Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr02 ID=Chr02-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: 62769430
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1067035 characters in sequence are not A, C, G, or T
File 164 of 206
Found at i:49681345 original size:16 final size:16
Alignment explanation
Indices: 49681300--49681336 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
49681290 TTAATTTACT
*
49681300 ATTACACATCTATTTC
1 ATTACACCTCTATTTC
49681316 ATTACACCTCTATTTC
1 ATTACACCTCTATTTC
49681332 ATTAC
1 ATTAC
49681337 GCCTTTATTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.30, C:0.27, G:0.00, T:0.43
Consensus pattern (16 bp):
ATTACACCTCTATTTC
Found at i:49684734 original size:42 final size:42
Alignment explanation
Indices: 49684678--49684757 Score: 115
Period size: 42 Copynumber: 1.9 Consensus size: 42
49684668 AAATGTTATG
* * *
49684678 TTTATAGTGGCGTTTTTGCGAGAAGCGCCGCTAAAGGTTTGT
1 TTTATAGAGGCGTTTGTGCGAAAAGCGCCGCTAAAGGTTTGT
* *
49684720 TTTATAGAGGCGTTTGTGGGAAAAGCGTCGCTAAAGGT
1 TTTATAGAGGCGTTTGTGCGAAAAGCGCCGCTAAAGGT
49684758 CTTGAGCTAT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 33 1.00
ACGTcount: A:0.23, C:0.12, G:0.33, T:0.33
Consensus pattern (42 bp):
TTTATAGAGGCGTTTGTGCGAAAAGCGCCGCTAAAGGTTTGT
Found at i:49684794 original size:20 final size:22
Alignment explanation
Indices: 49684754--49684794 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
49684744 GCGTCGCTAA
49684754 AGGTCTTGAGCTATAATAGCGTC
1 AGGTCTTGAGC-ATAATAGCGTC
49684777 AGGTCTTGAG-AT-ATAGCG
1 AGGTCTTGAGCATAATAGCG
49684795 GCATTTGTGG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 6 0.33
21 2 0.11
23 10 0.56
ACGTcount: A:0.27, C:0.15, G:0.29, T:0.29
Consensus pattern (22 bp):
AGGTCTTGAGCATAATAGCGTC
Found at i:49687075 original size:22 final size:23
Alignment explanation
Indices: 49687038--49687084 Score: 69
Period size: 22 Copynumber: 2.0 Consensus size: 23
49687028 ATTTTTTTTG
*
49687038 TTAATTTGAAATTTTAAGTATTTA
1 TTAATTT-AAATTTTAAGAATTTA
49687062 TTAATTT-AATTTTAAGAATTTA
1 TTAATTTAAATTTTAAGAATTTA
49687084 T
1 T
49687085 CAAATAATGT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 15 0.68
24 7 0.32
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.55
Consensus pattern (23 bp):
TTAATTTAAATTTTAAGAATTTA
Found at i:49693447 original size:18 final size:18
Alignment explanation
Indices: 49693424--49693466 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
49693414 TGCCAGGTGC
*
49693424 GTATCCTAACCCTTATAT
1 GTATCCTAACCATTATAT
49693442 GTATCCTAACCATTATAT
1 GTATCCTAACCATTATAT
*
49693460 GTTTCCT
1 GTATCCT
49693467 TTATTCAGTC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.26, C:0.26, G:0.07, T:0.42
Consensus pattern (18 bp):
GTATCCTAACCATTATAT
Found at i:49697299 original size:125 final size:125
Alignment explanation
Indices: 49697004--49697527 Score: 737
Period size: 125 Copynumber: 4.2 Consensus size: 125
49696994 TAAGGCCAAG
* * * * * * * *
49697004 TAGGAACTATTATAGAAAAAGAGTGTCCATGTGGGAGCTTTTTTCAGTAATTTTGTTGATAATGC
1 TAGGAACTACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTCTTCAATAATTTTGCTGATAGTGC
** * * *
49697069 ATCCTGCTTGAAGTGTTTTTGACACTATTTTTTTCAAAATTTTCTTCTCAAAATTATTTTT
66 ATCCTGCTTGAAGCATTTTTGACACTA-TTTTTTCAGAACTGTCTTCTCAAAATTATTTTT
*
49697130 TCAGGAACTACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTCTTCAATAATTTTGCTGATATTG
1 T-AGGAACTACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTCTTCAATAATTTTGCTGATAGTG
49697195 CATCCTGCTTGAAGCATTTTTGACACTATTTTTTCAGAACTGTCTTCTCAAAATTATTTTT
65 CATCCTGCTTGAAGCATTTTTGACACTATTTTTTCAGAACTGTCTTCTCAAAATTATTTTT
* *
49697256 TAGGAACTACTGTAGAAAAAGAGTGTCCACGTGGGAGCTTTCTTCAGTAATTTTGCTGATAGTGC
1 TAGGAACTACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTCTTCAATAATTTTGCTGATAGTGC
* * * *
49697321 ATCTTGCTTGAAGCATTTTTTACACTACTTTTTCAGAACTGTCCTCTCAAAATTATTTTT
66 ATCCTGCTTGAAGCATTTTTGACACTATTTTTTCAGAACTGTCTTCTCAAAATTATTTTT
** * *
49697381 TAGGAACTACTGTAGAAAAAGAGCGTCCACGTGAAAGCTTTTTTTCAATAATTTTGCTGACAGTG
1 TAGGAACTACTGTAGAAAAAGAGCGTCCACGTGGGAGC-TTTCTTCAATAATTTTGCTGATAGTG
* *
49697446 CATCCTGCTTGAAGCATTTTTGACATTATCTTTTCAGAA-TCGTCTTCTCAAAATTAATTTTT
65 CATCCTGCTTGAAGCATTTTTGACACTATTTTTTCAGAACT-GTCTTCTCAAAATT-ATTTTT
*
49697508 CT-GAAACTACTGTAGAAAAA
1 -TAGGAACTACTGTAGAAAAA
49697528 AAACAAAATC
Statistics
Matches: 360, Mismatches: 33, Indels: 9
0.90 0.08 0.02
Matches are distributed among these distances:
125 153 0.43
126 102 0.28
127 104 0.29
128 1 0.00
ACGTcount: A:0.28, C:0.16, G:0.16, T:0.39
Consensus pattern (125 bp):
TAGGAACTACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTCTTCAATAATTTTGCTGATAGTGC
ATCCTGCTTGAAGCATTTTTGACACTATTTTTTCAGAACTGTCTTCTCAAAATTATTTTT
Found at i:49697647 original size:34 final size:32
Alignment explanation
Indices: 49697593--49697722 Score: 145
Period size: 34 Copynumber: 3.9 Consensus size: 32
49697583 TAAACACAAA
*
49697593 AATTATTTAAAAAACTAAACCCTAATTTAATT
1 AATTTTTTAAAAAACTAAACCCTAATTTAATT
*
49697625 AATTTTCTTAAAAAATCGAAACCCTAATTTAATT
1 AATTTT-TTAAAAAA-CTAAACCCTAATTTAATT
** *
49697659 AATTTGTTTAAAACCCCTAAAACCTAATTTAATT
1 AATTT-TTTAAAA-AACTAAACCCTAATTTAATT
*
49697693 -ATTTTTTAAAAAACTTTAAAACCTAATTTA
1 AATTTTTTAAAAAAC--TAAACCCTAATTTA
49697723 TTTTTTAAAA
Statistics
Matches: 84, Mismatches: 8, Indels: 11
0.82 0.08 0.11
Matches are distributed among these distances:
31 1 0.01
32 12 0.14
33 26 0.31
34 44 0.52
35 1 0.01
ACGTcount: A:0.45, C:0.14, G:0.02, T:0.39
Consensus pattern (32 bp):
AATTTTTTAAAAAACTAAACCCTAATTTAATT
Found at i:49698366 original size:28 final size:28
Alignment explanation
Indices: 49698267--49698364 Score: 180
Period size: 28 Copynumber: 3.5 Consensus size: 28
49698257 AAATAATAAA
49698267 ATTTACCAAAATATTACAACTTTTTTTT
1 ATTTACCAAAATATTACAACTTTTTTTT
49698295 ATTTACCAAAATATTACAACTTTTTTTT
1 ATTTACCAAAATATTACAACTTTTTTTT
49698323 ATTTACCAAAATATATA-AACTTTTTTTT
1 ATTTACCAAAATAT-TACAACTTTTTTTT
49698351 ATTTACCAAAATAT
1 ATTTACCAAAATAT
49698365 ATCAAAAAAA
Statistics
Matches: 69, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
28 67 0.97
29 2 0.03
ACGTcount: A:0.39, C:0.13, G:0.00, T:0.48
Consensus pattern (28 bp):
ATTTACCAAAATATTACAACTTTTTTTT
Found at i:49698644 original size:19 final size:21
Alignment explanation
Indices: 49698606--49698644 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
49698596 AATAATTGAT
*
49698606 TATATTATTGTTATTATTTTG
1 TATATTATTGTTAATATTTTG
49698627 TATATT-TTG-TAATATTTT
1 TATATTATTGTTAATATTTT
49698645 TTGTTGTAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 8 0.47
20 3 0.18
21 6 0.35
ACGTcount: A:0.26, C:0.00, G:0.08, T:0.67
Consensus pattern (21 bp):
TATATTATTGTTAATATTTTG
Found at i:49698708 original size:3 final size:3
Alignment explanation
Indices: 49698690--49698733 Score: 70
Period size: 3 Copynumber: 14.3 Consensus size: 3
49698680 AAAATAAAAG
*
49698690 TAT TAGT TAG TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
49698734 GTTGTTGTTG
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
3 35 0.92
4 3 0.08
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:49698738 original size:3 final size:3
Alignment explanation
Indices: 49698732--49698796 Score: 130
Period size: 3 Copynumber: 21.7 Consensus size: 3
49698722 ATTATTATTA
49698732 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG
49698780 TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TT
49698797 AATGTATTAA
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 62 1.00
ACGTcount: A:0.00, C:0.00, G:0.32, T:0.68
Consensus pattern (3 bp):
TTG
Found at i:49699644 original size:18 final size:18
Alignment explanation
Indices: 49699601--49699645 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
49699591 TTGACATGGT
* *
49699601 TGGTGGTGAAGAAGAATG
1 TGGTGGCGAAGAAGAAGG
**
49699619 TGCCGGCGAAGAAGAAGG
1 TGGTGGCGAAGAAGAAGG
49699637 TGGTGGCGA
1 TGGTGGCGA
49699646 TCATTAGGAT
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.29, C:0.09, G:0.47, T:0.16
Consensus pattern (18 bp):
TGGTGGCGAAGAAGAAGG
Found at i:49705406 original size:28 final size:30
Alignment explanation
Indices: 49705361--49705423 Score: 71
Period size: 28 Copynumber: 2.1 Consensus size: 30
49705351 CATTTTTTCC
49705361 CTTTTTTTTTCCTTTCTTC-CCTCTTCT-TCTT
1 CTTTTTTTTTCC-TTCTTCTCCT-TTCTCT-TT
49705392 CTTTTTTTTT-C-TCTTCTCCTTTCTCTTT
1 CTTTTTTTTTCCTTCTTCTCCTTTCTCTTT
49705420 CTTT
1 CTTT
49705424 CCTTCTTTCT
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
28 15 0.50
29 4 0.13
30 1 0.03
31 10 0.33
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (30 bp):
CTTTTTTTTTCCTTCTTCTCCTTTCTCTTT
Found at i:49705408 original size:18 final size:18
Alignment explanation
Indices: 49705385--49705505 Score: 86
Period size: 18 Copynumber: 6.4 Consensus size: 18
49705375 TCTTCCCTCT
*
49705385 TCTTCTTCTTTTTTTTTC
1 TCTTCTTCTTTCTTTTTC
* *
49705403 TCTTCTCCTTTCTCTTTCTT
1 TCTTCTTCTTTCT-TTT-TC
49705423 TCCTTCTTTCTTTCTTTTT-
1 T-CTTC-TTCTTTCTTTTTC
*
49705442 TCTTC-TCTTCTCCTTTTC
1 TCTTCTTCTT-TCTTTTTC
49705460 TTCTTCTTTCTTTCCTTTTTTC
1 -TCTTC-TTCTTT-C-TTTTTC
* *
49705482 TCTTCTCCTTTCCTTTTC
1 TCTTCTTCTTTCTTTTTC
49705500 T-TTCTT
1 TCTTCTT
49705506 TCCTCTCCTT
Statistics
Matches: 83, Mismatches: 9, Indels: 23
0.72 0.08 0.20
Matches are distributed among these distances:
16 4 0.05
17 10 0.12
18 21 0.25
19 10 0.12
20 9 0.11
21 17 0.20
22 12 0.14
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (18 bp):
TCTTCTTCTTTCTTTTTC
Found at i:49705420 original size:44 final size:42
Alignment explanation
Indices: 49705367--49705511 Score: 140
Period size: 44 Copynumber: 3.4 Consensus size: 42
49705357 TTCCCTTTTT
49705367 TTTTCCTTTCTTCCCTCTTCTTCTTCTTTTTTTTTCTCTTCTCC
1 TTTT-CTTTCTT-CCTCTTCTTCTTCTTTTTTTTTCTCTTCTCC
* *
49705411 TTTCTCTTTCTTTC-CTTCTTTCTTTCTTTTTTCTTCTCTTCTCC
1 TTT-TCTTTCTTCCTCTTC-TTC-TTCTTTTTTTTTCTCTTCTCC
*
49705455 TTTTC-TTCTT-CT-TTCTT-TCCTTTTTTCTCTTCTCCTT-TCC
1 TTTTCTTTCTTCCTCTTCTTCTTCTTTTTT-T-TTCT-CTTCTCC
49705495 TTTTCTTTCTTTCCTCT
1 TTTTCTTTC-TTCCTCT
49705512 CCTTTCTTTC
Statistics
Matches: 86, Mismatches: 4, Indels: 22
0.77 0.04 0.20
Matches are distributed among these distances:
38 8 0.09
40 14 0.16
41 10 0.12
42 11 0.13
43 8 0.09
44 34 0.40
45 1 0.01
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (42 bp):
TTTTCTTTCTTCCTCTTCTTCTTCTTTTTTTTTCTCTTCTCC
