCTTAGACAGTACCAATGGTGTGTG-AGGTCTCAGAGGCTTCC
1 ACGCAACGTACCTTAGACAGTACCAATGGTGTGTGCA-GTCCCAAAGGCTTCC
55278605 ACGCAACGTACCTTAGACAGTACCAATGGTGTGTGCAGTCCCAAAGGCTTCC
1 ACGCAACGTACCTTAGACAGTACCAATGGTGTGTGCAGTCCCAAAGGCTTCC
55278657 CTGTCGTTCA
Statistics
Matches: 48, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
52 47 0.98
53 1 0.02
ACGTcount: A:0.25, C:0.27, G:0.26, T:0.22
Consensus pattern (52 bp):
ACGCAACGTACCTTAGACAGTACCAATGGTGTGTGCAGTCCCAAAGGCTTCC
Found at i:55281835 original size:11 final size:11
Alignment explanation
Indices: 55281819--55281844 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
55281809 AATATTTTTA
55281819 TTTTAAAATAC
1 TTTTAAAATAC
55281830 TTTTAAAATAC
1 TTTTAAAATAC
55281841 TTTT
1 TTTT
55281845 TTTAAATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (11 bp):
TTTTAAAATAC
Found at i:55281856 original size:10 final size:10
Alignment explanation
Indices: 55281841--55281903 Score: 53
Period size: 9 Copynumber: 6.4 Consensus size: 10
55281831 TTTAAAATAC
55281841 TTTTTTTAAA
1 TTTTTTTAAA
55281851 -TTTTTTAAA
1 TTTTTTTAAA
*
55281860 --TTTTAAAA
1 TTTTTTTAAA
55281868 TTTTTTTAAAA
1 TTTTTTT-AAA
55281879 TACTTTTTT-AA
1 T--TTTTTTAAA
*
55281890 TTTTTTTTAA
1 TTTTTTTAAA
55281900 TTTT
1 TTTT
55281904 ACAATACTTT
Statistics
Matches: 45, Mismatches: 2, Indels: 12
0.76 0.03 0.20
Matches are distributed among these distances:
8 7 0.16
9 15 0.33
10 10 0.22
11 7 0.16
13 6 0.13
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (10 bp):
TTTTTTTAAA
Found at i:55281864 original size:30 final size:29
Alignment explanation
Indices: 55281830--55281893 Score: 76
Period size: 30 Copynumber: 2.1 Consensus size: 29
55281820 TTTAAAATAC
*
55281830 TTTTAAAATACTTTTTTTAAAT-TTTTTAAA
1 TTTTAAAAT--TTTTTTAAAATATTTTTAAA
*
55281860 TTTTAAAATTTTTTTAAAATACTTTTTTAA
1 TTTTAAAATTTTTTTAAAATA-TTTTTAAA
55281890 TTTT
1 TTTT
55281894 TTTTAATTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
28 10 0.33
30 20 0.67
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.62
Consensus pattern (29 bp):
TTTTAAAATTTTTTTAAAATATTTTTAAA
Found at i:55281902 original size:32 final size:35
Alignment explanation
Indices: 55281830--55281936 Score: 100
Period size: 41 Copynumber: 3.1 Consensus size: 35
55281820 TTTAAAATAC
*
55281830 TTTTAAAATACTTTTTTTAAATTTTTTAAATTTTAAAATTT
1 TTTTAAAATACTTTTTTT-AA-TTTTT--GTTTT--AATTT
55281871 TTTTAAAATAC-TTTTTTAA-TTTT-TTTTAA---
1 TTTTAAAATACTTTTTTTAATTTTTGTTTTAATTT
*
55281900 TTTTACAATACTTTTTTTAATTTTTGTTTTAATTT
1 TTTTAAAATACTTTTTTTAATTTTTGTTTTAATTT
55281935 TT
1 TT
55281937 AAAATAAATT
Statistics
Matches: 59, Mismatches: 1, Indels: 18
0.76 0.01 0.23
Matches are distributed among these distances:
29 10 0.17
30 8 0.14
31 4 0.07
32 8 0.14
34 4 0.07
35 2 0.03
37 4 0.07
39 2 0.03
40 6 0.10
41 11 0.19
ACGTcount: A:0.30, C:0.04, G:0.01, T:0.65
Consensus pattern (35 bp):
TTTTAAAATACTTTTTTTAATTTTTGTTTTAATTT
Found at i:55281915 original size:41 final size:42
Alignment explanation
Indices: 55281807--55281915 Score: 145
Period size: 40 Copynumber: 2.7 Consensus size: 42
55281797 CCGAATATAA
*
55281807 TAAATATTTTT-ATTTTAAAATAC-TTTTAAAATACTTTTTT
1 TAAATTTTTTTAATTTTAAAATACTTTTTAAAATACTTTTTT
* *
55281847 TAAATTTTTTAAATTTTAAAAT-TTTTTTAAAATAC-TTTTT
1 TAAATTTTTTTAATTTTAAAATACTTTTTAAAATACTTTTTT
* *
55281887 TAATTTTTTTTAATTTTACAATACTTTTT
1 TAAATTTTTTTAATTTTAAAATACTTTTT
55281916 TTAATTTTTG
Statistics
Matches: 59, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
40 33 0.56
41 26 0.44
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.61
Consensus pattern (42 bp):
TAAATTTTTTTAATTTTAAAATACTTTTTAAAATACTTTTTT
