Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A11
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: 113101708
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2797742 characters in sequence are not A, C, G, or T
File 170 of 352
Found at i:55602952 original size:54 final size:54
Alignment explanation
Indices: 55602861--55603003 Score: 200
Period size: 54 Copynumber: 2.7 Consensus size: 54
55602851 GTGACGAAGT
* * *
55602861 CACCAGATACAGAT-ATTGT-GTAGAGCCACCAGAACAGATATATGTAGCAGAGC
1 CACCAGAT-CAGATAATTGTGGCATAGCCACCAGGACAGATATATGTAGCAGAGC
*
55602914 CACCAGATCAGATAATTGTGGCATAGCCACCAGGACAGATATATGTGGCAGAGC
1 CACCAGATCAGATAATTGTGGCATAGCCACCAGGACAGATATATGTAGCAGAGC
* * *
55602968 CACTAGATTAGATAATTATGGCATAGCCACCAGGAC
1 CACCAGATCAGATAATTGTGGCATAGCCACCAGGAC
55603004 GCTTCCTCCA
Statistics
Matches: 81, Mismatches: 7, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
52 5 0.06
53 13 0.16
54 63 0.78
ACGTcount: A:0.36, C:0.22, G:0.23, T:0.20
Consensus pattern (54 bp):
CACCAGATCAGATAATTGTGGCATAGCCACCAGGACAGATATATGTAGCAGAGC
Found at i:55602980 original size:27 final size:27
Alignment explanation
Indices: 55602861--55603000 Score: 137
Period size: 27 Copynumber: 5.2 Consensus size: 27
55602851 GTGACGAAGT
*
55602861 CACCAGATACAGATAT-TGT-GTAGAGC
1 CACCAGAT-CAGATATATGTGGCAGAGC
* *
55602887 CACCAGAACAGATATATGTAGCAGAGC
1 CACCAGATCAGATATATGTGGCAGAGC
*
55602914 CACCAGATCAGATA-ATTGTGGCATAGC
1 CACCAGATCAGATATA-TGTGGCAGAGC
55602941 CACCAGGA-CAGATATATGTGGCAGAGC
1 CACCA-GATCAGATATATGTGGCAGAGC
* * * *
55602968 CACTAGATTAGATA-ATTATGGCATAGC
1 CACCAGATCAGATATA-TGTGGCAGAGC
55602995 CACCAG
1 CACCAG
55603001 GACGCTTCCT
Statistics
Matches: 96, Mismatches: 11, Indels: 13
0.80 0.09 0.11
Matches are distributed among these distances:
25 7 0.07
26 14 0.15
27 72 0.75
28 3 0.03
ACGTcount: A:0.36, C:0.21, G:0.23, T:0.20
Consensus pattern (27 bp):
CACCAGATCAGATATATGTGGCAGAGC
Found at i:55604627 original size:26 final size:26
Alignment explanation
Indices: 55604596--55604703 Score: 180
Period size: 26 Copynumber: 4.2 Consensus size: 26
55604586 TGAAATACCC
*
55604596 ATCATGGAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAACCCATT
*
55604622 AGCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* *
55604648 ATCATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
55604674 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
55604700 ATCA
1 ATCA
55604704 ATTTGTACCA
Statistics
Matches: 75, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 75 1.00
ACGTcount: A:0.36, C:0.24, G:0.08, T:0.31
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:55607224 original size:48 final size:47
Alignment explanation
Indices: 55607086--55607224 Score: 165
Period size: 48 Copynumber: 2.9 Consensus size: 47
55607076 GTATATCGCG
* *
55607086 AGGCCGATGCATGTCCCAGACATGTCTTACACTAG-CTC-TCGTCTCA
1 AGGCCGATGCATGTCCCAGACATGTCTTACACTAGCCACAT-ATCTCA
* * * *
55607132 ATGCCGGTGCATGTCCCAGACATGTCTTACACTGGCCTAAATATCTCA
1 AGGCCGATGCATGTCCCAGACATGTCTTACACTAGCC-ACATATCTCA
* *
55607180 AGGCTGATGCATGTACCAGACATGTCTTACACTAGCACACATATC
1 AGGCCGATGCATGTCCCAGACATGTCTTACACTAGC-CACATATC
55607225 ACCCATTATC
Statistics
Matches: 77, Mismatches: 12, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
46 32 0.42
47 1 0.01
48 42 0.55
49 2 0.03
ACGTcount: A:0.26, C:0.29, G:0.19, T:0.26
Consensus pattern (47 bp):
AGGCCGATGCATGTCCCAGACATGTCTTACACTAGCCACATATCTCA
Found at i:55614461 original size:43 final size:41
Alignment explanation
Indices: 55614338--55614461 Score: 115
Period size: 41 Copynumber: 2.9 Consensus size: 41
55614328 TGGCATCAAT
* *
55614338 ATATGTGATTACGTGTAAGACCATGTATGAGACATCGGCATCG
1 ATATGTGA-TACGTGTAAGACCATGTATGGGACAT-GGCAACG
* * * * *
55614381 -TATTTGATTCGTGTAAGACCCTATTTGGGACAGTGGCAACG
1 ATATGTGATACGTGTAAGACCATGTATGGGACA-TGGCAACG
* *
55614422 ATATGTGACTACATGTAAGACCATGTCTGGGACGATGGCA
1 ATATGTGA-TACGTGTAAGACCATGTATGGGAC-ATGGCA
55614462 TTGTACGATA
Statistics
Matches: 64, Mismatches: 13, Indels: 8
0.75 0.15 0.09
Matches are distributed among these distances:
41 26 0.41
42 13 0.20
43 24 0.38
44 1 0.02
ACGTcount: A:0.28, C:0.17, G:0.27, T:0.28
Consensus pattern (41 bp):
ATATGTGATACGTGTAAGACCATGTATGGGACATGGCAACG
Found at i:55625741 original size:41 final size:45
Alignment explanation
Indices: 55625660--55625756 Score: 121
Period size: 41 Copynumber: 2.2 Consensus size: 45
55625650 CTGGGACGTT
**
55625660 GGCATCGATATATGTGATTACGTGTAAGACCATGTTTGGGACAAC
1 GGCATCGATATATGTGATTACGTGTAAGACCATGCCTGGGACAAC
* **
55625705 GGCATCG-TAT-T-TGATT-CGTGTAAGACCCTGCCTGGGACAGT
1 GGCATCGATATATGTGATTACGTGTAAGACCATGCCTGGGACAAC
55625746 GGCATCGATAT
1 GGCATCGATAT
55625757 GTGACTCCAT
Statistics
Matches: 46, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
41 27 0.59
42 8 0.17
43 1 0.02
44 3 0.07
45 7 0.15
ACGTcount: A:0.25, C:0.19, G:0.28, T:0.29
Consensus pattern (45 bp):
GGCATCGATATATGTGATTACGTGTAAGACCATGCCTGGGACAAC
Found at i:55628205 original size:20 final size:20
Alignment explanation
Indices: 55628168--55628206 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
55628158 GTATTGTATC
*
55628168 TGTGTGATGTGTTGTCTGTA
1 TGTGTGATGTGGTGTCTGTA
55628188 TGTGTGCATGTGGT-TCTGT
1 TGTGTG-ATGTGGTGTCTGT
55628207 GAAGCAATTG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.08, C:0.08, G:0.36, T:0.49
Consensus pattern (20 bp):
TGTGTGATGTGGTGTCTGTA
Found at i:55628732 original size:23 final size:23
Alignment explanation
Indices: 55628706--55628780 Score: 80
Period size: 23 Copynumber: 3.3 Consensus size: 23
55628696 CCTTTTTATT
55628706 ATATTCCAGAATGCCTTTGTGGC
1 ATATTCCAGAATGCCTTTGTGGC
* * *
55628729 ATATTCCGGAATACTTTTGTGGC
1 ATATTCCAGAATGCCTTTGTGGC
* *
55628752 ATATT-CTGTAATGCCTTTATGGC
1 ATATTCCAG-AATGCCTTTGTGGC
*
55628775 GTATTC
1 ATATTC
55628781 TGTAATGTCT
Statistics
Matches: 42, Mismatches: 8, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
22 2 0.05
23 40 0.95
ACGTcount: A:0.21, C:0.19, G:0.20, T:0.40
Consensus pattern (23 bp):
ATATTCCAGAATGCCTTTGTGGC
Found at i:55628781 original size:23 final size:23
Alignment explanation
Indices: 55628715--55628796 Score: 92
Period size: 23 Copynumber: 3.6 Consensus size: 23
55628705 TATATTCCAG
* * *
55628715 AATGCCTTTGTGGCATATTCCGG
1 AATGCCTTTATGGCATATTCTGT
* * *
55628738 AATACTTTTGTGGCATATTCTGT
1 AATGCCTTTATGGCATATTCTGT
*
55628761 AATGCCTTTATGGCGTATTCTGT
1 AATGCCTTTATGGCATATTCTGT
*
55628784 AATGTCTTTATGG
1 AATGCCTTTATGG
55628797 TAAGTTTTGT
Statistics
Matches: 50, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 50 1.00
ACGTcount: A:0.20, C:0.16, G:0.22, T:0.43
Consensus pattern (23 bp):
AATGCCTTTATGGCATATTCTGT
Found at i:55632409 original size:46 final size:47
Alignment explanation
Indices: 55632256--55632474 Score: 179
Period size: 46 Copynumber: 4.7 Consensus size: 47
55632246 TCACTTGTGT
* * **
55632256 GAGCTAGTGTAAGAAATGT-TAGGGACATGCATCGGCCAC-A-TTGTGA
1 GAGCTAGTGTAAGACATGTCT-GGGACATGCATCGGCCTCGAGACGT-A
* * * *
55632302 GAGCCAGTGTAAGACCATGTTTGGGACATGGCATTGGTACT-GAGACG-A
1 GAGCTAGTGTAAGA-CATGTCTGGGACAT-GCATCGG-CCTCGAGACGTA
* *
55632350 GTGCTAGTATAAGACATGTCTGGGACATGCATCGGCCTCGAGACGTA
1 GAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGACGTA
* *
55632397 -AGCTAGTGTAAGACATGTCTGGGACATGCATCAG-CTACGAGATGT-
1 GAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCT-CGAGACGTA
*
55632442 -ATC-AGTGTAAGACCATGTCTGGGACATGACATC
1 GAGCTAGTGTAAGA-CATGTCTGGGACATG-CATC
55632475 AGCACAGATA
Statistics
Matches: 144, Mismatches: 18, Indels: 22
0.78 0.10 0.12
Matches are distributed among these distances:
44 9 0.06
45 21 0.15
46 67 0.47
47 25 0.17
48 19 0.13
49 2 0.01
50 1 0.01
ACGTcount: A:0.28, C:0.18, G:0.30, T:0.24
Consensus pattern (47 bp):
GAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGACGTA
Found at i:55633552 original size:16 final size:16
Alignment explanation
Indices: 55633531--55633574 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 16
55633521 CCACACGGGC
*
55633531 GTGTTACGTTTATGGG
1 GTGTTACGTTTATGGA
**
55633547 GTGTTACGGATATGGA
1 GTGTTACGTTTATGGA
*
55633563 GTGTTACATTTA
1 GTGTTACGTTTA
55633575 GTGGTATTAG
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.20, C:0.07, G:0.32, T:0.41
Consensus pattern (16 bp):
GTGTTACGTTTATGGA
Found at i:55636990 original size:46 final size:46
Alignment explanation
Indices: 55636940--55637108 Score: 193
Period size: 46 Copynumber: 3.7 Consensus size: 46
55636930 TGAGCATCCA
55636940 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCG
1 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCG
* * * *
55636986 AACTCGTTGAGTTGAGTCCGAGTTC-GTGA--AATG-TAACTAGGCATCCG
1 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G--TCCG
* *
55637033 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCG
1 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCG
* *
55637079 AGCTCGTTGAGTTGAGTTCGAGTTCACTTA
1 AACTCGTTGAGTTGAGTCCGAGTTCACTTA
55637109 GGGGCGGGTT
Statistics
Matches: 102, Mismatches: 12, Indels: 18
0.77 0.09 0.14
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
45 3 0.03
46 56 0.55
47 29 0.28
48 3 0.03
50 3 0.03
51 2 0.02
ACGTcount: A:0.22, C:0.20, G:0.28, T:0.30
Consensus pattern (46 bp):
AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCG
Found at i:55637092 original size:93 final size:93
Alignment explanation
Indices: 55636933--55637103 Score: 297
Period size: 93 Copynumber: 1.8 Consensus size: 93
55636923 GGATGGTTGA
* *
55636933 GCATCCAAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCAAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
55636998 TGAGTCCGAGTTCGTGAAATGTAACTAG
66 TGAGTCCGAGTTCGTGAAATGTAACTAG
* *
55637026 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCAAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
*
55637091 TGAGTTCGAGTTC
66 TGAGTCCGAGTTC
55637104 ACTTAGGGGC
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.22, C:0.21, G:0.28, T:0.29
Consensus pattern (93 bp):
GCATCCAAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAAATGTAACTAG
Found at i:55642500 original size:46 final size:46
Alignment explanation
Indices: 55642351--55642526 Score: 183
Period size: 46 Copynumber: 3.8 Consensus size: 46
55642341 TCACTTGTGT
* * * * *
55642351 GAGCTAGTGTACGACATGTCAGGGACATGCATCGGCCACATTATGA
1 GAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCTCAATACGA
* * ** ** *
55642397 GAGCCAGTGTAAGACCATGTTTGGGACATGGCATCGGTATTGAGACGA
1 GAGCTAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCCTCAATACGA
* *
55642445 GTGCTAGTGTAAGACATGTCTGGGACATGGATCGGCCTCAATACGTA
1 GAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCTCAATACG-A
*