Found at i:49705424 original size:4 final size:4
Alignment explanation
Indices: 49705415--49705525 Score: 70
Period size: 4 Copynumber: 26.5 Consensus size: 4
49705405 TTCTCCTTTC
*
49705415 TCTT TCTT TCCT TCTT TCTT TCTT T-TT TCTT CTCTT CTCCTT T-TCT
1 TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT -TCTT -T-CTT TCT-T
*
49705461 TC-T TCTT TCTT TCCTT T-TT TCTCT TC-T CCTT TCCTTT TCTT TCTT
1 TCTT TCTT TCTT T-CTT TCTT TCT-T TCTT TCTT T-C-TT TCTT TCTT
*
49705506 TCCTCT CCTT TCTT TCTT TC
1 T-CT-T TCTT TCTT TCTT TC
49705526 CCTCCTTCTG
Statistics
Matches: 87, Mismatches: 6, Indels: 28
0.72 0.05 0.23
Matches are distributed among these distances:
3 12 0.14
4 48 0.55
5 20 0.23
6 7 0.08
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (4 bp):
TCTT
Found at i:49705470 original size:67 final size:67
Alignment explanation
Indices: 49705373--49705506 Score: 150
Period size: 67 Copynumber: 2.0 Consensus size: 67
49705363 TTTTTTTTCC
* * *
49705373 TTTCTTCCCTCTTCTTCTTCTTTTTTTTTCTCTT-CTCCTTTCTCTT-T-CTTTCCTTCTTTCTT
1 TTTCTTCCCTCTCCTTCTTCTTCTTCTTTCT-TTCCTCCTTTCTCTTCTCCTTTCC-T-TTTCTT
49705435 TCTTT
63 TCTTT
* **
49705440 TTTCTTCTCTTCTCCTT-TTCTTCTTCTTTCTTTCCTTTTTTCTCTTCTCCTTTCCTTTTCTTTC
1 TTTCTTC-CCTCTCCTTCTTCTTCTTCTTTCTTTCCTCCTTTCTCTTCTCCTTTCCTTTTCTTTC
49705504 TTT
65 TTT
49705507 CCTCTCCTTT
Statistics
Matches: 57, Mismatches: 6, Indels: 8
0.80 0.08 0.11
Matches are distributed among these distances:
66 2 0.04
67 40 0.70
68 9 0.16
69 6 0.11
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (67 bp):
TTTCTTCCCTCTCCTTCTTCTTCTTCTTTCTTTCCTCCTTTCTCTTCTCCTTTCCTTTTCTTTCT
TT
Found at i:49705506 original size:34 final size:34
Alignment explanation
Indices: 49705411--49705509 Score: 125
Period size: 35 Copynumber: 2.9 Consensus size: 34
49705401 TCTCTTCTCC
49705411 TTTCTCTT-T-CTTTCCTTCTTTCTTTCTTT--TTT
1 TTTCTCTTCTCCTTTCC-T-TTTCTTTCTTTCCTTT
* *
49705443 CTTCTCTTCTCCTTTTCTTCTTCTTTCTTTCCTTT
1 TTTCTCTTCTCCTTTCCTT-TTCTTTCTTTCCTTT
49705478 TTTCTCTTCTCCTTTCCTTTTCTTTCTTTCCT
1 TTTCTCTTCTCCTTTCCTTTTCTTTCTTTCCT
49705510 CTCCTTTCTT
Statistics
Matches: 58, Mismatches: 4, Indels: 8
0.83 0.06 0.11
Matches are distributed among these distances:
32 8 0.14
33 12 0.21
34 18 0.31
35 20 0.34
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (34 bp):
TTTCTCTTCTCCTTTCCTTTTCTTTCTTTCCTTT
Found at i:49705642 original size:27 final size:27
Alignment explanation
Indices: 49705560--49705633 Score: 121
Period size: 27 Copynumber: 2.7 Consensus size: 27
49705550 CCCCCCATAA
49705560 CACCAATTGGTGCCGCCAATGGTATTGG
1 CACC-ATTGGTGCCGCCAATGGTATTGG
*
49705588 CACCATTGGTGCCGCCAATGGTTTTGG
1 CACCATTGGTGCCGCCAATGGTATTGG
*
49705615 CACCTTTGGTGCCGCCAAT
1 CACCATTGGTGCCGCCAAT
49705634 ACCATTGGCG
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
27 40 0.91
28 4 0.09
ACGTcount: A:0.18, C:0.28, G:0.27, T:0.27
Consensus pattern (27 bp):
CACCATTGGTGCCGCCAATGGTATTGG
Found at i:49705769 original size:28 final size:29
Alignment explanation
Indices: 49705705--49705775 Score: 110
Period size: 28 Copynumber: 2.5 Consensus size: 29
49705695 GTTTTTTTAT
*
49705705 ATATTTTGGTAAATAAAAAGAAGGTTGTA
1 ATATTTTGGTAAATAAAAAGAAGATTGTA
49705734 ATATTTTGGTAAATAGAAAA-AA-ATTGTA
1 ATATTTTGGTAAATA-AAAAGAAGATTGTA
49705762 ATATTTTGGTAAAT
1 ATATTTTGGTAAAT
49705776 TTTTATTATT
Statistics
Matches: 40, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
28 19 0.47
29 17 0.43
30 4 0.10
ACGTcount: A:0.45, C:0.00, G:0.17, T:0.38
Consensus pattern (29 bp):
ATATTTTGGTAAATAAAAAGAAGATTGTA
Found at i:49705906 original size:9 final size:9
Alignment explanation
Indices: 49705881--49705919 Score: 51
Period size: 9 Copynumber: 4.2 Consensus size: 9
49705871 TAAAATTAAG
*
49705881 TTTTTAATA
1 TTTTTAATT
*
49705890 TTTATAATT
1 TTTTTAATT
49705899 TTTTTAATT
1 TTTTTAATT
49705908 TTTTTAAATT
1 TTTTT-AATT
49705918 TT
1 TT
49705920 ATTATTTGAG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
9 20 0.77
10 6 0.23
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (9 bp):
TTTTTAATT
Found at i:49706984 original size:18 final size:19
Alignment explanation
Indices: 49706964--49706998 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
49706954 TCAAACAAAT
49706964 TTTTTG-TTC-ATTTTCAA
1 TTTTTGTTTCAATTTTCAA
49706981 TTTTTGTTTCAATTTTCA
1 TTTTTGTTTCAATTTTCA
49706999 TTCATCAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
18 3 0.19
19 7 0.44
ACGTcount: A:0.17, C:0.11, G:0.06, T:0.66
Consensus pattern (19 bp):
TTTTTGTTTCAATTTTCAA
Found at i:49708026 original size:6 final size:6
Alignment explanation
Indices: 49708015--49708042 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
49708005 CAACTGCAGC
49708015 CTTTTA CTTTTA CTTTTA CTTTTA CTTT
1 CTTTTA CTTTTA CTTTTA CTTTTA CTTT
49708043 CAACTGTCAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.14, C:0.18, G:0.00, T:0.68
Consensus pattern (6 bp):
CTTTTA
Found at i:49709949 original size:111 final size:114
Alignment explanation
Indices: 49709737--49710067 Score: 392
Period size: 114 Copynumber: 2.9 Consensus size: 114
49709727 AAAATAAGAA
* * * * * * *
49709737 TTAGCGGCGCTTTTGCT-GAAGCGCCGC-AAAAAACT-AAGCCCAACGACGCCATTTTCTAAGAT
1 TTAGCGGCGCTTTT-ATGGAAGCGCCGCAAAAAAAATGAAACCCAACGACACCGTTTTCTTAGCT
* * *
49709799 TCCGGGGGGGTTTAGCGGCGTTTTTAATAATGCGCCGCTAATGCA-GGG-CT
65 TTC--AGGGGTTTAGCGGCGTTTTTAATAAAGCGCCGCTAATGCATGGGTCT
*
49709849 TTAGCGGCGTTTTTATGGAAGCGCCGC-AAAAAAATGAAACCCAACGACACCGTTTTCATT-GCT
1 TTAGCGGCGCTTTTATGGAAGCGCCGCAAAAAAAATGAAACCCAACGACACCGTTTTC-TTAGCT
* * *
49709912 TTC-GTGGGTTTAGCGGCGTTTTTAGTAAAGCGTCGCTAATG-ATGGGTTT
65 TTCAG-GGGTTTAGCGGCGTTTTTAATAAAGCGCCGCTAATGCATGGGTCT
* *
49709961 TTAGCGGCGCTTTTATGGAAGCGCCGCAAAAAAAAATTAAACCCAACGGCACCGTTTTCTTAGCT
1 TTAGCGGCGCTTTTATGGAAGCGCCGC-AAAAAAAATGAAACCCAACGACACCGTTTTCTTAGCT
*
49710026 TTCAGGGTTTTAGCGGCGTTTTTAATAAAGCGCCGCTAATGC
65 TTCAGGGGTTTAGCGGCGTTTTTAATAAAGCGCCGCTAATGC
49710068 TCAGGGATTT
Statistics
Matches: 189, Mismatches: 19, Indels: 19
0.83 0.08 0.08
Matches are distributed among these distances:
110 2 0.01
111 37 0.20
112 57 0.30
113 24 0.13
114 68 0.36
115 1 0.01
ACGTcount: A:0.25, C:0.22, G:0.25, T:0.28
Consensus pattern (114 bp):
TTAGCGGCGCTTTTATGGAAGCGCCGCAAAAAAAATGAAACCCAACGACACCGTTTTCTTAGCTT
TCAGGGGTTTAGCGGCGTTTTTAATAAAGCGCCGCTAATGCATGGGTCT
Found at i:49710424 original size:35 final size:35
Alignment explanation
Indices: 49710385--49710467 Score: 85
Period size: 35 Copynumber: 2.3 Consensus size: 35
49710375 TGGTTTTACA
* ***
49710385 GTTTAGGGTTTAAGGGTTATGCTCTAAGGTTTATG
1 GTTTAGGGTTTAAGAGTTACAATCTAAGGTTTATG
* * *
49710420 GTTTAAGATTTAAGAGTTACAATTTAAGGTTTATG
1 GTTTAGGGTTTAAGAGTTACAATCTAAGGTTTATG
*
49710455 GATTATGGGTTTA
1 GTTTA-GGGTTTA
49710468 GTGATTATGT
Statistics
Matches: 37, Mismatches: 10, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
35 32 0.86
36 5 0.14
ACGTcount: A:0.27, C:0.04, G:0.27, T:0.43
Consensus pattern (35 bp):
GTTTAGGGTTTAAGAGTTACAATCTAAGGTTTATG
Found at i:49713452 original size:52 final size:52
Alignment explanation
Indices: 49713380--49713584 Score: 177
Period size: 52 Copynumber: 4.1 Consensus size: 52
49713370 GTATATAACT
*
49713380 TAATACATAATAACACAATACATAA-TTGGTATATAAGCTTGCATAACTTACA
1 TAATACATAATAACACAATACATAACTT-ATATATAAGCTTGCATAACTTACA
*
49713432 TAATACATAATAACATAATACATAACTTATATATAAGCTTG--T-A--TAGC-
1 TAATACATAATAACACAATACATAACTTATATATAAGCTTGCATAACTTA-CA
* ** * *
49713479 T--TACATAAT-A-AC-TTATGTAACTTATATATAATCTGAT-AAT-ACATTACA
1 TAATACATAATAACACAATACATAACTTATATATAAGCT--TGCATAAC-TTACA
* *
49713527 TAATACATAATAACATAATACATAACTTATATTATAATCTTGCATAACTTACA
1 TAATACATAATAACACAATACATAACTTATA-TATAAGCTTGCATAACTTACA
49713580 TAATA
1 TAATA
49713585 ACTTACATAA
Statistics
Matches: 123, Mismatches: 12, Indels: 35
0.72 0.07 0.21
Matches are distributed among these distances:
42 18 0.15
43 1 0.01
44 2 0.02
45 10 0.08
47 4 0.03
48 4 0.03
49 1 0.01
50 9 0.07
51 1 0.01
52 38 0.31
53 25 0.20
54 10 0.08
ACGTcount: A:0.46, C:0.14, G:0.05, T:0.35
Consensus pattern (52 bp):
TAATACATAATAACACAATACATAACTTATATATAAGCTTGCATAACTTACA
Found at i:49713481 original size:21 final size:20
Alignment explanation
Indices: 49713453--49713509 Score: 60
Period size: 21 Copynumber: 2.8 Consensus size: 20
49713443 AACATAATAC
*
49713453 ATAACTTATATATAAGCTTGT
1 ATAACTTATATATAA-CTTAT
* *
49713474 ATAGCTTACATAATAACTTAT
1 ATAACTTATAT-ATAACTTAT
*
49713495 GTAACTTATATATAA
1 ATAACTTATATATAA
49713510 TCTGATAATA
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
20 4 0.14
21 21 0.72
22 4 0.14
ACGTcount: A:0.42, C:0.11, G:0.07, T:0.40
Consensus pattern (20 bp):
ATAACTTATATATAACTTAT
Found at i:49713531 original size:12 final size:14
Alignment explanation
Indices: 49713514--49713550 Score: 51
Period size: 15 Copynumber: 2.7 Consensus size: 14
49713504 ATATAATCTG
49713514 ATAATACAT-T-AC
1 ATAATACATATAAC
49713526 ATAATACATAATAAC
1 ATAATACAT-ATAAC
49713541 ATAATACATA
1 ATAATACATA
49713551 ACTTATATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
12 9 0.41
14 2 0.09
15 11 0.50
ACGTcount: A:0.57, C:0.14, G:0.00, T:0.30
Consensus pattern (14 bp):
ATAATACATATAAC
Found at i:49713536 original size:95 final size:96
Alignment explanation
Indices: 49713427--49713604 Score: 295
Period size: 96 Copynumber: 1.9 Consensus size: 96
49713417 CTTGCATAAC
* *
49713427 TTACATAATACATAATAACATAATACATAACTTATA-TATAAGCTTGTATAGCTTACATAATAAC
1 TTACATAATACATAATAACATAATACATAACTTATATTATAAGCTTGCATAACTTACATAATAAC
** *
49713491 TTATGTAACTTATATATAATCTGATAATACA
66 TTACATAACTTACATATAATCTGATAATACA
*
49713522 TTACATAATACATAATAACATAATACATAACTTATATTATAATCTTGCATAACTTACATAATAAC
1 TTACATAATACATAATAACATAATACATAACTTATATTATAAGCTTGCATAACTTACATAATAAC
49713587 TTACATAACTTACATATA
66 TTACATAACTTACATATA
49713605 TTCATTTACG
Statistics
Matches: 76, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
95 36 0.47
96 40 0.53
ACGTcount: A:0.46, C:0.14, G:0.03, T:0.37
Consensus pattern (96 bp):
TTACATAATACATAATAACATAATACATAACTTATATTATAAGCTTGCATAACTTACATAATAAC
TTACATAACTTACATATAATCTGATAATACA
Found at i:49713544 original size:8 final size:7
Alignment explanation
Indices: 49713514--49713551 Score: 53
Period size: 7 Copynumber: 5.6 Consensus size: 7
49713504 ATATAATCTG
49713514 ATAATAC
1 ATAATAC
49713521 AT--TAC
1 ATAATAC
49713526 ATAATAC
1 ATAATAC
49713533 ATAATAAC
1 ATAAT-AC
49713541 ATAATAC
1 ATAATAC
49713548 ATAA
1 ATAA