Found at i:55288935 original size:6 final size:6
Alignment explanation
Indices: 55288919--55288958 Score: 53
Period size: 6 Copynumber: 6.7 Consensus size: 6
55288909 CTTGGTTACT
* * *
55288919 GTCTTC TTCTTC GTCTTC GTCGTC GTCTTC GTCATC GTCT
1 GTCTTC GTCTTC GTCTTC GTCTTC GTCTTC GTCTTC GTCT
55288959 GGGCTTTCTT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.03, C:0.33, G:0.17, T:0.47
Consensus pattern (6 bp):
GTCTTC
Found at i:55289709 original size:12 final size:13
Alignment explanation
Indices: 55289677--55289713 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
55289667 AAATTATCCA
*
55289677 ACCCAACTCAATT
1 ACCCAACCCAATT
55289690 ACCCAACCCAATT
1 ACCCAACCCAATT
55289703 A-CCAACCCAAT
1 ACCCAACCCAAT
55289714 AAAACTAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 10 0.43
13 13 0.57
ACGTcount: A:0.41, C:0.43, G:0.00, T:0.16
Consensus pattern (13 bp):
ACCCAACCCAATT
Found at i:55289800 original size:38 final size:38
Alignment explanation
Indices: 55289695--55289810 Score: 196
Period size: 38 Copynumber: 3.0 Consensus size: 38
55289685 CAATTACCCA
*
55289695 ACCCAATTACCAACCCAATAAAACTAAAACTAAAGTTT
1 ACCCAATTACCAACCCAATAAAACTAAAACTAAAGTCT
55289733 ACCCAATTACCCAACCCAATAAAACTAAAACTAAAGTCT
1 ACCCAATTA-CCAACCCAATAAAACTAAAACTAAAGTCT
* *
55289772 ACCCAATTATCAACCCAATAAAAATAAAACTAAAGTCT
1 ACCCAATTACCAACCCAATAAAACTAAAACTAAAGTCT
55289810 A
1 A
55289811 ACTCTAAGTC
Statistics
Matches: 74, Mismatches: 3, Indels: 2
0.94 0.04 0.03
Matches are distributed among these distances:
38 37 0.50
39 37 0.50
ACGTcount: A:0.51, C:0.27, G:0.03, T:0.20
Consensus pattern (38 bp):
ACCCAATTACCAACCCAATAAAACTAAAACTAAAGTCT
Found at i:55289964 original size:17 final size:17
Alignment explanation
Indices: 55289944--55290004 Score: 50
Period size: 17 Copynumber: 3.4 Consensus size: 17
55289934 ATTTCAAGAC
55289944 TTATGTAATGTTTTTAA
1 TTATGTAATGTTTTTAA
* ***
55289961 TTATGTAGTGATTCAAAGA
1 TTATGTAATG-TTTTTA-A
*
55289980 CTTATGTAATATTTTTAA
1 -TTATGTAATGTTTTTAA
55289998 TTATGTA
1 TTATGTA
55290005 GTGATTCAAT
Statistics
Matches: 32, Mismatches: 9, Indels: 6
0.68 0.19 0.13
Matches are distributed among these distances:
17 16 0.50
18 4 0.12
19 4 0.12
20 8 0.25
ACGTcount: A:0.33, C:0.03, G:0.13, T:0.51
Consensus pattern (17 bp):
TTATGTAATGTTTTTAA
Found at i:55289980 original size:37 final size:37
Alignment explanation
Indices: 55289939--55290013 Score: 141
Period size: 37 Copynumber: 2.0 Consensus size: 37
55289929 TGTTAATTTC
*
55289939 AAGACTTATGTAATGTTTTTAATTATGTAGTGATTCA
1 AAGACTTATGTAATATTTTTAATTATGTAGTGATTCA
55289976 AAGACTTATGTAATATTTTTAATTATGTAGTGATTCA
1 AAGACTTATGTAATATTTTTAATTATGTAGTGATTCA
55290013 A
1 A
55290014 TTCGGGTAAT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.35, C:0.05, G:0.15, T:0.45
Consensus pattern (37 bp):
AAGACTTATGTAATATTTTTAATTATGTAGTGATTCA
Found at i:55290026 original size:9 final size:9
Alignment explanation
Indices: 55290012--55290052 Score: 64
Period size: 9 Copynumber: 4.6 Consensus size: 9
55290002 GTAGTGATTC
*
55290012 AATTCGGGT
1 AATTCGGTT
55290021 AATTCGGTT
1 AATTCGGTT
55290030 AATTCGGTT
1 AATTCGGTT
*
55290039 AATTTGGTT
1 AATTCGGTT
55290048 AATTC
1 AATTC
55290053 TTAACCAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 29 1.00
ACGTcount: A:0.24, C:0.10, G:0.22, T:0.44
Consensus pattern (9 bp):
AATTCGGTT
Found at i:55297132 original size:4 final size:4
Alignment explanation
Indices: 55297125--55297150 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
55297115 TTGAATTAAT
55297125 TTTC TTTC TTTC TTTC TTTC TTTC TT
1 TTTC TTTC TTTC TTTC TTTC TTTC TT