55642492 -AGCTAGTGTAAGACATGTCTTGGACATGCATCGGC
1 GAGCTAGTGTAAGACATGTCTGGGACATGCATCGGC
55642527 TACGAGATGT
Statistics
Matches: 103, Mismatches: 24, Indels: 6
0.77 0.18 0.05
Matches are distributed among these distances:
46 55 0.53
47 26 0.25
48 22 0.21
ACGTcount: A:0.27, C:0.19, G:0.30, T:0.24
Consensus pattern (46 bp):
GAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCTCAATACGA
Found at i:55653078 original size:39 final size:40
Alignment explanation
Indices: 55653035--55653132 Score: 108
Period size: 46 Copynumber: 2.3 Consensus size: 40
55653025 TATTGAATGC
*
55653035 ATACTTTCAATTTACTAA-AATAATAGATGAGTCCGAGAG
1 ATACTTTCAATTTACCAATAATAATAGATGAGTCCGAGAG
**
55653074 ATACTTTCAATTTTTTACCAATCTTTCTAATAGATGAGTCCGAGAG
1 ATACTTTCAA---TTTACCAA---TAATAATAGATGAGTCCGAGAG
55653120 ATACTTTCAATTT
1 ATACTTTCAATTT
55653133 TTTACTAAAT
Statistics
Matches: 49, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
39 10 0.20
42 7 0.14
43 3 0.06
46 29 0.59
ACGTcount: A:0.35, C:0.15, G:0.12, T:0.38
Consensus pattern (40 bp):
ATACTTTCAATTTACCAATAATAATAGATGAGTCCGAGAG
Found at i:55655445 original size:32 final size:31
Alignment explanation
Indices: 55655392--55655551 Score: 221
Period size: 32 Copynumber: 5.0 Consensus size: 31
55655382 TATAACTATG
*
55655392 CTACTTTTTTATATGGAAAACTAATGTATGAT
1 CTACTTTTTTATAT-GTAAACTAATGTATGAT
** *
55655424 CTACTTTTTCGTATGCTAAACTAATGTTTGAT
1 CTACTTTTTTATATG-TAAACTAATGTATGAT
*
55655456 CTACTTTTTTATATGTGAACCTAATGTATGAT
1 CTACTTTTTTATATGT-AAACTAATGTATGAT
*
55655488 CTACTTTTTTATATGCAAAACTAATGTATGAT
1 CTACTTTTTTATATG-TAAACTAATGTATGAT
55655520 CTACTTTTTTATATGTAAACCTAATGTATGAT
1 CTACTTTTTTATATGTAAA-CTAATGTATGAT
55655552 ATTTTTTATG
Statistics
Matches: 113, Mismatches: 11, Indels: 8
0.86 0.08 0.06
Matches are distributed among these distances:
31 5 0.04
32 108 0.96
ACGTcount: A:0.31, C:0.12, G:0.11, T:0.46
Consensus pattern (31 bp):
CTACTTTTTTATATGTAAACTAATGTATGAT
Found at i:55655493 original size:64 final size:64
Alignment explanation
Indices: 55655392--55655551 Score: 250
Period size: 64 Copynumber: 2.5 Consensus size: 64
55655382 TATAACTATG
* * * *
55655392 CTACTTTTTTATATG-GAAAACTAATGTATGATCTACTTTTTCGTATGCTAAACTAATGTTTGAT
1 CTACTTTTTTATATGTG-AACCTAATGTATGATCTACTTTTTCATATGCAAAACTAATGTATGAT
*
55655456 CTACTTTTTTATATGTGAACCTAATGTATGATCTACTTTTTTATATGCAAAACTAATGTATGAT
1 CTACTTTTTTATATGTGAACCTAATGTATGATCTACTTTTTCATATGCAAAACTAATGTATGAT
*
55655520 CTACTTTTTTATATGTAAACCTAATGTATGAT
1 CTACTTTTTTATATGTGAACCTAATGTATGAT
55655552 ATTTTTTATG
Statistics
Matches: 89, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
64 88 0.99
65 1 0.01
ACGTcount: A:0.31, C:0.12, G:0.11, T:0.46
Consensus pattern (64 bp):
CTACTTTTTTATATGTGAACCTAATGTATGATCTACTTTTTCATATGCAAAACTAATGTATGAT
Found at i:55657586 original size:21 final size:21
Alignment explanation
Indices: 55657560--55657612 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
55657550 CGCTGTTTCT
*
55657560 AATCTCACCGCTACAGTATCC
1 AATCTCACCGCTACAGTAACC
*
55657581 AATCTCACCGCTACAGTAACT
1 AATCTCACCGCTACAGTAACC
55657602 AATCTCACCGC
1 AATCTCACCGC
55657613 CACCACTGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.30, C:0.38, G:0.09, T:0.23
Consensus pattern (21 bp):
AATCTCACCGCTACAGTAACC
Found at i:55658752 original size:17 final size:17
Alignment explanation
Indices: 55658727--55658761 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
55658717 GATTGATACC
55658727 AAAAAA-TTTAATTTTA
1 AAAAAATTTTAATTTTA
55658743 AAAAATATTTTAATTTTA
1 AAAAA-ATTTTAATTTTA
55658761 A
1 A
55658762 TTTTTTATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.29
17 1 0.06
18 11 0.65
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
AAAAAATTTTAATTTTA
Found at i:55667455 original size:28 final size:27
Alignment explanation
Indices: 55667407--55667511 Score: 133
Period size: 27 Copynumber: 3.8 Consensus size: 27
55667397 CTGCCAGAAT
* *
55667407 AGATAATGTGACAGAGTCACCAGATAC
1 AGATAATGTGGCAGAGCCACCAGATAC
55667434 AGATAATCGTGGCAGAGCCACCAGA-AC
1 AGATAAT-GTGGCAGAGCCACCAGATAC
55667461 AGATATATGTGGCAGAGCCACCAGAT-C
1 AGATA-ATGTGGCAGAGCCACCAGATAC
*
55667488 AGATAATTTGTGGCATAGCCACCA
1 AGATAA--TGTGGCAGAGCCACCA
55667512 AGACACTTCC
Statistics
Matches: 70, Mismatches: 3, Indels: 9
0.85 0.04 0.11
Matches are distributed among these distances:
26 1 0.01
27 37 0.53
28 32 0.46
ACGTcount: A:0.36, C:0.22, G:0.24, T:0.18
Consensus pattern (27 bp):
AGATAATGTGGCAGAGCCACCAGATAC
Found at i:55667483 original size:55 final size:54
Alignment explanation
Indices: 55667400--55667511 Score: 154
Period size: 55 Copynumber: 2.1 Consensus size: 54
55667390 AGCATGGCTG
* *
55667400 CCAGAATAGATAATGTGACAGAGTCACCAGATACAGATAA-TCGTGGCAGAGCCA
1 CCAGAACAGATAATGTGACAGAGCCACCAGAT-CAGATAATTCGTGGCAGAGCCA
* * *
55667454 CCAGAACAGATATATGTGGCAGAGCCACCAGATCAGATAATTTGTGGCATAGCCA
1 CCAGAACAGATA-ATGTGACAGAGCCACCAGATCAGATAATTCGTGGCAGAGCCA
55667509 CCA
1 CCA
55667512 AGACACTTCC
Statistics
Matches: 51, Mismatches: 5, Indels: 3
0.86 0.08 0.05
Matches are distributed among these distances:
54 18 0.35
55 33 0.65
ACGTcount: A:0.37, C:0.22, G:0.23, T:0.18
Consensus pattern (54 bp):
CCAGAACAGATAATGTGACAGAGCCACCAGATCAGATAATTCGTGGCAGAGCCA
Found at i:55667964 original size:8 final size:8
Alignment explanation
Indices: 55667928--55667967 Score: 53
Period size: 8 Copynumber: 5.0 Consensus size: 8
55667918 ACCAAAATAC
55667928 CGGCTTTT
1 CGGCTTTT
*
55667936 CGGCATTT
1 CGGCTTTT
* *
55667944 CAGCATTT
1 CGGCTTTT
55667952 CGGCTTTT
1 CGGCTTTT
55667960 CGGCTTTT
1 CGGCTTTT
55667968 GCCGATCTAG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
8 28 1.00
ACGTcount: A:0.07, C:0.25, G:0.23, T:0.45
Consensus pattern (8 bp):
CGGCTTTT
Found at i:55670064 original size:14 final size:14
Alignment explanation
Indices: 55670045--55670071 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
55670035 TCAAAAATCA
55670045 AAATCACATATAAG
1 AAATCACATATAAG
55670059 AAATCACATATAA
1 AAATCACATATAA
55670072 CTCATATTTA
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:0.59, C:0.15, G:0.04, T:0.22
Consensus pattern (14 bp):
AAATCACATATAAG
Found at i:55670917 original size:26 final size:26
Alignment explanation
Indices: 55670873--55670932 Score: 77
Period size: 26 Copynumber: 2.3 Consensus size: 26
55670863 AATTTTCTCG
55670873 AAATTTTATCGAGGGTAAAACCATCA
1 AAATTTTATCGAGGGTAAAACCATCA
***
55670899 AAATTTTATC-AGGGATAAAATTGTCA
1 AAATTTTATCGAGGG-TAAAACCATCA
55670925 AAATTTTA
1 AAATTTTA
55670933 CAATTGTAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
25 4 0.13
26 26 0.87
ACGTcount: A:0.43, C:0.10, G:0.13, T:0.33
Consensus pattern (26 bp):
AAATTTTATCGAGGGTAAAACCATCA
Found at i:55672821 original size:19 final size:20
Alignment explanation
Indices: 55672797--55672835 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
55672787 ATGATCATGT
*
55672797 CAATGCTCATTTTGT-AAAA
1 CAATGCACATTTTGTGAAAA
*
55672816 CAATGCAGATTTTGTGAAAA
1 CAATGCACATTTTGTGAAAA
55672836 TAGTCCTACC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.38, C:0.13, G:0.15, T:0.33
Consensus pattern (20 bp):
CAATGCACATTTTGTGAAAA
Found at i:55679604 original size:26 final size:26
Alignment explanation
Indices: 55679565--55679633 Score: 84
Period size: 26 Copynumber: 2.7 Consensus size: 26
55679555 TTTACATCGT
* * *
55679565 TGCTTACAAAAGCTGTGAAACGGGTC
1 TGCTCACAAGAGCTGTGAAACGAGTC
* *
55679591 TGCTCACAAGAGCTGTAAAATGAGTC
1 TGCTCACAAGAGCTGTGAAACGAGTC
*
55679617 TGCTCACAGGAGCTGTG
1 TGCTCACAAGAGCTGTG
55679634 GGTCAGAATG
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 36 1.00
ACGTcount: A:0.29, C:0.20, G:0.28, T:0.23
Consensus pattern (26 bp):
TGCTCACAAGAGCTGTGAAACGAGTC
Found at i:55682242 original size:13 final size:12
Alignment explanation
Indices: 55682207--55682240 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
55682197 CTAAATCGTG
*
55682207 AGTCAGATTGGTT
1 AGTCA-ATTTGTT
55682220 AGTCAATTTGTT
1 AGTCAATTTGTT
55682232 AGTCAATTT
1 AGTCAATTT
55682241 TGGTAGGAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 15 0.75
13 5 0.25
ACGTcount: A:0.26, C:0.09, G:0.21, T:0.44
Consensus pattern (12 bp):
AGTCAATTTGTT
Found at i:55684760 original size:22 final size:22
Alignment explanation
Indices: 55684732--55684853 Score: 61
Period size: 22 Copynumber: 5.3 Consensus size: 22
55684722 TTCCACATCC
55684732 ATCACATTGGCCATTCGGCCTT
1 ATCACATTGGCCATTCGGCCTT
** * * *
55684754 ATCACATATATACACTTTC-ACATT
1 ATCACAT-T-GGC-CATTCGGCCTT
55684778 CATCACATTGGCCATTCGGCCTT
1 -ATCACATTGGCCATTCGGCCTT
* * * *
55684801 ATCTCATATATG-CATGTTC-ACATT
1 ATCACAT-T-GGCCA--TTCGGCCTT
55684825 CATCACATTGGCCATTCGGCCTT
1 -ATCACATTGGCCATTCGGCCTT
55684848 ATCACA
1 ATCACA
55684854 CATACACATG
Statistics
Matches: 70, Mismatches: 18, Indels: 24
0.62 0.16 0.21
Matches are distributed among these distances:
22 26 0.37
23 12 0.17
24 12 0.17
25 20 0.29
ACGTcount: A:0.25, C:0.30, G:0.11, T:0.34
Consensus pattern (22 bp):
ATCACATTGGCCATTCGGCCTT
Found at i:55684767 original size:47 final size:47
Alignment explanation
Indices: 55684704--55684964 Score: 373
Period size: 47 Copynumber: 5.5 Consensus size: 47
55684694 CCCTTCGGGA
* * *
55684704 CTTATCACATTTATACACTTCCACATCCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
55684751 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* *
55684798 CTTATCTCATATATGCA-TGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACT-TTCACATTCATCACATTGGCCATTCGGC
* * * *
55684845 CTTATCACACATACACA-TGTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACT-TTCACATTCATCACATTGGCCATTCGGC
* *
55684892 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
55684939 CTTATCACATATATATACACTTTCAC
1 CTTATCAC--ATATATACACTTTCAC
55684965 TAGGCCTTAT
Statistics
Matches: 197, Mismatches: 13, Indels: 6
0.91 0.06 0.03
Matches are distributed among these distances:
46 1 0.01
47 179 0.91
48 1 0.01
49 16 0.08
ACGTcount: A:0.28, C:0.30, G:0.09, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
Found at i:55684969 original size:31 final size:31
Alignment explanation
Indices: 55684934--55684995 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
55684924 CATCGGCCAT
55684934 TAGGCCTTATCACATATATATACACTTTCAC
1 TAGGCCTTATCACATATATATACACTTTCAC
55684965 TAGGCCTTATCACATATATATACACTTTCAC
1 TAGGCCTTATCACATATATATACACTTTCAC
55684996 ATTCATCACA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.32, C:0.26, G:0.06, T:0.35
Consensus pattern (31 bp):
TAGGCCTTATCACATATATATACACTTTCAC
Found at i:55685005 original size:80 final size:76
Alignment explanation
Indices: 55684887--55685042 Score: 267
Period size: 80 Copynumber: 2.0 Consensus size: 76