49713552 CTTATATTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
5 5 0.18
7 16 0.57
8 7 0.25
ACGTcount: A:0.58, C:0.13, G:0.00, T:0.29
Consensus pattern (7 bp):
ATAATAC
Found at i:49713572 original size:22 final size:21
Alignment explanation
Indices: 49713514--49713602 Score: 85
Period size: 22 Copynumber: 4.1 Consensus size: 21
49713504 ATATAATCTG
49713514 ATAAT-ACATTACATAA--TAC
1 ATAATAAC-TTACATAACTTAC
*
49713533 ATAATAACATAATACATAACTTAT
1 ATAATAAC-T--TACATAACTTAC
* *
49713557 ATTATAATCTTGCATAACTTAC
1 ATAATAA-CTTACATAACTTAC
49713579 ATAATAACTTACATAACTTAC
1 ATAATAACTTACATAACTTAC
49713600 ATA
1 ATA
49713603 TATTCATTTA
Statistics
Matches: 58, Mismatches: 6, Indels: 10
0.78 0.08 0.14
Matches are distributed among these distances:
19 5 0.09
20 4 0.07
21 16 0.28
22 23 0.40
24 9 0.16
25 1 0.02
ACGTcount: A:0.48, C:0.16, G:0.01, T:0.35
Consensus pattern (21 bp):
ATAATAACTTACATAACTTAC
Found at i:49713587 original size:12 final size:12
Alignment explanation
Indices: 49713570--49713594 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
49713560 ATAATCTTGC
49713570 ATAACTTACATA
1 ATAACTTACATA
49713582 ATAACTTACATA
1 ATAACTTACATA
49713594 A
1 A
49713595 CTTACATATA
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:0.52, C:0.16, G:0.00, T:0.32
Consensus pattern (12 bp):
ATAACTTACATA
Found at i:49713707 original size:92 final size:92
Alignment explanation
Indices: 49713597--49714072 Score: 911
Period size: 92 Copynumber: 5.2 Consensus size: 92
49713587 TTACATAACT
49713597 TACATATATTCATTTACGTATGTAAGCTATATTTAAATTTTATTAATAATAAATTTATAACTTAA
1 TACATATATTCATTTACGTATGTAAGCTATATTTAAATTTTATTAATAATAAATTTATAACTTAA
*
49713662 ATAAGTATTACTATTTTTTTAATATTA
66 ATAAGTATTACTATTTTTTTAATAGTA
49713689 TACATATATTCATTTACGTATGTAAGCTATATTTAAATTTTATTAATAATAAATTTATAACTTAA
1 TACATATATTCATTTACGTATGTAAGCTATATTTAAATTTTATTAATAATAAATTTATAACTTAA
49713754 ATAAGTATTACTATTTTTTTAATAGGT-
66 ATAAGTATTACTATTTTTTTAATA-GTA
49713781 TACATATATTCATTTACGTATGTAAGCTATATTTAAATTTTATTAATAATAAATTTATAACTTAA
1 TACATATATTCATTTACGTATGTAAGCTATATTTAAATTTTATTAATAATAAATTTATAACTTAA
49713846 ATAAGTATTACTATTTTTTTAATAGTA
66 ATAAGTATTACTATTTTTTTAATAGTA
49713873 TACATATATTCATTTACGTATGTAAGCTATATTTAAATTTTATTAATAATAAATTTATAACTTAA
1 TACATATATTCATTTACGTATGTAAGCTATATTTAAATTTTATTAATAATAAATTTATAACTTAA
49713938 ATAAGTATTACTATTTTTTTAATAGTA
66 ATAAGTATTACTATTTTTTTAATAGTA
49713965 TACATATATTCATTTACGTATGTAAGCTATATTTAAATTTTATTAATAATAAATTTATAACTTAA
1 TACATATATTCATTTACGTATGTAAGCTATATTTAAATTTTATTAATAATAAATTTATAACTTAA
*
49714030 ATAAGTATTACTA-TTTTTTAATATTA
66 ATAAGTATTACTATTTTTTTAATAGTA
49714056 TACATATATTCATTTAC
1 TACATATATTCATTTAC
49714073 ATAACACATA
Statistics
Matches: 380, Mismatches: 2, Indels: 5
0.98 0.01 0.01
Matches are distributed among these distances:
91 31 0.08
92 348 0.92
93 1 0.00
ACGTcount: A:0.40, C:0.07, G:0.05, T:0.48
Consensus pattern (92 bp):
TACATATATTCATTTACGTATGTAAGCTATATTTAAATTTTATTAATAATAAATTTATAACTTAA
ATAAGTATTACTATTTTTTTAATAGTA
Found at i:49714092 original size:9 final size:9
Alignment explanation
Indices: 49714069--49714400 Score: 133
Period size: 9 Copynumber: 37.9 Consensus size: 9
49714059 ATATATTCAT
49714069 TTACATAAC
1 TTACATAAC
49714078 --ACATAAC
1 TTACATAAC
49714085 TTACATAAC
1 TTACATAAC
* *
49714094 CTACTTAA-
1 TTACATAAC
*
49714102 -TATATAAC
1 TTACATAAC
*
49714110 TTGCATAAC
1 TTACATAAC
* *
49714119 TTAAATAAG
1 TTACATAAC
*
49714128 TTACGTAA-
1 TTACATAAC
49714136 TAATACATAA-
1 T--TACATAAC
*
49714146 -TACACAAC
1 TTACATAAC
*
49714154 TTTCATAA-
1 TTACATAAC
49714162 -TACAATAA-
1 TTAC-ATAAC
* *
49714170 -TACAGAGC
1 TTACATAAC
49714178 TTACATAAC
1 TTACATAAC
*
49714187 TTACATACC
1 TTACATAAC
* *
49714196 CTACATAAA
1 TTACATAAC
* *
49714205 TTAAATAAG
1 TTACATAAC
49714214 TTACATAA-
1 TTACATAAC
*
49714222 TAATACATACC
1 T--TACATAAC
* *
49714233 CTACATAAA
1 TTACATAAC
* *
49714242 TTAAATAAG
1 TTACATAAC
49714251 TTACATAA-
1 TTACATAAC
*
49714259 TAATACATACC
1 T--TACATAAC
* *
49714270 CTACATAAA
1 TTACATAAC
* *
49714279 TTAAATAAG
1 TTACATAAC
49714288 TTACATAA-
1 TTACATAAC
**
49714296 TAATACATATT
1 T--TACATAAC
49714307 TTACATAAC
1 TTACATAAC
49714316 TTACATAA-
1 TTACATAAC
*
49714324 -GACATAAC
1 TTACATAAC
*
49714332 TTACATAAG
1 TTACATAAC
*
49714341 TTTCATAA-
1 TTACATAAC
* *
49714349 -TACACATC
1 TTACATAAC
**
49714357 TTACGCAAC
1 TTACATAAC
*
49714366 TTACACAAC
1 TTACATAAC
49714375 TTACATAAC
1 TTACATAAC
49714384 TTACATAAC
1 TTACATAAC
49714393 TTACATAA
1 TTACATAA
49714401 TGTATATCTT
Statistics
Matches: 241, Mismatches: 58, Indels: 48
0.69 0.17 0.14
Matches are distributed among these distances:
7 32 0.13
8 11 0.05
9 173 0.72
10 24 0.10
11 1 0.00
ACGTcount: A:0.47, C:0.19, G:0.03, T:0.31
Consensus pattern (9 bp):
TTACATAAC
Found at i:49714184 original size:24 final size:23
Alignment explanation
Indices: 49714135--49714185 Score: 66
Period size: 24 Copynumber: 2.2 Consensus size: 23
49714125 AAGTTACGTA
*
49714135 ATAATACATAATACACAACTTTC
1 ATAATACATAATACACAACTTAC
* *
49714158 ATAATACAATAATACAGAGCTTAC
1 ATAATAC-ATAATACACAACTTAC
49714182 ATAA
1 ATAA
49714186 CTTACATACC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
23 7 0.29
24 17 0.71
ACGTcount: A:0.51, C:0.18, G:0.04, T:0.27
Consensus pattern (23 bp):
ATAATACATAATACACAACTTAC
Found at i:49714324 original size:37 final size:37
Alignment explanation
Indices: 49714188--49714304 Score: 234
Period size: 37 Copynumber: 3.2 Consensus size: 37
49714178 TTACATAACT
49714188 TACATACCCTACATAAATTAAATAAGTTACATAATAA
1 TACATACCCTACATAAATTAAATAAGTTACATAATAA
49714225 TACATACCCTACATAAATTAAATAAGTTACATAATAA
1 TACATACCCTACATAAATTAAATAAGTTACATAATAA
49714262 TACATACCCTACATAAATTAAATAAGTTACATAATAA
1 TACATACCCTACATAAATTAAATAAGTTACATAATAA
49714299 TACATA
1 TACATA
49714305 TTTTACATAA
Statistics
Matches: 80, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 80 1.00
ACGTcount: A:0.51, C:0.16, G:0.03, T:0.30
Consensus pattern (37 bp):
TACATACCCTACATAAATTAAATAAGTTACATAATAA
Found at i:49714328 original size:16 final size:16
Alignment explanation
Indices: 49714309--49714340 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
49714299 TACATATTTT
49714309 ACATAACTTACATAAG
1 ACATAACTTACATAAG
49714325 ACATAACTTACATAAG
1 ACATAACTTACATAAG
49714341 TTTCATAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.19, G:0.06, T:0.25
Consensus pattern (16 bp):
ACATAACTTACATAAG
Found at i:49714329 original size:25 final size:25
Alignment explanation
Indices: 49714295--49714401 Score: 106
Period size: 25 Copynumber: 4.2 Consensus size: 25
49714285 AAGTTACATA
**
49714295 ATAATACATATTTTACATAACTTAC
1 ATAATACATAACTTACATAACTTAC
* * *
49714320 ATAAGACATAACTTACATAAGTTTC
1 ATAATACATAACTTACATAACTTAC
* * **
49714345 ATAATACACATCTTACGCAACTTAC
1 ATAATACATAACTTACATAACTTAC
*
49714370 ACAACTTACATAACTTACATAACTTAC
1 ATAA--TACATAACTTACATAACTTAC
49714397 ATAAT
1 ATAAT
49714402 GTATATCTTG
Statistics
Matches: 62, Mismatches: 18, Indels: 4
0.74 0.21 0.05
Matches are distributed among these distances:
25 42 0.68
27 20 0.32
ACGTcount: A:0.44, C:0.21, G:0.03, T:0.33
Consensus pattern (25 bp):
ATAATACATAACTTACATAACTTAC
Found at i:49719956 original size:21 final size:21
Alignment explanation
Indices: 49719930--49719996 Score: 89
Period size: 21 Copynumber: 3.2 Consensus size: 21
49719920 CTACAACTTA
* *
49719930 AAGCAGAGGCGGAAGCGAGGG
1 AAGCAGAGGCTGCAGCGAGGG
*
49719951 AAGCAGCGGCTGCAGCGAGGG
1 AAGCAGAGGCTGCAGCGAGGG
* *
49719972 AAGCGGAGGCTGCAGCGAGAG
1 AAGCAGAGGCTGCAGCGAGGG
49719993 AAGC
1 AAGC
49719997 GGAGCAGAGC
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.30, C:0.19, G:0.48, T:0.03
Consensus pattern (21 bp):
AAGCAGAGGCTGCAGCGAGGG
Found at i:49720236 original size:14 final size:14
Alignment explanation
Indices: 49720217--49720250 Score: 68
Period size: 14 Copynumber: 2.4 Consensus size: 14
49720207 ATTGCTATTG
49720217 GTTGCTTTTGAATT
1 GTTGCTTTTGAATT
49720231 GTTGCTTTTGAATT
1 GTTGCTTTTGAATT
49720245 GTTGCT
1 GTTGCT
49720251 ACAGGAGGGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.12, C:0.09, G:0.24, T:0.56
Consensus pattern (14 bp):
GTTGCTTTTGAATT
Found at i:49720820 original size:7 final size:7
Alignment explanation
Indices: 49720810--49720841 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
49720800 ATAAATGCTA
49720810 AAACCCT
1 AAACCCT
49720817 AAACCCT
1 AAACCCT
49720824 AAACCCT
1 AAACCCT
49720831 AAACCCT
1 AAACCCT
49720838 AAAC
1 AAAC
49720842 TTGAGACCCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.47, C:0.41, G:0.00, T:0.12
Consensus pattern (7 bp):
AAACCCT
Found at i:49720851 original size:28 final size:28
Alignment explanation
Indices: 49720819--49720875 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 28
49720809 AAAACCCTAA
49720819 ACCCTAAACCCTAAACCC-TAAACTTGAG
1 ACCCTAAACCCTAAACCCTTAAA-TTGAG
** *
49720847 ACCCTAGGCCTTAAACCCTTAAATTGAG
1 ACCCTAAACCCTAAACCCTTAAATTGAG
49720875 A
1 A
49720876 GTTATAATAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 21 0.84
29 4 0.16
ACGTcount: A:0.37, C:0.32, G:0.11, T:0.21
Consensus pattern (28 bp):
ACCCTAAACCCTAAACCCTTAAATTGAG
Found at i:49721151 original size:21 final size:21
Alignment explanation
Indices: 49721113--49721169 Score: 53
Period size: 21 Copynumber: 2.7 Consensus size: 21
49721103 ATATTCCATA
** *
49721113 AATTTCAATTAAAAATAATAAG
1 AATTT-AATTAATTATAAAAAG
*
49721135 AATTTAATTAATTATAAAAAT
1 AATTTAATTAATTATAAAAAG
*
49721156 ATTTTAATT-ATTAT
1 AATTTAATTAATTAT
49721170 TAAATTGAAT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
20 5 0.17
21 20 0.67
22 5 0.17
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (21 bp):
AATTTAATTAATTATAAAAAG
Found at i:49722615 original size:31 final size:30
Alignment explanation
Indices: 49722556--49722615 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 30
49722546 ATAGCATCGA
*
49722556 TTTTAATAGTCTAGTGACTTAAATAAAAAC
1 TTTTAATAGTCTAGTGACTTAAACAAAAAC
*
49722586 TTTTAAATAGTTTAGTGA-TCTAAACAAAAA
1 TTTT-AATAGTCTAGTGACT-TAAACAAAAA
49722616 TTTACCTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 5 0.19
31 21 0.81
ACGTcount: A:0.45, C:0.08, G:0.10, T:0.37
Consensus pattern (30 bp):
TTTTAATAGTCTAGTGACTTAAACAAAAAC
Found at i:49730782 original size:13 final size:14
Alignment explanation
Indices: 49730763--49730800 Score: 51
Period size: 13 Copynumber: 2.7 Consensus size: 14
49730753 TACCTCCGAG