55297151 CCGATGGATC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTC
Found at i:55299392 original size:15 final size:15
Alignment explanation
Indices: 55299345--55299394 Score: 57
Period size: 15 Copynumber: 3.2 Consensus size: 15
55299335 CAATTCAAAT
*
55299345 AATCAATATATATTC
1 AATCAATATAAATTC
55299360 AAT-ATATATACCAATTC
1 AATCA-ATATA--AATTC
55299377 AATCAATATAAATTC
1 AATCAATATAAATTC
55299392 AAT
1 AAT
55299395 AAATTCATCA
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
14 1 0.03
15 16 0.53
17 12 0.40
18 1 0.03
ACGTcount: A:0.50, C:0.14, G:0.00, T:0.36
Consensus pattern (15 bp):
AATCAATATAAATTC
Found at i:55299417 original size:24 final size:24
Alignment explanation
Indices: 55299372--55299418 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
55299362 TATATATACC
55299372 AATTCAATCAATATAAATTCAATA
1 AATTCAATCAATATAAATTCAATA
55299396 AATTC-ATCACATACTAAA-TCAAT
1 AATTCAATCA-ATA-TAAATTCAAT
55299419 CCATTTCAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 4 0.19
24 13 0.62
25 4 0.19
ACGTcount: A:0.51, C:0.17, G:0.00, T:0.32
Consensus pattern (24 bp):
AATTCAATCAATATAAATTCAATA
Found at i:55312779 original size:20 final size:21
Alignment explanation
Indices: 55312754--55312800 Score: 64
Period size: 20 Copynumber: 2.3 Consensus size: 21
55312744 TAAAATATAA
55312754 ATTTTGAAATTTTT-ATAAA-T
1 ATTTTGAAATTTTTGA-AAATT
55312774 ATTTTG-AATTTTTGAAAATT
1 ATTTTGAAATTTTTGAAAATT
55312794 ATTTTGA
1 ATTTTGA
55312801 TTTTTTTTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
19 10 0.42
20 14 0.58
ACGTcount: A:0.36, C:0.00, G:0.09, T:0.55
Consensus pattern (21 bp):
ATTTTGAAATTTTTGAAAATT
Found at i:55312785 original size:19 final size:20
Alignment explanation
Indices: 55312754--55312805 Score: 65
Period size: 19 Copynumber: 2.6 Consensus size: 20
55312744 TAAAATATAA
55312754 ATTTTGAAATTTTT-ATAAA-T
1 ATTTTG-AATTTTTGA-AAATT
55312774 ATTTTGAATTTTTGAAAATT
1 ATTTTGAATTTTTGAAAATT
55312794 ATTTTG-ATTTTT
1 ATTTTGAATTTTT
55312806 TTTTGTAATT
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
19 16 0.53
20 14 0.47
ACGTcount: A:0.33, C:0.00, G:0.08, T:0.60
Consensus pattern (20 bp):
ATTTTGAATTTTTGAAAATT
Found at i:55320328 original size:36 final size:36
Alignment explanation
Indices: 55320287--55320375 Score: 87
Period size: 36 Copynumber: 2.5 Consensus size: 36
55320277 TAATTAAGCT
*
55320287 TAATATTATTTAATATACATATTTATTT-ATA-TTTAA
1 TAATATTATTTAATATA-ATA-TGATTTAATATTTTAA
*
55320323 TAATATAATATGTAATA-AATATGATTTAATATTTTAA
1 TAATAT--TATTTAATATAATATGATTTAATATTTTAA
*
55320360 CAA-ATTATTTAATATA
1 TAATATTATTTAATATA
55320376 TTTATAATAA
Statistics
Matches: 44, Mismatches: 4, Indels: 11
0.75 0.07 0.19
Matches are distributed among these distances:
34 8 0.18
35 6 0.14
36 14 0.32
37 8 0.18
38 8 0.18
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.49
Consensus pattern (36 bp):
TAATATTATTTAATATAATATGATTTAATATTTTAA
Found at i:55321752 original size:56 final size:56
Alignment explanation
Indices: 55321645--55321754 Score: 141
Period size: 56 Copynumber: 1.9 Consensus size: 56
55321635 AAATTTGGGT
* * * *
55321645 AAAAAAATTCGAGTTTTGGTCTGTCAATGGCCGGCACCAGAGTACGAAAAAAAGAA
1 AAAAAAATTCGAGTGTTGGCCTGTCAATGACCGGCACCACAGTACGAAAAAAAGAA
* *
55321701 AAAAAAATTTGGGTGTTGGCCTGTCAATGACCGGCACC-CAGTACAGTAAAAAAA
1 AAAAAAATTCGAGTGTTGGCCTGTCAATGACCGGCACCACAGTAC-G-AAAAAAA
55321755 ATTTTACTTT
Statistics
Matches: 46, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
55 5 0.11
56 34 0.74
57 7 0.15
ACGTcount: A:0.40, C:0.17, G:0.23, T:0.20
Consensus pattern (56 bp):
AAAAAAATTCGAGTGTTGGCCTGTCAATGACCGGCACCACAGTACGAAAAAAAGAA
Found at i:55321901 original size:113 final size:112