55684877 CATCGGCCAT
55684887 TAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATA
1 TAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC--ATA
55684952 TATACACTTTCAC
64 TATACACTTTCAC
*
55684965 TAGGCCTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTAGGCCTTATCACATA
1 TAGGCCTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATA
55685030 TATACACTTTCAC
64 TATACACTTTCAC
55685043 ATTTATTCAA
Statistics
Matches: 75, Mismatches: 1, Indels: 4
0.94 0.01 0.05
Matches are distributed among these distances:
78 29 0.39
80 46 0.61
ACGTcount: A:0.31, C:0.28, G:0.08, T:0.34
Consensus pattern (76 bp):
TAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATA
TACACTTTCAC
Found at i:55685723 original size:17 final size:17
Alignment explanation
Indices: 55685701--55685739 Score: 78
Period size: 17 Copynumber: 2.3 Consensus size: 17
55685691 ATAGGAAATT
55685701 TCTTTGCTCACAAGGTC
1 TCTTTGCTCACAAGGTC
55685718 TCTTTGCTCACAAGGTC
1 TCTTTGCTCACAAGGTC
55685735 TCTTT
1 TCTTT
55685740 TATAAGAAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.15, C:0.28, G:0.15, T:0.41
Consensus pattern (17 bp):
TCTTTGCTCACAAGGTC
Found at i:55686448 original size:56 final size:56
Alignment explanation
Indices: 55686381--55686500 Score: 231
Period size: 56 Copynumber: 2.1 Consensus size: 56
55686371 TATTAGTTTA
55686381 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
*
55686437 TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
55686493 TTGCCCAT
1 TTGCCCAT
55686501 CATCCCTTGT
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 63 1.00
ACGTcount: A:0.23, C:0.23, G:0.09, T:0.45
Consensus pattern (56 bp):
TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
Found at i:55698794 original size:31 final size:32
Alignment explanation
Indices: 55698743--55698804 Score: 83
Period size: 31 Copynumber: 2.0 Consensus size: 32
55698733 ATGTAGTTTG
*
55698743 TTTATTTTTTTAACACTATTATCATCATTATA
1 TTTATTTTTTTAACACTATTATCACCATTATA
*
55698775 TTTACTTTTTTTAA-A-TATTATTACCATTAT
1 TTTA-TTTTTTTAACACTATTATCACCATTAT
55698805 TTTTTAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
31 13 0.48
32 5 0.19
33 9 0.33
ACGTcount: A:0.31, C:0.11, G:0.00, T:0.58
Consensus pattern (32 bp):
TTTATTTTTTTAACACTATTATCACCATTATA
Found at i:55698808 original size:25 final size:25
Alignment explanation
Indices: 55698780--55698833 Score: 83
Period size: 25 Copynumber: 2.2 Consensus size: 25
55698770 TTATATTTAC
*
55698780 TTTTTTTAAA-TATTATTACCATTA
1 TTTTTTAAAATTATTATTACCATTA
*
55698804 TTTTTTAAAATTATTATTACTATTA
1 TTTTTTAAAATTATTATTACCATTA
55698829 TTTTT
1 TTTTT
55698834 ATTATCCGTC
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
24 9 0.33
25 18 0.67
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.63
Consensus pattern (25 bp):
TTTTTTAAAATTATTATTACCATTA
Found at i:55701034 original size:27 final size:27
Alignment explanation
Indices: 55700997--55701064 Score: 120
Period size: 26 Copynumber: 2.6 Consensus size: 27
55700987 AGAAACTATT
55700997 TTTAAAAATTATAAATTAGTAAAATTA
1 TTTAAAAATTATAAATTAGTAAAATTA
55701024 TTTAAAAATTAT-AATTAGTAAAATTA
1 TTTAAAAATTATAAATTAGTAAAATTA
*
55701050 TTTAAAATTTATAAA
1 TTTAAAAATTATAAA
55701065 ATTATTTAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
26 25 0.64
27 14 0.36
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (27 bp):
TTTAAAAATTATAAATTAGTAAAATTA
Found at i:55701064 original size:19 final size:19
Alignment explanation
Indices: 55701042--55701093 Score: 79
Period size: 19 Copynumber: 2.7 Consensus size: 19
55701032 TTATAATTAG
55701042 TAAAATTATTTAAAATTTA
1 TAAAATTATTTAAAATTTA
55701061 TAAAATTATTTAAAATTTA
1 TAAAATTATTTAAAATTTA
*
55701080 -AAATATTAATTAAA
1 TAAA-ATTATTTAAA
55701094 TGTTGATGTG
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
18 3 0.10
19 28 0.90
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (19 bp):
TAAAATTATTTAAAATTTA
Found at i:55710345 original size:25 final size:24
Alignment explanation
Indices: 55710289--55710364 Score: 80
Period size: 25 Copynumber: 2.9 Consensus size: 24
55710279 AAATTGAAAT
*
55710289 AAAAATTATAAATAATTAATATATAATT
1 AAAAA-TAT-AAT-ATTAATAT-TAATG
55710317 AAAAATATCAATATTAATATTAATG
1 AAAAATAT-AATATTAATATTAATG
*
55710342 AAAAATAATTATATTAATATTAA
1 AAAAAT-ATAATATTAATATTAA
55710365 AAAAAATTCC
Statistics
Matches: 44, Mismatches: 3, Indels: 5
0.85 0.06 0.10
Matches are distributed among these distances:
25 23 0.52
26 10 0.23
27 6 0.14
28 5 0.11
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.38
Consensus pattern (24 bp):
AAAAATATAATATTAATATTAATG
Found at i:55711008 original size:24 final size:24
Alignment explanation
Indices: 55710981--55711033 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
55710971 ATTTTTTTTA
**
55710981 AATATTAATATAATTGTTTTAATT
1 AATATTAATATAATAATTTTAATT
55711005 AATATTAATATAATAATTTTAATT
1 AATATTAATATAATAATTTTAATT
55711029 -ATATT
1 AATATT
55711034 GATTATTTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
23 5 0.19
24 22 0.81
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (24 bp):
AATATTAATATAATAATTTTAATT
Found at i:55711582 original size:2 final size:2
Alignment explanation
Indices: 55711575--55711600 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
55711565 TTTAATCTCC
55711575 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
55711601 GAGTATACTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:55716714 original size:24 final size:24
Alignment explanation
Indices: 55716681--55716739 Score: 77
Period size: 24 Copynumber: 2.5 Consensus size: 24
55716671 GATGTTGAAC
*
55716681 CTTTCATCTTTCTTAACTT-TTCA-
1 CTTTCATCTTCCTTAA-TTCTTCAT
55716704 CATTTCATCTTCCTTAATTCTTCAT
1 C-TTTCATCTTCCTTAATTCTTCAT
55716729 CTTTCATCTTC
1 CTTTCATCTTC
55716740 TTGTAATCAT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
23 3 0.09
24 28 0.88
25 1 0.03
ACGTcount: A:0.17, C:0.29, G:0.00, T:0.54
Consensus pattern (24 bp):
CTTTCATCTTCCTTAATTCTTCAT
Found at i:55719608 original size:19 final size:19
Alignment explanation
Indices: 55719576--55719615 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
55719566 GTTGAGAATG
* *
55719576 ATTTTCTTTTAGAAGCAAA
1 ATTTTATTTAAGAAGCAAA
55719595 ATTTTATTTAAGAAGCAAA
1 ATTTTATTTAAGAAGCAAA
55719614 AT
1 AT
55719616 GAAAAATTGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.42, C:0.07, G:0.10, T:0.40
Consensus pattern (19 bp):
ATTTTATTTAAGAAGCAAA
Found at i:55732570 original size:133 final size:133
Alignment explanation
Indices: 55732332--55732577 Score: 492
Period size: 133 Copynumber: 1.8 Consensus size: 133
55732322 GACTGTGTGT
55732332 CACACGCGGCCTAGACACACGCGCGTGTGTCTACCCGTGTGGACAATATAAGGCTTTCTACCAAG
1 CACACGCGGCCTAGACACACGCGCGTGTGTCTACCCGTGTGGACAATATAAGGCTTTCTACCAAG
55732397 CCTTTTGCCACCCTGACACACCATCTAATGCCAACCATTTCACATTCACACGACCAAGCAACATC
66 CCTTTTGCCACCCTGACACACCATCTAATGCCAACCATTTCACATTCACACGACCAAGCAACATC
55732462 TTG
131 TTG
55732465 CACACGCGGCCTAGACACACGCGCGTGTGTCTACCCGTGTGGACAATATAAGGCTTTCTACCAAG
1 CACACGCGGCCTAGACACACGCGCGTGTGTCTACCCGTGTGGACAATATAAGGCTTTCTACCAAG
55732530 CCTTTTGCCACCCTGACACACCATCTAATGCCAACCATTTCACATTCA
66 CCTTTTGCCACCCTGACACACCATCTAATGCCAACCATTTCACATTCA
55732578 TGAAAGACTA
Statistics
Matches: 113, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
133 113 1.00
ACGTcount: A:0.26, C:0.35, G:0.17, T:0.22
Consensus pattern (133 bp):
CACACGCGGCCTAGACACACGCGCGTGTGTCTACCCGTGTGGACAATATAAGGCTTTCTACCAAG
CCTTTTGCCACCCTGACACACCATCTAATGCCAACCATTTCACATTCACACGACCAAGCAACATC
TTG
Found at i:55733222 original size:47 final size:47
Alignment explanation
Indices: 55733152--55733427 Score: 201
Period size: 47 Copynumber: 5.8 Consensus size: 47
55733142 AAGGTATAAC
*
55733152 GTCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCATCCATCAA
1 GTCGATGCCATATCCCAGACATGGTCTTACACTGGCTCATCCATCAA
* * * *
55733199 GTCGATGCCATGTCCCAGGCATGGTCTTACACTGACT-ATCAAAATCAA
1 GTCGATGCCATATCCCAGACATGGTCTTACACTGGCTCATC--CATCAA
* * ** * *
55733247 GGCCGATGCCATATCCCAGATATGGTCTTACACTATC-CCTCACAT-ATCC
1 -GTCGATGCCATATCCCAGACATGGTCTTACACTGGCTCATC-CATCA--A
** * * * *
55733296 GTGCCGATGCCACGTCCTAGACATGGTCTTACACTGACACAT-C-TTATA
1 GT--CGATGCCATATCCCAGACATGGTCTTACACTGGCTCATCCATCA-A
* * *
55733344 GCCTATG-CATATCCCAGACAT-GTCTTACACTAGCTC-T-CATCTCAA
1 GTCGATGCCATATCCCAGACATGGTCTTACACTGGCTCATCCA--TCAA
55733389 TGTCGATGCCATATCCCAGACATGGTCTTACACTGGCTC
1 -GTCGATGCCATATCCCAGACATGGTCTTACACTGGCTC
55733428 TCATAGTGTG
Statistics
Matches: 179, Mismatches: 34, Indels: 31
0.73 0.14 0.13
Matches are distributed among these distances:
43 2 0.01
44 12 0.07
45 12 0.07
46 14 0.08
47 50 0.28
48 25 0.14
49 34 0.19
50 28 0.16
51 2 0.01
ACGTcount: A:0.25, C:0.31, G:0.17, T:0.27
Consensus pattern (47 bp):
GTCGATGCCATATCCCAGACATGGTCTTACACTGGCTCATCCATCAA
Found at i:55733416 original size:92 final size:96
Alignment explanation
Indices: 55733154--55733423 Score: 277
Period size: 92 Copynumber: 2.8 Consensus size: 96
55733144 GGTATAACGT
* *
55733154 CGATGCCATGTCCCAGACATGGTCTTACACT-G-GCTCATCCATCAA-GTCGATGCCATGTCCCA
1 CGATGCCATATCCCAGACATGGTCTTACACTAGCTCTCAT-C-TCAATGTCGATGCCATGTCCCA
* *
55733216 GGCATGGTCTTACACTGACTATCAAAATCAAGGC
64 GACATGGTCTTACACTGACCATCAAAAT-AAGGC
* * * * ** * * *
55733250 CGATGCCATATCCCAGATATGGTCTTACACTATCCCTCACATATCCGTGCCGATGCCACGTCCTA
1 CGATGCCATATCCCAGACATGGTCTTACACTA--GCTCTCATCTCAATGTCGATGCCATGTCCCA
**
55733315 GACATGGTCTTACACTGACACATC-TTAT-A-GC
64 GACATGGTCTTACACTGAC-CATCAAAATAAGGC
* *
55733346 CTATG-CATATCCCAGACAT-GTCTTACACTAGCTCTCATCTCAATGTCGATGCCATATCCCAGA
1 CGATGCCATATCCCAGACATGGTCTTACACTAGCTCTCATCTCAATGTCGATGCCATGTCCCAGA
55733409 CATGGTCTTACACTG
66 CATGGTCTTACACTG
55733424 GCTCTCATAG
Statistics
Matches: 142, Mismatches: 26, Indels: 16
0.77 0.14 0.09
Matches are distributed among these distances:
92 39 0.27
94 11 0.08
95 13 0.09
96 35 0.25
97 1 0.01
98 2 0.01
99 34 0.24
100 7 0.05
ACGTcount: A:0.26, C:0.31, G:0.17, T:0.27
Consensus pattern (96 bp):
CGATGCCATATCCCAGACATGGTCTTACACTAGCTCTCATCTCAATGTCGATGCCATGTCCCAGA
CATGGTCTTACACTGACCATCAAAATAAGGC
Found at i:55740665 original size:13 final size:13
Alignment explanation
Indices: 55740649--55740673 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
55740639 TATTTTGAAT
55740649 GGCACACGGGCTA
1 GGCACACGGGCTA
55740662 GGCACACGGGCT
1 GGCACACGGGCT
55740674 TATGATTGGT
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:0.20, C:0.32, G:0.40, T:0.08
Consensus pattern (13 bp):
GGCACACGGGCTA
Found at i:55744175 original size:28 final size:28
Alignment explanation
Indices: 55744139--55744231 Score: 75
Period size: 28 Copynumber: 3.3 Consensus size: 28
55744129 AGGAAGATTA
*