49730763 GTTAAAAAAATCGA
1 GTTAAAAAAATCGA
*
49730777 -TTAAAAAAATTGA
1 GTTAAAAAAATCGA
49730790 GTATAAAAAAA
1 GT-TAAAAAAA
49730801 AGAGAAAAGG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
13 12 0.57
14 1 0.05
15 8 0.38
ACGTcount: A:0.63, C:0.03, G:0.11, T:0.24
Consensus pattern (14 bp):
GTTAAAAAAATCGA
Found at i:49739010 original size:3 final size:3
Alignment explanation
Indices: 49739002--49739046 Score: 56
Period size: 3 Copynumber: 15.0 Consensus size: 3
49738992 TATAGAAAAT
* *
49739002 ATA ATA ATA GTA ATA ATAA ATA AT- ACA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA ATA
49739047 GAAAATCGTG
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
2 1 0.03
3 32 0.89
4 3 0.08
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:49739031 original size:24 final size:24
Alignment explanation
Indices: 49738999--49739044 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
49738989 ATATATAGAA
* *
49738999 AATATAATAATAGTAATAATAAAT
1 AATACAATAATAATAATAATAAAT
49739023 AATACAATAATAATAATAATAA
1 AATACAATAATAATAATAATAA
49739045 TAGAAAATCG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.30
Consensus pattern (24 bp):
AATACAATAATAATAATAATAAAT
Found at i:49744171 original size:75 final size:75
Alignment explanation
Indices: 49744048--49744202 Score: 310
Period size: 75 Copynumber: 2.1 Consensus size: 75
49744038 GGCAAAAGGG
49744048 GGCATTTGAGGGAGGACAGTTTTTCTCTTGAAAATAAAAACTAAAAGAAGAAAGTTGCATCCACC
1 GGCATTTGAGGGAGGACAGTTTTTCTCTTGAAAATAAAAACTAAAAGAAGAAAGTTGCATCCACC
49744113 GCTTGCAAGT
66 GCTTGCAAGT
49744123 GGCATTTGAGGGAGGACAGTTTTTCTCTTGAAAATAAAAACTAAAAGAAGAAAGTTGCATCCACC
1 GGCATTTGAGGGAGGACAGTTTTTCTCTTGAAAATAAAAACTAAAAGAAGAAAGTTGCATCCACC
49744188 GCTTGCAAGT
66 GCTTGCAAGT
49744198 GGCAT
1 GGCAT
49744203 ATCTGGTTCC
Statistics
Matches: 80, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
75 80 1.00
ACGTcount: A:0.35, C:0.16, G:0.23, T:0.25
Consensus pattern (75 bp):
GGCATTTGAGGGAGGACAGTTTTTCTCTTGAAAATAAAAACTAAAAGAAGAAAGTTGCATCCACC
GCTTGCAAGT
Found at i:49745979 original size:27 final size:27
Alignment explanation
Indices: 49745920--49745997 Score: 72
Period size: 27 Copynumber: 3.0 Consensus size: 27
49745910 GATGCTTAGT
* * *
49745920 AGTTGCTAGGT-GAGACTCTTAGGAGAA
1 AGTTGTTAGGTAG-GACTCTTAGAATAA
*
49745947 ATTTGTTAGGTAGGACTCTTAGAATAA
1 AGTTGTTAGGTAGGACTCTTAGAATAA
* *
49745974 AGTTGTT--TTAGGACTCTTAAAATA
1 AGTTGTTAGGTAGGACTCTTAGAATA
49745998 GATGTTGTGT
Statistics
Matches: 43, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
25 15 0.35
27 27 0.63
28 1 0.02
ACGTcount: A:0.32, C:0.09, G:0.24, T:0.35
Consensus pattern (27 bp):
AGTTGTTAGGTAGGACTCTTAGAATAA
Found at i:49753881 original size:50 final size:48
Alignment explanation
Indices: 49753744--49753882 Score: 152
Period size: 48 Copynumber: 2.8 Consensus size: 48
49753734 TTTTTATTGC
* * * *
49753744 AAGCCTCTCCTTATGCATCTGGGAGTAAGACCATAATTACCACATTTCAT
1 AAGCCTCTCC--ATGCGTCTGGGAGTAGGGCCATAATTACCACATTCCAT
* * * *
49753794 AAGCCTCTCCACGCGTCTGGGAGCAGGGTCATCATTACCACATTCCAT
1 AAGCCTCTCCATGCGTCTGGGAGTAGGGCCATAATTACCACATTCCAT
* *
49753842 AAGCCTCTTCCCATGCGTCTGGGAGTAGGGCCTTTATTACC
1 AAGCCTC-T-CCATGCGTCTGGGAGTAGGGCCATAATTACC
49753883 TTCCATAAGT
Statistics
Matches: 74, Mismatches: 13, Indels: 4
0.81 0.14 0.04
Matches are distributed among these distances:
48 37 0.50
49 1 0.01
50 36 0.49
ACGTcount: A:0.24, C:0.29, G:0.19, T:0.27
Consensus pattern (48 bp):
AAGCCTCTCCATGCGTCTGGGAGTAGGGCCATAATTACCACATTCCAT
Found at i:49753983 original size:49 final size:51
Alignment explanation
Indices: 49753861--49754001 Score: 148
Period size: 49 Copynumber: 2.8 Consensus size: 51
49753851 CCCATGCGTC
* * * *
49753861 TGGGAGTAGGG-CCTTTATTACCTTCCATAAGTTTGCCTCCTATTATGTGTT
1 TGGGAGTAGGGTCATTTATTACCTTCCATAAGTCT-CCTCCTACTATGAGTT
* * *
49753912 TGGGAGCAGGGTCACCTTATTACCTTTCATAAGTCT-C-CCT-CTATGAGTT
1 TGGGAGTAGGGTCA-TTTATTACCTTCCATAAGTCTCCTCCTACTATGAGTT
49753961 TGGGAGTAGGGTCATTTCATTACCTTCCATAAG-CGTCCTCC
1 TGGGAGTAGGGTCATTT-ATTACCTTCCATAAGTC-TCCTCC
49754002 CATCGCCTAG
Statistics
Matches: 74, Mismatches: 10, Indels: 12
0.77 0.10 0.12
Matches are distributed among these distances:
48 3 0.04
49 35 0.47
50 4 0.05
51 13 0.18
52 1 0.01
53 18 0.24
ACGTcount: A:0.19, C:0.23, G:0.21, T:0.36
Consensus pattern (51 bp):
TGGGAGTAGGGTCATTTATTACCTTCCATAAGTCTCCTCCTACTATGAGTT
Found at i:49755474 original size:14 final size:14
Alignment explanation
Indices: 49755455--49755494 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
49755445 TTGATTACCA
49755455 GTAAAATGTTTTCC
1 GTAAAATGTTTTCC
* *
49755469 GTAAAATGATTTCT
1 GTAAAATGTTTTCC
*
49755483 GGAAAATGTTTT
1 GTAAAATGTTTT
49755495 ACTTTTCTGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.42
Consensus pattern (14 bp):
GTAAAATGTTTTCC
Found at i:49755503 original size:20 final size:20
Alignment explanation
Indices: 49755478--49755517 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
49755468 CGTAAAATGA
*
49755478 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
49755498 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
49755518 GGAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:49755507 original size:34 final size:35
Alignment explanation
Indices: 49755463--49755529 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
49755453 CAGTAAAATG
*
49755463 TTTTCCGTAAAATGATTT-CTGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
*
49755497 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTT
49755530 CTGGTGTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.31, C:0.09, G:0.13, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
Found at i:49755533 original size:14 final size:15
Alignment explanation
Indices: 49755457--49755533 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
49755447 GATTACCAGT
* *
49755457 AAAATG-TTTTCCGT
1 AAAATGATTTTCTGG
49755471 AAAATGA-TTTCTGG
1 AAAATGATTTTCTGG
*
49755485 AAAATGTTTTACTTTTCTGT
1 AAAATG----A-TTTTCTGG
*
49755505 AAAATGATTTACTGG
1 AAAATGATTTTCTGG
49755520 AAAAT-ATTTTCTGG
1 AAAATGATTTTCTGG
49755534 TGTTTGATTG
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 25 0.50
15 11 0.22
16 1 0.02
18 1 0.02
20 12 0.24
ACGTcount: A:0.32, C:0.09, G:0.16, T:0.43
Consensus pattern (15 bp):
AAAATGATTTTCTGG
Found at i:49755930 original size:21 final size:21
Alignment explanation
Indices: 49755901--49755942 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
49755891 ACGGAAATTG
*
49755901 AAAAGGTAAGACATTTTCCCT
1 AAAAGGTAACACATTTTCCCT
* *
49755922 AAAATGTAACTCATTTTCCCT
1 AAAAGGTAACACATTTTCCCT
49755943 TGTTTTGGAG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.36, C:0.21, G:0.10, T:0.33
Consensus pattern (21 bp):
AAAAGGTAACACATTTTCCCT
Found at i:49759276 original size:26 final size:25
Alignment explanation
Indices: 49759240--49759290 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 25
49759230 ATTAAATACA
49759240 TAAAACTAATTAAATTATATATTTAAT
1 TAAAACTAATTAAATTAT-T-TTTAAT
49759267 TAAAA-TAATTAAATTATTTTTAAT
1 TAAAACTAATTAAATTATTTTTAAT
49759291 ATTTTTTATT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
24 6 0.25
25 1 0.04
26 12 0.50
27 5 0.21
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (25 bp):
TAAAACTAATTAAATTATTTTTAAT
Found at i:49760623 original size:16 final size:16
Alignment explanation
Indices: 49760604--49760648 Score: 81
Period size: 16 Copynumber: 2.8 Consensus size: 16
49760594 CTATTACTGC
49760604 TCTATTCCATTACACA
1 TCTATTCCATTACACA
*
49760620 TCTATTCCATTACACC
1 TCTATTCCATTACACA
49760636 TCTATTCCATTAC
1 TCTATTCCATTAC
49760649 GGCGAACCAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.27, C:0.33, G:0.00, T:0.40
Consensus pattern (16 bp):
TCTATTCCATTACACA
Found at i:49764140 original size:32 final size:32
Alignment explanation
Indices: 49764094--49764154 Score: 104
Period size: 32 Copynumber: 1.9 Consensus size: 32
49764084 CTTTTGACGT
*
49764094 TTGAGGGTTAGAGAATAATGGAGATCATTTTA
1 TTGAGGGTTAGAGAATAATAGAGATCATTTTA
*
49764126 TTGAGGGTTTGAGAATAATAGAGATCATT
1 TTGAGGGTTAGAGAATAATAGAGATCATT
49764155 CGATGGAGAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.34, C:0.03, G:0.28, T:0.34
Consensus pattern (32 bp):
TTGAGGGTTAGAGAATAATAGAGATCATTTTA
Found at i:49772190 original size:32 final size:31
Alignment explanation
Indices: 49772154--49772250 Score: 89
Period size: 32 Copynumber: 3.3 Consensus size: 31
49772144 ATTTTTCAAA
49772154 TAAAAAATAGCCAATTAATTGATCTCCTCTCT
1 TAAAAAATAGCCAATTAATT-ATCTCCTCTCT
* * ***
49772186 TAAAAAATA-TCAA-TCATT-T-T--TCAAA
1 TAAAAAATAGCCAATTAATTATCTCCTCTCT
49772211 TAAAAAATAGCCAATTAATTCATCTCCTCTCT
1 TAAAAAATAGCCAATTAATT-ATCTCCTCTCT
49772243 TAAAAAAT
1 TAAAAAAT
49772251 TGTAATGAAA
Statistics
Matches: 48, Mismatches: 10, Indels: 14
0.67 0.14 0.19
Matches are distributed among these distances:
25 11 0.23
26 3 0.06
27 5 0.10
28 1 0.02
29 1 0.02
30 5 0.10
31 3 0.06
32 19 0.40
ACGTcount: A:0.44, C:0.19, G:0.03, T:0.34
Consensus pattern (31 bp):
TAAAAAATAGCCAATTAATTATCTCCTCTCT
Found at i:49775009 original size:6 final size:6
Alignment explanation
Indices: 49774994--49775035 Score: 75
Period size: 6 Copynumber: 6.8 Consensus size: 6
49774984 TTTATAGGAA
49774994 AAAAAGG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAA
1 AAAAA-G AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAA
49775036 AGAGGGAGTT
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 30 0.86
7 5 0.14
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:49776057 original size:15 final size:15
Alignment explanation
Indices: 49776039--49776086 Score: 57
Period size: 15 Copynumber: 3.4 Consensus size: 15
49776029 CGGGTCGGGT
49776039 GGCGCCTCATAGAGA
1 GGCGCCTCATAGAGA
*
49776054 GGCGCC-AAT-GA-A
1 GGCGCCTCATAGAGA
*
49776066 GGTGCCTCATAGAGA
1 GGCGCCTCATAGAGA
49776081 GGCGCC
1 GGCGCC
49776087 AATGGTGGCA
Statistics
Matches: 26, Mismatches: 4, Indels: 6
0.72 0.11 0.17
Matches are distributed among these distances:
12 6 0.23
13 4 0.15
14 4 0.15
15 12 0.46
ACGTcount: A:0.25, C:0.27, G:0.35, T:0.12
Consensus pattern (15 bp):
GGCGCCTCATAGAGA
Found at i:49776230 original size:3 final size:3
Alignment explanation
Indices: 49776224--49776275 Score: 74
Period size: 3 Copynumber: 18.3 Consensus size: 3
49776214 GAGAGAAAGG
*
49776224 AGA AGA AG- AGA AGG AGA AGA AG- AGA AGA AGA AGA AG- AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