Alignment explanation
Indices: 55321756--55321974 Score: 307
Period size: 111 Copynumber: 1.9 Consensus size: 112
55321746 GTAAAAAAAA
* *
55321756 TTTTACTTTTTTTCGTGTCAGTATCAGGTATCAGCATACGAAAAAAGTAAAAAAAAAATTGAGGT
1 TTTTACTTTTTTTCGTGTCAATAGCAGGTATCAGCATACGAAAAAAGT--AAAAAAAATTGAGGT
*
55321821 GGCCTGCCAA-TGGCCGGCACCACCTTTTTTGGTGGAAAAAAATATTTTT
64 GGCCTGCCAATTGGCCGGCACCACC-TTTTTGGGGGAAAAAAATATTTTT
* ***** *
55321870 TTTTACTTTTTTT-GTGTCAATAGCAGGTATCAGTATACGAAAAAAGTAAATTTTTTTGTGGTGG
1 TTTTACTTTTTTTCGTGTCAATAGCAGGTATCAGCATACGAAAAAAGTAAAAAAAATTGAGGTGG
55321934 CCTGCCAATTGGCCGGCACCACCTTTTTGGGGGAAAAAAAT
66 CCTGCCAATTGGCCGGCACCACCTTTTTGGGGGAAAAAAAT
55321975 TTCGGATGCT
Statistics
Matches: 94, Mismatches: 10, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
111 36 0.38
112 14 0.15
113 31 0.33
114 13 0.14
ACGTcount: A:0.30, C:0.16, G:0.21, T:0.34
Consensus pattern (112 bp):
TTTTACTTTTTTTCGTGTCAATAGCAGGTATCAGCATACGAAAAAAGTAAAAAAAATTGAGGTGG
CCTGCCAATTGGCCGGCACCACCTTTTTGGGGGAAAAAAATATTTTT
Found at i:55322605 original size:53 final size:52
Alignment explanation
Indices: 55322544--55322715 Score: 238
Period size: 53 Copynumber: 3.2 Consensus size: 52
55322534 TAGAAACGAA
*
55322544 AATGAAAAAAAGGGTGCTAGATGTAGGAAAAAATTTTGAAATAAATGAGATTG
1 AATGAAAAAAAGGGTGTTAGATGTAGGAAAAAATTTT-AAATAAATGAGATTG
* * * *
55322597 AATGAAAAAAATGGTGTTAGATGTGGGAAAAAATTTAAAATATATGAGATTG
1 AATGAAAAAAAGGGTGTTAGATGTAGGAAAAAATTTTAAATAAATGAGATTG
*
55322649 AATGAAAAAAAAAGGGTGTTA-ATTGTAGGAAAAAAATTTTAAATAAATGAGACTG
1 AATG--AAAAAAAGGGTGTTAGA-TGTAGG-AAAAAATTTTAAATAAATGAGATTG
55322704 AATGAAAAAAAG
1 AATGAAAAAAAG
55322716 AGAGTGTCAG
Statistics
Matches: 105, Mismatches: 10, Indels: 8
0.85 0.08 0.07
Matches are distributed among these distances:
52 18 0.17
53 42 0.40
54 19 0.18
55 26 0.25
ACGTcount: A:0.52, C:0.01, G:0.22, T:0.25
Consensus pattern (52 bp):
AATGAAAAAAAGGGTGTTAGATGTAGGAAAAAATTTTAAATAAATGAGATTG
Found at i:55324627 original size:26 final size:27
Alignment explanation
Indices: 55324567--55324635 Score: 72
Period size: 28 Copynumber: 2.6 Consensus size: 27
55324557 ATATATTTAC
55324567 AAAATAGA-AAAAAAAATGTATAAGTAT
1 AAAATA-ATAAAAAAAATGTATAAGTAT
*
55324594 ATATATAATAAAAAAAAT-TATGAAG-AT
1 A-AAATAATAAAAAAAATGTAT-AAGTAT
*
55324621 AAAATAATAATAAAA
1 AAAATAATAAAAAAA
55324636 TATATAAAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
26 12 0.33
27 8 0.22
28 16 0.44
ACGTcount: A:0.68, C:0.00, G:0.07, T:0.25
Consensus pattern (27 bp):
AAAATAATAAAAAAAATGTATAAGTAT
Found at i:55324738 original size:3 final size:3
Alignment explanation
Indices: 55324723--55324784 Score: 63
Period size: 3 Copynumber: 19.3 Consensus size: 3
55324713 CGTATGGAAG
*
55324723 TAA TAA TAC TAA TAA TAA TAA TATA TAA TAAA TAA TATA TAA TACCA
1 TAA TAA TAA TAA TAA TAA TAA TA-A TAA T-AA TAA TA-A TAA TA--A
55324770 TAA T-A TAA TAA TAA T
1 TAA TAA TAA TAA TAA T
55324785 GCAATTCAAT
Statistics
Matches: 51, Mismatches: 2, Indels: 12
0.78 0.03 0.18
Matches are distributed among these distances:
2 2 0.04
3 37 0.73
4 9 0.18
5 3 0.06
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:55324756 original size:29 final size:29
Alignment explanation
Indices: 55324724--55324783 Score: 79
Period size: 29 Copynumber: 2.0 Consensus size: 29
55324714 GTATGGAAGT
55324724 AATAATACTAATAATA-ATAATAT-ATAATA
1 AATAATA-T-ATAATACATAATATAATAATA
55324753 AATAATATATAATACCATAATATAATAATA
1 AATAATATATAATA-CATAATATAATAATA
55324783 A
1 A
55324784 TGCAATTCAA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
27 6 0.21
28 1 0.04
29 14 0.50
30 7 0.25
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (29 bp):