55744139 TTTTGAAAGACATTTTCTATGTATCAAG
1 TTTTAAAAGACATTTTCTATGTATCAAG
* * * *
55744167 TTTTAAAAGAAACTTATT-TAGGAAGAT-TA-
1 TTTTAAAAGACA-TT-TTCTATG--TATCAAG
*
55744196 TTTTGAAAGACATTTTCTATGTATCAAG
1 TTTTAAAAGACATTTTCTATGTATCAAG
55744224 TTTTAAAA
1 TTTTAAAA
55744232 AAACTTAATT
Statistics
Matches: 47, Mismatches: 11, Indels: 14
0.65 0.15 0.19
Matches are distributed among these distances:
26 2 0.04
27 3 0.06
28 22 0.47
29 15 0.32
30 3 0.06
31 2 0.04
ACGTcount: A:0.38, C:0.08, G:0.13, T:0.42
Consensus pattern (28 bp):
TTTTAAAAGACATTTTCTATGTATCAAG
Found at i:55744255 original size:57 final size:57
Alignment explanation
Indices: 55744126--55744238 Score: 219
Period size: 57 Copynumber: 2.0 Consensus size: 57
55744116 TTTTGATAAT
55744126 TTTAGGAAGATTATTTTGAAAGACATTTTCTATGTATCAAGTTTTAAAAGAAACTTA
1 TTTAGGAAGATTATTTTGAAAGACATTTTCTATGTATCAAGTTTTAAAAGAAACTTA
55744183 TTTAGGAAGATTATTTTGAAAGACATTTTCTATGTATCAAGTTTTAAAA-AAACTTA
1 TTTAGGAAGATTATTTTGAAAGACATTTTCTATGTATCAAGTTTTAAAAGAAACTTA
55744239 ATTTCTTTTG
Statistics
Matches: 56, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
56 7 0.12
57 49 0.88
ACGTcount: A:0.39, C:0.07, G:0.13, T:0.41
Consensus pattern (57 bp):
TTTAGGAAGATTATTTTGAAAGACATTTTCTATGTATCAAGTTTTAAAAGAAACTTA
Found at i:55745984 original size:53 final size:53
Alignment explanation
Indices: 55745904--55746007 Score: 199
Period size: 53 Copynumber: 2.0 Consensus size: 53
55745894 TCTACAATTA
*
55745904 AACAAAGGTTCTACTTTCTCTTCTTATAAATTGATGGCACCGGTAGGGCATTC
1 AACAAAGGTTCTACTTTCTCTTCTTATAAATAGATGGCACCGGTAGGGCATTC
55745957 AACAAAGGTTCTACTTTCTCTTCTTATAAATAGATGGCACCGGTAGGGCAT
1 AACAAAGGTTCTACTTTCTCTTCTTATAAATAGATGGCACCGGTAGGGCAT
55746008 AACACATAAC
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 50 1.00
ACGTcount: A:0.28, C:0.20, G:0.19, T:0.33
Consensus pattern (53 bp):
AACAAAGGTTCTACTTTCTCTTCTTATAAATAGATGGCACCGGTAGGGCATTC
Found at i:55754514 original size:40 final size:38
Alignment explanation
Indices: 55754457--55754641 Score: 158
Period size: 40 Copynumber: 4.7 Consensus size: 38
55754447 TTGAATGATG
55754457 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAG-TGACCATA
1 TCCGGGCTAAGT-CCGAAGGCATTTGTGC-AAGAT-ACCA-A
* * *
55754497 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGATACTAA
1 TCCGGGCTAAG-TCCGAAGGCATTTGTGCAAGATACCAA
* * *
55754536 TCCGGGCTAAGCTCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAG-TCCGAAGGCATTTGTGCAAGATAC-CAA
* * * *
55754576 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA
1 TCCGGGCTAAGT-CCGAAGGCATTTGTGCAAGATACCA-A
* *
55754616 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGT-CCGAAGGCATTTG
55754642 AACGAGGAGC
Statistics
Matches: 127, Mismatches: 12, Indels: 12
0.84 0.08 0.08
Matches are distributed among these distances:
39 36 0.28
40 82 0.65
41 9 0.07
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (38 bp):
TCCGGGCTAAGTCCGAAGGCATTTGTGCAAGATACCAA
Found at i:55754593 original size:79 final size:81
Alignment explanation
Indices: 55754457--55754641 Score: 236
Period size: 79 Copynumber: 2.3 Consensus size: 81
55754447 TTGAATGATG
*
55754457 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
55754521 TGTGCGAGATACTA-A
66 TGTGCGAGATACTATA
* * * **
55754536 TCCGGGCTAAG-CTCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 TCCGGGCTAAGTC-CCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
*
55754598 TTTGTGCGAGTTACTATA
64 TTTGTGCGAGATACTATA
* *
55754616 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
55754642 AACGAGGAGC
Statistics
Matches: 92, Mismatches: 9, Indels: 9
0.84 0.08 0.08
Matches are distributed among these distances:
78 2 0.02
79 59 0.64
80 30 0.33
81 1 0.01
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
TGTGCGAGATACTATA
Found at i:55754663 original size:79 final size:79
Alignment explanation
Indices: 55754510--55754674 Score: 201
Period size: 79 Copynumber: 2.1 Consensus size: 79
55754500 GGACTAAGAT
* ** *
55754510 CCGAAGGCATTTGTGCGAGATACTAATCCGGGCTAAGCTCCGAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGATACTAAACCGGGCTAAGCTCCGAAGGCATTTGAACGAGTGACTAA
*
55754575 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
* *
55754589 CCGAAGGCATTTGTGCGAGTTACTATAACCGGGCTATG-TCCCGAAGGCATTTGAACGAG-GAGC
1 CCGAAGGCATTTGTGCGAGATACTA-AACCGGGCTAAGCT-CCGAAGGCATTTGAACGAGTGA-C
* *
55754652 TATATCC-GGTTAAATT
63 TAAATCCGGGTTAAATC
55754668 CCGAAGG
1 CCGAAGG
55754675 TACGTGATTT
Statistics
Matches: 74, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
79 40 0.54
80 34 0.46
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGATACTAAACCGGGCTAAGCTCCGAAGGCATTTGAACGAGTGACTAA
ATCCGGGTTAAATC
Found at i:55762489 original size:79 final size:78
Alignment explanation
Indices: 55762309--55762531 Score: 258
Period size: 79 Copynumber: 2.8 Consensus size: 78
55762299 TTGAATGATG
* * * *
55762309 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTA-AGTGACCATATCCGGACTAAGATCCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTATATCCGGGCTAAGACCCGAAGGCAT
55762372 TTGTGCGAGATACTA
64 TTGTGCGAGATACTA
*
55762387 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTA-ATTCCGGGCTAAG-CCCGAAGGCAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGATACTATA-TCCGGGCTAAGACCCGAAGGCAT
*
55762449 TTGTGCGAGTTACTAAA
64 TTGTGCGAGATACT--A
* * * * *
55762466 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAACCGGGCTATGTCCCGAAGGCATTT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTATATCCGGGCTAAGACCCGAAGGCATTT
55762531 G
66 G
55762532 AACGAGGAGC
Statistics
Matches: 125, Mismatches: 11, Indels: 16
0.82 0.07 0.11
Matches are distributed among these distances:
77 24 0.19
78 32 0.26
79 53 0.42
80 16 0.13
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.25
Consensus pattern (78 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTATATCCGGGCTAAGACCCGAAGGCATTT
GTGCGAGATACTA
Found at i:55762545 original size:40 final size:40
Alignment explanation
Indices: 55762310--55762531 Score: 244
Period size: 40 Copynumber: 5.6 Consensus size: 40
55762300 TGAATGATGT
* * * *
55762310 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAA
* *
55762350 CCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAT--
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATAA
* * *
55762388 CCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTA-ATT
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATA-A
55762428 CCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTA-AA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
55762466 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
55762507 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
55762532 AACGAGGAGC
Statistics
Matches: 162, Mismatches: 11, Indels: 18
0.85 0.06 0.09
Matches are distributed among these distances:
38 37 0.23
39 34 0.21
40 81 0.50
41 10 0.06
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
Found at i:55762553 original size:79 final size:78
Alignment explanation
Indices: 55762316--55762564 Score: 242
Period size: 79 Copynumber: 3.2 Consensus size: 78
55762306 ATGTCCGGGC
* * * *
55762316 TAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGAT-CCGAAGGCATTTGTGCG
1 TAAGTCCCGAAGGCATTTGTGC-GAGTTACTATATCCGGGCTAAG-TCCCGAAGGCATTTGTGCG
*
55762379 A-GA-TACTATCCGGAC
64 AGGACTA-TATCCGG-T
*
55762394 TAAGAT-CCGAAGGCATTTGTGCGAGATACTA-ATTCCGGGCTAAG-CCCGAAGGCATTTGTGCG
1 TAAG-TCCCGAAGGCATTTGTGCGAGTTACTATA-TCCGGGCTAAGTCCCGAAGGCATTTGTGCG
* *
55762456 AGTTACTAAATCCGGGT
64 AG-GACTATATCC-GGT
* * **
55762473 TAAGTCCCGAAGGCATTTGTGCGAGTTACTATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG
1 TAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAG
55762538 GAGCTATATCCGGT
66 GA-CTATATCCGGT
* *
55762552 TAAATTCCGAAGG
1 TAAGTCCCGAAGG
55762565 TACGTGATTT
Statistics
Matches: 142, Mismatches: 17, Indels: 23
0.78 0.09 0.13
Matches are distributed among these distances:
77 19 0.13
78 28 0.20
79 65 0.46
80 30 0.21
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.25
Consensus pattern (78 bp):
TAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAG
GACTATATCCGGT
Found at i:55767480 original size:27 final size:27
Alignment explanation
Indices: 55767448--55767499 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
55767438 CCACTGAATC
*
55767448 GGGGAATCAGCACTTAGCAACCCCTCG
1 GGGGAATCAGCACATAGCAACCCCTCG
55767475 GGGGAATCAGCACATAGCAACCCCT
1 GGGGAATCAGCACATAGCAACCCCT
55767500 TTTTATTTCA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.29, C:0.33, G:0.25, T:0.13
Consensus pattern (27 bp):
GGGGAATCAGCACATAGCAACCCCTCG
Found at i:55767681 original size:26 final size:26
Alignment explanation
Indices: 55767652--55767703 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
55767642 ACCAATGAAA
*
55767652 TCGGGGAATCAGCACTTAGCAACCCC
1 TCGGGGAATCAGCACATAGCAACCCC
55767678 TCGGGGAATCAGCACATAGCAACCCC
1 TCGGGGAATCAGCACATAGCAACCCC
55767704 CTTTCACATT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.29, C:0.35, G:0.23, T:0.13
Consensus pattern (26 bp):
TCGGGGAATCAGCACATAGCAACCCC
Found at i:55767726 original size:104 final size:103
Alignment explanation
Indices: 55767414--55767780 Score: 589
Period size: 102 Copynumber: 3.6 Consensus size: 103
55767404 TAGCCGTTAT
** *
55767414 TGGTGGATCCCGCACTTAGCACCACCACTGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
1 TGGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
*
55767479 AATCAGCACATAGCAA-CCCCTTTTTATTTCAAAGATA
66 AATCAGCACATAGCAACCCCCTTTTCATTTCAAAGATA
55767516 TGGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
1 TGGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
55767581 AATCAGCACATAGCAACCCCCTTTTCATTTCAAAGATA
66 AATCAGCACATAGCAACCCCCTTTTCATTTCAAAGATA
55767619 TGGTGGATATCGCACTTAGCACCACCAATGAAATCGGGGAATCAGCACTTAGCAACCCCTC-GGG
1 TGGTGGATATCGCACTTAGCACCACCAATG-AATCGGGGAATCAGCACTTAGCAACCCCTCGGGG
*
55767683 GAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATA
65 GAATCAGCACATAGCAACCCCCTTT-TCATTTCAAAGATA
* * * **
55767723 TGGTGGATCA-CGCACATAGCA-CACCCATAAATCGGGGAATCAGCACACAGCAACCCCT
1 TGGTGGAT-ATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCT
55767781 TTTATATACA
Statistics
Matches: 251, Mismatches: 10, Indels: 8
0.93 0.04 0.03
Matches are distributed among these distances:
102 105 0.42
103 84 0.33
104 61 0.24
105 1 0.00
ACGTcount: A:0.31, C:0.29, G:0.20, T:0.20
Consensus pattern (103 bp):
TGGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
AATCAGCACATAGCAACCCCCTTTTCATTTCAAAGATA
Found at i:55768142 original size:29 final size:29
Alignment explanation
Indices: 55768109--55768172 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 29