49776269 AGA AGA A
1 AGA AGA A
49776276 AGAAAAAAAA
Statistics
Matches: 44, Mismatches: 2, Indels: 6
0.85 0.04 0.12
Matches are distributed among these distances:
2 6 0.14
3 38 0.86
ACGTcount: A:0.63, C:0.00, G:0.37, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:49776234 original size:17 final size:16
Alignment explanation
Indices: 49776212--49776280 Score: 60
Period size: 14 Copynumber: 4.6 Consensus size: 16
49776202 AGAAAAAAAA
49776212 AAGAGAGAAAGGAGAAG
1 AAGA-AGAAAGGAGAAG
49776229 AAG-AG-AAGGAGAAG
1 AAGAAGAAAGGAGAAG
*
49776243 AAG-AG-AAGAAGAAG
1 AAGAAGAAAGGAGAAG
*
49776257 AAG-AG-AAGAAGAAG
1 AAGAAGAAAGGAGAAG
49776271 AAGAAAGAAA
1 AAG-AAGAAA
49776281 AAAAAAGGTA
Statistics
Matches: 48, Mismatches: 1, Indels: 6
0.87 0.02 0.11
Matches are distributed among these distances:
14 39 0.81
15 2 0.04
16 2 0.04
17 5 0.10
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (16 bp):
AAGAAGAAAGGAGAAG
Found at i:49776237 original size:14 final size:14
Alignment explanation
Indices: 49776224--49776279 Score: 96
Period size: 14 Copynumber: 4.1 Consensus size: 14
49776214 GAGAGAAAGG
*
49776224 AGAAGAAGAGAAGG
1 AGAAGAAGAGAAGA
49776238 AGAAGAAGAGAAGA
1 AGAAGAAGAGAAGA
49776252 AGAAGAAGAGAAGA
1 AGAAGAAGAGAAGA
49776266 AGAAGAAGA-AAGA
1 AGAAGAAGAGAAGA
49776279 A
1 A
49776280 AAAAAAAGGT
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
13 5 0.12
14 36 0.88
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (14 bp):
AGAAGAAGAGAAGA
Found at i:49776243 original size:11 final size:11
Alignment explanation
Indices: 49776227--49776271 Score: 58
Period size: 11 Copynumber: 4.1 Consensus size: 11
49776217 AGAAAGGAGA
49776227 AGAAG-AGAAGG
1 AGAAGAAGAA-G
49776238 AGAAGAAG-AG
1 AGAAGAAGAAG
49776248 AAGAAGAAGAAG
1 -AGAAGAAGAAG
49776260 AGAAGAAGAAG
1 AGAAGAAGAAG
49776271 A
1 A
49776272 AGAAAGAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
10 1 0.03
11 26 0.84
12 4 0.13
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (11 bp):
AGAAGAAGAAG
Found at i:49776446 original size:19 final size:19
Alignment explanation
Indices: 49776422--49776639 Score: 139
Period size: 19 Copynumber: 11.2 Consensus size: 19
49776412 TTTGGATTAG
49776422 AATTTTGTATGAATATTGT
1 AATTTTGTATGAATATTGT
*
49776441 AATTTTTTATGAATATTGT
1 AATTTTGTATGAATATTGT
*
49776460 AATTATTTTAT-AATTAAATTTGT
1 AATT-TTGTATGAA-T--A-TTGT
* * *
49776483 -ATTTATAGTTTTGGAT-TAGT
1 AATTT-T-G-TATGAATATTGT
49776503 -ATTTTGTATGAATATTGT
1 AATTTTGTATGAATATTGT
49776521 AATTTTTTGTATGAATATTGT
1 AA--TTTTGTATGAATATTGT
49776542 AATTTTGTATGAATATTGT
1 AATTTTGTATGAATATTGT
49776561 AATTTTTTTGTATGAATATTGT
1 AA---TTTTGTATGAATATTGT
* * **
49776583 AATATTATAAT-TTTATATG-
1 AATTTTGT-ATGAATAT-TGT
*
49776602 AATATTG--T-AATATTGT
1 AATTTTGTATGAATATTGT
*
49776618 AATTTTGTATGAATATTAT
1 AATTTTGTATGAATATTGT
49776637 AAT
1 AAT
49776640 GTCGAGATAT
Statistics
Matches: 160, Mismatches: 17, Indels: 44
0.72 0.08 0.20
Matches are distributed among these distances:
15 2 0.01
16 10 0.06
17 5 0.03
18 5 0.03
19 68 0.43
20 18 0.11
21 20 0.12
22 24 0.15
23 4 0.03
24 3 0.02
25 1 0.01
ACGTcount: A:0.33, C:0.00, G:0.12, T:0.55
Consensus pattern (19 bp):
AATTTTGTATGAATATTGT
Found at i:49776588 original size:8 final size:8
Alignment explanation
Indices: 49776575--49776626 Score: 51
Period size: 8 Copynumber: 7.1 Consensus size: 8
49776565 TTTTTGTATG
49776575 AATATTGT
1 AATATTGT
*
49776583 AATATTAT
1 AATATTGT
49776591 AAT-TT-T
1 AATATTGT
49776597 -ATA-TG-
1 AATATTGT
49776602 AATATTGT
1 AATATTGT
49776610 AATATTGT
1 AATATTGT
*
49776618 AATTTTGT
1 AATATTGT
49776626 A
1 A
49776627 TGAATATTAT
Statistics
Matches: 37, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
5 3 0.08
6 4 0.11
7 4 0.11
8 26 0.70
ACGTcount: A:0.38, C:0.00, G:0.10, T:0.52
Consensus pattern (8 bp):
AATATTGT
Found at i:49776604 original size:27 final size:27
Alignment explanation
Indices: 49776566--49776639 Score: 121
Period size: 27 Copynumber: 2.7 Consensus size: 27
49776556 ATTGTAATTT
*
49776566 TTTTGTATGAATATTGTAATATTATAA
1 TTTTGTATGAATATTGTAATATTGTAA
*
49776593 TTTTATATGAATATTGTAATATTGTAA
1 TTTTGTATGAATATTGTAATATTGTAA
*
49776620 TTTTGTATGAATATTATAAT
1 TTTTGTATGAATATTGTAAT
49776640 GTCGAGATAT
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 43 1.00
ACGTcount: A:0.36, C:0.00, G:0.11, T:0.53
Consensus pattern (27 bp):
TTTTGTATGAATATTGTAATATTGTAA
Found at i:49776893 original size:36 final size:37
Alignment explanation
Indices: 49776831--49776910 Score: 135
Period size: 36 Copynumber: 2.2 Consensus size: 37
49776821 CATATAAAGT
49776831 TTATAAAAAAAATAAAAATCATTTTATTAAAAGTTTAA
1 TTAT-AAAAAAATAAAAATCATTTTATTAAAAGTTTAA
*
49776869 TTATAAAAAATTAAAAATCA-TTTATTAAAAGTTTAA
1 TTATAAAAAAATAAAAATCATTTTATTAAAAGTTTAA
49776905 TTATAA
1 TTATAA
49776911 CTGACTTTTT
Statistics
Matches: 41, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
36 22 0.54
37 15 0.37
38 4 0.10
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.39
Consensus pattern (37 bp):
TTATAAAAAAATAAAAATCATTTTATTAAAAGTTTAA
Found at i:49778631 original size:18 final size:18
Alignment explanation
Indices: 49778610--49778644 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
49778600 GCATCATGCA
*
49778610 CCAGAGCCAGAGCCAGTG
1 CCAGAGCCAGAGACAGTG
*
49778628 CCAGTGCCAGAGACAGT
1 CCAGAGCCAGAGACAGT
49778645 ACTACATTCT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.31, G:0.31, T:0.09
Consensus pattern (18 bp):
CCAGAGCCAGAGACAGTG
Found at i:49779010 original size:28 final size:28
Alignment explanation
Indices: 49778965--49779033 Score: 122
Period size: 28 Copynumber: 2.5 Consensus size: 28
49778955 ACCTCATATT
49778965 TAATGG-TTTTTTATGTAAATAAAATTA
1 TAATGGTTTTTTTATGTAAATAAAATTA
49778992 TAATGGTTTTTTTATGTAAATAAAATTA
1 TAATGGTTTTTTTATGTAAATAAAATTA
*
49779020 TAATGTTTTTTTTA
1 TAATGGTTTTTTTA
49779034 ATTTTGTAAT
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
27 6 0.15
28 34 0.85
ACGTcount: A:0.36, C:0.00, G:0.10, T:0.54
Consensus pattern (28 bp):
TAATGGTTTTTTTATGTAAATAAAATTA
Found at i:49783059 original size:216 final size:216
Alignment explanation
Indices: 49782668--49783331 Score: 784
Period size: 216 Copynumber: 3.0 Consensus size: 216
49782658 NNCTTCCTAG
*
49782668 AAGAGCTTGTTCTTTTCCATCTCATTCATAGTTTCTCTTGAGTTTTCAGTTATTGAAG-GGGTTT
1 AAGAGCTTGTTCTTTTCCATCTCATTCATGGTTTCTCTTGAGTTTTCAGTTA-TGAAGAGGG-TT
* *
49782732 CTTTTCTTTCCCAAAGAACTAAAAAATACGATGATGCATAACAAAAAGAAAAAGAGGACTAGTGA
64 CTTTTCTTTTCCAAAGAACTAAAAAATACGATGATGCATAACAAAAAGAAAAAGAGGACTGGTGA
* * **
49782797 AAGCCTATTTGGCTAGCGAGGAAAAAAATAACAAGAAACGAAAAAAAGAGGCG-AGGAAGAAAGT
129 AAGCCTGTTTGGCTAGCGAGGAAAAAAATAACAAGAAAAGAAAAAAAGAGG-GAAGGAAGAAAAC
*
49782861 CCATATTTTCTAGGAAGCCAAA-A
193 CCAGATTTTCTAGGAAGCCAAACA
* * *
49782884 AAGAGCTTGTTCTTTTCCATCTCATTCATGGCTTCTTTTAAGTTTTCAGTTGATGAAGAGGGTTC
1 AAGAGCTTGTTCTTTTCCATCTCATTCATGGTTTCTCTTGAGTTTTCAGTT-ATGAAGAGGGTTC
*
49782949 TTTTCTTTTCCAAAGAACTAAAAAATA-GGTGATGCATAACAAAAAG-AAAAGAGGACTGGTGAA
65 TTTTCTTTTCCAAAGAACTAAAAAATACGATGATGCATAACAAAAAGAAAAAGAGGACTGGTGAA
* ** *
49783012 AGCCTGTTTGGCTAGTGAGGAAAAAAATGAATGAGAAAAGAAAAAAAAGTGGGAAGGAAGAAAAC
130 AGCCTGTTTGGCTAGCGAGGAAAAAAAT-AACAAGAAAAG-AAAAAAAGAGGGAAGGAAGAAAAC
49783077 CCAGATTTTCTAGGAAGCCAAACA
193 CCAGATTTTCTAGGAAGCCAAACA
* * * *
49783101 ATCTTCCTAGAAGAACATATTCTTTTCCATCTCATTCATGGTTTCTCATGAGTTTTCAGTTAAAG
1 A-------AG-AG--CTTGTTCTTTTCCATCTCATTCATGGTTTCTCTTGAGTTTTCAGTT-ATG
* * *
49783166 AAAAAGGTTTCTTTTC-TTTCCAAAAGAACTAAAAAATATGATGATGCATAACAAAAAGAAAAAG
55 -AAGAGGGTTCTTTTCTTTTCC-AAAGAACTAAAAAATACGATGATGCATAACAAAAAGAAAAAG
* * * * * *
49783230 AGGACTGATGAAAGCTTGTTTGGCTAGCAAGAAAAGTAAAAGAATAA-AAAAGAAAAAAAGGAGG
118 AGGACTGGTGAAAGCCTGTTTGGCTAGCGAGGAAA--AAAATAACAAGAAAAGAAAAAAA-GAGG
** **
49783294 GAAAAAAGAAAACTGAGATTTTCTAGGAAGCCAAACA
180 GAAGGAAGAAAACCCAGATTTTCTAGGAAGCCAAACA
49783331 A
1 A
49783332 GCTTAAGAGA
Statistics
Matches: 386, Mismatches: 39, Indels: 32
0.84 0.09 0.07
Matches are distributed among these distances:
214 42 0.11
215 27 0.07
216 121 0.31
217 6 0.02
224 2 0.01
225 2 0.01
227 47 0.12
228 29 0.08
229 25 0.06
230 77 0.20
231 4 0.01
232 4 0.01
ACGTcount: A:0.41, C:0.13, G:0.20, T:0.26
Consensus pattern (216 bp):
AAGAGCTTGTTCTTTTCCATCTCATTCATGGTTTCTCTTGAGTTTTCAGTTATGAAGAGGGTTCT
TTTCTTTTCCAAAGAACTAAAAAATACGATGATGCATAACAAAAAGAAAAAGAGGACTGGTGAAA
GCCTGTTTGGCTAGCGAGGAAAAAAATAACAAGAAAAGAAAAAAAGAGGGAAGGAAGAAAACCCA
GATTTTCTAGGAAGCCAAACA
Found at i:49786159 original size:30 final size:31
Alignment explanation
Indices: 49786091--49786168 Score: 81
Period size: 29 Copynumber: 2.5 Consensus size: 31
49786081 TTCGAGGCTC
**
49786091 TAGAAACACTTTAGAAACAATTCGAGACTAAAT
1 TAGAAACA-TTTA-AAACAATTCGAGAAAAAAT
49786124 TAGAAACATTTAAAAC-ATT-GAGAAAAAAGT
1 TAGAAACATTTAAAACAATTCGAGAAAAAA-T
*
49786154 TAGAAA-AATTAAAAC
1 TAGAAACATTTAAAAC
49786169 TGTAGGGTCA
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
29 15 0.37
30 10 0.24
31 4 0.10
32 4 0.10
33 8 0.20
ACGTcount: A:0.55, C:0.10, G:0.12, T:0.23
Consensus pattern (31 bp):
TAGAAACATTTAAAACAATTCGAGAAAAAAT
Found at i:49786462 original size:17 final size:17
Alignment explanation
Indices: 49786439--49786481 Score: 77
Period size: 17 Copynumber: 2.5 Consensus size: 17
49786429 ACTACAAGGG
49786439 ACACACGGTCGTGTGTC
1 ACACACGGTCGTGTGTC
*
49786456 GCACACGGTCGTGTGTC
1 ACACACGGTCGTGTGTC
49786473 ACACACGGT
1 ACACACGGT
49786482 TGAGACACAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.19, C:0.30, G:0.30, T:0.21
Consensus pattern (17 bp):
ACACACGGTCGTGTGTC
Found at i:49787214 original size:82 final size:82
Alignment explanation
Indices: 49787077--49787239 Score: 281
Period size: 82 Copynumber: 2.0 Consensus size: 82
49787067 CCCAATCGAT
* *
49787077 CTTTCCGATGACCTACAGGAAAAGAAAAAAACTAACGTAAGCAATAATGGTTAGTAAGTTCATAT
1 CTTTCCGATGACCTACAGGAAAAGAAAAAAACTAACGTAAGAAATAATGCTTAGTAAGTTCATAT
49787142 AAAGGTAACCTAACTAG
66 AAAGGTAACCTAACTAG
* *
49787159 CTTTCCGATGACCTACAGGAAAAGAAAACAACTAACGTAAGAAATAATGCTTAGTAAGTTCGTAT
1 CTTTCCGATGACCTACAGGAAAAGAAAAAAACTAACGTAAGAAATAATGCTTAGTAAGTTCATAT
*
49787224 ATAGGTAACCTAACTA
66 AAAGGTAACCTAACTA
49787240 CTGAACATAT
Statistics
Matches: 76, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
82 76 1.00
ACGTcount: A:0.43, C:0.17, G:0.17, T:0.24
Consensus pattern (82 bp):
CTTTCCGATGACCTACAGGAAAAGAAAAAAACTAACGTAAGAAATAATGCTTAGTAAGTTCATAT