AATAATATATAATACATAATATAATAATA
Found at i:55327081 original size:13 final size:13
Alignment explanation
Indices: 55327063--55327087 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
55327053 GATCGCGACA
55327063 ATTTTAATTTTTT
1 ATTTTAATTTTTT
55327076 ATTTTAATTTTT
1 ATTTTAATTTTT
55327088 ACTTTCTTAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (13 bp):
ATTTTAATTTTTT
Found at i:55327152 original size:18 final size:19
Alignment explanation
Indices: 55327115--55327152 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
55327105 TATGTAAATA
*
55327115 TTTCTTTTATTTTTACATT
1 TTTCTTTTATTTTAACATT
*
55327134 TTTCTTTT-TTTTAATATT
1 TTTCTTTTATTTTAACATT
55327152 T
1 T
55327153 ATTTAATGGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.16, C:0.08, G:0.00, T:0.76
Consensus pattern (19 bp):
TTTCTTTTATTTTAACATT
Found at i:55327735 original size:56 final size:55
Alignment explanation
Indices: 55327663--55327812 Score: 183
Period size: 56 Copynumber: 2.7 Consensus size: 55
55327653 AAAACTCGAA
* * **
55327663 TTTTTTTACTGTACTGGGTGCCGGCCATTGACAGGCTAGCACCCAATTTTTTTTTTCC
1 TTTTTTT-C-GTACTGGGTGCCGGCCATTGACAGACCAGCACCCAAAATTTTTTTT-C
*
55327721 TTTTTTTCGTACTGGGTGTCGGCCATTGACAGACCAGCACCCAAAATTTTTTTTC
1 TTTTTTTCGTACTGGGTGCCGGCCATTGACAGACCAGCACCCAAAATTTTTTTTC
* ** *
55327776 TTTTTTTCGTACTCTGGTGCCTACCATTAACAGACCA
1 TTTTTTTCGTACT-GGGTGCCGGCCATTGACAGACCA
55327813 AAACTCGAAT
Statistics
Matches: 81, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
55 14 0.17
56 59 0.73
57 1 0.01
58 7 0.09
ACGTcount: A:0.19, C:0.25, G:0.17, T:0.39
Consensus pattern (55 bp):
TTTTTTTCGTACTGGGTGCCGGCCATTGACAGACCAGCACCCAAAATTTTTTTTC
Found at i:55332531 original size:22 final size:23
Alignment explanation
Indices: 55332506--55332550 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
55332496 ATAGCAACGT
55332506 ATTTATGATTA-ATTTA-TATAAA
1 ATTTATGA-TACATTTATTATAAA
*
55332528 ATTTATTATACATTTATTATAAA
1 ATTTATGATACATTTATTATAAA
55332551 GATCAATATT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 2 0.10
22 12 0.60
23 6 0.30
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.51
Consensus pattern (23 bp):
ATTTATGATACATTTATTATAAA
Found at i:55338144 original size:41 final size:41
Alignment explanation
Indices: 55338082--55338165 Score: 159
Period size: 41 Copynumber: 2.0 Consensus size: 41
55338072 CGAATGATCC
55338082 TTAAGCTTGTTTTATTATATCTTGATTTCTACTTATTGAAA
1 TTAAGCTTGTTTTATTATATCTTGATTTCTACTTATTGAAA
*
55338123 TTAATCTTGTTTTATTATATCTTGATTTCTACTTATTGAAA
1 TTAAGCTTGTTTTATTATATCTTGATTTCTACTTATTGAAA
55338164 TT
1 TT
55338166 GGGAAAAGTA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.26, C:0.10, G:0.08, T:0.56
Consensus pattern (41 bp):
TTAAGCTTGTTTTATTATATCTTGATTTCTACTTATTGAAA
Found at i:55358557 original size:17 final size:17
Alignment explanation
Indices: 55358505--55358557 Score: 52
Period size: 19 Copynumber: 3.0 Consensus size: 17
55358495 TATGGAAACA
* *
55358505 TAATCTTCGAGGATATG
1 TAATCTTAGAAGATATG
* *
55358522 CAATCGTAGATATGATATG
1 TAATCTTAGA-A-GATATG
55358541 TAATCTTAGAAGATATG
1 TAATCTTAGAAGATATG
55358558 ATTTTGTAAT
Statistics
Matches: 28, Mismatches: 6, Indels: 4
0.74 0.16 0.11
Matches are distributed among these distances:
17 13 0.46
18 1 0.04
19 14 0.50
ACGTcount: A:0.36, C:0.09, G:0.21, T:0.34
Consensus pattern (17 bp):
TAATCTTAGAAGATATG
Found at i:55358557 original size:22 final size:23
Alignment explanation
Indices: 55358529--55358573 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
55358519 ATGCAATCGT
*
55358529 AGATATGA-TATGTAATCTTAGA
1 AGATATGATTATGTAATATTAGA
*
55358551 AGATATGATTTTGTAATATTAGA