55768099 TAATCCACCA
55768109 CCCAACTTTTTG-AAAATTACAATTTTGCC
1 CCCAAC-TTTTGCAAAATTACAATTTTGCC
* * *
55768138 CCCAAACTTTTGCATAATTACACTTTTGTC
1 CCC-AACTTTTGCAAAATTACAATTTTGCC
55768168 CCCAA
1 CCCAA
55768173 GCTCGGAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
29 10 0.33
30 20 0.67
ACGTcount: A:0.30, C:0.28, G:0.06, T:0.36
Consensus pattern (29 bp):
CCCAACTTTTGCAAAATTACAATTTTGCC
Found at i:55768146 original size:30 final size:30
Alignment explanation
Indices: 55768116--55768172 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
55768106 CCACCCAACT
55768116 TTTTG-AAAATTACAATTTTGCCCCCAAAC
1 TTTTGCAAAATTACAATTTTGCCCCCAAAC
* * *
55768145 TTTTGCATAATTACACTTTTGTCCCCAA
1 TTTTGCAAAATTACAATTTTGCCCCCAA
55768173 GCTCGGAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 5 0.21
30 19 0.79
ACGTcount: A:0.30, C:0.25, G:0.07, T:0.39
Consensus pattern (30 bp):
TTTTGCAAAATTACAATTTTGCCCCCAAAC
Found at i:55769081 original size:45 final size:44
Alignment explanation
Indices: 55769030--55769158 Score: 136
Period size: 45 Copynumber: 2.9 Consensus size: 44
55769020 GCTATACACC
* *
55769030 TAAAATGAGTGAGACCATAA-TAGAAAGACGCTAT-AGCATCATGAT
1 TAAAATGAGTAAGACCATAACT-GAAAGACGCTATGA-CATCAT-AA
* * *
55769075 TAAAATGAGTAAGACTATAACTGAAATATGCTATGACATCATAA
1 TAAAATGAGTAAGACCATAACTGAAAGACGCTATGACATCATAA
** *
55769119 TATAAATGAGTAAGACCATGGCTAAAAGACGCTATGACAT
1 TA-AAATGAGTAAGACCATAACTGAAAGACGCTATGACAT
55769159 TATGTGAAAG
Statistics
Matches: 70, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
44 3 0.04
45 65 0.93
46 2 0.03
ACGTcount: A:0.45, C:0.13, G:0.18, T:0.24
Consensus pattern (44 bp):
TAAAATGAGTAAGACCATAACTGAAAGACGCTATGACATCATAA
Found at i:55771943 original size:26 final size:26
Alignment explanation
Indices: 55771914--55772028 Score: 88
Period size: 26 Copynumber: 4.3 Consensus size: 26
55771904 TTAGTTTACC
*
55771914 AAATTACTAAAATACCCCC-AGTTGTA
1 AAATTACCAAAATACCCCCGA-TTGTA
* * *
55771940 AAATTACCAAAGTACCCCCGGTTTATA
1 AAATTACCAAAATACCCCC-GATTGTA
* **
55771967 AAATTACCGAAATACCATCGATTGTA
1 AAATTACCAAAATACCCCCGATTGTA
** * *
55771993 AAATTACTGAAATGCCCTCGATTTGTA
1 AAATTACCAAAATACCCCCGA-TTGTA
*
55772020 GAATTACCA
1 AAATTACCA
55772029 TTTTAGCCTC
Statistics
Matches: 70, Mismatches: 16, Indels: 5
0.77 0.18 0.05
Matches are distributed among these distances:
26 40 0.57
27 30 0.43
ACGTcount: A:0.39, C:0.22, G:0.11, T:0.28
Consensus pattern (26 bp):
AAATTACCAAAATACCCCCGATTGTA
Found at i:55771968 original size:27 final size:25
Alignment explanation
Indices: 55771914--55771982 Score: 75
Period size: 27 Copynumber: 2.6 Consensus size: 25
55771904 TTAGTTTACC
* *
55771914 AAATTACTAAAATACCCCCAGTTGTA
1 AAATTAC-CAAATACCCCCAGTTATA
*
55771940 AAATTACCAAAGTACCCCCGGTTTATA
1 AAATTACCAAA-TACCCCCAG-TTATA
55771967 AAATTACCGAAATACC
1 AAATTACC-AAATACC
55771983 ATCGATTGTA
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
25 3 0.08
26 15 0.41
27 16 0.43
28 3 0.08
ACGTcount: A:0.42, C:0.25, G:0.09, T:0.25
Consensus pattern (25 bp):
AAATTACCAAATACCCCCAGTTATA
Found at i:55772038 original size:27 final size:27
Alignment explanation
Indices: 55772007--55772176 Score: 180
Period size: 27 Copynumber: 6.3 Consensus size: 27
55771997 TACTGAAATG
* *
55772007 CCCTCGATTTGTAGAATTACCATTTTA
1 CCCTCGATTTATAAAATTACCATTTTA
* * ** *
55772034 GCCTCGATTTATAGAATTACGGTTTCA
1 CCCTCGATTTATAAAATTACCATTTTA
** * *
55772061 CCCTTAATTTACAAAATTACCGTTTTA
1 CCCTCGATTTATAAAATTACCATTTTA
* *
55772088 CCCTTGATTTATAGAATTACCATTTTA
1 CCCTCGATTTATAAAATTACCATTTTA
*
55772115 CCTTCGATTTA-AAAATTACCATTTTA
1 CCCTCGATTTATAAAATTACCATTTTA
* * *
55772141 CCCTCAATTTACAAAATTATCATTTTA
1 CCCTCGATTTATAAAATTACCATTTTA
55772168 CCCTCGATT
1 CCCTCGATT
55772177 GTGAAATTAC
Statistics
Matches: 119, Mismatches: 23, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
26 23 0.19
27 96 0.81
ACGTcount: A:0.30, C:0.22, G:0.08, T:0.41
Consensus pattern (27 bp):
CCCTCGATTTATAAAATTACCATTTTA
Found at i:55772151 original size:53 final size:54
Alignment explanation
Indices: 55772021--55772176 Score: 181
Period size: 53 Copynumber: 2.9 Consensus size: 54
55772011 CGATTTGTAG
* ** * *
55772021 AATTACCATTTTAGCCTCGATTTATAGAATTACGGTTTCACCCTT-AATTTACAA
1 AATTACCATTTTACCCTCGATTTATAGAATTACCATTTTA-CCTTCGATTTACAA
* *
55772075 AATTACCGTTTTACCCTTGATTTATAGAATTACCATTTTACCTTCGATTTA-AA
1 AATTACCATTTTACCCTCGATTTATAGAATTACCATTTTACCTTCGATTTACAA
* * * * *
55772128 AATTACCATTTTACCCTCAATTTACAAAATTATCATTTTACCCTCGATT
1 AATTACCATTTTACCCTCGATTTATAGAATTACCATTTTACCTTCGATT
55772177 GTGAAATTAC
Statistics
Matches: 87, Mismatches: 14, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
53 48 0.55
54 39 0.45
ACGTcount: A:0.31, C:0.21, G:0.06, T:0.41
Consensus pattern (54 bp):
AATTACCATTTTACCCTCGATTTATAGAATTACCATTTTACCTTCGATTTACAA
Found at i:55772198 original size:27 final size:27
Alignment explanation
Indices: 55772168--55772276 Score: 109
Period size: 27 Copynumber: 4.1 Consensus size: 27
55772158 TATCATTTTA
*
55772168 CCCTCGATTGTGAAATTACTAAAATAC
1 CCCTCGATTGTGAAATTACCAAAATAC
*
55772195 CCCT-G-TAG-GATAAATTACCAAAATAC
1 CCCTCGATTGTG--AAATTACCAAAATAC
* * *
55772221 CCCTAGTTTGTAAAATTACCAAAATAC
1 CCCTCGATTGTGAAATTACCAAAATAC
*
55772248 CCCTC-ATTTGTGAAATTACCGAAATAC
1 CCCTCGA-TTGTGAAATTACCAAAATAC
55772275 CC
1 CC
55772277 TTGTAGGGTA
Statistics
Matches: 68, Mismatches: 8, Indels: 12
0.77 0.09 0.14
Matches are distributed among these distances:
24 1 0.01
25 2 0.03
26 19 0.28
27 44 0.65
28 2 0.03
ACGTcount: A:0.38, C:0.25, G:0.10, T:0.28
Consensus pattern (27 bp):
CCCTCGATTGTGAAATTACCAAAATAC
Found at i:55772291 original size:27 final size:27
Alignment explanation
Indices: 55772189--55772534 Score: 389
Period size: 27 Copynumber: 12.9 Consensus size: 27
55772179 GAAATTACTA
* *
55772189 AAATACCCCTGTAGGATA-AATTACCA
1 AAATACCCCTGTAGGGTAGAATTACCG
** * *
55772215 AAATACCCCTAGT-TTGTAAAATTACCA
1 AAATACCCCT-GTAGGGTAGAATTACCG
* **
55772242 AAATACCCCT-CATTTGT-GAAATTACCG
1 AAATACCCCTGTA-GGGTAG-AATTACCG
* *
55772269 AAATACCCTTGTAGGGTAGAATTATCG
1 AAATACCCCTGTAGGGTAGAATTACCG
*
55772296 AAATACCCCTGTAGGGTAGAATTACTG
1 AAATACCCCTGTAGGGTAGAATTACCG
*
55772323 AAATACCCCTGTAGGGTAGAATTATCG
1 AAATACCCCTGTAGGGTAGAATTACCG
* *
55772350 GAATACCCCTGTAGGGTAGAATTA-CT
1 AAATACCCCTGTAGGGTAGAATTACCG
55772376 AGAATACCCCTGTAGGGTAGAATTACC-
1 A-AATACCCCTGTAGGGTAGAATTACCG
*
55772403 AGAATACCCCTGTAGGATAGAATTACCG
1 A-AATACCCCTGTAGGGTAGAATTACCG
* * *
55772431 GAATACCCCTGTACGGTAGAATTATCG
1 AAATACCCCTGTAGGGTAGAATTACCG
* *
55772458 CAATACCCCTGTAAGGTAGAATTACCG
1 AAATACCCCTGTAGGGTAGAATTACCG
**
55772485 AAATACCCCTGTAGGGTAGAATTACTA
1 AAATACCCCTGTAGGGTAGAATTACCG
*
55772512 AAATACCCCTGTAGGGTGGAATT
1 AAATACCCCTGTAGGGTAGAATT
55772535 GCTGAGATAC
Statistics
Matches: 278, Mismatches: 32, Indels: 19
0.84 0.10 0.06
Matches are distributed among these distances:
26 13 0.05
27 262 0.94
28 3 0.01
ACGTcount: A:0.34, C:0.21, G:0.19, T:0.26
Consensus pattern (27 bp):
AAATACCCCTGTAGGGTAGAATTACCG
Found at i:55773042 original size:22 final size:22
Alignment explanation
Indices: 55772990--55773054 Score: 69
Period size: 22 Copynumber: 3.0 Consensus size: 22
55772980 TTAAAGCCTT
* *
55772990 CTGATTATGGCTTTGTGTCAAC
1 CTGATTATGGCTCTGTGCCAAC
* *
55773012 CT-ACATATGGCTCTATGCCAAC
1 CTGA-TTATGGCTCTGTGCCAAC
*
55773034 CTGATTATGGCTGTGTGCCAA
1 CTGATTATGGCTCTGTGCCAA
55773055 ATGTATTTGC
Statistics
Matches: 34, Mismatches: 7, Indels: 4
0.76 0.16 0.09
Matches are distributed among these distances:
21 1 0.03
22 32 0.94
23 1 0.03
ACGTcount: A:0.22, C:0.23, G:0.22, T:0.34
Consensus pattern (22 bp):
CTGATTATGGCTCTGTGCCAAC
Found at i:55773243 original size:27 final size:27
Alignment explanation
Indices: 55773213--55773314 Score: 116
Period size: 27 Copynumber: 3.8 Consensus size: 27
55773203 ATTTTGTTAA
* *
55773213 GTGGCTTTGCCACATTATCTGTTTCTG
1 GTGGCTATGCCACAATATCTGTTTCTG
55773240 GTGGCTATGCCACAAATATCTG-TTCTG
1 GTGGCTATGCCAC-AATATCTGTTTCTG
* * *
55773267 GTGGCTCTGCCACAATATCTGTATCTA
1 GTGGCTATGCCACAATATCTGTTTCTG
* * *
55773294 GTGACTCTGTCACAATATCTG
1 GTGGCTATGCCACAATATCTG
55773315 ATAACTGAGC
Statistics
Matches: 66, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
26 8 0.12
27 51 0.77
28 7 0.11
ACGTcount: A:0.20, C:0.24, G:0.21, T:0.36
Consensus pattern (27 bp):
GTGGCTATGCCACAATATCTGTTTCTG
Found at i:55773272 original size:54 final size:53
Alignment explanation
Indices: 55773213--55773314 Score: 132
Period size: 54 Copynumber: 1.9 Consensus size: 53
55773203 ATTTTGTTAA
* * * * *
55773213 GTGGCTTTGCCACATTATCTGTTTCTGGTGGCTATGCCACAAATATCTGTTCTG
1 GTGGCTCTGCCACAATATCTGTATCTAGTGACTATGCCAC-AATATCTGTTCTG
* *
55773267 GTGGCTCTGCCACAATATCTGTATCTAGTGACTCTGTCACAATATCTG
1 GTGGCTCTGCCACAATATCTGTATCTAGTGACTATGCCACAATATCTG
55773315 ATAACTGAGC
Statistics
Matches: 41, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
53 8 0.20
54 33 0.80
ACGTcount: A:0.20, C:0.24, G:0.21, T:0.36
Consensus pattern (53 bp):
GTGGCTCTGCCACAATATCTGTATCTAGTGACTATGCCACAATATCTGTTCTG
Found at i:55773489 original size:6 final size:6
Alignment explanation
Indices: 55773452--55773531 Score: 65
Period size: 6 Copynumber: 12.8 Consensus size: 6
55773442 TGCATTCACC
* * *
55773452 TTCTGA TTTTTGA TTCTG- TTACATGA TACTGA TTCTGA TTTTGA TTCTG-
1 TTCTGA -TTCTGA TTCTGA TT-C-TGA TTCTGA TTCTGA TTCTGA TTCTGA
*
55773501 TTACCTGA TACTGA TTCTGA TTCTGA TTCTG
1 TT--CTGA TTCTGA TTCTGA TTCTGA TTCTG
55773532 TCACCTAATT
Statistics
Matches: 59, Mismatches: 8, Indels: 13
0.74 0.10 0.16
Matches are distributed among these distances:
5 4 0.07
6 42 0.71
7 11 0.19
8 2 0.03
ACGTcount: A:0.19, C:0.15, G:0.16, T:0.50
Consensus pattern (6 bp):
TTCTGA
Found at i:55773497 original size:31 final size:31
Alignment explanation
Indices: 55773452--55773532 Score: 135
Period size: 31 Copynumber: 2.6 Consensus size: 31
55773442 TGCATTCACC
55773452 TTCTGATTTTTGATTCTGTTACATGATACTGA
1 TTCTGA-TTTTGATTCTGTTACATGATACTGA
*
55773484 TTCTGATTTTGATTCTGTTACCTGATACTGA
1 TTCTGATTTTGATTCTGTTACATGATACTGA
*
55773515 TTCTGATTCTGATTCTGT
1 TTCTGATTTTGATTCTGT
55773533 CACCTAATTT
Statistics
Matches: 47, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
31 41 0.87
32 6 0.13
ACGTcount: A:0.19, C:0.15, G:0.16, T:0.51
Consensus pattern (31 bp):
TTCTGATTTTGATTCTGTTACATGATACTGA
Found at i:55773547 original size:31 final size:31
Alignment explanation
Indices: 55773452--55773555 Score: 118
Period size: 31 Copynumber: 3.3 Consensus size: 31
55773442 TGCATTCACC
* * * *
55773452 TTCTGATTTTTGATTCTGTTACATGATACTGA
1 TTCTGA-TTCTGATTCTGTCACCTAATACTGA
* * *
55773484 TTCTGATTTTGATTCTGTTACCTGATACTGA
1 TTCTGATTCTGATTCTGTCACCTAATACTGA