AAAGGTAACCTAACTAG
Found at i:49791725 original size:22 final size:21
Alignment explanation
Indices: 49791699--49791771 Score: 89
Period size: 22 Copynumber: 3.5 Consensus size: 21
49791689 TCGAAATGCT
49791699 AATAGAGGCACCGTAGTGCAA
1 AATAGAGGCACCGTAGTGCAA
49791720 ATATAGAGGCACCGTAGTGCAA
1 A-ATAGAGGCACCGTAGTGCAA
* *
49791742 ACA-A-AGGCATCGAAGTGC-A
1 A-ATAGAGGCACCGTAGTGCAA
49791761 AATAGAGGCAC
1 AATAGAGGCAC
49791772 TTCTTATTTT
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
18 1 0.02
19 3 0.07
20 17 0.38
21 2 0.04
22 22 0.49
ACGTcount: A:0.40, C:0.19, G:0.27, T:0.14
Consensus pattern (21 bp):
AATAGAGGCACCGTAGTGCAA
Found at i:49791769 original size:20 final size:20
Alignment explanation
Indices: 49791699--49791771 Score: 83
Period size: 20 Copynumber: 3.5 Consensus size: 20
49791689 TCGAAATGCT
*
49791699 AATAGAGGCACCGTAGTGCAA
1 AATAGAGGCACCGAAGTGC-A
*
49791720 ATATAGAGGCACCGTAGTGCA
1 A-ATAGAGGCACCGAAGTGCA
* * *
49791741 AACAAAGGCATCGAAGTGCA
1 AATAGAGGCACCGAAGTGCA
49791761 AATAGAGGCAC
1 AATAGAGGCAC
49791772 TTCTTATTTT
Statistics
Matches: 44, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
20 23 0.52
21 3 0.07
22 18 0.41
ACGTcount: A:0.40, C:0.19, G:0.27, T:0.14
Consensus pattern (20 bp):
AATAGAGGCACCGAAGTGCA
Found at i:49796755 original size:13 final size:13
Alignment explanation
Indices: 49796734--49796763 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
49796724 GAGCAAACAT
*
49796734 AAAACATAACTTA
1 AAAAAATAACTTA
49796747 AAAAAATAACTTA
1 AAAAAATAACTTA
49796760 AAAA
1 AAAA
49796764 CAAAATTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.70, C:0.10, G:0.00, T:0.20
Consensus pattern (13 bp):
AAAAAATAACTTA
Found at i:49808745 original size:22 final size:21
Alignment explanation
Indices: 49808703--49808745 Score: 50
Period size: 22 Copynumber: 2.0 Consensus size: 21
49808693 TAGTTTTAGG
***
49808703 TTTAGTTTTCTCTAGGTTTTC
1 TTTAGTTTTCTCTACACTTTC
49808724 TTTAGTTTTTCTCTACACTTTC
1 TTTAG-TTTTCTCTACACTTTC
49808746 CTAGGTTTTA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.12, C:0.19, G:0.09, T:0.60
Consensus pattern (21 bp):
TTTAGTTTTCTCTACACTTTC
Found at i:49824552 original size:25 final size:25
Alignment explanation
Indices: 49824524--49824582 Score: 100
Period size: 25 Copynumber: 2.4 Consensus size: 25
49824514 TCACAAATCG
49824524 TGTGAGCATTCTGATTCAAAGCTCA
1 TGTGAGCATTCTGATTCAAAGCTCA
* *
49824549 TGTGAGCATTCTGATTCATAGCTCC
1 TGTGAGCATTCTGATTCAAAGCTCA
49824574 TGTGAGCAT
1 TGTGAGCAT
49824583 ACAGGTACAG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.24, C:0.20, G:0.22, T:0.34
Consensus pattern (25 bp):
TGTGAGCATTCTGATTCAAAGCTCA
Found at i:49830804 original size:15 final size:16
Alignment explanation
Indices: 49830786--49830815 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
49830776 TTGTGCCTTG
49830786 TTGAT-ATGTGTTAAT
1 TTGATAATGTGTTAAT
49830801 TTGATAATGTGTTAA
1 TTGATAATGTGTTAA
49830816 AGGATGTTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.30, C:0.00, G:0.20, T:0.50
Consensus pattern (16 bp):
TTGATAATGTGTTAAT
Found at i:49834063 original size:294 final size:294
Alignment explanation
Indices: 49833529--49834111 Score: 925
Period size: 294 Copynumber: 2.0 Consensus size: 294
49833519 CCTTAATGGA
* * * * *
49833529 CTTAGAAGTTAAGGGTACCTTCTTTTTGCAAAGAAGAACTCCGGTAGCATCTGGCTTAGTCAAAC
1 CTTAAAAGTTAAGGGTACCTTCTTCTTGCAAACAAGAACTCCAGTAGCATCTGACTTAGTCAAAC
* * * *
49833594 TGGCATAGAACTTTCGAACTAACTTCTCATCGGGTAATAATCGTGCATCACAAAAATAATTCCAA
66 TGGCATAGAACTCTCAAACTAACTCCTCATCGGGTAATAATCATGCATCACAAAAATAATTCCAA
* * *
49833659 TTGAGGGCATCAATTGTCTTTCGAATCGGCAAAGACACAACCATCTTATCATTGCTTTCCAAGTT
131 TTGAGGGCATCAATCGTCTTTCAAATCAGCAAAGACACAACCATCTTATCATTGCTTTCCAAGTT
*
49833724 GAAACCTTTTTTCGGCATCATAGGTTGATTCTTAAAGATTGAATCAAACCTCTCTTTCACTTTTT
196 GAAACCTTTTTTCGGCATCATAGGTTGATTCTTAAAGATTGAATCAAACCTCTCTTTCACTTCTT
*
49833789 CATCTTGAACCACAATGGTATTTTCGGCAAAGGT
261 CATCTAGAACCACAATGGTATTTTCGGCAAAGGT
* * *
49833823 CTTAAAAGTTAAGGGTACCTTCTTCTTGCCAACAAGAACTTCAGTAGCATCTGACTTAGTCAAAT
1 CTTAAAAGTTAAGGGTACCTTCTTCTTGCAAACAAGAACTCCAGTAGCATCTGACTTAGTCAAAC
* * *
49833888 TGGCATAGAACTCTCAAACTAACTCCTCATTGGGTAATCATTATGCATCACAAAAATAATTCCAA
66 TGGCATAGAACTCTCAAACTAACTCCTCATCGGGTAATAATCATGCATCACAAAAATAATTCCAA
* *
49833953 TTGAGGGCATCAATCGTCTTTCAAATCAGCAAAGGCACAATCATCTTATCATTGCTTTCCAAGTT
131 TTGAGGGCATCAATCGTCTTTCAAATCAGCAAAGACACAACCATCTTATCATTGCTTTCCAAGTT
*
49834018 GAAACC-TTTTTCTTGCATCATAGGTTGATTCTTAAAGATTGAATCAAACCTCTCTTTCACTTCT
196 GAAACCTTTTTTC-GGCATCATAGGTTGATTCTTAAAGATTGAATCAAACCTCTCTTTCACTTCT
* *
49834082 TCATCTAGAATCACAATGGTATTTTTGGCA
260 TCATCTAGAACCACAATGGTATTTTCGGCA
49834112 GTGGCTTGGA
Statistics
Matches: 263, Mismatches: 25, Indels: 2
0.91 0.09 0.01
Matches are distributed among these distances:
293 6 0.02
294 257 0.98
ACGTcount: A:0.31, C:0.21, G:0.15, T:0.33
Consensus pattern (294 bp):
CTTAAAAGTTAAGGGTACCTTCTTCTTGCAAACAAGAACTCCAGTAGCATCTGACTTAGTCAAAC
TGGCATAGAACTCTCAAACTAACTCCTCATCGGGTAATAATCATGCATCACAAAAATAATTCCAA
TTGAGGGCATCAATCGTCTTTCAAATCAGCAAAGACACAACCATCTTATCATTGCTTTCCAAGTT
GAAACCTTTTTTCGGCATCATAGGTTGATTCTTAAAGATTGAATCAAACCTCTCTTTCACTTCTT
CATCTAGAACCACAATGGTATTTTCGGCAAAGGT
Found at i:49839055 original size:21 final size:21
Alignment explanation
Indices: 49839031--49839071 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
49839021 ATTCTTCAAT
* *
49839031 GTTGTTTCTTGGCTTTGGATC
1 GTTGTTGCTTGACTTTGGATC
49839052 GTTGTTGCTTGACTTTGGAT
1 GTTGTTGCTTGACTTTGGAT
49839072 GAAGACATCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.07, C:0.12, G:0.29, T:0.51
Consensus pattern (21 bp):
GTTGTTGCTTGACTTTGGATC
Found at i:49840422 original size:4 final size:4
Alignment explanation
Indices: 49840413--49840447 Score: 70
Period size: 4 Copynumber: 8.8 Consensus size: 4
49840403 ATTAGGGTTA
49840413 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
49840448 AATAAAAACC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:49841752 original size:23 final size:23
Alignment explanation
Indices: 49841720--49841770 Score: 84
Period size: 23 Copynumber: 2.2 Consensus size: 23
49841710 TTACTAAAAA
*
49841720 TGTAATACCCCGAAAATTACTAC
1 TGTAACACCCCGAAAATTACTAC
49841743 TGTAACACCCCGAAAATTACTAC
1 TGTAACACCCCGAAAATTACTAC
*
49841766 AGTAA
1 TGTAA
49841771 GAAAGTAGGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.41, C:0.25, G:0.10, T:0.24
Consensus pattern (23 bp):
TGTAACACCCCGAAAATTACTAC
Found at i:49845718 original size:25 final size:25
Alignment explanation
Indices: 49845685--49845738 Score: 72
Period size: 25 Copynumber: 2.2 Consensus size: 25
49845675 ATTCTTTTTG
* * *
49845685 GCCTATGTGGCTTATTCTGTATGTT
1 GCCTATGTGACGTATTCTGCATGTT
*
49845710 GCCTTTGTGACGTATTCTGCATGTT
1 GCCTATGTGACGTATTCTGCATGTT
49845735 GCCT
1 GCCT
49845739 CTCTGGCATA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.11, C:0.20, G:0.24, T:0.44
Consensus pattern (25 bp):
GCCTATGTGACGTATTCTGCATGTT
Found at i:49852338 original size:62 final size:61
Alignment explanation
Indices: 49852233--49852454 Score: 248
Period size: 61 Copynumber: 3.6 Consensus size: 61
49852223 TATTCTCCAT
* * * ** * * * *
49852233 AAAGGCTTTCCTATCCAGAGCTTTTCCACAAAGGTGTTCCTTTACATTTAATGCTCGCCAC
1 AAAGGCTTTCCTGTCCAAAGTTTTTCCACAAAGGCATTTCTTTACATTCAGTACTCGCCAC
* *
49852294 AAAGGCTTTCTTGTCCAAAGTTTTTTCCACAAAGGCATTTCTTTACATTCAGTACTCGCTAC
1 AAAGGCTTTCCTGTCCAAAG-TTTTTCCACAAAGGCATTTCTTTACATTCAGTACTCGCCAC
* * * * *
49852356 AGAGGCTTTCCTGTCTAGAGTTTTTCCATAAAGGCA-ATCTTTTACATTCAGTACTCGCCAC
1 AAAGGCTTTCCTGTCCAAAGTTTTTCCACAAAGGCATTTC-TTTACATTCAGTACTCGCCAC
* * *
49852417 AAATGCTTTCCTATCCAAAGCTTTTCCACAAAGGCATT
1 AAAGGCTTTCCTGTCCAAAGTTTTTCCACAAAGGCATT
49852455 CTTAAACAAA
Statistics
Matches: 132, Mismatches: 26, Indels: 5
0.81 0.16 0.03
Matches are distributed among these distances:
60 2 0.02
61 81 0.61
62 49 0.37
ACGTcount: A:0.26, C:0.26, G:0.14, T:0.34
Consensus pattern (61 bp):
AAAGGCTTTCCTGTCCAAAGTTTTTCCACAAAGGCATTTCTTTACATTCAGTACTCGCCAC
Found at i:49854690 original size:129 final size:129
Alignment explanation
Indices: 49854460--49854694 Score: 407
Period size: 129 Copynumber: 1.8 Consensus size: 129
49854450 GAAGAACCTA
* *
49854460 AGCATTAAGCAGATAGCCAAAAACCATTCAAAGTGTCCACTTCCTATAAATACATTCTCGGTCCC
1 AGCATTAAGCAGATAGCCAAAAACCATTCAAAGTGTCCACTTCCCATAAATACATTCTCGATCCC
49854525 CTGATTTCCTTACCTAATCCAGGGTAGGTAAAAGAAAATCTAGTGATGATTAACCTCACTGTTG
66 CTGATTTCCTTACCTAATCCAGGGTAGGTAAAAGAAAATCTAGTGATGATTAACCTCACTGTTG
* * * *
49854589 AGCATTAAGTAGATAGCCAAAAACCATTCCAAGTGTCCACTTCCCATAAATATATTCTCGATCTC
1 AGCATTAAGCAGATAGCCAAAAACCATTCAAAGTGTCCACTTCCCATAAATACATTCTCGATCCC
*
49854654 CTGATTTCCTTACCTAATCTAGGGTAGGTAAAAGAAAATCT
66 CTGATTTCCTTACCTAATCCAGGGTAGGTAAAAGAAAATCT
49854695 GGCAAAAATA
Statistics
Matches: 99, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
129 99 1.00
ACGTcount: A:0.34, C:0.23, G:0.14, T:0.29
Consensus pattern (129 bp):
AGCATTAAGCAGATAGCCAAAAACCATTCAAAGTGTCCACTTCCCATAAATACATTCTCGATCCC
CTGATTTCCTTACCTAATCCAGGGTAGGTAAAAGAAAATCTAGTGATGATTAACCTCACTGTTG
Found at i:49867785 original size:43 final size:43
Alignment explanation
Indices: 49867737--49867851 Score: 126
Period size: 43 Copynumber: 2.7 Consensus size: 43
49867727 ATCTCGTACA
** * *
49867737 ATGCCAACGTCCCAGACGTGGTCTTACATGCAATCACATATCG
1 ATGCCAACGTCCCAGACGTGGTCTTACACACAAACACAAATCG
* *
49867780 ATGCC-ACTGTTCCAGACAG-GGTCTTACACATAAACACAAATCG
1 ATGCCAAC-GTCCCAGAC-GTGGTCTTACACACAAACACAAATCG
* *
49867823 ATGTCAACGTCCCATACGTGGTCTTACAC
1 ATGCCAACGTCCCAGACGTGGTCTTACAC
49867852 GAAAAGCACA
Statistics
Matches: 59, Mismatches: 9, Indels: 8
0.78 0.12 0.11
Matches are distributed among these distances:
42 3 0.05
43 53 0.90
44 3 0.05
ACGTcount: A:0.30, C:0.30, G:0.17, T:0.23
Consensus pattern (43 bp):
ATGCCAACGTCCCAGACGTGGTCTTACACACAAACACAAATCG
Found at i:49870227 original size:87 final size:86
Alignment explanation
Indices: 49870123--49870306 Score: 260
Period size: 87 Copynumber: 2.1 Consensus size: 86
49870113 TTCAGAAAAT
* ***
49870123 AAACGCCACTAAAGACCATGACCTTTAGCGGCGCTTTTCCCACAAATGTCGCTAAAGACCATGAC
1 AAACGCCACTAAAGACCATAACCTTTAGCGGCGCTTTTCCCACAAACACCGCTAAAGACCATGAC
49870188 CTTTAGCTGCGCTTTTCCCAC
66 CTTTAGCTGCGCTTTTCCCAC
* *
49870209 AAACGCCGGCTAAAGACCATAACCTTTAGCGGCGCTTTTGCCACAAACACCGCTAAAGACCATGA
1 AAACGCC-ACTAAAGACCATAACCTTTAGCGGCGCTTTTCCCACAAACACCGCTAAAGACCATGA