1 AGATATGATTATGTAATATTAGA
55358574 GATTTTATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 8 0.40
23 12 0.60
ACGTcount: A:0.40, C:0.02, G:0.18, T:0.40
Consensus pattern (23 bp):
AGATATGATTATGTAATATTAGA
Found at i:55363692 original size:17 final size:17
Alignment explanation
Indices: 55363640--55363692 Score: 61
Period size: 19 Copynumber: 3.0 Consensus size: 17
55363630 TATGGAAACA
*
55363640 TAATCTTTGAAGATATG
1 TAATCTTAGAAGATATG
* *
55363657 CAATCGTAGATATGATATG
1 TAATCTTAGA-A-GATATG
55363676 TAATCTTAGAAGATATG
1 TAATCTTAGAAGATATG
55363693 ATTTTGTAAT
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
17 13 0.45
18 2 0.07
19 14 0.48
ACGTcount: A:0.38, C:0.08, G:0.19, T:0.36
Consensus pattern (17 bp):
TAATCTTAGAAGATATG
Found at i:55363692 original size:22 final size:21
Alignment explanation
Indices: 55363664--55363721 Score: 80
Period size: 22 Copynumber: 2.7 Consensus size: 21
55363654 ATGCAATCGT
*
55363664 AGATATGATATGTAATCTTAG
1 AGATATGATTTGTAATCTTAG
55363685 AAGATATGATTTTGTAATCTTAG
1 -AGATATGA-TTTGTAATCTTAG
*
55363708 AGATTTGATTTGTA
1 AGATATGATTTGTA
55363722 GATACCTTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
21 6 0.18
22 15 0.45
23 12 0.36
ACGTcount: A:0.34, C:0.03, G:0.19, T:0.43
Consensus pattern (21 bp):
AGATATGATTTGTAATCTTAG
Found at i:55368257 original size:21 final size:21
Alignment explanation
Indices: 55368232--55368273 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
55368222 TGGTCATTTT
55368232 ACCACCTAAGGTTAAACTATC
1 ACCACCTAAGGTTAAACTATC
55368253 ACCACCTAAGGTTAAACTATC
1 ACCACCTAAGGTTAAACTATC
55368274 CCAATTTTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.38, C:0.29, G:0.10, T:0.24
Consensus pattern (21 bp):
ACCACCTAAGGTTAAACTATC
Found at i:55368940 original size:23 final size:22
Alignment explanation
Indices: 55368895--55368940 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
55368885 CGAAAATATA
*
55368895 TTAAATATATATATTTTTATTT
1 TTAAATATATATAGTTTTATTT
*
55368917 TTAAA-ATATACTAGTTTTAGTT
1 TTAAATATATA-TAGTTTTATTT
55368939 TT
1 TT
55368941 GTTTTAAGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 5 0.24
22 16 0.76
ACGTcount: A:0.35, C:0.02, G:0.04, T:0.59
Consensus pattern (22 bp):
TTAAATATATATAGTTTTATTT
Found at i:55369088 original size:40 final size:36
Alignment explanation
Indices: 55368995--55369093 Score: 110
Period size: 40 Copynumber: 2.6 Consensus size: 36
55368985 TTAAAACAAT
* *
55368995 TAACAATTAATAATTTGATAATTTTACTAACAATTAA
1 TAACAATTAATAA-TTAATAATTTTACTAAAAATTAA
* *
55369032 T-ACAATTAACAATTAATAATTTTACTAAAGAAATGTTAG
1 TAACAATTAATAATTAATAATTTTACT-AA-AAA--TTAA
55369071 TAACAATTAATAATTAATAATTT
1 TAACAATTAATAATTAATAATTT
55369094 GATATAATTT
Statistics
Matches: 52, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
35 13 0.25
36 12 0.23
37 3 0.06
39 4 0.08
40 20 0.38
ACGTcount: A:0.49, C:0.07, G:0.04, T:0.39
Consensus pattern (36 bp):
TAACAATTAATAATTAATAATTTTACTAAAAATTAA
Found at i:55371597 original size:2 final size:2
Alignment explanation
Indices: 55371590--55371631 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
55371580 AAAACAAGCA
55371590 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
55371632 CTCTCAATTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:55373075 original size:37 final size:37
Alignment explanation
Indices: 55373025--55373100 Score: 134
Period size: 37 Copynumber: 2.1 Consensus size: 37
55373015 TGGTTTATCA
*
55373025 TTAGGGAGAGCTCAGTCACGATACTATAGTGGATGAC
1 TTAGGGAAAGCTCAGTCACGATACTATAGTGGATGAC
*
55373062 TTAGGGAAAGCTCAGTCACGATTCTATAGTGGATGAC
1 TTAGGGAAAGCTCAGTCACGATACTATAGTGGATGAC
55373099 TT