**
55773515 TTCTGATTCTGATTCTGTCACCTAATTTTGA
1 TTCTGATTCTGATTCTGTCACCTAATACTGA
55773546 TTCTGATTCT
1 TTCTGATTCT
55773556 AGTTCTAATA
Statistics
Matches: 66, Mismatches: 6, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
31 60 0.91
32 6 0.09
ACGTcount: A:0.19, C:0.16, G:0.14, T:0.50
Consensus pattern (31 bp):
TTCTGATTCTGATTCTGTCACCTAATACTGA
Found at i:55775186 original size:47 final size:48
Alignment explanation
Indices: 55775118--55775285 Score: 179
Period size: 48 Copynumber: 3.6 Consensus size: 48
55775108 TATGCTAGTA
* * *
55775118 TAAGA-CATGTCCGGGACAT-GCATCGGCCACGTTATGA-GAGCCAGTG
1 TAAGACCATGTCTGGGACATGGCATCGGCCACG-TATGAGGTGACAGTG
* * *
55775164 TAAGACCATGTCTGGGACAT-GCATCGGCTACG-A-GATGTGTCAGTG
1 TAAGACCATGTCTGGGACATGGCATCGGCCACGTATGAGGTGACAGTG
* * *
55775209 TAAGACCATGTCTTGGACATGGCATCGG-CATGTATAGAGGTGATAGTG
1 TAAGACCATGTCTGGGACATGGCATCGGCCACGTAT-GAGGTGACAGTG
*
55775257 TAAGACCATGTTTGGGACATGGCATCGGC
1 TAAGACCATGTCTGGGACATGGCATCGGC
55775286 ATAGATATGT
Statistics
Matches: 103, Mismatches: 12, Indels: 11
0.82 0.10 0.09
Matches are distributed among these distances:
44 2 0.02
45 29 0.28
46 13 0.13
47 24 0.23
48 35 0.34
ACGTcount: A:0.26, C:0.20, G:0.31, T:0.24
Consensus pattern (48 bp):
TAAGACCATGTCTGGGACATGGCATCGGCCACGTATGAGGTGACAGTG
Found at i:55775319 original size:50 final size:48
Alignment explanation
Indices: 55775160--55775328 Score: 165
Period size: 48 Copynumber: 3.5 Consensus size: 48
55775150 TATGAGAGCC
* * *
55775160 AGTGTAAGACCATGTCTGGGACAT-GCATCGGC-TACGAGATGT-GTC-
1 AGTGTAAGACCATGTTTGGGACATGGCATCGGCATA-GATATGTAGACT
*
55775205 AGTGTAAGACCATGTCTT-GGACATGGCATCGGCAT-GTATAGAGGT-GA-T
1 AGTGTAAGACCATGT-TTGGGACATGGCATCGGCATAG-AT--ATGTAGACT
55775253 AGTGTAAGACCATGTTTGGGACATGGCATCGGCATAGATATGTAAGAACT
1 AGTGTAAGACCATGTTTGGGACATGGCATCGGCATAGATATGT-AG-ACT
* *
55775303 AGTGTAAAACCATGTTTGGTACATGG
1 AGTGTAAGACCATGTTTGGGACATGG
55775329 TGTCAGCCTC
Statistics
Matches: 104, Mismatches: 7, Indels: 21
0.79 0.05 0.16
Matches are distributed among these distances:
45 22 0.21
46 13 0.12
47 3 0.03
48 39 0.38
49 2 0.02
50 25 0.24
ACGTcount: A:0.28, C:0.15, G:0.30, T:0.27
Consensus pattern (48 bp):
AGTGTAAGACCATGTTTGGGACATGGCATCGGCATAGATATGTAGACT
Found at i:55781572 original size:15 final size:15
Alignment explanation
Indices: 55781554--55781587 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
55781544 TTATATGCTA
55781554 AATTCAGTAAGAGTG
1 AATTCAGTAAGAGTG
55781569 AATTCAGTAAGAGTG
1 AATTCAGTAAGAGTG
55781584 AATT
1 AATT
55781588 TTGGTTAAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.41, C:0.06, G:0.24, T:0.29
Consensus pattern (15 bp):
AATTCAGTAAGAGTG
Found at i:55785108 original size:48 final size:47
Alignment explanation
Indices: 55785049--55785470 Score: 170
Period size: 48 Copynumber: 8.9 Consensus size: 47
55785039 ACCACGTTAT
*
55785049 GAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGAGA
1 GAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGAGA
* ** * * *
55785096 CGAGAGCTAGTGTAAGA-CATGTTTAAGACAT-GCATCAGCCTCGAGA
1 -GAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGAGA
* * * *
55785142 TATAAACCAGTGTAAGA-CATGTCTGGGACAT-GCATCGG--TT-ACGA
1 GA-GAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGA-GA
* * * * *
55785186 GACGTGTTAGTGTAAGACCATGCCTTGGACAAGGCATCGGCACGTAT-AGA
1 GA-GAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCA--T-TGAGA
* * ** *
55785236 G-GTG-TCAGTGTAAGACCATGTTTGGGACATGGCATCGGCACGGATA
1 GAGAGCT-AGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGAGA
* * * * * ** *
55785282 GAG-GTGTCAGTGTAAGACCATGTTTGGGACATTGTATCTGCACGGATA
1 GAGAG-CT-AGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGAGA
* * * * * ****
55785330 TGTAAGACCTAGTGTAACACCATGTCTGGGACATGGCGTCAGCCTCGTTTTT
1 -G--AGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCAT--TGAGA
* * * * *
55785382 GATAG-TAAGTTTAAGACCATGTATGGGACATGGTATCGAC-TTGATG-
1 GAGAGCT-AGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGA-GA
* * *
55785428 GATGAGCCACTGTAAGACCATGTCTGGGACATGGCATCAGCAT
1 GA-GAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCAT
55785471 CAAATCCTAT
Statistics
Matches: 279, Mismatches: 70, Indels: 50
0.70 0.18 0.13
Matches are distributed among these distances:
43 1 0.00
44 13 0.05
45 12 0.04
46 54 0.19
47 42 0.15
48 90 0.32
49 29 0.10
50 31 0.11
51 6 0.02
52 1 0.00
ACGTcount: A:0.27, C:0.18, G:0.29, T:0.25
Consensus pattern (47 bp):
GAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGAGA
Found at i:55785187 original size:46 final size:45
Alignment explanation
Indices: 55785011--55785187 Score: 119
Period size: 46 Copynumber: 3.8 Consensus size: 45
55785001 TTGTGTGCTT
* * *
55785011 GTGTAAGACATGTCTGAGACATGCATC-G-ACCACGTTATGAGAGCCA
1 GTGTAAGACATGTCTGAGACATGCATCGGTTCGA-GATAT-A-AGCCA
* * * *
55785057 GTGTAAGACCATGTCTGGGACATGGCATCGGCATT-GAGACGA-GAGCTA
1 GTGTAAGA-CATGTCTGAGACAT-GCATCGG--TTCGAGA-TATAAGCCA
* * ** *
55785105 GTGTAAGACATGTTTAAGACATGCATCAGCCTCGAGATATAAACCA
1 GTGTAAGACATGTCTGAGACATGCATC-GGTTCGAGATATAAGCCA
*
55785151 GTGTAAGACATGTCTGGGACATGCATCGGTTACGAGA
1 GTGTAAGACATGTCTGAGACATGCATCGGTT-CGAGA
55785188 CGTGTTAGTG
Statistics
Matches: 99, Mismatches: 21, Indels: 22
0.70 0.15 0.15
Matches are distributed among these distances:
45 4 0.04
46 49 0.49
47 25 0.25
48 17 0.17
49 1 0.01
50 1 0.01
51 2 0.02
ACGTcount: A:0.31, C:0.19, G:0.28, T:0.23
Consensus pattern (45 bp):
GTGTAAGACATGTCTGAGACATGCATCGGTTCGAGATATAAGCCA
Found at i:55791198 original size:15 final size:15
Alignment explanation
Indices: 55791178--55791222 Score: 72
Period size: 15 Copynumber: 3.0 Consensus size: 15
55791168 TATGATATTG
55791178 TATCTTGGATTTCTT
1 TATCTTGGATTTCTT
*
55791193 TATCTTGGATTTCTC
1 TATCTTGGATTTCTT
*
55791208 TATCTTGGACTTCTT
1 TATCTTGGATTTCTT
55791223 AATCCTAATT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.13, C:0.18, G:0.13, T:0.56
Consensus pattern (15 bp):
TATCTTGGATTTCTT
Found at i:55794311 original size:43 final size:43
Alignment explanation
Indices: 55794246--55794329 Score: 105
Period size: 43 Copynumber: 2.0 Consensus size: 43
55794236 GGAATTAAGA
* * * *
55794246 AATCTGAGCTCGTTGAGCGGTCCGAGTTTGTGATATATGTGAG
1 AATCTGAACTCGTCGAGCGGTCCAAGTTCGTGATATATGTGAG
* * *
55794289 AATCTGAACTTGTCGAGTGGTCCAAGTTCGTGATCTATGTG
1 AATCTGAACTCGTCGAGCGGTCCAAGTTCGTGATATATGTG
55794330 GCATCCGAGC
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
43 34 1.00
ACGTcount: A:0.21, C:0.15, G:0.30, T:0.33
Consensus pattern (43 bp):
AATCTGAACTCGTCGAGCGGTCCAAGTTCGTGATATATGTGAG
Found at i:55798080 original size:58 final size:63
Alignment explanation
Indices: 55797972--55798088 Score: 165
Period size: 58 Copynumber: 1.9 Consensus size: 63
55797962 GGAAAGGCGT
* *
55797972 CAAGTAAGGATAAGTAGATACATTGATCAAAAAGTACAATTACTCGAAAAGTAATAATAAGTA
1 CAAGTAAGGATAAGTAGATACATTGATCAAAAAGTACAAGTACTCGAAAAGTAAGAATAAGTA
55798035 CAAGTAAGGATAAG-A-A-A-A-TGATCAAAAAGTACAAGTACT-GCAAAAGTAAGAATA
1 CAAGTAAGGATAAGTAGATACATTGATCAAAAAGTACAAGTACTCG-AAAAGTAAGAATA
55798089 TTATTAAGGA
Statistics
Matches: 51, Mismatches: 2, Indels: 7
0.85 0.03 0.12
Matches are distributed among these distances:
57 1 0.02
58 32 0.63
59 1 0.02
60 1 0.02
61 1 0.02
62 1 0.02
63 14 0.27
ACGTcount: A:0.53, C:0.09, G:0.17, T:0.21
Consensus pattern (63 bp):
CAAGTAAGGATAAGTAGATACATTGATCAAAAAGTACAAGTACTCGAAAAGTAAGAATAAGTA
Found at i:55806354 original size:26 final size:26
Alignment explanation
Indices: 55806324--55806380 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 26
55806314 ACATTCTCTC
*
55806324 AAGCCATATAA-CAGGAAGTTCACAAA
1 AAGCCAT-TAATCAGGAAGCTCACAAA
* *
55806350 GAGCCATTAATCGGGAAGCTCACAAA
1 AAGCCATTAATCAGGAAGCTCACAAA
55806376 AAGCC
1 AAGCC
55806381 TATCAAGAAG
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
25 3 0.12
26 23 0.88
ACGTcount: A:0.44, C:0.23, G:0.19, T:0.14
Consensus pattern (26 bp):
AAGCCATTAATCAGGAAGCTCACAAA
Found at i:55806475 original size:26 final size:26
Alignment explanation
Indices: 55806429--55806493 Score: 71
Period size: 26 Copynumber: 2.5 Consensus size: 26
55806419 ATAAGAGTCA
* *
55806429 TAATCAGGAAGTTCACAAAGAACTTT
1 TAATCAGGAAGCTCACAAAGAACCTT
* *
55806455 TAATTAGGAAGCTCA-AGAAGAGCCTT
1 TAATCAGGAAGCTCACA-AAGAACCTT
55806481 TAATCAGG-AGCTC
1 TAATCAGGAAGCTC
55806494 TGGATAGCCA
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
25 6 0.18
26 27 0.82
ACGTcount: A:0.38, C:0.17, G:0.20, T:0.25
Consensus pattern (26 bp):
TAATCAGGAAGCTCACAAAGAACCTT
Found at i:55807549 original size:28 final size:28
Alignment explanation
Indices: 55807518--55807573 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
55807508 TAACTAGGGT
55807518 TTCCATGTCTTTTTAATTGGGAAAGATG
1 TTCCATGTCTTTTTAATTGGGAAAGATG
55807546 TTCCATGTCTTTTTAATTGGGAAAGATG
1 TTCCATGTCTTTTTAATTGGGAAAGATG
55807574 AACATAAATG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.25, C:0.11, G:0.21, T:0.43
Consensus pattern (28 bp):
TTCCATGTCTTTTTAATTGGGAAAGATG
Found at i:55811584 original size:15 final size:16
Alignment explanation
Indices: 55811564--55811593 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
55811554 ATTTAGTTGA
55811564 GAAAATT-ATTTAATT
1 GAAAATTAATTTAATT
55811579 GAAAATTAATTTAAT
1 GAAAATTAATTTAAT
55811594 AAAATAATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.50, C:0.00, G:0.07, T:0.43
Consensus pattern (16 bp):
GAAAATTAATTTAATT
Found at i:55827621 original size:22 final size:22
Alignment explanation
Indices: 55827572--55827615 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
55827562 TGACTGGCCA
55827572 TGGCATTTATATATATATATAT
1 TGGCATTTATATATATATATAT
55827594 TGGCATTTATATATATATATAT
1 TGGCATTTATATATATATATAT
55827616 ATGCATGCAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.36, C:0.05, G:0.09, T:0.50
Consensus pattern (22 bp):
TGGCATTTATATATATATATAT
Found at i:55834168 original size:11 final size:11
Alignment explanation
Indices: 55834152--55834182 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
55834142 AAGTATGGGT
55834152 AGGTATGGGAA
1 AGGTATGGGAA
*
55834163 AGGTATGGGCA
1 AGGTATGGGAA
55834174 AGGTATGGG
1 AGGTATGGG
55834183 GTATGGGTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.29, C:0.03, G:0.48, T:0.19
Consensus pattern (11 bp):
AGGTATGGGAA
Found at i:55838259 original size:18 final size:18
Alignment explanation
Indices: 55838236--55838328 Score: 150
Period size: 18 Copynumber: 5.2 Consensus size: 18
55838226 CCCAACTACT
*
55838236 GTATACGTGAACAGTACC
1 GTATACGTGAATAGTACC
*
55838254 GTATACGTGAATAGTGCC
1 GTATACGTGAATAGTACC
*
55838272 GTATACGTGAATAGTACT
1 GTATACGTGAATAGTACC
*
55838290 GTATACGTGAATAGTGCC