** * * *
49870274 CCTTTAGAGGCGCTTCTACCGC
65 CCTTTAGCTGCGCTTTTCCCAC
49870296 AAACGCCACTA
1 AAACGCCACTA
49870307 TAAGTCATAA
Statistics
Matches: 85, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
86 10 0.12
87 75 0.88
ACGTcount: A:0.29, C:0.33, G:0.17, T:0.21
Consensus pattern (86 bp):
AAACGCCACTAAAGACCATAACCTTTAGCGGCGCTTTTCCCACAAACACCGCTAAAGACCATGAC
CTTTAGCTGCGCTTTTCCCAC
Found at i:49870236 original size:44 final size:43
Alignment explanation
Indices: 49870123--49870302 Score: 252
Period size: 43 Copynumber: 4.2 Consensus size: 43
49870113 TTCAGAAAAT
*
49870123 AAACGCCACTAAAGACCATGACCTTTAGCGGCGCTTTTCCCAC
1 AAACGCCGCTAAAGACCATGACCTTTAGCGGCGCTTTTCCCAC
* * *
49870166 AAATGTCGCTAAAGACCATGACCTTTAGCTGCGCTTTTCCCAC
1 AAACGCCGCTAAAGACCATGACCTTTAGCGGCGCTTTTCCCAC
* *
49870209 AAACGCCGGCTAAAGACCATAACCTTTAGCGGCGCTTTTGCCAC
1 AAACGCC-GCTAAAGACCATGACCTTTAGCGGCGCTTTTCCCAC
* * * * *
49870253 AAACACCGCTAAAGACCATGACCTTTAGAGGCGCTTCTACCGC
1 AAACGCCGCTAAAGACCATGACCTTTAGCGGCGCTTTTCCCAC
49870296 AAACGCC
1 AAACGCC
49870303 ACTATAAGTC
Statistics
Matches: 120, Mismatches: 16, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
43 81 0.68
44 39 0.32
ACGTcount: A:0.28, C:0.33, G:0.18, T:0.21
Consensus pattern (43 bp):
AAACGCCGCTAAAGACCATGACCTTTAGCGGCGCTTTTCCCAC
Found at i:49876395 original size:15 final size:14
Alignment explanation
Indices: 49876377--49876459 Score: 62
Period size: 14 Copynumber: 5.8 Consensus size: 14
49876367 CCCTGAATCT
*
49876377 CTAAACCTTAAATCC
1 CTAAACCTT-AACCC
49876392 CT-AACTCTTAACCC
1 CTAAAC-CTTAACCC
*
49876406 CT-AACGTCTAACCC
1 CTAAACCT-TAACCC
49876420 CTAAACCCTTAACCC
1 CTAAA-CCTTAACCC
* **
49876435 CTAAATCTTAAATC
1 CTAAACCTTAACCC
*
49876449 CTAACCCTTAA
1 CTAAACCTTAA
49876460 ACCATAATCC
Statistics
Matches: 56, Mismatches: 8, Indels: 9
0.77 0.11 0.12
Matches are distributed among these distances:
13 1 0.02
14 35 0.62
15 18 0.32
16 2 0.04
ACGTcount: A:0.35, C:0.37, G:0.01, T:0.27
Consensus pattern (14 bp):
CTAAACCTTAACCC
Found at i:49876409 original size:14 final size:14
Alignment explanation
Indices: 49876390--49876459 Score: 70
Period size: 14 Copynumber: 4.9 Consensus size: 14
49876380 AACCTTAAAT
49876390 CCCTAACTCTTAAC
1 CCCTAACTCTTAAC
49876404 CCCTAACGTC-TAAC
1 CCCTAAC-TCTTAAC
*
49876418 CCCTAAACCCTTAAC
1 CCCT-AACTCTTAAC
* *
49876433 CCCTAAATCTTAAA
1 CCCTAACTCTTAAC
* *
49876447 TCCTAACCCTTAA
1 CCCTAACTCTTAA
49876460 ACCATAATCC
Statistics
Matches: 46, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
14 33 0.72
15 13 0.28
ACGTcount: A:0.33, C:0.40, G:0.01, T:0.26
Consensus pattern (14 bp):
CCCTAACTCTTAAC
Found at i:49876460 original size:14 final size:16
Alignment explanation
Indices: 49876441--49876486 Score: 55
Period size: 14 Copynumber: 3.1 Consensus size: 16
49876431 ACCCCTAAAT
49876441 CTTAAATCC-TAA-CC
1 CTTAAATCCATAATCC
49876455 CTTAAA-CCATAATCC
1 CTTAAATCCATAATCC
*
49876470 C-TAAATCCATACTCC
1 CTTAAATCCATAATCC
49876485 CT
1 CT
49876487 AACCTTAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
13 2 0.07
14 13 0.48
15 12 0.44
ACGTcount: A:0.35, C:0.37, G:0.00, T:0.28
Consensus pattern (16 bp):
CTTAAATCCATAATCC
Found at i:49876462 original size:29 final size:28
Alignment explanation
Indices: 49876377--49876459 Score: 87
Period size: 29 Copynumber: 2.9 Consensus size: 28
49876367 CCCTGAATCT
* *
49876377 CTAAACCTTAAATCCCTAACTCTTAACCC
1 CTAAATCTTAAAT-CCTAACCCTTAACCC
* **
49876406 CTAACGTC-TAACCCCTAAACCCTTAACCC
1 CTAA-ATCTTAAATCCT-AACCCTTAACCC
49876435 CTAAATCTTAAATCCTAACCCTTAA
1 CTAAATCTTAAATCCTAACCCTTAA
49876460 ACCATAATCC
Statistics
Matches: 43, Mismatches: 8, Indels: 7
0.74 0.14 0.12
Matches are distributed among these distances:
28 14 0.33
29 28 0.65
30 1 0.02
ACGTcount: A:0.35, C:0.37, G:0.01, T:0.27
Consensus pattern (28 bp):
CTAAATCTTAAATCCTAACCCTTAACCC
Found at i:49876479 original size:15 final size:15
Alignment explanation
Indices: 49876443--49876488 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 15
49876433 CCCTAAATCT
49876443 TAAATCC-TAA-CCC
1 TAAATCCATAATCCC
49876456 TTAAA-CCATAATCCC
1 -TAAATCCATAATCCC
*
49876471 TAAATCCATACTCCC
1 TAAATCCATAATCCC
49876486 TAA
1 TAA
49876489 CCTTAAAATA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
13 2 0.07
14 11 0.39
15 15 0.54
ACGTcount: A:0.39, C:0.35, G:0.00, T:0.26
Consensus pattern (15 bp):
TAAATCCATAATCCC
Found at i:49876756 original size:7 final size:7
Alignment explanation
Indices: 49876744--49876783 Score: 53
Period size: 7 Copynumber: 5.7 Consensus size: 7
49876734 AACCCTTAAA
49876744 CCATAAT
1 CCATAAT
49876751 CCATAAT
1 CCATAAT
49876758 CCATAAT
1 CCATAAT
* *
49876765 CCCTAAC
1 CCATAAT
*
49876772 CCATACT
1 CCATAAT
49876779 CCATA
1 CCATA
49876784 TACCTTAAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.38, C:0.38, G:0.00, T:0.25
Consensus pattern (7 bp):
CCATAAT
Found at i:49876852 original size:297 final size:286
Alignment explanation
Indices: 49876281--49876857 Score: 754
Period size: 297 Copynumber: 2.0 Consensus size: 286
49876271 TTTGATTTAC
*
49876281 TATTATCTCTTTTACAATTATATAAGAACATATTTAAAATATAAATTAAAAAAATAATTAATCTA
1 TATTATATCTTTTACAATTATATAAGAACATATTTAAAATATAAATTAAAAAAATAATTAATCTA
* * *
49876346 AACTCAAAACCTTAACTCGACCCCTGAATCTCTAAACCTTAAATCCCTAACTCTTAACCCCTAAC
66 AACTCAAAACCCTAACTCGACCCCTGAATCTCTAAACCTTAAATCCCTAACCCTAAACCCCTAAC
* * * *
49876411 GTCTAACCCCTAAACCCTTAACCCCTAAATCTTAAATCCTAACCCTTAAACCATAATCCCTAAAT
131 CTCTAACCCCTAAACCCTTAACCCCTAAACCTTAAATCCTAACCCATAAACCATAATCCCTAAAC
* * *
49876476 CCATACTCCCTAACCTTAAAATATGAACTCCTAAACCGGCCTTAAGTCTTAAATTAATCATATAC
196 CCATACTCCATAACCTTAAAATATGAACTCCTAAACCGGCCTTAAATCTTAAATAAATCATATAC
*
49876541 CCTAAACTAAAAACCCTAAACAAATT
261 CCTAAACCAAAAACCCTAAACAAATT
49876567 TATTATATCTTTTACAATTATATAAGATTAACATATTTAAAATATAAATTAAAAAAATAATTAAT
1 TATTATATCTTTTACAATTATATAAG---AACATATTTAAAATATAAATTAAAAAAATAATTAAT
* * *
49876632 CTAAACTCAAAACCCTAACTCGA-CCCTGAATCCCTAACTTTTAACCCTT-AGTGCATCTAACCC
63 CTAAACTCAAAACCCTAACTCGACCCCTGAAT--CT--C---TAAACCTTAAAT-C-CCTAA-CC
* * * *
49876695 CTAAACCCTTAACCCTCTAACCCCTAAA-CCTTAAATCCC-AACCCTTAAA-CCATAATCCATAA
118 CTAAACCCCTAA-CCTCTAACCCCTAAACCCTT-AACCCCTAAACCTTAAATCC-TAACCCATAA
* *
49876757 TCCATAATCCCT-AACCCATACTCCATATACCTTAAAATA-GTAACTCCTAAACTGGCCTTAAAT
180 ACCATAATCCCTAAACCCATACTCCATA-ACCTTAAAATATG-AACTCCTAAACCGGCCTTAAAT
49876820 CTTAAATAAATCATATACCCTAAACCAAAAACCCTAAA
243 CTTAAATAAATCATATACCCTAAACCAAAAACCCTAAA
49876858 TTATAATGAT
Statistics
Matches: 252, Mismatches: 21, Indels: 25
0.85 0.07 0.08
Matches are distributed among these distances:
286 25 0.10
288 8 0.03
289 58 0.23
290 2 0.01
292 1 0.00
294 2 0.01
295 8 0.03
296 20 0.08
297 109 0.43
298 19 0.08
ACGTcount: A:0.41, C:0.27, G:0.03, T:0.29
Consensus pattern (286 bp):
TATTATATCTTTTACAATTATATAAGAACATATTTAAAATATAAATTAAAAAAATAATTAATCTA
AACTCAAAACCCTAACTCGACCCCTGAATCTCTAAACCTTAAATCCCTAACCCTAAACCCCTAAC
CTCTAACCCCTAAACCCTTAACCCCTAAACCTTAAATCCTAACCCATAAACCATAATCCCTAAAC
CCATACTCCATAACCTTAAAATATGAACTCCTAAACCGGCCTTAAATCTTAAATAAATCATATAC
CCTAAACCAAAAACCCTAAACAAATT
Found at i:49877092 original size:73 final size:73
Alignment explanation
Indices: 49877002--49877143 Score: 232
Period size: 73 Copynumber: 1.9 Consensus size: 73
49876992 AATACTATCT
49877002 CTTTCTTAAAAACGCCGCTAAATCCCCGAAAGCTCAAAAAACGGCGA-CGTTGGGCTTAGATTTT
1 CTTTCTTAAAAACGCCGCTAAATCCCCGAAAGCTCAAAAAACGGC-ATCGTTGGGCTTAGATTTT
49877066 TTTGCGGCG
65 TTTGCGGCG
* * * *
49877075 CTTTCTTGAAAATGCCGCTAAATCCCCGAAAGCTCAGAAAACGGCATCGTTGGGCTTAGGTTTTT
1 CTTTCTTAAAAACGCCGCTAAATCCCCGAAAGCTCAAAAAACGGCATCGTTGGGCTTAGATTTTT
49877140 TTGC
66 TTGC
49877144 CCGAAAGCTC
Statistics
Matches: 64, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
72 1 0.02
73 63 0.98
ACGTcount: A:0.26, C:0.24, G:0.22, T:0.28
Consensus pattern (73 bp):
CTTTCTTAAAAACGCCGCTAAATCCCCGAAAGCTCAAAAAACGGCATCGTTGGGCTTAGATTTTT
TTGCGGCG
Found at i:49877159 original size:73 final size:73
Alignment explanation
Indices: 49877010--49877161 Score: 191
Period size: 73 Copynumber: 2.1 Consensus size: 73
49877000 CTCTTTCTTA
*
49877010 AAAACGCCGCTAAATCCCCGAAAGCTCAAAAAACGGCGACGTTGGGCTTAGATTTTTTTGCGGCG
1 AAAACGCCGCTAAATCCCCGAAAGCTCAAAAAACGGCGACGTTGGGCTTAGATTTTTTTGCGCCG
**** *
49877075 CTTTCTTG
66 AAAGCTAG
* * *
49877083 AAAATGCCGCTAAATCCCCGAAAGCTCAGAAAACGGC-ATCGTTGGGCTTAGGTTTTTTTGC-CC
1 AAAACGCCGCTAAATCCCCGAAAGCTCAAAAAACGGCGA-CGTTGGGCTTAGATTTTTTTGCGCC
49877146 GAAAGCTCAG
65 GAAAGCT-AG
49877156 AAAACG
1 AAAACG
49877162 GCGTCGTTGG
Statistics
Matches: 67, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
72 5 0.07
73 62 0.93
ACGTcount: A:0.29, C:0.24, G:0.23, T:0.24
Consensus pattern (73 bp):
AAAACGCCGCTAAATCCCCGAAAGCTCAAAAAACGGCGACGTTGGGCTTAGATTTTTTTGCGCCG
AAAGCTAG
Found at i:49877205 original size:44 final size:44
Alignment explanation
Indices: 49877099--49877187 Score: 169
Period size: 44 Copynumber: 2.0 Consensus size: 44
49877089 CCGCTAAATC
49877099 CCCGAAAGCTCAGAAAACGGCATCGTTGGGCTTAGGTTTTTTTG
1 CCCGAAAGCTCAGAAAACGGCATCGTTGGGCTTAGGTTTTTTTG
*
49877143 CCCGAAAGCTCAGAAAACGGCGTCGTTGGGCTTAGGTTTTTTTG
1 CCCGAAAGCTCAGAAAACGGCATCGTTGGGCTTAGGTTTTTTTG
49877187 C
1 C
49877188 GGCGCTTTCT
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.21, C:0.21, G:0.28, T:0.29
Consensus pattern (44 bp):
CCCGAAAGCTCAGAAAACGGCATCGTTGGGCTTAGGTTTTTTTG
Found at i:49879069 original size:19 final size:20
Alignment explanation
Indices: 49879023--49879066 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
49879013 TGGTATGATA
49879023 ATTTTTATAATTCTTTTACG
1 ATTTTTATAATTCTTTTACG
*
49879043 AATTTTATAATTC-TTTAC-
1 ATTTTTATAATTCTTTTACG
49879061 ATTTTT
1 ATTTTT
49879067 TATCATTTTC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 5 0.23
19 5 0.23
20 12 0.55
ACGTcount: A:0.27, C:0.09, G:0.02, T:0.61
Consensus pattern (20 bp):
ATTTTTATAATTCTTTTACG
Found at i:49879162 original size:30 final size:30
Alignment explanation
Indices: 49879128--49879206 Score: 88
Period size: 29 Copynumber: 2.7 Consensus size: 30
49879118 TATAGTTTAT
*
49879128 AATATTTTTTCTAATTTTTAATAAAAATTA
1 AATATTTTTTATAATTTTTAATAAAAATTA
* * * *
49879158 AATATTTCTTAT-ATTTTTTATTAAAATTT
1 AATATTTTTTATAATTTTTAATAAAAATTA
**
49879187 AATATAGTTTATAATTTTTA
1 AATATTTTTTATAATTTTTA
49879207 TTTTTTTAAT
Statistics
Matches: 39, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
29 23 0.59