1 TT
55373101 CGTGACTAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.29, C:0.16, G:0.28, T:0.28
Consensus pattern (37 bp):
TTAGGGAAAGCTCAGTCACGATACTATAGTGGATGAC
Found at i:55375047 original size:16 final size:16
Alignment explanation
Indices: 55375026--55375067 Score: 61
Period size: 16 Copynumber: 2.8 Consensus size: 16
55375016 AATCAAGTTG
*
55375026 AGAAAATTATTTAATT
1 AGAAAATTAATTAATT
55375042 AGAAAATTAATTAATT
1 AGAAAATTAATTAATT
55375058 --AAAATTAATT
1 AGAAAATTAATT
55375068 TATAATTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 10 0.40
16 15 0.60
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.40
Consensus pattern (16 bp):
AGAAAATTAATTAATT
Found at i:55377582 original size:12 final size:12
Alignment explanation
Indices: 55377565--55377589 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
55377555 AAAGATTAGA
55377565 AAAATAAAGAAG
1 AAAATAAAGAAG
55377577 AAAATAAAGAAG
1 AAAATAAAGAAG
55377589 A
1 A
55377590 TAGATGGAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.76, C:0.00, G:0.16, T:0.08
Consensus pattern (12 bp):
AAAATAAAGAAG
Found at i:55379817 original size:2 final size:2
Alignment explanation
Indices: 55379810--55379853 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
55379800 TAAGTAAACA
55379810 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
55379852 AT
1 AT
55379854 TACTTCTCTT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:55382139 original size:3 final size:3
Alignment explanation
Indices: 55382131--55382156 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
55382121 TCCCTCACTG
55382131 CTT CTT CTT CTT CTT CTT CTT CTT CT
1 CTT CTT CTT CTT CTT CTT CTT CTT CT
55382157 AATTCTAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
CTT
Found at i:55391618 original size:21 final size:20
Alignment explanation
Indices: 55391590--55391628 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
55391580 TTGTTAAATG
55391590 AAATAATAA-AAATAATTGTT
1 AAATAATAATAAA-AATTGTT
55391610 AAATGAATAATAAAAATTG
1 AAAT-AATAATAAAAATTG
55391629 AGCTAATAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 4 0.24
21 10 0.59
22 3 0.18
ACGTcount: A:0.62, C:0.00, G:0.08, T:0.31
Consensus pattern (20 bp):
AAATAATAATAAAAATTGTT
Found at i:55391623 original size:24 final size:25
Alignment explanation
Indices: 55391580--55391626 Score: 87
Period size: 24 Copynumber: 1.9 Consensus size: 25
55391570 GGAAAGGATT
55391580 TTGTTAAATGAAATAATAAAAATAA
1 TTGTTAAATGAAATAATAAAAATAA
55391605 TTGTTAAATG-AATAATAAAAAT
1 TTGTTAAATGAAATAATAAAAAT
55391627 TGAGCTAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 12 0.55
25 10 0.45
ACGTcount: A:0.57, C:0.00, G:0.09, T:0.34
Consensus pattern (25 bp):
TTGTTAAATGAAATAATAAAAATAA
Found at i:55391848 original size:28 final size:25
Alignment explanation
Indices: 55391793--55391858 Score: 114
Period size: 25 Copynumber: 2.6 Consensus size: 25
55391783 AAAAACTTAC
55391793 ACGGCGATGCAGCAGAGGAGTGTCG
1 ACGGCGATGCAGCAGAGGAGTGTCG
55391818 ACGGCGATGCAGCAGAGGAGTGTCG
1 ACGGCGATGCAGCAGAGGAGTGTCG
* *
55391843 ACGACGATGCAACAGA
1 ACGGCGATGCAGCAGA
55391859 TAGTCGGGGA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
25 39 1.00
ACGTcount: A:0.29, C:0.21, G:0.39, T:0.11
Consensus pattern (25 bp):
ACGGCGATGCAGCAGAGGAGTGTCG
Found at i:55392049 original size:40 final size:40
Alignment explanation
Indices: 55391994--55392135 Score: 178
Period size: 40 Copynumber: 3.5 Consensus size: 40
55391984 TAAAATGATA
55391994 TTTTGCGGCATTTTTCTCATAGCGTCGCTAATGCTTGACC
1 TTTTGCGGCATTTTTCTCATAGCGTCGCTAATGCTTGACC
* * *
55392034 TTTTGCGGCATTTTTCTCATAGTGTAGCTAATGCTTGACA