1 GTATACGTGAATAGTACC
55838308 GTATACGTGAATAGTACC
1 GTATACGTGAATAGTACC
55838326 GTA
1 GTA
55838329 AACGGTCGTA
Statistics
Matches: 68, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 68 1.00
ACGTcount: A:0.31, C:0.16, G:0.25, T:0.28
Consensus pattern (18 bp):
GTATACGTGAATAGTACC
Found at i:55838288 original size:36 final size:36
Alignment explanation
Indices: 55838236--55838328 Score: 168
Period size: 36 Copynumber: 2.6 Consensus size: 36
55838226 CCCAACTACT
*
55838236 GTATACGTGAACAGTACCGTATACGTGAATAGTGCC
1 GTATACGTGAATAGTACCGTATACGTGAATAGTGCC
*
55838272 GTATACGTGAATAGTACTGTATACGTGAATAGTGCC
1 GTATACGTGAATAGTACCGTATACGTGAATAGTGCC
55838308 GTATACGTGAATAGTACCGTA
1 GTATACGTGAATAGTACCGTA
55838329 AACGGTCGTA
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 54 1.00
ACGTcount: A:0.31, C:0.16, G:0.25, T:0.28
Consensus pattern (36 bp):
GTATACGTGAATAGTACCGTATACGTGAATAGTGCC
Found at i:55838888 original size:11 final size:11
Alignment explanation
Indices: 55838872--55838902 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
55838862 AAGTATGGGT
55838872 AGGTATGGGAA
1 AGGTATGGGAA
*
55838883 AGGTATGGGCA
1 AGGTATGGGAA
55838894 AGGTATGGG
1 AGGTATGGG
55838903 GTATGGGTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.29, C:0.03, G:0.48, T:0.19
Consensus pattern (11 bp):
AGGTATGGGAA
Found at i:55843197 original size:16 final size:17
Alignment explanation
Indices: 55843149--55843211 Score: 65
Period size: 17 Copynumber: 3.6 Consensus size: 17
55843139 TCAATGAAAA
*
55843149 ATTAAAATTAAAAAA-T
1 ATTAAAAATAAAAAATT
*
55843165 ATATATAAATGAAAAAAATT
1 AT-TAAAAAT--AAAAAATT
*
55843185 ATTTAAAATAAAAAATT
1 ATTAAAAATAAAAAATT
55843202 ATTAAAAATA
1 ATTAAAAATA
55843212 TATAAAAATA
Statistics
Matches: 38, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
16 2 0.05
17 22 0.58
19 11 0.29
20 3 0.08
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.32
Consensus pattern (17 bp):
ATTAAAAATAAAAAATT
Found at i:55843218 original size:19 final size:19
Alignment explanation
Indices: 55843179--55843237 Score: 68
Period size: 19 Copynumber: 3.2 Consensus size: 19
55843169 ATAAATGAAA
*
55843179 AAAATTATTTAAAATA-A-
1 AAAATTATTAAAAATATAT
55843196 AAAATTATTAAAAATATAT
1 AAAATTATTAAAAATATAT
* * *
55843215 AAAAATATTCAAAATTTAT
1 AAAATTATTAAAAATATAT
55843234 AAAA
1 AAAA
55843238 ACATATAGAA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
17 15 0.42
18 1 0.03
19 20 0.56
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (19 bp):
AAAATTATTAAAAATATAT
Found at i:55843238 original size:10 final size:10
Alignment explanation
Indices: 55843192--55843271 Score: 54
Period size: 10 Copynumber: 7.9 Consensus size: 10
55843182 ATTATTTAAA
*
55843192 ATAAAAAATT
1 ATAAAAATTT
*
55843202 ATTAAAAATAT
1 A-TAAAAATTT
*
55843213 ATAAAAATAT
1 ATAAAAATTT
*
55843223 -TCAAAATTT
1 ATAAAAATTT
**
55843232 ATAAAAACAT
1 ATAAAAATTT
*
55843242 ATAGAAAACTT
1 ATA-AAAATTT
*
55843253 CTAAAAATTT
1 ATAAAAATTT
*
55843263 AAAAAAATT
1 ATAAAAATT
55843272 CTTAAAAACA
Statistics
Matches: 55, Mismatches: 12, Indels: 6
0.75 0.16 0.08
Matches are distributed among these distances:
9 7 0.13
10 32 0.58
11 16 0.29
ACGTcount: A:0.62, C:0.05, G:0.01, T:0.31
Consensus pattern (10 bp):
ATAAAAATTT
Found at i:55843243 original size:21 final size:20
Alignment explanation
Indices: 55843192--55843243 Score: 61
Period size: 19 Copynumber: 2.5 Consensus size: 20
55843182 ATTATTTAAA
55843192 ATAAAAAATTATTAAAAATAT
1 ATAAAAAA-TATTAAAAATAT
* *
55843213 AT-AAAAATATTCAAAATTT
1 ATAAAAAATATTAAAAATAT
55843232 ATAAAAACATAT
1 ATAAAAA-ATAT
55843244 AGAAAACTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
19 12 0.44
20 9 0.33
21 6 0.22
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (20 bp):
ATAAAAAATATTAAAAATAT
Found at i:55843265 original size:29 final size:28
Alignment explanation
Indices: 55843203--55843267 Score: 69
Period size: 29 Copynumber: 2.2 Consensus size: 28
55843193 TAAAAAATTA
* *
55843203 TTAAAAATATATAAAAATATTCAAAATT
1 TTAAAAACATATAAAAATATTCAAAAAT
*
55843231 TATAAAAACATATAGAAAA-CTTCTAAAAAT
1 T-TAAAAACATATA-AAAATATTC-AAAAAT
55843261 TTAAAAA
1 TTAAAAA
55843268 AATTCTTAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
28 1 0.03
29 20 0.65
30 10 0.32
ACGTcount: A:0.62, C:0.06, G:0.02, T:0.31
Consensus pattern (28 bp):
TTAAAAACATATAAAAATATTCAAAAAT
Found at i:55843286 original size:19 final size:19
Alignment explanation
Indices: 55843233--55843287 Score: 56
Period size: 20 Copynumber: 2.7 Consensus size: 19
55843223 TCAAAATTTA
55843233 TAAAAACATATAGAAAACTTC
1 TAAAAACATA-A-AAAACTTC
** *
55843254 TAAAAATTTAAAAAAATTC
1 TAAAAACATAAAAAACTTC
55843273 TTAAAAACATAAAAA
1 -TAAAAACATAAAAA
55843288 TTAAAATTTA
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
19 7 0.25
20 13 0.46
21 8 0.29
ACGTcount: A:0.64, C:0.09, G:0.02, T:0.25
Consensus pattern (19 bp):
TAAAAACATAAAAAACTTC
Found at i:55843778 original size:19 final size:18
Alignment explanation
Indices: 55843739--55843779 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
55843729 GAAATGAAGG
*
55843739 AATATATTTAGATATGCA
1 AATATATTTAAATATGCA
*
55843757 AATATATGTTAAATATGTA
1 AATATAT-TTAAATATGCA
55843776 AATA
1 AATA
55843780 ATATATTTAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 7 0.35
19 13 0.65
ACGTcount: A:0.49, C:0.02, G:0.10, T:0.39
Consensus pattern (18 bp):
AATATATTTAAATATGCA
Found at i:55847687 original size:20 final size:20
Alignment explanation
Indices: 55847662--55847727 Score: 66
Period size: 20 Copynumber: 3.4 Consensus size: 20
55847652 CAAGGTTTAC
55847662 CAAACTAATTGGCATTATTT
1 CAAACTAATTGGCATTATTT
* ***
55847682 CAAACTAA--GTCACTT-GCC
1 CAAACTAATTGGCA-TTATTT
55847700 CAAACTAATTGGCATTATTT
1 CAAACTAATTGGCATTATTT
55847720 CAAACTAA
1 CAAACTAA
55847728 GTCACTTGCC
Statistics
Matches: 34, Mismatches: 8, Indels: 8
0.68 0.16 0.16
Matches are distributed among these distances:
18 11 0.32
19 4 0.12
20 19 0.56
ACGTcount: A:0.38, C:0.21, G:0.09, T:0.32
Consensus pattern (20 bp):
CAAACTAATTGGCATTATTT
Found at i:55847703 original size:38 final size:38
Alignment explanation
Indices: 55847661--55847737 Score: 154
Period size: 38 Copynumber: 2.0 Consensus size: 38
55847651 CCAAGGTTTA
55847661 CCAAACTAATTGGCATTATTTCAAACTAAGTCACTTGC
1 CCAAACTAATTGGCATTATTTCAAACTAAGTCACTTGC
55847699 CCAAACTAATTGGCATTATTTCAAACTAAGTCACTTGC
1 CCAAACTAATTGGCATTATTTCAAACTAAGTCACTTGC
55847737 C
1 C
55847738 TACCAAAACA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.34, C:0.25, G:0.10, T:0.31
Consensus pattern (38 bp):
CCAAACTAATTGGCATTATTTCAAACTAAGTCACTTGC
Found at i:55849068 original size:42 final size:42
Alignment explanation
Indices: 55848990--55849165 Score: 167
Period size: 42 Copynumber: 4.2 Consensus size: 42
55848980 ATAAAAGTTG
* *
55848990 AACAGAAACTCATAAGAGTTGAACAGAATCTCGTAAGAGCTA
1 AACAGAAACTCATAAGAGTTTAACAGAAGCTCGTAAGAGCTA
* * * *
55849032 AACAAAAACTCATAAGAGTTTAATAGAAGCTTGTAAGAGCTG
1 AACAGAAACTCATAAGAGTTTAACAGAAGCTCGTAAGAGCTA
* * * *
55849074 AACAGAAACTTATAAGA-TTTGAACAGAAGCTCGCAAGAACTG
1 AACAGAAACTCATAAGAGTTT-AACAGAAGCTCGTAAGAGCTA
* * * * * *
55849116 AACAGAAGCTCGA-AAGAGCTAAATAGAACCTCGAAAGAGCTA
1 AACAGAAACTC-ATAAGAGTTTAACAGAAGCTCGTAAGAGCTA
*
55849158 AAAAGAAA
1 AACAGAAA
55849166 GTAAAACACT
Statistics
Matches: 108, Mismatches: 23, Indels: 6
0.79 0.17 0.04
Matches are distributed among these distances:
41 3 0.03
42 103 0.95
43 2 0.02
ACGTcount: A:0.48, C:0.15, G:0.19, T:0.18
Consensus pattern (42 bp):
AACAGAAACTCATAAGAGTTTAACAGAAGCTCGTAAGAGCTA
Found at i:55849069 original size:63 final size:61
Alignment explanation
Indices: 55848950--55849080 Score: 163
Period size: 63 Copynumber: 2.1 Consensus size: 61
55848940 TAGATATACC
* *
55848950 AACAGAAGCTCGAAAGCTAAACAAAAGCTCATAAAAGTTGAACAGAAACTCATAAGAGTTG
1 AACAGAAGCTCGAAAGCTAAACAAAAACTCATAAAAGTTGAACAGAAACTCATAAGAGCTG
* * * * * **
55849011 AACAGAATCTCGTAAGAGCTAAACAAAAACTCATAAGAGTTTAATAGAAGCTTGTAAGAGCTG
1 AACAGAAGCTCG-AA-AGCTAAACAAAAACTCATAAAAGTTGAACAGAAACTCATAAGAGCTG
55849074 AACAGAA
1 AACAGAA
55849081 ACTTATAAGA
Statistics
Matches: 59, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
61 11 0.19
62 2 0.03
63 46 0.78
ACGTcount: A:0.48, C:0.15, G:0.18, T:0.18
Consensus pattern (61 bp):
AACAGAAGCTCGAAAGCTAAACAAAAACTCATAAAAGTTGAACAGAAACTCATAAGAGCTG
Found at i:55849099 original size:21 final size:21
Alignment explanation
Indices: 55848969--55849101 Score: 124
Period size: 21 Copynumber: 6.3 Consensus size: 21
55848959 TCGAAAGCTA
*
55848969 AACA-AAAGCTCATAAAAGTTG
1 AACAGAAA-CTCATAAGAGTTG
55848990 AACAGAAACTCATAAGAGTTG
1 AACAGAAACTCATAAGAGTTG
* * * *
55849011 AACAGAATCTCGTAAGAGCTA
1 AACAGAAACTCATAAGAGTTG
* *
55849032 AACAAAAACTCATAAGAGTTT
1 AACAGAAACTCATAAGAGTTG
* * ** *
55849053 AATAGAAGCTTGTAAGAGCTG
1 AACAGAAACTCATAAGAGTTG
* *
55849074 AACAGAAACTTATAAGATTTG
1 AACAGAAACTCATAAGAGTTG
55849095 AACAGAA
1 AACAGAA
55849102 GCTCGCAAGA
Statistics
Matches: 89, Mismatches: 22, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
21 86 0.97
22 3 0.03
ACGTcount: A:0.48, C:0.14, G:0.17, T:0.21
Consensus pattern (21 bp):
AACAGAAACTCATAAGAGTTG
Found at i:55849111 original size:21 final size:21
Alignment explanation
Indices: 55849093--55849153 Score: 77
Period size: 21 Copynumber: 2.9 Consensus size: 21
55849083 TTATAAGATT
*
55849093 TGAACAGAAGCTCGCAAGAAC
1 TGAACAGAAGCTCGAAAGAAC
*
55849114 TGAACAGAAGCTCGAAAGAGC
1 TGAACAGAAGCTCGAAAGAAC
* * *
55849135 TAAATAGAACCTCGAAAGA
1 TGAACAGAAGCTCGAAAGA
55849154 GCTAAAAAGA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.46, C:0.20, G:0.23, T:0.11
Consensus pattern (21 bp):
TGAACAGAAGCTCGAAAGAAC
Found at i:55849133 original size:84 final size:84
Alignment explanation
Indices: 55848988--55849143 Score: 206
Period size: 84 Copynumber: 1.9 Consensus size: 84
55848978 TCATAAAAGT
* * * * *
55848988 TGAACAGAAACTCATAAGAGTTGAACAGAATCTCGTAAGAGCTAAACAAAAACTCATAAGAGTTT
1 TGAACAGAAACTCATAAGAGTTGAACAGAAGCTCGCAAGAACTAAACAAAAACTCATAAGAGCTA
55849053 AATAGAAGCTTGTAAGAGC
66 AATAGAAGCTTGTAAGAGC
* * * * *
55849072 TGAACAGAAACTTATAAGATTTGAACAGAAGCTCGCAAGAACTGAACAGAAGCTCGA-AAGAGCT
1 TGAACAGAAACTCATAAGAGTTGAACAGAAGCTCGCAAGAACTAAACAAAAACTC-ATAAGAGCT
55849136 AAATAGAA
65 AAATAGAA
55849144 CCTCGAAAGA
Statistics
Matches: 61, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
84 60 0.98
85 1 0.02
ACGTcount: A:0.46, C:0.15, G:0.20, T:0.19
Consensus pattern (84 bp):
TGAACAGAAACTCATAAGAGTTGAACAGAAGCTCGCAAGAACTAAACAAAAACTCATAAGAGCTA
AATAGAAGCTTGTAAGAGC
Found at i:55849154 original size:21 final size:21
Alignment explanation
Indices: 55849119--55849164 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