30 16 0.41
ACGTcount: A:0.39, C:0.03, G:0.01, T:0.57
Consensus pattern (30 bp):
AATATTTTTTATAATTTTTAATAAAAATTA
Found at i:49879425 original size:88 final size:91
Alignment explanation
Indices: 49879323--49879519 Score: 226
Period size: 92 Copynumber: 2.2 Consensus size: 91
49879313 TGCATTTTAG
* * *
49879323 CAATTGAGTGAAAAA-AA-AAGTAGGGGCCT-A-ATTGCTTTTTTGAAAATG-TTTGAGTGTCTT
1 CAATTGAGTGAAAAACAACAA-TAAGGGCCTAATATTGCTTTTTTGAAAATGTTTTAAG-GCCTT
* *
49879383 TTTAATGCATTTTGATAGTTCAAGTA-C
64 TTTAATACATTTTGAAAGTTCAAGTATC
* **
49879410 CTAATTGAGTGAAAAACAACAATAAGGGCTTAATTATTTTTTTTTTGAAAATGTTTTAAGGCCTT
1 C-AATTGAGTGAAAAACAACAATAAGGGCCTAA-TATTGCTTTTTTGAAAATGTTTTAAGGCCTT
* *
49879475 TTTAATATATTTTGAAAGTTTAAGTATC
64 TTTAATACATTTTGAAAGTTCAAGTATC
49879503 CAATTGAGTGAAAAACA
1 CAATTGAGTGAAAAACA
49879520 GAGATTTAAT
Statistics
Matches: 92, Mismatches: 10, Indels: 11
0.81 0.09 0.10
Matches are distributed among these distances:
87 1 0.01
88 14 0.15
89 9 0.10
90 3 0.03
92 58 0.63
93 7 0.08
ACGTcount: A:0.36, C:0.09, G:0.17, T:0.39
Consensus pattern (91 bp):
CAATTGAGTGAAAAACAACAATAAGGGCCTAATATTGCTTTTTTGAAAATGTTTTAAGGCCTTTT
TAATACATTTTGAAAGTTCAAGTATC
Found at i:49893513 original size:11 final size:11
Alignment explanation
Indices: 49893499--49893534 Score: 56
Period size: 12 Copynumber: 3.3 Consensus size: 11
49893489 AAAAGAAAAG
49893499 AAAAAAATGGAA
1 AAAAAAATGG-A
49893511 AAAAAAATGGA
1 AAAAAAATGGA
49893522 AAAAAAAT-GA
1 AAAAAAATGGA
49893532 AAA
1 AAA
49893535 CCTAAACTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 5 0.21
11 9 0.38
12 10 0.42
ACGTcount: A:0.78, C:0.00, G:0.14, T:0.08
Consensus pattern (11 bp):
AAAAAAATGGA
Found at i:49893514 original size:12 final size:12
Alignment explanation
Indices: 49893499--49893528 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
49893489 AAAAGAAAAG
49893499 AAAAAAATGGAA
1 AAAAAAATGGAA
49893511 AAAAAAATGGAA
1 AAAAAAATGGAA
49893523 AAAAAA
1 AAAAAA
49893529 TGAAAACCTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.80, C:0.00, G:0.13, T:0.07
Consensus pattern (12 bp):
AAAAAAATGGAA
Found at i:49895309 original size:135 final size:134
Alignment explanation
Indices: 49895095--49895364 Score: 441
Period size: 135 Copynumber: 2.0 Consensus size: 134
49895085 TCAATGTCAA
* * *
49895095 ATATAGAATGGAGTACTAAATCTCTCGATCGAAATAATGAATAATGTCACTCACAAAGGTAGATA
1 ATATAGAATGGAGTAATAAATCTCTCAATCGAAATAATGAATAATGTCACTCACAAAGGCAGATA
* ** *
49895160 ACGGAAATAATTCAATATTAGAAAAGAATTCTTGGATAGAAATTGATTCCAAGAGGAAAATTAAA
66 ACGGAAATAATTCAATATT-GAAAAGAATTCTTGAATAGAAACCGATTCCAAGAGGAAAATCAAA
49895225 GAGTT
130 GAGTT
49895230 ATATAGAATGGAGTAATAAATCTCTCAATCGAAATAATGAATAATGTCACTCACAAAGGCAGATA
1 ATATAGAATGGAGTAATAAATCTCTCAATCGAAATAATGAATAATGTCACTCACAAAGGCAGATA
* * *
49895295 ATGGAAATACTTCAATATTGAAAAGAATTCTTGAATTGAAACCGATTCCAAGAGGAAAATCAAAG
66 ACGGAAATAATTCAATATTGAAAAGAATTCTTGAATAGAAACCGATTCCAAGAGGAAAATCAAAG
49895360 AGTT
131 AGTT
49895364 A
1 A
49895365 ATGAAAAAAG
Statistics
Matches: 125, Mismatches: 10, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
134 46 0.37
135 79 0.63
ACGTcount: A:0.46, C:0.11, G:0.17, T:0.26
Consensus pattern (134 bp):
ATATAGAATGGAGTAATAAATCTCTCAATCGAAATAATGAATAATGTCACTCACAAAGGCAGATA
ACGGAAATAATTCAATATTGAAAAGAATTCTTGAATAGAAACCGATTCCAAGAGGAAAATCAAAG
AGTT
Found at i:49906417 original size:15 final size:15
Alignment explanation
Indices: 49906397--49906435 Score: 69
Period size: 15 Copynumber: 2.6 Consensus size: 15
49906387 AGTGCTAAGG
49906397 ATTGCTCCAATATCA
1 ATTGCTCCAATATCA
*
49906412 ATTGCTCCAATATCG
1 ATTGCTCCAATATCA
49906427 ATTGCTCCA
1 ATTGCTCCA
49906436 TATTGAATGG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.28, C:0.28, G:0.10, T:0.33
Consensus pattern (15 bp):
ATTGCTCCAATATCA
Found at i:49907740 original size:64 final size:64
Alignment explanation
Indices: 49907662--49907815 Score: 206
Period size: 52 Copynumber: 2.6 Consensus size: 64
49907652 AGTCTAAAGA
*
49907662 TTTTCATCTGCAAAAATTTGATGACCGATTAAGATTTTGTTACCAAATTGAAATTCAGTACAGG
1 TTTTCATCTGCAAAAATTTGATGACCGATTAAGATTTTGTTACCAAATTGAAATTCAGTACAGC
*
49907726 TTTTCATCTGCAAAAA--TG--G---G--T-A-A-TTTGTTACCAAATTGAAATTCAGTATAGC
1 TTTTCATCTGCAAAAATTTGATGACCGATTAAGATTTTGTTACCAAATTGAAATTCAGTACAGC
49907778 TTTTCATCTGCAAAAATTTGATGACCGATTAAGATTTT
1 TTTTCATCTGCAAAAATTTGATGACCGATTAAGATTTT
49907816 AGCTTGGGAA
Statistics
Matches: 76, Mismatches: 2, Indels: 24
0.75 0.02 0.24
Matches are distributed among these distances:
52 43 0.57
53 1 0.01
54 3 0.04
55 1 0.01
56 1 0.01
57 1 0.01
59 1 0.01
60 1 0.01
61 1 0.01
62 3 0.04
63 1 0.01
64 19 0.25
ACGTcount: A:0.34, C:0.14, G:0.15, T:0.38
Consensus pattern (64 bp):
TTTTCATCTGCAAAAATTTGATGACCGATTAAGATTTTGTTACCAAATTGAAATTCAGTACAGC
Found at i:49912762 original size:18 final size:19
Alignment explanation
Indices: 49912739--49912779 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
49912729 GTAGAAATTA
*
49912739 AAAACTACT-AAATTAAAT
1 AAAACTAATGAAATTAAAT
*
49912757 AAAACTAATGAAATTAAGT
1 AAAACTAATGAAATTAAAT
49912776 AAAA
1 AAAA
49912780 TAACCAAACC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 8 0.40
19 12 0.60
ACGTcount: A:0.63, C:0.07, G:0.05, T:0.24
Consensus pattern (19 bp):
AAAACTAATGAAATTAAAT
Found at i:49921634 original size:50 final size:49
Alignment explanation
Indices: 49921517--49921695 Score: 155
Period size: 50 Copynumber: 3.6 Consensus size: 49
49921507 ACATGCCAAA
* * * *
49921517 GCCATGTCCCAAAAATGGTCTTACATGGGATGTTTCTTGTAC--TGTCAAT
1 GCCATGTCCCAGACATGGTCTTACATGGGAT-TTTCATAT-CGGTGTCAAT
* * * *
49921566 GCCATATCCCAGATATGGTCTTACATGGGAGTTTTCATATCGGTGCCCAT
1 GCCATGTCCCAGACATGGTCTTACATGGGA-TTTTCATATCGGTGTCAAT
** * * * *
49921616 GCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGGTGTCAAC
1 GCCATGTCCCAGACATGGTCTTACATGGGA-TTTTCATATCGGTGTCAAT
** *
49921666 GCCATGTCAAAGACATGGTCCTACATGGGA
1 GCCATGTCCCAGACATGGTCTTACATGGGA
49921696 CCTCTCATAA
Statistics
Matches: 104, Mismatches: 23, Indels: 5
0.79 0.17 0.04
Matches are distributed among these distances:
48 1 0.01
49 33 0.32
50 70 0.67
ACGTcount: A:0.23, C:0.25, G:0.23, T:0.28
Consensus pattern (49 bp):
GCCATGTCCCAGACATGGTCTTACATGGGATTTTCATATCGGTGTCAAT
Found at i:49931676 original size:54 final size:53
Alignment explanation
Indices: 49931563--49931676 Score: 147
Period size: 54 Copynumber: 2.1 Consensus size: 53
49931553 TCGTCCTTTA
* * * * *
49931563 TCTTCTTTCCCTACATAATGCCATAGTCGCAGACTAGGTCTTACACTATGTGG
1 TCTTCTTTCCCTACATAATGCCATAGTCCCAAACTAGGTCTAACACTATATAG
* * *
49931616 TATTCTTATCCCTATATAATGCCATAGTCCCAAAGTAGGTCTAACACTATATAG
1 TCTTCTT-TCCCTACATAATGCCATAGTCCCAAACTAGGTCTAACACTATATAG
49931670 TCTTCTT
1 TCTTCTT
49931677 GCCATAGCCA
Statistics
Matches: 51, Mismatches: 9, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
53 6 0.12
54 45 0.88
ACGTcount: A:0.26, C:0.25, G:0.13, T:0.36
Consensus pattern (53 bp):
TCTTCTTTCCCTACATAATGCCATAGTCCCAAACTAGGTCTAACACTATATAG
Found at i:49938522 original size:7 final size:7
Alignment explanation
Indices: 49938510--49938546 Score: 56
Period size: 7 Copynumber: 5.1 Consensus size: 7
49938500 TAATAAGAAT
49938510 TAATATA
1 TAATATA
49938517 TAATATA
1 TAATATA
49938524 TAATATA
1 TAATATA
*
49938531 AAATATA
1 TAATATA
49938538 TTAATATA
1 -TAATATA
49938546 T
1 T
49938547 TTTTTTCTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
7 21 0.78
8 6 0.22
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (7 bp):
TAATATA
Found at i:49938527 original size:14 final size:15
Alignment explanation
Indices: 49938508--49938546 Score: 62
Period size: 14 Copynumber: 2.7 Consensus size: 15
49938498 GTTAATAAGA
49938508 ATTAATATATAATAT
1 ATTAATATATAATAT
*
49938523 A-TAATATAAAATAT
1 ATTAATATATAATAT
49938537 ATTAATATAT
1 ATTAATATAT
49938547 TTTTTTCTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
14 13 0.62
15 8 0.38
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
ATTAATATATAATAT
Found at i:49938671 original size:15 final size:16
Alignment explanation
Indices: 49938644--49938673 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
49938634 GAGAACAATT
49938644 AATATATATTATATAA
1 AATATATATTATATAA
49938660 AATATA-ATTATATA
1 AATATATATTATATA
49938674 TTAGTTGTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
AATATATATTATATAA
Found at i:49963028 original size:45 final size:45
Alignment explanation
Indices: 49962964--49963054 Score: 146
Period size: 45 Copynumber: 2.0 Consensus size: 45
49962954 GAGTGAAGTG
* * *
49962964 AGAGCATATACTTCATGTATTCTTGCGACTCGTCTTCTTGGCGCT
1 AGAGCATACACTTCATGTATTCCTGCGACTCGTCTTCCTGGCGCT
*
49963009 AGAGCATCCACTTCATGTATTCCTGCGACTCGTCTTCCTGGCGCT
1 AGAGCATACACTTCATGTATTCCTGCGACTCGTCTTCCTGGCGCT
49963054 A
1 A
49963055 CTTGATTGGT
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.18, C:0.29, G:0.20, T:0.34
Consensus pattern (45 bp):
AGAGCATACACTTCATGTATTCCTGCGACTCGTCTTCCTGGCGCT
Found at i:49974865 original size:18 final size:18
Alignment explanation
Indices: 49974827--49974876 Score: 66
Period size: 19 Copynumber: 2.8 Consensus size: 18
49974817 ATCAAAACTT
49974827 GTTTCTCCAAAGTTTTAAA
1 GTTTCTCCAAA-TTTTAAA
*
49974846 GTTTCTCCAAATTTTTAA
1 GTTTCTCCAAATTTTAAA
*
49974864 GTTT-TCAAAATTT
1 GTTTCTCCAAATTT
49974877 AAGTTTTAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.28
18 10 0.34
19 11 0.38
ACGTcount: A:0.30, C:0.14, G:0.08, T:0.48
Consensus pattern (18 bp):
GTTTCTCCAAATTTTAAA
Found at i:49974889 original size:14 final size:15
Alignment explanation
Indices: 49974859--49974890 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
49974849 TCTCCAAATT
49974859 TTTAAGTTTTCAAAA
1 TTTAAGTTTTCAAAA
49974874 TTTAAGTTTT-AAAA
1 TTTAAGTTTTCAAAA
49974888 TTT
1 TTT
49974891 TTATTAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.41
15 10 0.59
ACGTcount: A:0.38, C:0.03, G:0.06, T:0.53
Consensus pattern (15 bp):
TTTAAGTTTTCAAAA
Found at i:49975079 original size:21 final size:22
Alignment explanation
Indices: 49975055--49975099 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 22
49975045 AAATTTCTAA
*
49975055 AAATTTATTATG-AAATAATTT
1 AAATTGATTATGTAAATAATTT
*
49975076 AAATTGATTATGTTAATAATTT
1 AAATTGATTATGTAAATAATTT
49975098 AA
1 AA
49975100 GTGCAAATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 11 0.52
22 10 0.48
ACGTcount: A:0.47, C:0.00, G:0.07, T:0.47
Consensus pattern (22 bp):
AAATTGATTATGTAAATAATTT
Done.