1 TTTTGCGGCATTTTTCTCATAGCGTCGCTAATGCTTGACC
* * * *
55392074 TTTTGCGTCGTTTGTCTCATAAACG-CTGCTAATGCTTGACC
1 TTTTGCGGCATTTTTCTCAT-AGCGTC-GCTAATGCTTGACC
**
55392115 TTTTGCGGTGTTTTTCTCATA
1 TTTTGCGGCATTTTTCTCATA
55392136 AACGCCGCTG
Statistics
Matches: 87, Mismatches: 13, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
40 55 0.63
41 32 0.37
ACGTcount: A:0.16, C:0.21, G:0.20, T:0.43
Consensus pattern (40 bp):
TTTTGCGGCATTTTTCTCATAGCGTCGCTAATGCTTGACC
Found at i:55392162 original size:41 final size:41
Alignment explanation
Indices: 55391996--55392188 Score: 140
Period size: 40 Copynumber: 4.8 Consensus size: 41
55391986 AAATGATATT
* * * * *
55391996 TTGCGGCATTTTTCTCAT-AGCGTCGCTAATGCTTGACCTT
1 TTGCGGCGTTTTTCTCATAAACGCCGCTAATGATTGACCTA
* ** ** * * *
55392036 TTGCGGCATTTTTCTCAT-AGTGTAGCTAATGCTTGACATT
1 TTGCGGCGTTTTTCTCATAAACGCCGCTAATGATTGACCTA
* * * * *
55392076 TTGCGTCGTTTGTCTCATAAACGCTGCTAATGCTTGACCTT
1 TTGCGGCGTTTTTCTCATAAACGCCGCTAATGATTGACCTA
* ** *
55392117 TTGCGGTGTTTTTCTCATAAACGCCGCTGTTGATTTACCTA
1 TTGCGGCGTTTTTCTCATAAACGCCGCTAATGATTGACCTA
* * *
55392158 TTGCGGCGTTTTAC-CATTAGCGCCGCTAATG
1 TTGCGGCGTTTTTCTCATAAACGCCGCTAATG
55392189 TATAATATTT
Statistics
Matches: 126, Mismatches: 26, Indels: 2
0.82 0.17 0.01
Matches are distributed among these distances:
40 65 0.52
41 61 0.48
ACGTcount: A:0.17, C:0.23, G:0.21, T:0.39
Consensus pattern (41 bp):
TTGCGGCGTTTTTCTCATAAACGCCGCTAATGATTGACCTA
Found at i:55394920 original size:12 final size:12
Alignment explanation
Indices: 55394903--55394952 Score: 52
Period size: 12 Copynumber: 4.2 Consensus size: 12
55394893 TTTTGTAAAA
55394903 TATATATTTAAT
1 TATATATTTAAT
55394915 TATATATTTAA-
1 TATATATTTAAT
55394926 TAT-TAATTT-AT
1 TATAT-ATTTAAT
*
55394937 TTTATATTTTAAT
1 TATATA-TTTAAT
55394950 TAT
1 TAT
55394953 TTTAATATAA
Statistics
Matches: 31, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
10 2 0.06
11 10 0.32
12 15 0.48
13 4 0.13
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (12 bp):
TATATATTTAAT
Found at i:55394927 original size:23 final size:24
Alignment explanation
Indices: 55394901--55394958 Score: 63
Period size: 23 Copynumber: 2.6 Consensus size: 24
55394891 AATTTTGTAA
55394901 AATATATATTTAATTATATA-TTT
1 AATATATATTTAATTATATATTTT
*
55394924 AATAT-TAATTT-ATTTTATATTTT
1 AATATAT-ATTTAATTATATATTTT
55394947 AAT-TAT-TTTAAT
1 AATATATATTTAAT
55394959 ATAAATAAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 9
0.75 0.03 0.22
Matches are distributed among these distances:
21 3 0.10
22 11 0.37
23 16 0.53
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (24 bp):
AATATATATTTAATTATATATTTT
Found at i:55394960 original size:17 final size:17
Alignment explanation
Indices: 55394903--55394956 Score: 58
Period size: 16 Copynumber: 3.1 Consensus size: 17
55394893 TTTTGTAAAA
55394903 TATATATTTAATTATATATT
1 TATAT-TTTAATT-TAT-TT
*
55394923 TA-ATATTAATTTATTT
1 TATATTTTAATTTATTT
55394939 TATATTTTAA-TTATTT
1 TATATTTTAATTTATTT
55394955 TA
1 TA
55394957 ATATAAATAA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
16 12 0.39
17 9 0.29
18 6 0.19
19 2 0.06
20 2 0.06
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (17 bp):
TATATTTTAATTTATTT
Found at i:55405584 original size:20 final size:20
Alignment explanation
Indices: 55405546--55405583 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
55405536 TTTCGCACTT
55405546 GTTTTGGATTTTTGTTTTTG
1 GTTTTGGATTTTTGTTTTTG
*
55405566 GTTTTGGGTTTTT-TTTTT
1 GTTTTGGATTTTTGTTTTT
55405584 TCATATTTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.03, C:0.00, G:0.24, T:0.74
Consensus pattern (20 bp):
GTTTTGGATTTTTGTTTTTG
Done.