55849109 AGAACTGAAC
* *
55849119 AGAAGCTCGAAAGAGCTAAAT
1 AGAACCTCGAAAGAGCTAAAA
55849140 AGAACCTCGAAAGAGCTAAAA
1 AGAACCTCGAAAGAGCTAAAA
55849161 AGAA
1 AGAA
55849165 AGTAAAACAC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.52, C:0.15, G:0.22, T:0.11
Consensus pattern (21 bp):
AGAACCTCGAAAGAGCTAAAA
Found at i:55850082 original size:5 final size:5
Alignment explanation
Indices: 55850072--55850097 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
55850062 TTCTTATGTT
55850072 TTTAA TTTAA TTTAA TTTAA TTTAA T
1 TTTAA TTTAA TTTAA TTTAA TTTAA T
55850098 CCATCAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (5 bp):
TTTAA
Found at i:55851305 original size:28 final size:28
Alignment explanation
Indices: 55851274--55851369 Score: 72
Period size: 29 Copynumber: 3.3 Consensus size: 28
55851264 AGAAATTTAA
55851274 TAATTTTATGTATTTTTATATTTTATAT
1 TAATTTTATGTATTTTTATATTTTATAT
* * *
55851302 TAATTTTTTATAATTTTTAAATGTTTAT-T
1 TAATTTTATGT-ATTTTTATAT-TTTATAT
* *
55851331 ATATTTTTATG-ATTTTTTATAAATTTT-TAA
1 -TAATTTTATGTA-TTTTTAT--ATTTTATAT
55851361 TAATTTTAT
1 TAATTTTAT
55851370 ATTTTATAAT
Statistics
Matches: 52, Mismatches: 9, Indels: 13
0.70 0.12 0.18
Matches are distributed among these distances:
28 10 0.19
29 25 0.48
30 15 0.29
31 2 0.04
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (28 bp):
TAATTTTATGTATTTTTATATTTTATAT
Found at i:55851311 original size:20 final size:18
Alignment explanation
Indices: 55851286--55851478 Score: 89
Period size: 19 Copynumber: 10.2 Consensus size: 18
55851276 ATTTTATGTA
55851286 TTTTTATATTTTATATTAAT
1 TTTTTATATTTT-TA-TAAT
55851306 TTTTTATAATTTTTA-AAT
1 TTTTTAT-ATTTTTATAAT
*
55851324 GTTTATTATATTTTTATGAT
1 -TTT-TTATATTTTTATAAT
55851344 TTTTTATAAATTTTTAATAA-
1 TTTTTAT--ATTTTT-ATAAT
55851364 -TTTTATA-TTTTATAAT
1 TTTTTATATTTTTATAAT
**
55851380 AAAATTTACT-TTTTTATATAT
1 --TTTTTA-TATTTTTATA-AT
*
55851401 TTTTAATAGTTTTGTATAAAT
1 TTTTTATA-TTTT-TAT-AAT
*
55851422 TTTTTA-AATTTT-TAAT
1 TTTTTATATTTTTATAAT
* *
55851438 TTTTAATAAATTTT-TAAT
1 TTTTTAT-ATTTTTATAAT
*
55851456 ATTTTAATATTATTTAT-AT
1 -TTTTTATATT-TTTATAAT
55851475 TTTT
1 TTTT
55851479 AAAATAATTT
Statistics
Matches: 140, Mismatches: 10, Indels: 48
0.71 0.05 0.24
Matches are distributed among these distances:
15 4 0.03
16 12 0.09
17 2 0.01
18 25 0.18
19 41 0.29
20 35 0.25
21 20 0.14
22 1 0.01
ACGTcount: A:0.33, C:0.01, G:0.02, T:0.64
Consensus pattern (18 bp):
TTTTTATATTTTTATAAT
Found at i:55851367 original size:19 final size:19
Alignment explanation
Indices: 55851345--55851461 Score: 63
Period size: 18 Copynumber: 6.3 Consensus size: 19
55851335 TTTTATGATT
55851345 TTTTATAAATTTTTAATAA
1 TTTTATAAATTTTTAATAA
55851364 TTTTAT--ATTTTATAATAA
1 TTTTATAAATTTT-TAATAA
** * *
55851382 AATT-T-ACTTTTTTATATA
1 TTTTATAAATTTTTAATA-A
55851400 TTTT-TAATAGTTTTGT-ATAAA
1 TTTTATAA-A-TTTT-TAAT-AA
*
55851421 TTTTTTAAATTTTTAAT--
1 TTTTATAAATTTTTAATAA
55851438 TTTTAATAAATTTTTAAT-A
1 TTTT-ATAAATTTTTAATAA
55851457 TTTTA
1 TTTTA
55851462 ATATTATTTA
Statistics
Matches: 78, Mismatches: 8, Indels: 25
0.70 0.07 0.23
Matches are distributed among these distances:
17 14 0.18
18 29 0.37
19 12 0.15
20 6 0.08
21 12 0.15
22 5 0.06
ACGTcount: A:0.36, C:0.01, G:0.02, T:0.62
Consensus pattern (19 bp):
TTTTATAAATTTTTAATAA
Found at i:55851368 original size:48 final size:45
Alignment explanation
Indices: 55851275--55851480 Score: 159
Period size: 48 Copynumber: 4.4 Consensus size: 45
55851265 GAAATTTAAT
* * * *
55851275 AATTTTA-TGTATTTTTATATTTTATATTAATTTTTTATAATTTTTA
1 AATTTTATTATATTTTTA-ATTTTTTATAAATTTTTAATAA-TTTTA
55851321 AATGTTTATTATATTTTTATGATTTTTTATAAATTTTTAATAATTTTA
1 AAT-TTTATTATATTTTTA--ATTTTTTATAAATTTTTAATAATTTTA
* * ** * * *
55851369 TATTTTATAATAAAATTTACTTTTTTATATATTTTTAATAGTTTTGTATA
1 AATTTTATTAT-ATTTTTAATTTTTTATAAATTTTTAATA--ATT-T-TA
* *
55851419 AATTTT-TTAAATTTTTAATTTTTAATAAATTTTTAAT-ATTTT-
1 AATTTTATTATATTTTTAATTTTTTATAAATTTTTAATAATTTTA
*
55851461 AATATTATTTATATTTTTAA
1 AATTTTA-TTATATTTTTAA
55851481 AATAATTTTC
Statistics
Matches: 127, Mismatches: 23, Indels: 22
0.74 0.13 0.13
Matches are distributed among these distances:
42 5 0.04
43 1 0.01
44 12 0.09
45 2 0.02
46 22 0.17
47 11 0.09
48 45 0.35
49 22 0.17
50 7 0.06
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.63
Consensus pattern (45 bp):
AATTTTATTATATTTTTAATTTTTTATAAATTTTTAATAATTTTA
Found at i:55851374 original size:28 final size:30
Alignment explanation
Indices: 55851271--55851371 Score: 95
Period size: 30 Copynumber: 3.5 Consensus size: 30
55851261 AATAGAAATT
*
55851271 TAATAATTTTATGTATTTTTAT--ATTTTA
1 TAATAATTTTATATATTTTTATAAATTTTA
* * *
55851299 TATTAATTTTTTATAATTTT-TAAATGTTTA
1 TAATAATTTTATATATTTTTATAAAT-TTTA
* *
55851329 TTATATTTTTATGAT-TTTTTATAAATTTT-
1 TAATAATTTTAT-ATATTTTTATAAATTTTA
55851358 TAATAATTTTATAT
1 TAATAATTTTATAT
55851372 TTTATAATAA
Statistics
Matches: 57, Mismatches: 11, Indels: 10
0.73 0.14 0.13
Matches are distributed among these distances:
27 1 0.02
28 18 0.32
29 12 0.21
30 19 0.33
31 7 0.12
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (30 bp):
TAATAATTTTATATATTTTTATAAATTTTA
Found at i:55851400 original size:66 final size:64
Alignment explanation
Indices: 55851301--55851478 Score: 177
Period size: 66 Copynumber: 2.7 Consensus size: 64
55851291 ATATTTTATA
* *
55851301 TTAATTTTTTAT-AATTTTTAA-ATGTTTATTATATTTTTATGATTTTTTATAAATTTTTAATAA
1 TTAATTTTTAATAAATATTTAATAT-TTTA-TATATTTTTAT-ATTTTTTATAAATTTTTAA-AA
55851364 -TT
62 TTT
* * * *
55851366 TTATATTTTATAATAAA-ATTTACTTTTTTATATATTTTTAATAGTTTTGTATAAATTTTTTAAA
1 TTA-ATTTT-TAATAAATATTTAATATTTTATATATTTTT-ATA-TTTTTTATAAATTTTTAAAA
55851430 TTT
62 TTT
*
55851433 TTAATTTTTAATAAATTTTTAATATTTTA-ATATTATTTATATTTTT
1 TTAATTTTTAATAAATATTTAATATTTTATATATT-TTTATATTTTT
55851479 AAAATAATTT
Statistics
Matches: 94, Mismatches: 10, Indels: 19
0.76 0.08 0.15
Matches are distributed among these distances:
64 4 0.04
65 18 0.19
66 35 0.37
67 34 0.36
68 3 0.03
ACGTcount: A:0.34, C:0.01, G:0.02, T:0.63
Consensus pattern (64 bp):
TTAATTTTTAATAAATATTTAATATTTTATATATTTTTATATTTTTTATAAATTTTTAAAATTT
Found at i:55851462 original size:19 final size:18
Alignment explanation
Indices: 55851426--55851494 Score: 70
Period size: 18 Copynumber: 3.7 Consensus size: 18
55851416 ATAAATTTTT
55851426 TAAATTTTTAATTTTTAA
1 TAAATTTTTAATTTTTAA
55851444 TAAATTTTTAATATTTTAA
1 TAAATTTTTAAT-TTTTAA
55851463 T--ATTATTTATATTTTTAA
1 TAAATT-TTTA-ATTTTTAA
* *
55851481 AATAATTTTCAATT
1 TA-AATTTTTAATT
55851495 ATTTTTCGCA
Statistics
Matches: 43, Mismatches: 2, Indels: 11
0.77 0.04 0.20
Matches are distributed among these distances:
17 3 0.07
18 22 0.51
19 12 0.28
20 3 0.07
21 3 0.07
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.59
Consensus pattern (18 bp):
TAAATTTTTAATTTTTAA
Found at i:55860743 original size:24 final size:22
Alignment explanation
Indices: 55860710--55860753 Score: 61
Period size: 24 Copynumber: 1.9 Consensus size: 22
55860700 GATCCTTCTA
55860710 CCCTTAAAATATTTTCACTATTAT
1 CCCTTAAAAT-TTTTCA-TATTAT
*
55860734 CCCTTCAAATTTTTCATATT
1 CCCTTAAAATTTTTCATATT
55860754 TACACTTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 4 0.21
23 6 0.32
24 9 0.47
ACGTcount: A:0.30, C:0.23, G:0.00, T:0.48
Consensus pattern (22 bp):
CCCTTAAAATTTTTCATATTAT
Found at i:55860786 original size:30 final size:31
Alignment explanation
Indices: 55860718--55860776 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 31
55860708 TACCCTTAAA
*
55860718 ATATTTTCACTATTATCCCTTCAAATTTTTC
1 ATATTTACACTATTATCCCTTCAAATTTTTC
55860749 ATATTTACACT-TTAATCCC-TCAAATTTT
1 ATATTTACACTATT-ATCCCTTCAAATTTT
55860777 GAGTATTTAC
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 11 0.42
31 15 0.58
ACGTcount: A:0.29, C:0.22, G:0.00, T:0.49
Consensus pattern (31 bp):
ATATTTACACTATTATCCCTTCAAATTTTTC
Found at i:55862050 original size:17 final size:17
Alignment explanation
Indices: 55862015--55862053 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
55862005 TTAAGATAAG
*
55862015 TATTAAATTTAATTTAA
1 TATTAAATTTAATTAAA
55862032 TATTAAATTT-ATTAAAA
1 TATTAAATTTAATT-AAA
55862049 TATTA
1 TATTA
55862054 TTATATTTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 3 0.15
17 17 0.85
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
TATTAAATTTAATTAAA
Found at i:55870038 original size:93 final size:93
Alignment explanation
Indices: 55869925--55870096 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
55869915 CGCCCATAAG
* *
55869925 CGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
55869990 ACGAGTTCGGATGCCTAGTTACATCTCA
66 ACGAGTTCGGATGCCTAGTTACATCTCA
*
55870018 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
55870083 ACGAGTTCGGATGC
66 ACGAGTTCGGATGC
55870097 TCAACCATCC
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.28, C:0.30, G:0.22, T:0.21
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATCTCA
Found at i:55870093 original size:46 final size:46
Alignment explanation
Indices: 55869918--55870093 Score: 216
Period size: 46 Copynumber: 3.8 Consensus size: 46
55869908 TGTAACCCGC
* * *
55869918 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
* *
55869964 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
*
55870014 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
55870057 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA
55870094 TGCTCAACCA
Statistics
Matches: 111, Mismatches: 10, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 2 0.02
46 63 0.57
47 29 0.26
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.30, G:0.21, T:0.20
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:55886750 original size:6 final size:6
Alignment explanation
Indices: 55886733--55886775 Score: 50
Period size: 6 Copynumber: 7.0 Consensus size: 6
55886723 GCAAATGAAA
* * *
55886733 CATTTCT CATTTT CATTTT CATTTC CATTTC CATTTC CATTTT
1 CATTT-T CATTTT CATTTT CATTTT CATTTT CATTTT CATTTT
55886776 AAGAAAATTA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
6 29 0.85
7 5 0.15
ACGTcount: A:0.16, C:0.26, G:0.00, T:0.58
Consensus pattern (6 bp):
CATTTT
Found at i:55886756 original size:12 final size:12
Alignment explanation
Indices: 55886733--55886775 Score: 59
Period size: 12 Copynumber: 3.5 Consensus size: 12
55886723 GCAAATGAAA
*
55886733 CATTTCTCATTTT
1 CATTT-TCATTTC
55886746 CATTTTCATTTC
1 CATTTTCATTTC
*
55886758 CATTTCCATTTC
1 CATTTTCATTTC
55886770 CATTTT
1 CATTTT
55886776 AAGAAAATTA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
12 22 0.81
13 5 0.19
ACGTcount: A:0.16, C:0.26, G:0.00, T:0.58
Consensus pattern (12 bp):
CATTTTCATTTC
Done.